bluuebunny/crossref_metadata_2025_split huggingface dataset:
DNA Pyrosequencing-Based Bacterial Pathogen Identification in a Pediatric Hospital Setting
Authors: Luna Ruth Ann , Fasciano Lea R. , Jones Shaunte C. , Boyanton Bobby L. , Ton Trang T. , Versalovic James 
Published: July 2007

ABSTRACT
Sole reliance on biochemical methods can limit the clinical microbiology laboratory's ability to identify bacterial pathogens. This study describes the incorporation of DNA pyrosequencing-based identification for routine pathogen identification of atypical clinical isolates in a large children's hospital. The assay capitalized on the highly conserved nature of 16S rRNA genes by positioning amplification and sequencing primers in conserved target sequences flanking the variable V1 and V3 regions. A total of 414 isolates of 312 pediatric patients were tested by DNA pyrosequencing during the time period from December 2003 to July 2006. Seventy-eight different genera were specified by DNA pyrosequencing, and isolates were derived from diverse specimen types. By integrating DNA sequencing of bacterial pathogens with conventional microbiologic methods, isolates that lacked a definitive identification by biochemical testing yielded genus- or species-level identifications in approximately 90% of cases by pyrosequencing. Improvements incorporated into the assay process during the period of clinical testing included software enhancements, improvements in sequencing reagents, and refinements in database search strategies. Coupled with isolation by bacteriologic culture and biochemical testing, DNA pyrosequencing-based bacterial identification was a valuable tool that markedly improved bacterial pathogen identification in a pediatric hospital setting.
Catheter-Related Fungemia Due to Fluconazole-Resistant
Candida nivariensis
Authors: Fujita Shin-ichi , Senda Yasuko , Okusi Tikako , Ota Yumi , Takada Hideaki , Yamada Kazunori , Kawano Mitsuhiro 
Published: July 2007

ABSTRACT

We report on a case of fungemia due to fluconazole-resistant
Candida nivariensis
(MIC, ≥128 μg/ml). Internal transcribed spacer PCR followed by microchip gel electrophoresis with a blood culture that tested positive revealed a unique pattern different from those of other pathogenic yeasts.
Binding of Kaposi's Sarcoma-Associated Herpesvirus K-bZIP to Interferon-Responsive Factor 3 Elements Modulates Antiviral Gene Expression
Authors: Lefort Sylvain , Soucy-Faulkner Anton , Grandvaux Nathalie , Flamand Louis 
Published: July 2007

ABSTRACT

Kaposi's sarcoma-associated herpesvirus encodes numerous regulatory proteins capable of modulating viral and cellular gene expression and affecting host cell functions. K-bZIP, a leucine zipper-containing transcription factor encoded by ORFK8, is one such protein. During infection, transcription of the ORFK8 early gene is turned on by the immediate-early replication and transcription factor activator (RTA). One described function of the K-bZIP nuclear protein is to interact with and repress RTA-mediated transactivation of viral promoters, including that of the
K8
gene. In the present work, we provide evidence that the expression of K-bZIP results in the activation of the
ifn
-β gene. Of interest,
ifn
-β gene activation by K-bZIP is independent of interferon (IFN)-responsive factor 3 (IRF-3) and nuclear factor κB (NF-κB) activation. Using a DNA binding affinity assay and electromobility shift assay, we report that K-bZIP binds efficiently to the PRDIII-I region of the beta IFN (IFN-β) promoter, and, in doing so, it prevents the attachment of activated IRF-3 but not that of NF-κB or ATF2/c-Jun to the IFN-β promoter sequence. As a consequence,
ifn
-β gene activation in response to IFN inducers such as Sendai virus infection or expression of retinoic acid-inducible gene I, mitochondrial antiviral signaling protein, or TANK-binding kinase 1 (TBK-1) is severely impaired (>90%) by the presence of K-bZIP. K-bZIP also prevents the activation of RANTES and CXCL11, whose promoters are also regulated by IRF-3. Lysine 158 (target for SUMO conjugation), threonine 111, and serine 167 (targets for phosphorylation) mutants of K-bZIP were equally effective as wild-type K-bZIP in mediating the repression of TBK-1-activated
ifn
-β gene expression. Lastly, the overexpression of CREB binding protein could not reverse the K-bZIP repression of TBK-1-activated
ifn
-β gene expression. In all, our results indicate that K-bZIP binds directly to the PRDIII-I region of the IFN-β promoter and, as a consequence, causes a low level of
ifn
-β gene transcription. In doing so, K-bZIP prevents IRF-3 from binding to the IFN-β promoter and precludes the formation of the enhanceosome, which is required for maximal
ifn
-β gene transcription. A new role for K-bZIP as a protein involved in immune evasion is therefore uncovered.
Emerin Is Hyperphosphorylated and Redistributed in Herpes Simplex Virus Type 1-Infected Cells in a Manner Dependent on both UL34 and US3
Authors: Leach Natalie , Bjerke Susan L. , Christensen Desire K. , Bouchard Jacques M. , Mou Fan , Park Richard , Baines Joel , Haraguchi Tokuko , Roller Richard J. 
Published: July 2007

ABSTRACT
Cells infected with wild-type herpes simplex virus type 1 (HSV-1) show disruption of the organization of the nuclear lamina that underlies the nuclear envelope. This disruption is reflected in changes in the localization and phosphorylation of lamin proteins. Here, we show that HSV-1 infection causes relocalization of the LEM domain protein emerin. In cells infected with wild-type virus, emerin becomes more mobile in the nuclear membrane, and in cells infected with viruses that fail to express UL34 protein (pUL34) and US3 protein (pUS3), emerin no longer colocalizes with lamins, suggesting that infection causes a loss of connection between emerin and the lamina. Infection causes hyperphosphorylation of emerin in a manner dependent upon both pUL34 and pUS3. Some emerin hyperphosphorylation can be inhibited by the protein kinase Cδ (PKCδ) inhibitor rottlerin. Emerin and pUL34 interact physically, as shown by pull-down and coimmunoprecipitation assays. Emerin expression is not, however, necessary for infection, since virus growth is not impaired in cells derived from emerin-null transgenic mice. The results suggest a model in which pUS3 and PKCδ that has been recruited by pUL34 hyperphosphorylate emerin, leading to disruption of its connections with lamin proteins and contributing to the disruption of the nuclear lamina. Changes in emerin localization, nuclear shape, and lamin organization characteristic of cells infected with wild-type HSV-1 also occur in cells infected with recombinant virus that does not make viral capsids, suggesting that these changes occur independently of capsid envelopment.
Molecular Profiling of Ovine Prion Diseases by Using Thermolysin-Resistant PrP
Sc
and Endogenous C2 PrP Fragments
Authors: Owen Jonathan P. , Rees Helen C. , Maddison Ben C. , Terry Linda A. , Thorne Leigh , Jackman Roy , Whitelam Garry C. , Gough Kevin C. 
Published: July 2007

ABSTRACT

Disease-associated PrP fragments produced upon in vitro or in vivo proteolysis can provide significant insight into the causal strain of prion disease. Here we describe a novel molecular strain typing assay that used thermolysin digestion of caudal medulla samples to produce PrP
res
signatures on Western blots that readily distinguished experimental sheep bovine spongiform encephalopathy (BSE) from classical scrapie. Furthermore, the accumulation of such PrP
res
species within the cerebellum also appeared to be dependent upon the transmissible spongiform encephalopathy (TSE) strain, allowing discrimination between two experimental strains of scrapie and grouping of natural scrapie isolates into two profiles. The occurrence of endogenously produced PrP fragments, namely, glycosylated and unglycosylated C2, within different central nervous system (CNS) regions is also described; this is the first detailed description of such scrapie-associated fragments within a natural host. The advent of C2 fragments within defined CNS regions, compared between BSE and scrapie cases and also between two experimental scrapie strains, appeared to be largely dependent upon the TSE strain. The combined analyses of C2 fragments and thermolysin-resistant PrP species within caudal medulla, cerebellum, and spinal cord samples allowed natural scrapie isolates to be separated into four distinct molecular profiles: most isolates produced C2 and PrP
res
in all CNS regions, a second group lacked detectable cerebellar C2 fragments, one isolate lacked both cerebellar PrP
res
and C2, and a further isolate lacked detectable C2 within all three CNS regions and also lacked cerebellar PrP
res
. This CNS region-specific deposition of disease-associated PrP species may reflect the natural heterogeneity of scrapie strains in the sheep population in the United Kingdom.
Adenovirus Virus-Associated RNAII-Derived Small RNAs Are Efficiently Incorporated into the RNA-Induced Silencing Complex and Associate with Polyribosomes
Authors: Xu Ning , Segerman Bo , Zhou Xiaofu , Akusjärvi Göran 
Published: July 2007

ABSTRACT
Adenovirus type 5 encodes two highly structured short RNAs, the virus-associated (VA) RNAI and RNAII. Both are processed by Dicer into small RNAs that are incorporated into the RNA-induced silencing complex (RISC). We show here, by cloning of small RNAs, that approximately 80% of Ago2-containing RISC immunopurified from late-infected cells is associated with VA RNA-derived small RNAs (mivaRNAs). Most surprisingly, VA RNAII, which is expressed at 20-fold lower levels compared to that of VA RNAI, appears to be the preferred substrate for Dicer and accounts for approximately 60% of all small RNAs in RISC. The mivaRNAs are derived from the 3′ strand of the terminal stems of the VA RNAs, with the major fraction of VA RNAII starting at position 138. The small RNAs derived from VA RNAI were more heterogeneous in size, with the two predominant small RNAs starting at positions 137 and 138. Collectively, our results suggest that the mivaRNAs are efficiently used for RISC assembly in late-infected cells. Potentially, they function as miRNAs, regulating translation of cellular mRNAs. In support of this hypothesis, we detected a fraction of the VA RNAII-derived mivaRNAs on polyribosomes.
Persistent Host Markers in Pandemic and H5N1 Influenza Viruses
Authors: Finkelstein David B. , Mukatira Suraj , Mehta Perdeep K. , Obenauer John C. , Su Xiaoping , Webster Robert G. , Naeve Clayton W. 
Published: July 2007

ABSTRACTAvian influenza viruses have adapted to human hosts, causing pandemics in humans. The key host-specific amino acid mutations required for an avian influenza virus to function in humans are unknown. Through multiple-sequence alignment and statistical testing of each aligned amino acid, we identified markers that discriminate human influenza viruses from avian influenza viruses. We applied strict thresholds to select only markers which are highly preserved in human influenza virus isolates over time. We found that a subset of these persistent host markers exist in all human pandemic influenza virus sequences from 1918, 1957, and 1968, while others are acquired as the virus becomes a seasonal influenza virus. We also show that human H5N1 influenza viruses are significantly more likely to contain the amino acid predominant in human strains for a few persistent host markers than avian H5N1 influenza viruses. This sporadic enrichment of amino acids present in human-hosted viruses may indicate that some H5N1 viruses have made modest adaptations to their new hosts in the recent past. The markers reported here should be useful in monitoring potential pandemic influenza viruses.
Endoribonuclease-Prepared Short Interfering RNAs Induce Effective and Specific Inhibition of Human Immunodeficiency Virus Type 1 Replication
Authors: Gimenez-Barcons Mireia , Clotet Bonaventura , Martinez Miguel Angel 
Published: July 2007

ABSTRACT

Short interfering RNAs (siRNAs) targeting viral or cellular genes can efficiently inhibit human immunodeficiency virus type 1 (HIV-1) replication. Nevertheless, optimal HIV-1 gene silencing by siRNA requires precise complementarity with most of the target sequence. The emergence of mutations in the targeted gene could lead to rapid viral escape from the siRNA. In the present study,
Escherichia coli
endoribonuclease III (RNase III) or mammalian Dicer was used to cleave double-stranded RNA into endoribonuclease-prepared siRNA (esiRNA). esiRNAs generate a variety of siRNAs which can efficiently and specifically target multiple sites in the cognate RNA. esiRNAs targeting the region encoding the HIV-1 reverse transcriptase (RT) reduced viral replication by 90%. The inhibition was dose dependent and sequence specific because several irrelevant esiRNAs did not inhibit HIV-1 replication. Importantly, esiRNAs obtained from the prototypic RT sequence of the HXB2 strain and from highly mutated RT sequences showed similar degrees of viral inhibition, suggesting that the heterogeneous population of esiRNAs could overcome individual mismatches in the RT sequence. Finally, esiRNAs generated by Dicer cleavage were five times more potent than those generated by bacterial RNase III digestion. These results show that esiRNAs are potent HIV-1 inhibitors. Moreover, sequence targets do not need to be highly conserved to reach a high level of viral replication inhibition.
Single Amino Acid Changes in the Nipah and Hendra Virus Attachment Glycoproteins Distinguish EphrinB2 from EphrinB3 Usage
Authors: Negrete Oscar A. , Chu David , Aguilar Hector C. , Lee Benhur 
Published: July 2007

ABSTRACT
The henipaviruses, Nipah virus (NiV) and Hendra virus (HeV), are lethal emerging paramyxoviruses. EphrinB2 and ephrinB3 have been identified as receptors for henipavirus entry. NiV and HeV share similar cellular tropisms and likely use an identical receptor set, although a quantitative comparison of receptor usage by NiV and HeV has not been reported. Here we show that (i) soluble NiV attachment protein G (sNiV-G) bound to cell surface-expressed ephrinB3 with a 30-fold higher affinity than that of sHeV-G, (ii) NiV envelope pseudotyped reporter virus (NiVpp) entered ephrinB3-expressing cells much more efficiently than did HeV pseudotyped particles (HeVpp), and (iii) NiVpp but not HeVpp entry was inhibited efficiently by soluble ephrinB3. These data underscore the finding that NiV uses ephrinB3 more efficiently than does HeV. Henipavirus G chimeric protein analysis implicated residue 507 in the G ectodomain in efficient ephrinB3 usage. Curiously, alternative versions of published HeV-G sequences show variations at residue 507 that can clearly affect ephrinB3 but not ephrinB2 usage. We further defined surrounding mutations (W504A and E505A) that diminished ephrinB3-dependent binding and viral entry without compromising ephrinB2 receptor usage and another mutation (E533Q) that abrogated both ephrinB2 and -B3 usage. Our results suggest that ephrinB2 and -B3 binding determinants on henipavirus G are distinct and dissociable. Global expression analysis showed that ephrinB3, but not ephrinB2, is expressed in the brain stem. Thus, ephrinB3-mediated viral entry and pathology may underlie the severe brain stem neuronal dysfunction seen in fatal Nipah viral encephalitis. Characterizing the determinants of ephrinB2 versus -B3 usage will further our understanding of henipavirus pathogenesis.
The
Mx1
Gene Protects Mice against the Pandemic 1918 and Highly Lethal Human H5N1 Influenza Viruses
Authors: Tumpey Terrence M. , Szretter Kristy J. , Van Hoeven Neal , Katz Jacqueline M. , Kochs Georg , Haller Otto , García-Sastre Adolfo , Staeheli Peter 
Published: July 2007

ABSTRACT

Mice carrying a wild-type
Mx1
gene (
Mx1

+/+

) differ from standard laboratory mice (
Mx1
−/−
) in being highly resistant to infection with common laboratory strains of influenza A virus. We report that
Mx1
also protects mice against the pandemic human 1918 influenza virus and a highly lethal human H5N1 strain from Vietnam. Resistance to H5N1 of
Mx1

+/+

but not
Mx1
−/−
mice was enhanced if the animals were treated with a single dose of exogenous alpha interferon before infection. Thus, the interferon-induced resistance factor Mx1 represents a key component of the murine innate immune system that mediates protection against epidemic and pandemic influenza viruses.
Incorporation of Functional HN-F Glycoprotein-Containing Complexes into Newcastle Disease Virus Is Dependent on Cholesterol and Membrane Lipid Raft Integrity
Authors: Laliberte Jason P. , McGinnes Lori W. , Morrison Trudy G. 
Published: July 2007

ABSTRACT
Newcastle disease virus assembles in plasma membrane domains with properties of membrane lipid rafts, and disruption of these domains by cholesterol extraction with methyl-β-cyclodextrin resulted in the release of virions with irregular protein composition, abnormal particle density, and reduced infectivity (J. P. Laliberte, L. W. McGinnes, M. E. Peeples, and T. G. Morrison, J. Virol. 80:10652-10662, 2006). In the present study, these results were confirmed using Niemann-Pick syndrome type C cells, which are deficient in normal membrane rafts due to mutations affecting cholesterol transport. Furthermore, cholesterol extraction of infected cells resulted in the release of virions that attached to target cells at normal levels but were defective in virus-cell membrane fusion. The reduced fusion capacity of particles released from cholesterol-extracted cells correlated with significant loss of HN-F glycoprotein-containing complexes detected in the virion envelopes of these particles and with detection of cell-associated HN-F protein-containing complexes in extracts of cholesterol-extracted cells. Extraction of cholesterol from purified virions had no effect on virus-cell attachment, virus-cell fusion, particle infectivity, or the levels of glycoprotein-containing complexes. Taken together, these results suggest that cholesterol and membrane rafts are required for the formation or maintenance of HN-F glycoprotein-containing complexes in cells but not the stability of preformed glycoprotein complexes once assembled into virions.
Flow perturbation folding in shear zones
Authors: Alsop G. I. , Holdsworth R. E. 
Published: July 2007

Abstract
Variable patterns of displacement in shear zones may result in arcuate fold and fault traces as recognized by Mike Coward and co-workers in the early 1980s. Within such deformation zones, localized perturbations in flow may undergo acceleration (surging flow) or deceleration (slackening flow) with respect to the adjacent regions. Such flow cells may govern the orientation and geometries of folds and fabrics and thereby provide evidence of the scale and nature of deformation associated with heterogeneous flow in the high-strain zones. The length/width ratio of individual flow cells (measured in the direction of flow) may vary from <1 to >1 for situations when flow cells are, respectively, dominated by layer-parallel shear (LPS) or layer-normal shear (LNS). Folds initiating at high angles to transport are associated with LPS, whereas LNS may generate folds with slight clockwise (sinistral LNS) or anticlockwise (dextral LNS) trends relative to flow. Continued progressive deformation may subsequently modify and reduce angular relationships between folds and fabrics, but these geometric obliquities are generally preserved. Using examples from the Moine metasediments of northern Scotland, we show that folding displays predictable geometric patterns that can be related to the development of flow perturbation cells associated with Caledonian ductile thrusting under mid-crustal conditions. The differing relative timing of folds and individual ductile thrusts reflects the complexity of flow cells within ductile imbricates and additionally highlights the progressive foreland-directed propagation of ductile thrusting. These geometric relationships developed during contractional shear are compared with those generated in extensional systems, to provide an overall framework for the study of perturbation patterns. The geometric arrangement of mean fold axial planes about the flow direction results in their intersection forming parallel to the transport direction. This relationship permits transport directions to be calculated via the axial-planar intersection method (AIM), and also allows comparison with other techniques devised primarily for the study of soft-sediment deformation and palaeoslope analysis.
Analysis of a mesoscopic duplex in SW Tuscany, Italy: implications for thrust system development during positive tectonic inversion
Authors: Casini Giulio , Decandia Francesco Antonio , Tavarnelli Enrico 
Published: July 2007

Abstract
The advances in the field of inversion tectonics, pioneered by Mike Coward and co-workers, have shown that many thrust belts originated at the expense of pre-orogenic rift basins that originally had complex extensional architectures. These architectures are reflected by significant lateral thickness and facies changes within the deformed stratigraphic sequences. Although these changes are widely documented from the restoration of balanced sections across thrust fans, they are significantly less well documented from restoration of duplex structures. As a consequence, most available duplex models assume layer-cake stratigraphic sequences. In this contribution a peculiar mesoscopic duplex is described. This structure developed across a single irregular, previously extended quartzite layer of the Arenarie di Poggio al Carpino Formation (Upper Permian-Lower Triassic), during the Late Tertiary orogenic event that led to development of the Apennine chain. Through comparison of the analysed duplex with macroscopic analogues, it is proposed that similar structures may occur on a wide variety of scales, in the Apennines as well as in other orogenic belts.
Structural style and hydrocarbon prospectivity in fold and thrust belts: a global review
Authors: Cooper Mark 
Published: July 2007

Abstract
A statistical analysis of reserves in fold and thrust belts, grouped by their geological attributes, indicates which of the world's fold and thrust belts are the most prolific hydrocarbon provinces. The Zagros Fold Belt contains 490f reserves in fold and thrust belts and has been isolated during the analysis to avoid bias. Excluding the Zagros Fold Belt, most of the reserves are in thin-skinned fold and thrust belts that have no salt detachment or salt seal, are partially buried by syn- or post-orogenic sediments, are sourced by Cretaceous source rocks and underwent their last phase of deformation during the Tertiary. A significant observation is that the six most richly endowed fold and thrust belts have no common set of geological attributes, implying that these fold belts all have different structural characteristics. The implication is that deformation style is a not critical factor for the hydrocarbon endowment of fold and thrust belts; other elements of the petroleum system must be more significant. Other fold and thrust belts may share the structural attributes but the resource-rich fold belts overwhelmingly dominate the total reserves in that group of fold belts. There is nothing intrinsic in fold and thrust belts that differentiates them from other oil- and gas-rich provinces other than the prolific development of potential hydrocarbon traps. Many of the prolific, proven fold and thrust belts still have significant remaining exploration potential as a result of politically challenging access and remote locations.