bluuebunny/crossref_metadata_2025 huggingface dataset:
Evidence of Distinct Populations and Specific Subpopulations within the SpeciesOenococcus oeni
Authors: Bridier Julen , Claisse Olivier , Coton Monika , Coton Emmanuel , Lonvaud-Funel Aline
Published: October 2010

Among the lactic acid bacteria (LAB) present in the oenological microbial ecosystem,Oenococcus oeni, an acidophilic lactic acid bacterium, is essential during winemaking. It outclasses all other bacterial species during malolactic fermentation (MLF). Oenological performances, such as malic acid degradation rate and sensorial impact, vary significantly according to the strain. The genetic diversity of theO. oenispecies was evaluated using a multilocus sequence typing (MLST) scheme. Seven housekeeping genes were sequenced for a collection of 258 strains that had been isolated all over the world (particularly Burgundy, Champagne, and Aquitaine, France, Chile, South Africa, and Italy) and in several wine types (red wines, white wines, and champagne) and cider. The allelic diversity was high, with an average of 20.7 alleles per locus, many of them being rare alleles. The collection comprised 127 sequence types, suggesting an important genotypic diversity. The neighbor-joining phylogenetic tree constructed from the concatenated sequence of the seven housekeeping genes showed two major phylogenetic groups, named A and B. One unique strain isolated from cider composed a third group, rooting the phylogenetic tree. However, all other strains isolated from cider were in group B. Eight phylogenetic subgroups were statistically differentiated and could be delineated by the analysis of only 32 mutations instead of the 600 mutations observed in the concatenated sequence of the seven housekeeping genes. Interestingly, in group A, several phylogenetic subgroups were composed mostly of strains coming from a precise geographic origin. Three subgroups were identified, composed of strains from Chile, South Africa, and eastern France.
Identification of DysI, the Immunity Factor of the Streptococcal Bacteriocin Dysgalacticin
Authors: Swe Pearl M. , Heng Nicholas C. K. , Cook Gregory M. , Tagg John R. , Jack Ralph W.
Published: October 2010

DysI is identified as the protein that confers specific immunity to dysgalacticin, a plasmid-encoded streptococcal bacteriocin.
dysI
is transcribed as part of the
copG
-
repB
-
dysI
replication-associated operon. DysI appears to function at the membrane level to prevent the inhibitory effects of dysgalacticin on glucose transport, membrane integrity, and intracellular ATP content.
Functional Characterization of Replication and Stability Factors of an Incompatibility Group P-1 Plasmid from
Xylella fastidiosa
Authors: Lee Min Woo , Rogers Elizabeth E. , Stenger Drake C.
Published: October 2010

Xylella fastidiosa
strain riv11 harbors a 25-kbp plasmid (pXF-RIV11) belonging to the IncP-1 incompatibility group. Replication and stability factors of pXF-RIV11 were identified and used to construct plasmids able to replicate in
X. fastidiosa
and
Escherichia coli
. Replication in
X. fastidiosa
required a 1.4-kbp region from pXF-RIV11 containing a replication initiation gene (
trfA
) and the adjacent origin of DNA replication (
oriV
). Constructs containing
trfA
and
oriV
from pVEIS01, a related IncP-1 plasmid of the earthworm symbiont
Verminephrobacter eiseniae
, also were competent for replication in
X. fastidiosa
. Constructs derived from pXF-RIV11 but not pVEIS01 replicated in
Agrobacterium tumefaciens
,
Xanthomonas campestris
, and
Pseudomonas syringae
. Although plasmids bearing replication elements from pXF-RIV11 or pVEIS01 could be maintained in
X. fastidiosa
under antibiotic selection, removal of selection resulted in plasmid extinction after 3 weekly passages. Addition of a toxin-antitoxin addiction system (
pemI
/
pemK
) from pXF-RIV11 improved plasmid stability such that >80 to 90% of
X. fastidiosa
cells retained plasmid after 5 weekly passages in the absence of antibiotic selection. Expression of PemK in
E. coli
was toxic for cell growth, but toxicity was nullified by coexpression of PemI antitoxin. Deletion of N-terminal sequences of PemK containing the conserved motif RGD abolished toxicity.
In vitro
assays revealed a direct interaction of PemI with PemK, suggesting that antitoxin activity of PemI is mediated by toxin sequestration. IncP-1 plasmid replication and stability factors were added to an
E. coli
cloning vector to constitute a stable 6.0-kbp shuttle vector (pXF20-PEMIK) suitable for use in
X. fastidiosa
.
Antibody Responses in Mice Stimulated by Various Doses of the Potato-Derived Major Surface Antigen of Hepatitis B Virus
Authors: Youm Jung Won , Won Young Suk , Jeon Jae Heung , Moon Ki Beom , Kim Hyoung Chin , Shin Kee-Sun , Joung Hyouk , Kim Hyun Soon
Published: October 2010

The ability of potato-derived major surface antigen of hepatitis B virus (P-HBsAg) to elicit antibody responses to different dosages of P-HBsAg ranging from 0.02 to 30 μg administered orally in mice was examined. All immunized groups produced specific serum IgG and fecal IgA antibodies against P-HBsAg, even at low levels (<5 μg), after administration of a 0.5-μg yeast-derived HBsAg (Y-HBsAg; LG Life Sciences, Republic of Korea) booster.
Evaluation of Gamma Interferon Release Assays Using
Mycobacterium tuberculosis
Antigens for Diagnosis of Latent and Active Tuberculosis in
Mycobacterium bovis
BCG-Vaccinated Populations
Authors: Zhang Shu , Shao Lingyun , Mo Ling , Chen Jiazhen , Wang Feifei , Meng Chengyan , Zhong Min , Qiu Lihua , Wu Meiying , Weng Xinhua , Zhang Wenhong
Published: October 2010

T-cell-based gamma interferon (IFN-γ) release assays (IGRAs) using
Mycobacterium tuberculosis
-specific antigens have shown higher sensitivity and specificity than the routine tuberculin skin test (TST). However, the effects of
Mycobacterium bovis
BCG vaccination and anti-tuberculosis (TB) treatment on dynamic T-cell responses to
M. tuberculosis
-specific antigens in active TB cases have rarely been investigated in regions where TB is endemic. Eighty-nine patients with active pulmonary TB (ATB) and 57 healthy controls (HC) from China were recruited and tested by sputum smear and culture, TSTs, and IGRAs with
M. tuberculosis
-specific antigens ESAT-6 and CFP-10 (T-SPOT.TB) as well as purified protein derivative (PPD) stimulation. All 146 participants were screened by the T-SPOT.TB assay at recruitment. T-SPOT.TB-positive rates in ATB and HC groups were 87.6% (78/89) and 21.1% (12/57), respectively. Of 38 ATB patients who were both TST and T-SPOT.TB tested, the positive rates were 73.7% (28/38) and 94.7% (36/38), respectively (
P
= 0.0215), and those in the HC group were 62.3% (33/53) and 18.9% (10/53), respectively (
P
< 0.0001). The T-SPOT.TB-positive rates declined during TB treatment and were 94.4% (51/54), 86.4% (19/22), and 61.5% (8/13) for ATB patients receiving 0- to 1-month, 1- to 3-month, and 3- to 6-month anti-TB treatment, respectively. The IGRA is a most promising test for both active TB and latent TB infection (LTBI) diagnosis due to the improvement of its specificity and convenience, especially in the
Mycobacterium bovis
BCG-vaccinated population. Furthermore, the T-SPOT.TB assay using ESAT-6 and CFP-10 in ATB patients during anti-TB treatment could serve as a potential predictor of therapeutic efficacy.
FliZ Induces a Kinetic Switch in Flagellar Gene Expression
Authors: Saini Supreet , Koirala Santosh , Floess Emily , Mears Patrick J. , Chemla Yann R. , Golding Ido , Aldridge Christine , Aldridge Phillip D. , Rao Christopher V.
Published: October 2010

FliZ is an activator of class 2 flagellar gene expression inSalmonella enterica. To understand its role in flagellar assembly, we investigated how FliZ affects gene expression dynamics. We demonstrate that FliZ participates in a positive-feedback loop that induces a kinetic switch in class 2 gene expression.
Shadowing the Actions of a Predator: Backlit Fluorescent Microscopy Reveals Synchronous Nonbinary Septation of Predatory
Bdellovibrio
inside Prey and Exit through Discrete Bdelloplast Pores
Authors: Fenton A. K. , Kanna M. , Woods R. D. , Aizawa S.-I. , Sockett R. E.
Published: October 2010

The
Bdellovibrio
are miniature “living antibiotic” predatory bacteria which invade, reseal, and digest other larger Gram-negative bacteria, including pathogens. Nutrients for the replication of
Bdellovibrio
bacteria come entirely from the digestion of the single invaded bacterium, now called a bdelloplast, which is bound by the original prey outer membrane.
Bdellovibrio
bacteria are efficient digesters of prey cells, yielding on average 4 to 6 progeny from digestion of a single prey cell of a genome size similar to that of the
Bdellovibrio
cell itself. The developmental intrabacterial cycle of
Bdellovibrio
is largely unknown and has never been visualized “live.” Using the latest motorized
xy
stage with a very defined
z
-axis control and engineered periplasmically fluorescent prey allows, for the first time, accurate return and visualization without prey bleaching of developing
Bdellovibrio
cells using solely the inner resources of a prey cell over several hours. We show that
Bdellovibrio
bacteria do not follow the familiar pattern of bacterial cell division by binary fission. Instead, they septate synchronously to produce both odd and even numbers of progeny, even when two separate
Bdellovibrio
cells have invaded and develop within a single prey bacterium, producing two different amounts of progeny. Evolution of this novel septation pattern, allowing odd progeny yields, allows optimal use of the finite prey cell resources to produce maximal replicated, predatory bacteria. When replication is complete,
Bdellovibrio
cells exit the exhausted prey and are seen leaving via discrete pores rather than by breakdown of the entire outer membrane of the prey.
Influence of Extraction Protocol on Physical Properties of Parvovirus B19 DNA
Authors: Matz Bertfried , Kupfer Bernd , Kreil Thomas R. , Eis-Hübinger Anna Maria
Published: October 2010

While establishing a quantification standard for parvovirus B19 diagnostics, we extracted viral DNA from a high-titered human plasma by using three commercial kits. Despite similar viral DNA yields being obtained, striking differences in electrophoretic mobilities of the extracted nucleic acids were observed.
First Report of
Salmonella enterica
Serotype Paratyphi A Azithromycin Resistance Leading to Treatment Failure
Authors: Molloy Aoife , Nair Satheesh , Cooke Fiona J. , Wain John , Farrington Mark , Lehner Paul J. , Torok M. Estee
Published: October 2010

The prevalence of
Salmonella enterica
serotype Paratyphi A infection is increasing, and multidrug resistance is a well-recognized problem. Resistance to fluoroquinolones is common and leads to more frequent use of newer agents like azithromycin. We report the first case of azithromycin resistance and treatment failure in a patient with
S
. Paratyphi A infection.
TROCAI (Tropism Coreceptor Assay Information): a New Phenotypic Tropism Test and Its Correlation with Trofile Enhanced Sensitivity and Genotypic Approaches
Authors: Gonzalez-Serna Alejandro , Leal Manuel , Genebat Miguel , Abad Maria Antonia , Garcia-Perganeda Antonio , Ferrando-Martinez Sara , Ruiz-Mateos Ezequiel
Published: October 2010

The only clinically validated assay available to determine HIV tropism is Trofile, an assay that possesses some limitations. Our first aim was to develop a new phenotypic tropism test (TROCAI [tropism coreceptor assay information]) and to categorize results generated by this test according to the virological response to a short-term exposure to the CCR5 receptor antagonist maraviroc (maraviroc clinical test). Our second aim was to compare TROCAI results to those obtained by Trofile enhanced sensitivity (ES) and to different genotypic algorithms. TROCAI assayed HIV tropism in 33 HIV-infected patient viral isolates obtained from a modified coculture, followed by multiple infection cycles of indicator cells. TROCAI obtained a reportable result in all patients with viral loads of >500 HIV RNA copies/ml and in 3/6 patients with <500 HIV RNA copies/ml (30/33 patients, 91.9%). Patients who responded to maraviroc had an X4-using virus proportion in indicator cell supernatant of 0 to 0.41%. Hence, we used the threshold of 0.5% to categorize TROCAI results as R5 (<0.5%) or dual/mixed (>0.5%). The concordance between TROCAI and Trofile (ES) was 22/24 (91.6%), and with genotypic approaches it was 22/26 (84.6%). TROCAI results, which were categorized in this study by the maraviroc clinical test, could be used as a test in addition to those currently used to select patients for treatment with CCR5 antagonists.
Complete Nucleotide Sequence Analysis of Plasmids in Strains of
Staphylococcus aureus
Clone USA300 Reveals a High Level of Identity among Isolates with Closely Related Core Genome Sequences
Authors: Kennedy Adam D. , Porcella Stephen F. , Martens Craig , Whitney Adeline R. , Braughton Kevin R. , Chen Liang , Craig Carly T. , Tenover Fred C. , Kreiswirth Barry N. , Musser James M. , DeLeo Frank R.
Published: October 2010

A community-associated methicillin-resistant
Staphylococcus aureus
(CA-MRSA) strain known as pulsed-field type USA300 (USA300) is epidemic in the United States. Previous comparative whole-genome sequencing studies demonstrated that there has been recent clonal emergence of a subset of USA300 isolates, which comprise the epidemic clone. Although the core genomes of these isolates are closely related, the level of diversity among USA300 plasmids was not resolved. Inasmuch as these plasmids might contribute to significant gene diversity among otherwise closely related USA300 isolates, we performed
de novo
sequencing of endogenous plasmids from 10 previously characterized USA300 clinical isolates obtained from different geographic locations in the United States. All isolates tested contained small (2- to 3-kb) and/or large (27- to 30-kb) plasmids. The large plasmids encoded heavy metal and/or antimicrobial resistance elements, including those that confer resistance to cadmium, bacitracin, macrolides, penicillin, kanamycin, and streptothricin, although all isolates were sensitive to minocycline, doxycycline, trimethoprim-sulfamethoxazole, vancomycin, teicoplanin, and linezolid. One of the USA300 isolates contained an archaic plasmid that encoded staphylococcal enterotoxins R, J, and P. Notably, the large plasmids (27 to 28 kb) from 8 USA300 isolates—those that comprise the epidemic USA300 clone—were virtually identical (99% identity) and similar to a large plasmid from strain USA300_TCH1516 (a previously sequenced USA300 strain from Houston, TX). These plasmids are largely divergent from the 37-kb plasmid of FPR3757, the first sequenced USA300 strain. The high level of plasmid sequence identity among the majority of closely related USA300 isolates is consistent with the recent clonal emergence hypothesis for USA300.
Clinical Features of Infections and Colonization by
Acinetobacter
Genospecies 3
Authors: Molina José , Cisneros José Miguel , Fernández-Cuenca Felipe , Rodríguez-Baño Jesús , Ribera Anna , Beceiro Alejandro , Martínez-Martínez Luis , Pascual Álvaro , Bou Germán , Vila Jordi , Pachón Jerónimo
Published: October 2010

Two hundred twenty-one isolates of
Acinetobacter baumannii
and 15 of
Acinetobacter
genospecies 3 (AG3) were consecutively collected in a 30-day period during the nationwide project GEIH-Ab2000. Nosocomial acquisition (
P
= 0.01), intensive care unit admission (
P
= 0.02), and antibiotic pressure (
P
= 0.03) were observed to be lower in the AG3 group. AG3 isolates were more frequently implied in wound infections (
P
= 0.05), while
A. baumannii
tended to be recovered from respiratory samples (
P
= 0.08). To our knowledge, this is the first report analyzing the clinical differences among
Acinetobacter
genospecies, with our findings suggesting that clinical features of AG3 may not be equivalent to those traditionally described for
A. baumannii
.
Differential Circulation of
Streptococcus pneumoniae
Serotype 6C Clones in Two Israeli Pediatric Populations
Authors: Porat Nurith , Park In Ho , Nahm Moon H. , Dagan Ron
Published: October 2010

We genotyped
Streptococcus pneumoniae
serotype 6C (Sp6C) isolates collected from Jewish and Bedouin children in southern Israel during the decade before vaccination. Sp6C constituted 8.2% of the presumed Sp6A isolates. All of the Sp6C clonal clusters were associated with serogroup 6, mainly Sp6A. Different clonal distributions were found in the two subpopulations.
Roles of Vaccinia Virus Genes E3L and K3L and Host Genes PKR and RNase L during Intratracheal Infection of C57BL/6 Mice
Authors: Rice Amanda D. , Turner Peter C. , Embury Jennifer E. , Moldawer Lyle L. , Baker Henry V. , Moyer Richard W.
Published: October 2010

The importance of the 2′-5′ oligoadenylate synthetase (OAS)/RNase L and double-stranded RNA (dsRNA)-dependent protein kinase (PKR) pathways in host interferon induction resulting from virus infection in response to dsRNA has been well documented. In poxvirus infections, the interactions between the vaccinia virus (VV) genes E3L and K3L, which target RNase L and PKR, respectively, serve to prevent the induction of the dsRNA-dependent induced interferon response in cell culture. To determine the importance of these host genes in controlling VV infections, mouse single-gene knockouts of RNase L and PKR and double-knockout mice were studied following intratracheal infection with VV, VVΔK3L, or VVΔE3L. VV caused lethal disease in all mouse strains. The single-knockout animals were more susceptible than wild-type animals, while the RNase L
−/−
PKR
−/−
mice were the most susceptible. VVΔE3L infections of wild-type mice were asymptomatic, demonstrating that E3L plays a critical role in controlling the host immune response. RNase L
−/−
mice showed no disease, whereas 20% of the PKR
−/−
mice succumbed at a dose of 10
8
PFU. Lethal disease was routinely observed in RNase L
−/−
PKR
−/−
mice inoculated with 10
8
PFU of VVΔE3L, with a distinct pathology. VVΔK3L infections exhibited no differences in virulence among any of the mouse constructs, suggesting that PKR is not the exclusive target of K3L. Surprisingly, VVΔK3L did not disseminate to other tissues from the lung. Hence, the cause of death in this model is respiratory disease. These results also suggest that an unanticipated role of the K3L gene is to facilitate virus dissemination.
NFAT and CREB Regulate Kaposi's Sarcoma-Associated Herpesvirus-Induced Cyclooxygenase 2 (COX-2)
Authors: Sharma-Walia Neelam , George Paul Arun , Patel Kinjan , Chandran Karthic , Ahmad Waseem , Chandran Bala
Published: October 2010

COX-2 has been implicated in Kaposi's sarcoma-associated herpesvirus (KSHV) latency and pathogenesis (A. George Paul, N. Sharma-Walia, N. Kerur, C. White, and B. Chandran, Cancer Res. 70:3697-3708, 2010; P. P. Naranatt, H. H. Krishnan, S. R. Svojanovsky, C. Bloomer, S. Mathur, and B. Chandran, Cancer Res. 64:72-84, 2004; N. Sharma-Walia, A. G. Paul, V. Bottero, S. Sadagopan, M. V. Veettil, N. Kerur, and B. Chandran, PLoS Pathog. 6:e1000777, 2010; N. Sharma-Walia, H. Raghu, S. Sadagopan, R. Sivakumar, M. V. Veettil, P. P. Naranatt, M. M. Smith, and B. Chandran, J. Virol. 80:6534-6552, 2006). However, the precise regulatory mechanisms involved in COX-2 induction during KSHV infection have never been explored. Here, we identifiedcis-acting elements involved in the transcriptional regulation of COX-2 upon KSHVdenovoinfection. Promoter analysis using human COX-2 promoter deletion and mutation reporter constructs revealed that nuclear factor of activated T cells (NFAT) and the cyclic AMP (cAMP) response element (CRE) modulate KSHV-mediated transcriptional regulation of COX-2. Along with multiple KSHV-induced signaling pathways, infection-induced prostaglandin E2(PGE2) also augmented COX-2 transcription. Infection of endothelial cells markedly induced COX-2 expression via a cyclosporine A-sensitive, calcineurin/NFAT-dependent pathway. KSHV infection increased intracellular cAMP levels and activated protein kinase A (PKA), which phosphorylated the CRE-binding protein (CREB) at serine 133, which probably led to interaction with CRE in the COX-2 promoter, thereby enhancing COX-2 transcription. PKA selective inhibitor H-89 pretreatment strongly inhibited CREB serine 133, indicating the involvement of a cAMP-PKA-CREB-CRE loop in COX-2 transcriptional regulation. In contrast to phosphatidylinositol 3-kinase and protein kinase C, inhibition of FAK and Src effectively reduced KSHV infection-induced COX-2 transcription and protein levels. Collectively, our study indicates that mediation of COX-2 transcription upon KSHV infection is a paradigm of a complex regulatory milieu involving the interplay of multiple signal cascades and transcription factors. Intervention at each step of COX-2/PGE2induction can be used as a potential therapeutic target to treat KSHV-associated neoplasm and control inflammatory sequels of KSHV infection.
The Early Whole-Blood Transcriptional Signature of Dengue Virus and Features Associated with Progression to Dengue Shock Syndrome in Vietnamese Children and Young Adults
Authors: Hoang Long Truong , Lynn David J. , Henn Matt , Birren Bruce W. , Lennon Niall J. , Le Phuong Thi , Duong Kien Thi Hue , Nguyen Tham Thi Hong , Mai Lanh Ngoc , Farrar Jeremy J. , Hibberd Martin L. , Simmons Cameron P.
Published: October 2010

Dengue is a pantropic public health problem. In children, dengue shock syndrome (DSS) is the most common life-threatening complication. The ability to predict which patients may develop DSS may improve triage and treatment. To this end, we conducted a nested case-control comparison of the early host transcriptional features in 24 DSS patients and 56 sex-, age-, and virus serotype-matched uncomplicated (UC) dengue patients. In the first instance, we defined the “early dengue” profile. The transcriptional signature in acute rather than convalescent samples (≤72 h post-illness onset) was defined by an overabundance of interferon-inducible transcripts (31% of the 551 overabundant transcripts) and canonical gene ontology terms that included the following: response to virus, immune response, innate immune response, and inflammatory response. Pathway and network analyses identified STAT1, STAT2, STAT3, IRF7, IRF9, IRF1, CEBPB, and SP1 as key transcriptional factors mediating the early response. Strikingly, the only difference in the transcriptional signatures of early DSS and UC dengue cases was the greater abundance of several neutrophil-associated transcripts in patients who progressed to DSS, a finding supported by higher plasma concentrations of several canonical proteins associated with neutrophil degranulation (bactericidal/permeability-increasing protein [BPI], elastase 2 [ELA2], and defensin 1 alpha [DEF1A]). Elevated levels of neutrophil-associated transcripts were independent of the neutrophil count and also of the genotype of the infecting virus, as genome-length sequences of dengue virus serotype 1 (DENV-1) (
n
= 15) and DENV-2 (
n
= 3) sampled from DSS patients were phylogenetically indistinguishable from those sampled from uncomplicated dengue patients (32 DENV-1 and 9 DENV-2 sequences). Collectively, these data suggest a hitherto unrecognized association between neutrophil activation, pathogenesis, and the development of DSS and point to future strategies for guiding prognosis.
Determinants of Strain-Specific Differences in Efficiency of Reovirus Entry
Authors: Sarkar Payel , Danthi Pranav
Published: October 2010

Cell entry of reovirus requires a series of ordered steps, which include conformational changes in outer capsid protein μ1 and its autocleavage. The μ1N fragment released as a consequence of these events interacts with host cell membranes and mediates their disruption, leading to delivery of the viral core into the cytoplasm. The prototype reovirus strains T1L and T3D exhibit differences in the efficiency of autocleavage, in the propensity to undergo conformational changes required for membrane penetration, and in the capacity for penetrating host cell membranes. To better understand how polymorphic differences in μ1 influence reovirus entry events, we generated recombinant viruses that express chimeric T1L-T3D μ1 proteins and characterized them for the capacity to efficiently complete each step required for membrane penetration. Our studies revealed two important functions for the central δ region of μ1. First, we found that μ1 autocleavage is regulated by the N-terminal portion of δ, which forms an α-helical pedestal structure. Second, we observed that the C-terminal portion of δ, which forms a jelly-roll β barrel structure, regulates membrane penetration by influencing the efficiency of ISVP* formation. Thus, our studies highlight the molecular basis for differences in the membrane penetration efficiency displayed by prototype reovirus strains and suggest that distinct portions of the reovirus δ domain influence different steps during entry.
Identification of Basic Amino Acids at the N-Terminal End of the Core Protein That Are Crucial for Hepatitis C Virus Infectivity
Authors: Alsaleh Khaled , Delavalle Pierre-Yves , Pillez André , Duverlie Gilles , Descamps Véronique , Rouillé Yves , Dubuisson Jean , Wychowski Czeslaw
Published: October 2010

A major function of the hepatitis C virus (HCV) core protein is the interaction with genomic RNA to form the nucleocapsid, an essential component of the virus particle. Analyses to identify basic amino acid residues of HCV core protein, important for capsid assembly, were initially performed with a cell-free system, which did not indicate the importance of these residues for HCV infectivity. The development of a cell culture system for HCV (HCVcc) allows a more precise analysis of these core protein amino acids during the HCV life cycle. In the present study, we used a mutational analysis in the context of the HCVcc system to determine the role of the basic amino acid residues of the core protein in HCV infectivity. We focused our analysis on basic residues located in two clusters (cluster 1, amino acids [aa]6 to 23; cluster 2, aa 39 to 62) within the N-terminal 62 amino acids of the HCV core protein. Our data indicate that basic residues of the first cluster have little impact on replication and are dispensable for infectivity. Furthermore, only four basic amino acids residues of the second cluster (R50, K51, R59, and R62) were essential for the production of infectious viral particles. Mutation of these residues did not interfere with core protein subcellular localization, core protein-RNA interaction, or core protein oligomerization. Moreover, these mutations had no effect on core protein envelopment by intracellular membranes. Together, these data indicate that R50, K51, R59, and R62 residues play a major role in the formation of infectious viral particles at a post-nucleocapsid assembly step.
Interaction of Poxvirus Intracellular Mature Virion Proteins with the TPR Domain of Kinesin Light Chain in Live Infected Cells Revealed by Two-Photon-Induced Fluorescence Resonance Energy Transfer Fluorescence Lifetime Imaging Microscopy
Authors: Jeshtadi Ananya , Burgos Pierre , Stubbs Christopher D. , Parker Anthony W. , King Linda A. , Skinner Michael A. , Botchway Stanley W.
Published: October 2010

Using two-photon-induced fluorescence lifetime imaging microscopy, we corroborate an interaction (previously demonstrated by yeast two-hybrid domain analysis) of full-length vaccinia virus (VACV; an orthopoxvirus) A36 protein with the cellular microtubule motor protein kinesin. Quenching of enhanced green fluorescent protein (EGFP), fused to the C terminus of VACV A36, by monomeric red fluorescent protein (mDsRed), fused to the tetratricopeptide repeat (TPR) domain of kinesin, was observed in live chicken embryo fibroblasts infected with either modified vaccinia virus Ankara (MVA) or wild-type fowlpox virus (FWPV; an avipoxvirus), and the excited-state fluorescence lifetime of EGFP was reduced from 2.5 ± 0.1 ns to 2.1 ± 0.1 ns due to resonance energy transfer to mDsRed. FWPV does not encode an equivalent of intracellular enveloped virion surface protein A36, yet it is likely that this virus too must interact with kinesin to facilitate intracellular virion transport. To investigate possible interactions between innate FWPV proteins and kinesin, recombinant FWPVs expressing EGFP fused to the N termini of FWPV structural proteins Fpv140, Fpv168, Fpv191, and Fpv198 (equivalent to VACV H3, A4, p4c, and A34, respectively) were generated. EGFP fusions of intracellular mature virion (IMV) surface protein Fpv140 and type II membrane protein Fpv198 were quenched by mDsRed-TPR in recombinant FWPV-infected cells, indicating that these virion proteins are found within 10 nm of mDsRed-TPR. In contrast, and as expected, EGFP fusions of the IMV core protein Fpv168 did not show any quenching. Interestingly, the p4c-like protein Fpv191, which demonstrates late association with preassembled IMV, also did not show any quenching.
MyD88 Signaling Is Indispensable for Primary Influenza A Virus Infection but Dispensable for Secondary Infection
Authors: Seo Sang-Uk , Kwon Hyung-Joon , Song Joo-Hye , Byun Young-Ho , Seong Baik Lin , Kawai Taro , Akira Shizuo , Kweon Mi-Na
Published: October 2010

Recent studies have revealed that innate immunity is involved in the development of adaptive immune responses; however, its role in protection is not clear. In order to elucidate the exact role of Toll-like receptor (TLR) or RIG-I-like receptor (RLR) signaling on immunogenicity and protective efficacy against influenza A virus infection (A/PR/8/34 [PR8]; H1N1), we adapted several innate signal-deficient mice (e.g., TRIF−/−, MyD88−/−, MyD88−/−TRIF−/−, TLR3−/−TLR7−/−, and IPS-1−/−). In this study, we found that MyD88 signaling was required for recruitment of CD11b+granulocytes, production of early inflammatory cytokines, optimal proliferation of CD4 T cells, and production of Th1 cytokines by T cells. However, PR8 virus-specific IgG and IgA antibody levels in both systemic and mucosal compartments were normal in TLR- and RLR-deficient mice. To further assess the susceptibility of these mice to influenza virus infection, protective efficacy was determined after primary or secondary lethal challenge. We found that MyD88−/−and MyD88−/−TRIF−/−mice were more susceptible to primary influenza virus infection than the B6 mice but were fully protected against homologous (H1N1) and heterosubtypic (H5N2) secondary infection when primed with a nonlethal dose of PR8 virus. Taken together, these results show that MyD88 signaling plays an important role for resisting primary influenza virus infection but is dispensable for protection against a secondary lethal challenge.
Discovery and Characterization of Mammalian Endogenous Parvoviruses
Authors: Kapoor Amit , Simmonds Peter , Lipkin W. Ian
Published: October 2010

Public databases of nucleotide sequences contain exponentially increasing amounts of sequence data from mammalian genomes. Through the use of large-scale bioinformatic screening for sequences homologous to exogenous mammalian viruses, we found several sequences related to human and animal parvoviruses (PVs) in the
Parvovirus
and
Dependovirus
genera within genomes of several mammals, including rats, wallabies, opossums, guinea pigs, hedgehogs, African elephants, and European rabbits. However, phylogenetic analysis of these endogenous parvovirus (EnPV) sequences demonstrated substantial genetic divergence from exogenous mammalian PVs characterized to date. Entire nonstructural and capsid gene sequences of a novel EnPV were amplified and genetically characterized from rat (
Rattus norvegicus
) genomic DNA. Rat EnPV sequences were most closely related to members of the genus
Parvovirus
, with >70% and 65% amino acid identities to nonstructural and capsid proteins of canine parvovirus, respectively. Integration of EnPV into chromosome 5 of rats was confirmed by PCR cloning and sequence analysis of the viral and chromosomal junctions. Using inverse PCR, we determined that the rat genome contains a single copy of rat EnPV. Considering mammalian phylogeny, we estimate that EnPV integrated into the rat genome less than 30 million years ago. Comparative phylogenetic analysis done using all known representative exogenous parvovirus (ExPV) and EnPV sequences showed two major genetic groups of EnPVs, one genetically more similar to genus
Parvovirus
and the other genetically more similar to the genus
Dependovirus
. The full extent of the genetic diversity of parvoviruses that have undergone endogenization during evolution of mammals and other vertebrates will be recognized only once complete genomic sequences from a wider range of classes, orders, and species of animals become available.
Ultrastructural Analysis of Virion Formation and Intraaxonal Transport of Herpes Simplex Virus Type 1 in Primary Rat Neurons
Authors: Negatsch Alexandra , Granzow Harald , Maresch Christina , Klupp Barbara G. , Fuchs Walter , Teifke Jens P. , Mettenleiter Thomas C.
Published: October 2010

After primary replication at the site of entry into the host, alphaherpesviruses infect and establish latency in neurons. To this end, they are transported within axons retrograde from the periphery to the cell body for replication and in an anterograde direction to synapses for infection of higher-order neurons or back to the periphery. Retrograde transport of incoming nucleocapsids is well documented. In contrast, there is still significant controversy on the mode of anterograde transport. By high-resolution transmission electron microscopy of primary neuronal cultures from embryonic rat superior cervical ganglia infected by pseudorabies virus (PrV), we observed the presence of enveloped virions in axons within vesicles supporting the “married model” of anterograde transport of complete virus particles within vesicles (C. Maresch, H. Granzow, A. Negatsch, B.G. Klupp, W. Fuchs, J.P. Teifke, and T.C. Mettenleiter, J. Virol.
84:
5528-5539, 2010). We have now extended these analyses to the related human herpes simplex virus type 1 (HSV-1). We have demonstrated that in neurons infected by HSV-1 strains HFEM, 17+ or SC16, approximately 75% of virus particles observed intraaxonally or in growth cones late after infection constitute enveloped virions within vesicles, whereas approximately 25% present as naked capsids. In general, the number of HSV-1 particles in the axons was significantly less than that observed after PrV infection.
The threshold level of urinary cadmium associated with increased urinary excretion of retinol-binding protein and β2-microglobulin: a re-assessment in a large cohort of nickel-cadmium battery workers
Authors: Chaumont Agnès , De Winter Frédéric , Dumont Xavier , Haufroid Vincent , Bernard Alfred
Published: October 2010

Objective

To evaluate the threshold value of urinary cadmium (CdU) for renal dysfunction on the basis of relationships unconfounded by protein degradation, diuresis and the renal effects associated with chronic smoking.

Methods

We studied 599 workers (451 men, mean age 45.4 years) who were employed in four nickel-cadmium battery plants for 18.8 years on average. After adjustment for covariates by multiple regression, the CdU threshold values for increased concentrations of retinol-binding protein (RBPU) and b2-microglobulin (b2-mU) were assessed by logistic regression and benchmark dose analyses using as referents workers with CdU<1 μg/g creatinine.

Results

Relationships between urinary proteins and CdU (μg/g creatinine) were influenced by sex, age, diuresis and especially smoking. When considering all workers, odds for abnormal RBPU and b2-mU were significantly increased from CdU of 6-10 and >10, respectively. The benchmark dose (BMD5) and the benchmark dose lower limit (BMDL5) for a 5% excess in the background prevalence of abnormal RBPU and b2-mU were estimated at 5.1/3.0 and 9.6/5.9. When excluding ever smokers, odds for abnormal RBPU and b2-mU were both increased only among workers with CdU>10 (OR, 21.8, 95% CI, 6.4-74.4 and OR, 15.1, 95% CI, 3.6-63.1, respectively). In never smokers, these BMD5/BMDL5 of CdU were estimated at 12.6/6.6 and 12.2/5.5 while in ever smokers they were 6.2/4.9 and 4.3/3.5.

Conclusions

On the basis of associations undistorted by smoking and adjusted for covariates, the BMDL5 of CdU for low-molecular-weight proteinuria induced by occupational exposure to Cd can be reliably estimated between 5.5 and 6.6 μg/g creatinine.
A meta-analysis of leukaemia risk from protracted exposure to low-dose gamma radiation
Authors: Daniels R D , Schubauer-Berigan M K
Published: October 2010

Context

More than 400 000 workers annually receive a measurable radiation dose and may be at increased risk of radiation-induced leukaemia. It is unclear whether leukaemia risk is elevated with protracted, low-dose exposure.

Objective

We conducted a meta-analysis examining the relationship between protracted low-dose ionising radiation exposure and leukaemia.

Data sources

Reviews by the National Academies and United Nations provided a summary of informative studies published before 2005. PubMed and Embase databases were searched for additional occupational and environmental studies published between 2005 and 2009.

Study selection

We selected 23 studies that: (1) examined the association between protracted exposures to ionising radiation and leukaemia excluding chronic lymphocytic subtype; (2) were a cohort or nested case–control design without major bias; (3) reported quantitative estimates of exposure; and (4) conducted exposure–response analyses using relative or excess RR per unit exposure.

Methods

Studies were further screened to reduce information overlap. Random effects models were developed to summarise between-study variance and obtain an aggregate estimate of the excess RR at 100 mGy. Publication bias was assessed by trim and fill and Rosenthal's file drawer methods.

Results

We found an ERR at 100 mGy of 0.19 (95% CI 0.07 to 0.32) by modelling results from 10 studies and adjusting for publication bias. Between-study variance was not evident (p=0.99).

Conclusions

Protracted exposure to low-dose gamma radiation is significantly associated with leukaemia. Our estimate agreed well with the leukaemia risk observed among exposed adults in the Life Span Study (LSS) of atomic bomb survivors, providing increased confidence in the current understanding of leukaemia risk from ionising radiation. However, unlike the estimates obtained from the LSS, our model provides a precise, quantitative summary of the direct estimates of excess risk from studies of protracted radiation exposures.
Job stress and the use of antidepressant medicine: a 3.5-year follow-up study among Danish employees
Authors: Thielen Karsten , Nygaard Else , Rugulies Reiner , Diderichsen Finn
Published: October 2010

Objectives

To investigate if exposure to adverse psychological job characteristics predicts incident use of antidepressants, taking into account differential misclassification and residual confounding.

Methods

A prospective cohort study with a 3.5-year follow-up of 4661 Danish employees, aged 40 and 50 years, drawn from a 10% random sample of the Danish population was carried out. Job characteristics were the predictor variables and use of antidepressants was the outcome variable. Survey data on psychosocial work environment were linked with register data on dispensing of antidepressant medicine between June 2000 and December 2003. Respondents with major depression at baseline, with antidepressant use in the 5 years preceding baseline, or not employed at baseline were excluded.

Results

Among men, the OR for antidepressant use was significantly increased for high quantitative demands (OR 2.12, 95% CI 1.29 to 3.48) and low social support from colleagues (OR 2.28, 95% 1.36 to 3.82) after adjustment for lifestyle factors, socio-demographic factors, co-morbidity, other work factors and depressive symptoms at baseline. Both effects were dose dependent. An interaction effect with high demands was found for high anticipated private social support and living with children. Among women, no effect of job characteristics on antidepressant use was found.

Conclusion

Among men, but not among women, high quantitative demands and low social support from colleagues were predictive of incident use of antidepressants, indicating incident depressive episodes, even after taking into account differential misclassification and residual confounding. The effects were buffered for those with high anticipated private social support and for those having children.
Quantifying tooth variation within a single population ofAlbertosaurus sarcophagus(Theropoda: Tyrannosauridae) and implications for identifying isolated teeth of tyrannosauridsThis article is one of a series of papers published in this Special Issue on the themeAlbertosaurus.
Authors: Buckley Lisa G. , Larson Derek W. , Reichel Miriam , Samman Tanya
Published: October 2010

Documenting variation in theropod dinosaurs is usually hindered by the lack of a large sample size and specimens representing several ontogenetic stages. Here, variation within 140 disassociated and seven in situ tyrannosaur teeth from the Upper Cretaceous (lower Maastrichtian) monodominant Albertosaurus sarcophagus (Theropoda: Tyrannosauridae) bonebed is documented. This sample represents the largest data set of teeth from one population of A. sarcophagus containing both adult and juvenile specimens. Tooth variation was assessed using multivariate analyses (principal component, discriminant, and canonical variate analyses). Heterodonty in the teeth of A. sarcophagus contributes to the large amount of variation in the data set. Premaxillary teeth are significantly different from maxillary and dentary teeth, but there is no quantifiable difference between a priori identified maxillary and dentary teeth. Juvenile and adult teeth of A. sarcophagus show apparent quantitative differences that are size dependent on closer investigation, suggesting a cautious approach when interpreting multivariate analyses to identify novel tooth morphologies. Multivariate analyses on teeth of A. sarcophagus and published tooth data from other North American tyrannosaurid species reveals species-level clusters with little separation. The degree of separation among tooth clusters may reveal a phylogenetic signal in tyrannosaurid teeth.
Stratigraphy, sedimentology, and taphonomy of the Albertosaurus bonebed (upper Horseshoe Canyon Formation; Maastrichtian), southern Alberta, CanadaThis article is one of a series of papers published in this Special Issue on the theme Albertosaurus.
Authors: Eberth David A. , Currie Philip J.
Published: October 2010

The Albertosaurus bonebed provides evidence for the mass-mortality of at least 12 Albertosaurus . Albertosaurus, other vertebrates, and trees are concentrated on upper point bar surfaces of a small meandering paleochannel. Throughout the field area, Albertosaurus, other vertebrates, and coalified plants are also preserved patchily in overbank mudstones at the same horizon. Although the bonebed is dominated by Albertosaurus, there are also sparse macrofossil remains of Hypacrosaurus and Albertonykus . The basal lag yields vertebrate microfossils containing at least 19 additional taxa. Freshwater invertebrates are preserved at and below the base of the paleochannel. Large elements are over represented at the site, whereas smaller elements are under represented, suggesting hydraulic sorting. The taphonomic signature of the site suggests that death, disarticulation, and burial took place within one year. We conclude that one or more storms of large intensity downed trees and temporarily drowned the paleolandscape, ultimately killing the tyrannosaurids directly or indirectly. Logs and carcasses were reworked on a point bar during the waning stages of the storm and over subsequent years. Scavenging and breakage of remains by large carnivores was probably inhibited by the mixed log and bone jam. Remains of smaller scavengers (small theropods and snails) are plentiful suggesting these forms were more successful at accessing remains. Juvenile Albertosaurus are under represented at the site suggesting the possibility of age segregation. Because the group of Albertosaurus may have been forced together by rising floodwaters, it is not possible to assess the degree to which the taxon was gregarious from these data alone.
A history of Albertosaurus discoveries in Alberta, CanadaThis article is one of a series of papers published in this Special Issue on the theme Albertosaurus.
Authors: Tanke Darren H. , Currie Philip J.
Published: October 2010

After many years of taxonomic uncertainty, Albertosaurus was established as a new genus in 1905, the year Alberta became a province of Canada. Gorgosaurus is a closely related tyrannosaurid from the Judithian beds of southern Alberta that was subsequently synonymized with Albertosaurus. Although most researchers consider the genera as distinct, there has been considerable confusion over the temporal and geographic range of Albertosaurus. Albertosaurus sarcophagus is only known from 13 skulls and (or) skeletons of varying completeness, and one (possibly two) bonebeds, all from the Horseshoe Canyon Formation (Campanian–Maastrichtian) of Alberta. Many of the major Albertosaurus specimens are scientifically compromised due to poor collection techniques, incomplete locality and stratigraphic information, politics, vandalism, accidents, gunplay, and landowner issues. The background of each specimen is discussed to eliminate some of the sources of confusion and to document how much of each specimen is preserved.
Upper Cretaceous palynostratigraphy of the Dry Island areaThis article is one of a series of papers published in this Special Issue on the themeAlbertosaurus.
Authors: Koppelhus E. B. , Braman D. R.
Published: October 2010

The overall palynology of the upper Horseshoe Canyon Formation to lower Scollard Formation within the Edmonton Group is reviewed providing new insights into biostratigraphic relationships for the interval, including the recognition of unconformities in the stratigraphic package. The palynomorph recovery from the Horseshoe Canyon Formation and overlying units documents a number of significant events that allow the subdivision of the section. The Albertosaurus bonebed occurs within the lower Maastrichtian portion of the Edmonton Group. The bonebed is situated just below the base of the Scollardia trapaformis Palynomorph Zone, an important marker assemblage that has been documented from areas of the Yukon, Northwest Territories, Alberta, and Saskatchewan. This indicates that the bonebed lies at the top of the Mancicorpus vancampoi Zone. The transition between the zones is marked by a colour change in the sediments, the appearance of coals and organic-rich sediments above the transition, a decrease in numbers of vertebrate fossils, and the appearance of new pollen species. It is inferred that the observed changes reflect a climatic switch from dry to wetter conditions. At a large scale, palynomorph assemblages across this transition do not clearly indicate marked differences that can be attributed to the climatic change, with the exception of the appearance of Scollardia trapaformis and Mancicorpus gibbus in the assemblages. On a microscale of a few metres, there are changes in relative abundance of plant groups.
Modular incorporation of 1-benzyltryptophan into dipeptide hosts that bind acetylcholine in pure water
Authors: Beshara Cory S. , Hof Fraser
Published: October 2010

Proteins that recognize and bind quaternary ammonium ions depend on “aromatic-cage” structural motifs that use multiple aromatic residues to engage the side chain’s ammonium cation. We introduce herein the use of 1-benzyltryptophan (Trp(Bn)) residues as synthetic, unnatural partial analogues of natural aromatic cages. We demonstrate the modular incorporation of these building blocks into simple dipeptide hosts and show that they are capable of binding quaternary ammonium ions in buffered water and in chloroform.