bluuebunny/crossref_metadata_2025 huggingface dataset:
Herpes Simplex Virus VP16, but Not ICP0, Is Required To Reduce Histone Occupancy and Enhance Histone Acetylation on Viral Genomes in U2OS Osteosarcoma Cells
Authors: Hancock Meaghan H. , Cliffe Anna R. , Knipe David M. , Smiley James R.
Published: November 2009

The herpes simplex virus (HSV) genome rapidly becomes associated with histones after injection into the host cell nucleus. The viral proteins ICP0 and VP16 are required for efficient viral gene expression and have been implicated in reducing the levels of underacetylated histones on the viral genome, raising the possibility that high levels of underacetylated histones inhibit viral gene expression. The U2OS osteosarcoma cell line is permissive for replication of ICP0 and VP16 mutants and appears to lack an innate antiviral repression mechanism present in other cell types. We therefore used chromatin immunoprecipitation to determine whether U2OS cells are competent to load histones onto HSV DNA and, if so, whether ICP0 and/or VP16 are required to reduce histone occupancy and enhance acetylation in this cell type. High levels of underacetylated histone H3 accumulated at several locations on the viral genome in the absence of VP16 activation function; in contrast, an ICP0 mutant displayed markedly reduced histone levels and enhanced acetylation, similar to wild-type HSV. These results demonstrate that U2OS cells are competent to load underacetylated histones onto HSV DNA and uncover an unexpected role for VP16 in modulating chromatin structure at viral early and late loci. One interpretation of these findings is that ICP0 and VP16 affect viral chromatin structure through separate pathways, and the pathway targeted by ICP0 is defective in U2OS cells. We also show that HSV infection results in decreased histone levels on some actively transcribed genes within the cellular genome, demonstrating that viral infection alters cellular chromatin structure.
Mutations in Sensor 1 and Walker B in the Bovine Papillomavirus E1 Initiator Protein Mimic the Nucleotide-Bound State
Authors: Liu Xiaofei , Stenlund Arne
Published: November 2009

Viral replication initiator proteins are multifunctional proteins that utilize ATP binding and hydrolysis by their AAA+ modules for multiple functions in the replication of their viral genomes. These proteins are therefore of particular interest for understanding how AAA+ proteins carry out multiple ATP driven functions. We have performed a comprehensive mutational analysis of the residues involved in ATP binding and hydrolysis in the papillomavirus E1 initiator protein based on the recent structural data. Ten of the eleven residues that were targeted were defective for ATP hydrolysis, and seven of these were also defective for ATP binding. The three mutants that could still bind nucleotide represent the Walker B motif (D478 and D479) and Sensor 1 (N523), three residues that are in close proximity to each other and generally are considered to be involved in ATP hydrolysis. Surprisingly, however, two of these mutants, D478A and N523A, mimicked the nucleotide bound state and were capable of binding DNA in the absence of nucleotide. However, these mutants could not form the E1 double trimer in the absence of nucleotide, demonstrating that there are two qualitatively different consequences of ATP binding by E1, one that can be mimicked by D478A and N523A and one which cannot.
Protease Cleavage Sites in HIV-1 gp120 Recognized by Antigen Processing Enzymes Are Conserved and Located at Receptor Binding Sites
Authors: Yu Bin , Fonseca Dora P. A. J. , O'Rourke Sara M. , Berman Phillip W.
Published: November 2009

The identification of vaccine immunogens able to elicit broadly neutralizing antibodies (bNAbs) is a major goal in HIV vaccine research. Although it has been possible to produce recombinant envelope glycoproteins able to adsorb bNAbs from HIV-positive sera, immunization with these proteins has failed to elicit antibody responses effective against clinical isolates of HIV-1. Thus, the epitopes recognized by bNAbs are present on recombinant proteins, but they are not immunogenic. These results led us to consider the possibility that changes in the pattern of antigen processing might alter the immune response to the envelope glycoprotein to better elicit protective immunity. In these studies, we have defined protease cleavage sites on HIV gp120 recognized by three major human proteases (cathepsins L, S, and D) important for antigen processing and presentation. Remarkably, six of the eight sites identified in gp120 were highly conserved and clustered in regions of the molecule associated with receptor binding and/or the binding of neutralizing antibodies. These results suggested that HIV may have evolved to take advantage of major histocompatibility complex (MHC) class II antigen processing enzymes in order to evade or direct the antiviral immune response.
The Minor Envelope Glycoproteins GP2a and GP4 of Porcine Reproductive and Respiratory Syndrome Virus Interact with the Receptor CD163
Authors: Das Phani B. , Dinh Phat X. , Ansari Israrul H. , de Lima Marcelo , Osorio Fernando A. , Pattnaik Asit K.
Published: November 2009

Porcine reproductive and respiratory syndrome virus (PRRSV) contains the major glycoprotein, GP5, as well as three other minor glycoproteins, namely, GP2a, GP3, and GP4, on the virion envelope, all of which are required for generation of infectious virions. To study their interactions with each other and with the cellular receptor for PRRSV, we have cloned each of the viral glycoproteins and CD163 receptor in expression vectors and examined their expression and interaction with each other in transfected cells by coimmunoprecipitation (co-IP) assay using monospecific antibodies. Our results show that a strong interaction exists between the GP4 and GP5 proteins, although weak interactions among the other minor envelope glycoproteins and GP5 have been detected. Both GP2a and GP4 proteins were found to interact with all the other GPs, resulting in the formation of multiprotein complex. Our results further show that the GP2a and GP4 proteins also specifically interact with the CD163 molecule. The carboxy-terminal 223 residues of the CD163 molecule are not required for interactions with either the GP2a or the GP4 protein, although these residues are required for conferring susceptibility to PRRSV infection in BHK-21 cells. Overall, we conclude that the GP4 protein is critical for mediating interglycoprotein interactions and, along with GP2a, serves as the viral attachment protein that is responsible for mediating interactions with CD163 for virus entry into susceptible host cell.
Molecular Determinants of Adaptation of Highly Pathogenic Avian Influenza H7N7 Viruses to Efficient Replication in the Human Host
Authors: de Wit Emmie , Munster Vincent J. , van Riel Debby , Beyer Walter E. P. , Rimmelzwaan Guus F. , Kuiken Thijs , Osterhaus Albert D. M. E. , Fouchier Ron A. M.
Published: November 2009

Two viruses isolated during the highly pathogenic avian influenza (HPAI) H7N7 virus outbreak in The Netherlands in 2003, one isolated from a person with conjunctivitis and one from a person who died as the result of infection, were used for an
in vitro
study of influenza A virus pathogenicity factors. The two HPAI H7N7 viruses differed in 15 amino acid positions in five gene segments. Assays were designed to investigate the role of each of these substitutions in attachment and entry, transcription and genome replication, and virus production and release as determined by hemagglutinin (HA), polymerase proteins, nonstructural protein 1 (NS1), and neuraminidase (NA). These
in vitro
studies confirmed the roles of the E627K substitution in basic polymerase 2 (PB2) and the A143T substitution in HA in pathogenicity observed in a mouse model previously. However, the
in vitro
studies identified a contribution of acidic polymerase (PA) and NA to the efficient replication in human cells of the fatal case virus, despite the fact that these are rarely marked as determinants of pathogenicity in
in vivo
studies. With the exception of PB2 E627K, all substitutions contributing to enhanced replication of the fatal case virus
in vitro
were present in poultry viruses prior to transmission to the human fatal case, indicating that viruses with enhanced replication efficiency in the mammalian host can be generated in poultry. Thus, detailed
in vitro
analyses of mutations facilitating replication of avian influenza viruses in mammalian cells are important to assess the zoonotic risk posed by these viruses and, in addition, highlight the value of
in vitro
studies to complement animal models.
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

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

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

How 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

Replication 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

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

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

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

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

Aim

The 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.

Method

23 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.

Results

All 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.

Conclusion

Candidaemia, 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

Objectives

Hypospadias 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.

Methods

This 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.

Results

Multivariable 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.

Conclusions

Our findings provide preliminary evidence of an association between exposure to EDCs with oestrogenic or anti-androgenic properties and increased risk of hypospadias.
Recent studies in environmental applications of ultrasoundA paper submitted to the Journal of Environmental Engineering and Science.
Authors: Pham Thuy Duong , Shrestha Reena Amatya , Virkutyte Jurate , Sillanpää Mika
Published: November 2009

As a young, new, and rapidly growing science, the applications of ultrasound in environmental technology hold a promising future. Compared with conventional methods, ultrasonication can bring several benefits such as environmentally friendly (no toxic chemicals are used or produced), low cost, and compact (allowing on-site treatment). Beside an overview on ultrasonic background, this paper summarizes main findings and innovations of recent studies that used ultrasound in environmental analysis, water and sludge treatment, soil and sediment remediation, and air purification.
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.
Simulated safety performance of rear-end and angled vehicle interactions at isolated intersections
Authors: Cunto Flávio , Saccomanno Frank F.
Published: November 2009

This paper applies a calibrated microscopic simulation model to assess the safety implications of signalization at a stop-controlled isolated intersection. Safety performance is measured in terms of a crash potential index (CPI) that makes use of time-specific vehicle parameters, such as deceleration rates, spacing, and speed profiles. Four performance measures are obtained: (i) average CPI/vehicle, (ii) CPI 85th percentile, (iii) number of vehicles with CPI > 0 (defined as interacting), and (iv) number of conflicts (defined in terms of a given CPI threshold). Two types of interactions are considered, namely rear end and angled. For rear-end interactions, CPI/vehicle was found to be significantly higher following the introduction of fixed signal controls. For angled interactions, CPI/vehicle was found to decrease with signalization. For both types of interactions, the CPI 85th percentile was found to decrease nonlinearly with signalization, especially for higher assumed volumes on the major approach. Rear-end vehicle interactions increased significantly following signalization and with increasing volume, whereas no such increase was observed for angled interactions. The key observation is that the number of vehicles subject to angled interactions was found to decrease after signalization.
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.
Behaviour of flexural plastic hinges under high seismic shear with consideration of concrete strength
Authors: Elmenshawi Abdelsamie , Brown Tom , Loov Robert
Published: November 2009

A successful seismic design for a reinforced concrete element is one that can postpone the shear failure until the required ductility and deformation capacity are obtained. After flexural yielding, shear deformations are the main causes for strength and stiffness degradation. An experimental program was carried out to explore the shear behaviour of flexural plastic hinges of elements constructed with different concrete strengths (30–175 MPa) tested under load reversals. The specimen represented a beam–column assembly and was designed to have the inelastic deformation at the beam end only. The research investigated the effect of shear deformations on the hysteretic behaviour and stiffness deterioration, cyclic shear demands, shear resisting mechanisms, and the effect of concrete strength on the hinge shear strength. It was found that the effect of concrete strength on beam shear strength under cyclic loading differs from that under unidirectional loading.
Multi-stage response to contaminant ingress into water distribution systems and probability quantification
Authors: Shen Hailiang , McBean Edward A. , Ghazali Mirnader
Published: November 2009

A multi-stage response procedure for identifying possible ingress nodes (PINs) and quantifying the likelihood that a PIN in a given water distribution system is the actual point of ingress is described. The procedure uses data mining to successively decrease the number of PINs based on a pre-constructed database. In each stage, query sentences are executed to locate the PINs and a Euclidean distance is proposed to estimate the probability, to allow the identification of locations with the highest probabilities of being the true ingress location. As demonstrated in a case study, the ranges of PINs are reduced in the 1st, 2nd, and 3rd stages; except the first sensor alarm, the Euclidean distance metric can identify the true ingress node with the program run-time of less than 2 min; the multi-stage procedure saves roughly 3 h in identifying the true ingress node after the second sensor alarm, instead of waiting for a third sensor alarm to provide the location information. The multi-stage response procedure is shown to be an effective and efficient way for identification and probability quantification of PINs.
Project success indicators focusing on residential projects: Are schedule performance index and cost performance index accurate measures in earned value?
Authors: Kim Sang-chul
Published: November 2009

As a concept of project control that provides a quantitative measure of schedule and cost information, earned value (EV) can evaluate work progress by identifying potential delays and cost overruns. When EV is used as a construction control technique, the schedule performance index (SPI) and the cost performance index (CPI) are the core factors in the EV system. The standard is only 1, i.e., 1.0 above or below. Though the two indices have important roles in the EV system, those indices do always show the project status exactly; for example, when planned value (PV), EV, and actual cost (AC) are not collected in a timely manner. Additionally, there is no guideline on how each value in SPI and CPI is understood or how to read the hidden meaning behind the construction status. Therefore, this study first speculates about the meaning of the two indices, then suggests a practical application, and finally shows the framework where the two indices apply to various types of construction.
Microstructure of red brick dust and ground basaltic pumice blended cement mortars exposed to magnesium sulphate solutions
Authors: Binici Hanifi , Arocena Joselito , Kapur Selim , Aksogan Orhan , Kaplan Hasan
Published: November 2009

This paper presents a laboratory study on the deterioration of blended cement combinations of plain Portland cement (PPC) with red brick dust (RBD) and ground basaltic pumice (GBP). The compressive strength and the magnesium sulphate resistance of cements have been experimentally determined. The development of the microstructure and the secondary minerals in the plain and blended cements were studied via scanning electron microscope (SEM) analysis. A series of mechanical tests of cement mortars were undertaken on all specimens. A large quantity of sheet-like C-S-H was found in the mortars that have developed by the addition of RBD and GBP. The results indicated that the increase in the additive content caused a significant increase in the sulphate resistance of the mortars. Hence, the studied RBD and GBP can be recommended for use as admixtures in cement production.
Tsunami loading of near-shoreline structures: a primer
Authors: Palermo Dan , Nistor Ioan , Nouri Younes , Cornett Andrew
Published: November 2009

The effects and estimation of tsunami-induced loading on near-shoreline structures located within inundation zones have recently gained significant interest from researchers, engineers, and government agencies. Building codes, namely the 2005 National building code of Canada, do not explicitly consider tsunami loading, as it is understood that inland structures can be protected by proper site planning. However, recent catastrophic events (Indian Ocean, 2004; Solomon Islands, 2007) indicate that tsunami loading should be considered in structural design. Presented herein is a review of force components that arise from tsunami-induced hydraulic bores running inland, along with proposed loading combinations and load cases readily applicable for building codes. Test results from a comprehensive experimental program conducted in a large-scale flume are also provided. A comparison of experimental results with force components provided in readily available design documents is presented, and suggestions for improvements are further discussed.
Prediction of interaction between a side overflow and bed-load transport in a channel with semi-empirical approaches
Authors: Rosier Burkhard , Boillat Jean-Louis , Schleiss Anton J.
Published: November 2009

Side weirs are free overflow regulation and diversion structures commonly encountered in flood protection engineering. The lateral loss of water reduces the bed-load transport capacity in the main channel, leading to local sediment deposition near the side overflow. As a consequence, the design overflow is increased in an uncontrolled way. Since this flow–sediment interaction in such a channel has not been studied so far, systematic flume experiments have been performed. Based on these experiments, a two-dimensional empirical model to describe the longitudinal evolution of the aggraded channel reach near the weir has been developed. In addition, a simple and straightforward approach for direct estimation of the side overflow in presence of bed-load transport has been established. To be generally applicable in engineering practice, all input variables are expressed in terms of dimensionless parameters. Finally, the application of the models is demonstrated in a case study on the Rhone River in Switzerland.
Noise measuring technique and field evaluation based on the effects of vehicles and pavement types
Authors: Mun Sungho , Cho Dae-Seung
Published: November 2009

A measuring technique for tire–pavement interaction noise (coast-by noise) that uses a proposed close proximity (CPX) method equipped with surface microphones has been employed to perform pavement noise evaluations on nine different pavement sections as well as two on-site highways. Through field tests, the appropriate noise measuring procedures have been developed and validated for evaluating light and heavy vehicles and various pavement surfaces at varying vehicle speeds. The results show that tire–pavement noise levels vary widely according to the various surface types, vehicle types, and vehicle speeds. In addition, it was found that power-by noise (power-train plus tire–pavement interaction noise) measurements, based on the proposed CPX method, were able to determine the sound power levels used for outdoor sound propagation models.
Spatial distribution of ammonia-oxidizing bacteria in the biofilm and suspended growth biomass of the full- and partial-bed biological aerated filtersA paper submitted to the Journal of Environmental Engineering and Science.
Authors: Fatihah S. , Donnelly T.
Published: November 2009

The extent of comparable nitrogen removal in the full- and partial-bed biological aerated reactors needs further microbiological evidence, specifically the existence of ammonia-oxidizing bacteria (AOB). The nitrogen removal process in such systems is typically initiated by chemoliautotrophic ammonia-oxidizing bacteria converting ammonia to nitrite and traces of oxidized nitrogen gases. The formation of a dense biofilm as a result of higher turbulence would account for the higher number of AOB cells enumerated in the biofilm samples from the partial-bed reactor (4.3 × 105 ± 1.9 × 105No. of AOB cells/mL sample) as compared with those from the full-bed reactor (1.5 × 105 ± 8.0 × 104No. of AOB cells/mL sample).
Characterization of a self-compacting sand concrete using the quarry waste
Authors: Abidelah A. , Bouchaïr A. , Kerdal D. , Ayed K.
Published: November 2009

Self-compacting sand concrete (SCSC) can be made by using the quarry waste, thus helping to reduce the actual deficit in aggregates in Algeria and contribute to the solution of an acute environmental problem. The SCSC presented in this paper is made with aggregates whose maximum size is less than 5 mm. Several mixes were prepared by varying parameters, such as water volume, weight and nature of cement, weight of sand, nature of admixtures, and shape of aggregates. Each one of the SCSC mixes has been analyzed by considering its rheological behavior in the fresh state and its mechanical behavior in the hardened state. In the fresh state, the elaborated SCSC satisfies the recommendations of the Association Française de Génie Civil (AFGC) and in the hardened state, its mechanical performance is good.
Intake shape and boundary-related considerations in the operation and design of storm-sewer drop structures
Authors: Auckland A. , Nistor I. , Townsend R.
Published: November 2009

This paper presents the results of an experimental investigation into the hydraulic efficiency of a vertically oriented water intake. Under low submergence conditions, the operation of such an intake is affected significantly by the formation of surface vortices, which result in significant flow reduction and the downstream entrainment of air and swirl. The experimental work considered the fact that vortex formation is governed by the geometrical characteristics of the intake, including the diameter, local shape, submergence, surrounding boundary, etc, and the velocity distribution in the approaching flow. Therefore, an experimental study was conducted to investigate the influence that the local shape and the proximity to nearby boundaries have on the hydraulic performance of a vertical water intake. The results of this experimental investigation will hopefully lead to a better understanding of the phenomena governing the flow in such structures and to the elaboration of improved engineering design guidelines.
FACTORS AFFECTING THE INCORPORATION OF RADIOACTIVE PHOSPHATE INTO THE PHOSPHOLIPIDS OF SLICES OF CAT BRAIN
Authors: Strickland K. P.
Published: November 2009

Slices of cat brain respiring in a Krebs–Ringer bicarbonate medium were found to incorporate radioactive inorganic phosphate (P32) into the phospholipid fraction. The addition of glucose or mannose increased the incorporation of P32into the phospholipids. Fructose caused a small increase, whereas galactose was without effect. Pyruvate and lactate increased the incorporation of P32into the phospholipids. Succinate, L (+)-glutamate, D (−)-glutamate, α keto-glutarate, citrate, and L-malate failed to support the incorporation.Anaerobic conditions and homogenization of the tissue prevented the in vitro incorporation of P32into the phospholipids of cat brain. A wide range of metabolic inhibitors (cyanide, azide, malononitrile, chloretone, nembutal, iodoacetate, and fluoride), in concentrations that inhibit the oxygen consumption of brain slices, inhibited the incorporation. The incorporation was also inhibited by 2,4-dinitrophenol in concentrations that do not decrease the oxygen consumption of brain slices.These findings indicated that the incorporation of P32into the phospholipids of slices of cat brain is a metabolic phenomenon and is dependent upon the maintenance of an adequate phosphorylating mechanism within the slice.
THE DETERMINATION OF SERUM PROTEIN FRACTIONS ON FILTER PAPER ELECTROPHEROGRAMS BY THE BIURET REACTION, AND SOME OBSERVATIONS ON THE SERUM PROTEINS OF THE ESTROGENIZED IMMATURE PULLET
Authors: McKinley W. P. , Maw W. A. , Oliver W. F. , Common R. H.
Published: December 2009

An application of the biuret reaction to the determination of protein fractions on filter paper electropherograms of serum is described. The relative mobilities of the serum protein fractions of the domestic fowl and of man are compared. Values are reported for serum protein fractions as separated by filter paper electrophoresis in a methanolic veronal buffer. Some observations on the serum proteins of the estrogenized immature pullet are reported; and it is tentatively suggested that another fraction as well as serum phosphoprotein appears in the serum of the pullet as a consequence of treatment with estrogen.
ENZYMATIC DECARBOXYLATION OF 2,6- AND 2,3-DIHYDROXYPHENYLALANINE
Authors: Sourkes Theodore L.
Published: December 2009

The action of dihydroxyphenylalanine (dopa) decarboxylase of guinea pig kidney and of tyrosine decarboxylase of Streptococcus faecalis R on 2,3- and 2,6-dopa has been studied. Compared with 3,4-dopa, these substrates are decarboxylated by the kidney enzyme at rates decreasing in the order: 2,3-, 3,4-, 2,6-dopa. The bacterial enzyme employed as an acetonized powder decarboxylates 2,3-dopa but not the di-ortho isomer. The significance of these results in clarifying the substrate specificity of the two enzymes is discussed.