bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fusion-Deficient Insertion Mutants of Herpes Simplex Virus Type 1 Glycoprotein B Adopt the Trimeric Postfusion Conformation
Authors: Silverman Jessica L. , Sharma Sapna , Cairns Tina M. , Heldwein Ekaterina E. 
Published: November 2009

ABSTRACT
Glycoprotein B (gB) enables the fusion of viral and cell membranes during entry of herpesviruses. However, gB alone is insufficient for membrane fusion; the gH/gL heterodimer is also required. The crystal structure of the herpes simplex virus type 1 (HSV-1) gB ectodomain, gB730, has demonstrated similarities between gB and other viral fusion proteins, leading to the hypothesis that gB is a fusogen, presumably directly involved in bringing the membranes together by refolding from its initial or prefusion form to its final or postfusion form. The only available crystal structure likely represents the postfusion form of gB; the prefusion form has not yet been determined. Previously, a panel of HSV-1 gB mutants was generated by using random 5-amino-acid-linker insertion mutagenesis. Several mutants were unable to mediate cell-cell fusion despite being expressed on the cell surface. Mapping of the insertion sites onto the crystal structure of gB730 suggested that several insertions might not be accommodated in the postfusion form. Thus, we hypothesized that some insertion mutants were nonfunctional due to being “trapped” in a prefusion form. Here, we generated five insertion mutants as soluble ectodomains and characterized them biochemically. We show that the ectodomains of all five mutants assume conformations similar to that of the wild-type gB730. Four mutants have biochemical properties and overall structures that are indistinguishable from those of the wild-type gB730. We conclude that these mutants undergo only minor local conformational changes to relieve the steric strain resulting from the presence of 5 extra amino acids. Interestingly, one mutant, while able to adopt the overall postfusion structure, displays significant conformational differences in the vicinity of fusion loops, relative to wild-type gB730. Moreover, this mutant has a diminished ability to associate with liposomes, suggesting that the fusion loops in this mutant have decreased functional activity. We propose that these insertions cause a fusion-deficient phenotype not by preventing conversion of gB to a postfusion-like conformation but rather by interfering with other gB functions.
Inactivation of
Burkholderia cepacia
Complex Phage KS9 gp41 Identifies the Phage Repressor and Generates Lytic Virions
Authors: Lynch Karlene H. , Seed Kimberley D. , Stothard Paul , Dennis Jonathan J. 
Published: November 2009

ABSTRACT

The
Burkholderia cepacia
complex (BCC) is made up of at least 17 species of Gram-negative opportunistic bacterial pathogens that cause fatal infections in patients with cystic fibrosis and chronic granulomatous disease. KS9 (vB_BcenS_KS9), one of a number of temperate phages isolated from BCC species, is a prophage of
Burkholderia pyrrocinia
LMG 21824. Transmission electron micrographs indicate that KS9 belongs to the family
Siphoviridae
and exhibits the B1 morphotype. The 39,896-bp KS9 genome, comprised of 50 predicted genes, integrates into the 3′ end of the LMG 21824 GTP cyclohydrolase II open reading frame. The KS9 genome is most similar to uncharacterized prophage elements in the genome of
B. cenocepacia
PC184 (vB_BcenZ_ PC184), as well as
Burkholderia thailandensis
phage φE125 and
Burkholderia pseudomallei
phage φ1026b. Using molecular techniques, we have disrupted KS9 gene
41
, which exhibits similarity to genes encoding phage repressors, producing a lytic mutant named KS9c. This phage is incapable of stable lysogeny in either LMG 21824 or
B. cenocepacia
strain K56-2 and rescues a
Galleria mellonella
infection model from experimental
B. cenocepacia
K56-2 infections at relatively low multiplicities of infection. These results readily demonstrate that temperate phages can be genetically engineered to lytic form and that these modified phages can be used to treat bacterial infections
in vivo
.
Tpl2/AP-1 Enhances Murine Gammaherpesvirus 68 Lytic Replication
Authors: Li Xudong , Feng Jun , Chen Shijia , Peng Li , He Wei-Wu , Qi Jing , Deng Hongyu , Sun Ren 
Published: November 2009

ABSTRACTHow cellular factors regulate gammaherpesvirus lytic replication is not well understood. Here, through functional screening of a cellular kinase expression library, we identified mitogen-activated protein kinase kinase kinase 8 (MAP3K8/Tpl2) as a positive regulator of murine gammaherpesvirus 68 (MHV-68 or γHV-68) lytic gene expression and replication. Tpl2 enhances MHV-68 lytic replication by upregulating lytic gene expression and promoter activities of viral lytic genes, including RTA and open reading frame 57 (ORF57). By screening a cellular transcription factor library, we identified the Fos AP-1 transcription factor as a downstream factor that is both necessary and sufficient for mediating the enhancement of MHV-68 lytic replication by Tpl2. In addition, Tpl2 stimulates the promoter activities of key viral lytic genes, including RTA and ORF57, in an AP-1-dependent manner. We identified an AP-1-responsive element on the MHV-68 RTA promoter as theciselement mediating the upregulation of RTA promoter activity by Tpl2. MHV-68 lytic infection upregulates Fos expression, AP-1 activity, and RTA promoter activity in a Tpl2-dependent manner. We constructed a mutant MHV-68 virus that abolished this AP-1-responsive element. This mutant virus exhibited attenuated lytic replication kinetics, indicative of a critical role of this AP-1-responsive element during lytic replication. Moreover, Tpl2 knockdown inhibited the lytic replication of wild-type MHV-68 (MHV-68-WT) but not that of the MHV-68 mutant virus, indicating that endogenous Tpl2 promotes efficient virus lytic replication through AP-1-dependent upregulation of RTA expression. In summary, through tandem functional screens, we identified the Tpl2/AP-1 signaling transduction pathway as a positive regulator of MHV-68 lytic replication.
Cellular Corepressor TLE2 Inhibits Replication-and-Transcription- Activator-Mediated Transactivation and Lytic Reactivation of Kaposi's Sarcoma-Associated Herpesvirus
Authors: He Zhiheng , Liu Yunhua , Liang Deguang , Wang Zhuo , Robertson Erle S. , Lan Ke 
Published: November 2009

ABSTRACTReplication and transcription activator (RTA) encoded by open reading frame 50 (ORF50) of Kaposi's sarcoma-associated herpesvirus (KSHV) is essential and sufficient to initiate lytic reactivation. RTA activates its target genes through direct binding with high affinity to its responsive elements or by interaction with cellular factors, such as RBP-Jκ, Ap-1, C/EBP-α, and Oct-1. In this study, we identified transducin-like enhancer of split 2 (TLE2) as a novel RTA binding protein by using yeast two-hybrid screening of a human spleen cDNA library. The interaction between TLE2 and RTA was confirmed by glutathioneS-transferase (GST) binding and coimmunoprecipitation assays. Immunofluorescence analysis showed that TLE2 and RTA were colocalized in the same nuclear compartment in KSHV-infected cells. This interaction recruited TLE2 to RTA bound to its recognition sites on DNA and repressed RTA auto-activation and transactivation activity. Moreover, TLE2 also inhibited the induction of lytic replication and virion production driven by RTA. We further showed that the Q (Gln-rich), SP (Ser-Pro-rich), and WDR (Trp-Asp repeat) domains of TLE2 and the Pro-rich domain of RTA were essential for this interaction. RBP-Jκ has been shown previously to bind to the same Pro-rich domain of RTA, and this binding can be subject to competition by TLE2. In addition, TLE2 can form a complex with RTA to access the cognate DNA sequence of the RTA-responsive element at different promoters. Intriguingly, the transcription level of TLE2 could be upregulated by RTA during the lytic reactivation process. In conclusion, we identified a new RTA binding protein, TLE2, and demonstrated that TLE2 inhibited replication and transactivation mediated by RTA. This provides another potentially important mechanism for maintenance of KSHV viral latency through interaction with a host protein.
Conformational Changes in the Hepatitis B Virus Core Protein Are Consistent with a Role for Allostery in Virus Assembly
Authors: Packianathan Charles , Katen Sarah P. , Dann Charles E. , Zlotnick Adam 
Published: November 2009

ABSTRACT
In infected cells, virus components must be organized at the right place and time to ensure assembly of infectious virions. From a different perspective, assembly must be prevented until all components are available. Hypothetically, this can be achieved by allosterically controlling assembly. Consistent with this hypothesis, here we show that the structure of the hepatitis B virus (HBV) core protein dimer, which can spontaneously self-assemble, is incompatible with capsid assembly. Systematic differences between core protein dimer and capsid conformations demonstrate linkage between the intradimer interface and interdimer contact surface. These structures also provide explanations for the capsid-dimer selectivity of some antibodies and the activities of assembly effectors. Solution studies suggest that the assembly-inactive state is more accurately an ensemble of conformations. Simulations show that allostery supports controlled assembly and results in capsids that are resistant to dissociation. We propose that allostery, as demonstrated in HBV, is common to most self-assembling viruses.
Simian Rotaviruses Possess Divergent Gene Constellations That Originated from Interspecies Transmission and Reassortment
Authors: Matthijnssens Jelle , Taraporewala Zenobia F. , Yang Hongyan , Rao Shujing , Yuan Lijuan , Cao Dianjun , Hoshino Yasutaka , Mertens Peter P. C. , Carner Gerry R. , McNeal Monica , Sestak Karol , Van Ranst Marc , Patton John T. 
Published: November 2009

ABSTRACT
Although few simian rotaviruses (RVs) have been isolated, such strains have been important for basic research and vaccine development. To explore the origins of simian RVs, the complete genome sequences of strains PTRV (G8P[1]), RRV (G3P[3]), and TUCH (G3P[24]) were determined. These data allowed the genotype constellations of each virus to be determined and the phylogenetic relationships of the simian strains with each other and with nonsimian RVs to be elucidated. The results indicate that PTRV was likely transmitted from a bovine or other ruminant into pig-tailed macaques (its host of origin), since its genes have genotypes and encode outer-capsid proteins similar to those of bovine RVs. In contrast, most of the genes of rhesus-macaque strains, RRV and TUCH, have genotypes more typical of canine-feline RVs. However, the sequences of the canine and/or feline (canine/feline)-like genes of RRV and TUCH are only distantly related to those of modern canine/feline RVs, indicating that any potential transmission of a progenitor of these viruses from a canine/feline host to a simian host was not recent. The remaining genes of RRV and TUCH appear to have originated through reassortment with bovine, human, or other RV strains. Finally, comparison of PTRV, RRV, and TUCH genes with those of the vervet-monkey RV SA11-H96 (G3P[2]) indicates that SA11-H96 shares little genetic similarity to other simian strains and likely has evolved independently. Collectively, our data indicate that simian RVs are of diverse ancestry with genome constellations that originated largely by interspecies transmission and reassortment with nonhuman animal RVs.
Tiered Categorization of a Diverse Panel of HIV-1 Env Pseudoviruses for Assessment of Neutralizing Antibodies
Authors: Seaman Michael S. , Janes Holly , Hawkins Natalie , Grandpre Lauren E. , Devoy Colleen , Giri Ayush , Coffey Rory T. , Harris Linda , Wood Blake , Daniels Marcus G. , Bhattacharya Tanmoy , Lapedes Alan , Polonis Victoria R. , McCutchan Francine E. , Gilbert Peter B. , Self Steve G. , Korber Bette T. , Montefiori David C. , Mascola John R. 
Published: November 2009

ABSTRACT

The restricted neutralization breadth of vaccine-elicited antibodies is a major limitation of current human immunodeficiency virus-1 (HIV-1) candidate vaccines. In order to permit the efficient identification of vaccines with enhanced capacity for eliciting cross-reactive neutralizing antibodies (NAbs) and to assess the overall breadth and potency of vaccine-elicited NAb reactivity, we assembled a panel of 109 molecularly cloned HIV-1 Env pseudoviruses representing a broad range of genetic and geographic diversity. Viral isolates from all major circulating genetic subtypes were included, as were viruses derived shortly after transmission and during the early and chronic stages of infection. We assembled a panel of genetically diverse HIV-1-positive (HIV-1
+
) plasma pools to assess the neutralization sensitivities of the entire virus panel. When the viruses were rank ordered according to the average sensitivity to neutralization by the HIV-1
+
plasmas, a continuum of average sensitivity was observed. Clustering analysis of the patterns of sensitivity defined four subgroups of viruses: those having very high (tier 1A), above-average (tier 1B), moderate (tier 2), or low (tier 3) sensitivity to antibody-mediated neutralization. We also investigated potential associations between characteristics of the viral isolates (clade, stage of infection, and source of virus) and sensitivity to NAb. In particular, higher levels of NAb activity were observed when the virus and plasma pool were matched in clade. These data provide the first systematic assessment of the overall neutralization sensitivities of a genetically and geographically diverse panel of circulating HIV-1 strains. These reference viruses can facilitate the systematic characterization of NAb responses elicited by candidate vaccine immunogens.
Glutamine Metabolism Is Essential for Human Cytomegalovirus Infection
Authors: Chambers Jeremy W. , Maguire Tobi G. , Alwine James C. 
Published: November 2009

ABSTRACT
Human fibroblasts infected with human cytomegalovirus (HCMV) were more viable than uninfected cells during glucose starvation, suggesting that an alternate carbon source was used. We have determined that infected cells require glutamine for ATP production, whereas uninfected cells do not. This suggested that during infection, glutamine is used to fill the tricarboxylic acid (TCA) cycle (anaplerosis). In agreement with this, levels of glutamine uptake and ammonia production increased in infected cells, as did the activities of glutaminase and glutamate dehydrogenase, the enzymes needed to convert glutamine to α-ketoglutarate to enter the TCA cycle. Infected cells starved for glutamine beginning 24 h postinfection failed to produce infectious virions. Both ATP and viral production could be rescued in glutamine-starved cells by the TCA intermediates α-ketoglutarate, oxaloacetate, and pyruvate, confirming that in infected cells, a program allowing glutamine to be used anaplerotically is induced. Thus, HCMV infection activates the mechanisms needed to switch the anaplerotic substrate from glucose to glutamine to accommodate the biosynthetic and energetic needs of the viral infection and to allow glucose to be used biosynthetically.
Postmortem candidaemia: marker of disseminated disease
Authors: Thorn Jennifer L , Gilchrist Kevin B , Sobonya Richard E , Gaur Nand K , Lipke Peter N , Klotz Stephen A 
Published: November 2009

AimThe significance of findingCandidaspecies in heart blood cultures obtained at postmortem examination has never been studied. This article describes the findings of autopsy patients with postmortem candidaemia and it compares them with findings in autopsy patients with antemortem candidaemia.Method23 patients withCandidaspecies isolated from heart blood at autopsy were identified over a 10-year period. These patients were compared with 10 autopsy patients found during the same time period with antemortem blood cultures isolatingCandidaspecies, but not positive postmortem heart blood cultures. Antemortem and postmortem records were reviewed.ResultsAll 23 patients withCandidaspecies isolated from postmortem blood culture had one or more antemortem risk factors for disseminated candidiasis, such as positive antemortem blood cultures, isolation ofCandidafrom sterile internal sites, neutropenia, recent abdominal surgery, broad-spectrum antibiotic administration or the use of central venous catheters or other invasive devices. Eight patients showed histological proof of invasive candidiasis in addition to the positive heart blood cultures. This group did not differ with respect to risk factors from 10 autopsy patients with disseminated candidiasis and antemortem blood cultures withCandidaspecies. However, all the patients with antemortem candidaemia had histological evidence of disseminated candidiasis at autopsy.ConclusionCandidaemia, when documented by heart blood culture performed at autopsy or by antemortem blood culture, is an insensitive, but highly specific, indicator of disseminated candidiasis.
Parental occupational exposure to potential endocrine disrupting chemicals and risk of hypospadias in infants
Authors: Nassar Natasha , Abeywardana Prashan , Barker Andrew , Bower Carol 
Published: November 2009

ObjectivesHypospadias is a urogenital birth defect affecting infant boys. Periconceptual parental occupational exposure to endocrine disrupting chemicals (EDCs) with oestrogenic or anti-androgenic properties may adversely affect male genital development in utero. The aim of this study was to investigate the association between both maternal and paternal occupational exposures to EDCs and hypospadias.MethodsThis registry-based case–control study considered 1202 cases of hypospadias in children born in Western Australia between 1980 and 2000 and 2583 male controls randomly selected from birth records for whom information regarding parental occupation was available from the Western Australian Maternal and Child Health Research Database. Occupational exposures to seven groups of potential EDCs were independently coded by two researchers according to a validated job–exposure matrix.ResultsMultivariable analysis showed a strong association with potential maternal occupational exposure to heavy metals with an over twofold increased risk of hypospadias (OR 2.6; 95% CI 1.3 to 5.2), and women exposed to phthalates were more likely to have an affected son (OR 1.2; 95% CI 0.8 to 1.7). Compared with mild or isolated cases, the risks of moderate–severe hypospadias or multiple defects were increased up to two- and fivefold, respectively, with maternal exposure to most types of EDCs. Paternal occupational exposures to polychlorinated organic (OR 1.3; 95% CI 1.0 to 1.8) and bi-phenolic (OR 1.6; 95% CI 1.0 to 2.6) compounds were also possible risk factors.ConclusionsOur findings provide preliminary evidence of an association between exposure to EDCs with oestrogenic or anti-androgenic properties and increased risk of hypospadias.
Correlation between innovation and performance of construction firms
Authors: Choi Seokin , Jang Hyounseung , Hyun Joonsik 
Published: November 2009

This paper studies the performance of 118 major Korean construction companies between 1997 and 2003 to verify empirically the existence of a direct relationship between innovations of firms and their performance. This time period was selected because there had been a radical change in the market leadership of the construction industry due to the Asian Financial Crisis of the late 1990s. The AMOS analysis and the research demonstrated that innovation of a firm has an indirect relationship with its performance through mediating variables — firm product and process fits. While innovations of a firm are contingent to the external factors, product fit and process fit have direct impact on firm performance, suggesting that the product fit and the process fit are two significant indicators of the success or failure of a firm.
Behaviour of adhesive steel anchors under impulse-type loading
Authors: Braimah Abass , Contestabile Ettore , Guilbeault Rick 
Published: November 2009

The dynamic behaviour of adhesive anchors embedded in concrete is not well established, neither is their behaviour in stone masonry. This paper presents an experimental program designed to study the dynamic behaviour of adhesive anchor – substrate systems under impulse-type loading. The adhesive anchor – substrate systems consisted of steel rods bonded to concrete and limestone with an epoxy-based adhesive. Two steel anchor diameters (6.4 and 9.5 mm), two embedment depths (89 and 114 mm), and two angles of substrate penetration (90° and 45°) were investigated. The predominant failure mode observed for the steel anchor – concrete substrate samples was steel fracture, whereas for the steel anchor – limestone substrate samples, both steel fracture and limestone substrate failure modes were observed. The test results show that in most cases the dynamic increase factor (DIF) of adhesive anchors decreases with an increase in the embedment depth. Also, a substrate penetration angle of 45° increases the DIF in comparison with samples with 90° penetration angle. The DIFs of 1.2 and 2.5 are recommended for adhesive anchors with normal and 45° limestone substrate penetrations, respectively, while for concrete substrate, the recommended DIFs are 1.2 and 3.2 for normal and 45° substrate penetrations, respectively.
Bacillusspore uptake onto heavily corroded iron pipe in a drinking water distribution system simulatorA paper submitted to the Journal of Environmental Engineering and Science.
Authors: Szabo Jeffrey G. , Muhammad Nur , Packard Benjamin , Meiners Greg , Kefauver Paul , Hall John 
Published: November 2009

A dechlorinated drinking water distribution system simulator containing 15-year old unlined iron pipe was contaminated with Bacillus globigii spores. Bulk phase spore density decreased by 1.5–2.0 log105 min after injection and declined by 1.8–3.4 log10after 4 d. Spores were detected on the iron pipe interior at 2 and 22 CFU/cm2after it was decontaminated and disassembled. These results support previous bench-scale studies that show that spores can persist on corroded surfaces in a drinking water environment.
Total expected cost design method for reinforced concrete members based on current Canadian code provisions
Authors: Feldman Lisa R. , Christensen Paul N. , Boulfiza Mohamed , Sparks Gordon A. 
Published: November 2009

Reliability-based provisions for the design and evaluation of reinforced concrete members provided in the National building code of Canada and Canadian standard A23.3 are integrated with a corrosion deterioration model and a life-cycle cost analysis. The resulting model offers a simplified total expected cost design method that can be readily implemented by practicing engineers. The model is illustrated in the context of a 400 mm deep, 4.0 m long steel reinforced concrete cantilever slab that serves as a balcony adjacent to a party room of a condominium building. Nine design options for the slab were assessed. The near-surface chloride concentration and the oxygen concentration in the pore solution are the only two parameters that influence the selection of the balcony slab design. The design option with moderate concrete compressive strength and the largest clear cover considered was shown to be the most cost effective design regardless of the analysis method considered. Other model applications are also briefly presented.