bluuebunny/crossref_metadata_2025 huggingface dataset:
Antibodies to gp350/220 Enhance the Ability of Epstein-Barr Virus To Infect Epithelial Cells
Authors: Turk Susan M. , Jiang Ru , Chesnokova Liudmila S. , Hutt-Fletcher Lindsey M.
Published: September 2006

Epstein-Barr virus (EBV) is a persistent, orally transmitted herpesvirus that replicates in B cells and epithelial cells and is associated with lymphoid and epithelial malignancies. The virus binds to CD21 on B cells via glycoprotein gp350/220 and infects efficiently. Infection of cultured epithelial cells has not typically been efficient but can occur in the absence of gp350/220 and CD21 and in vivo is thought to be important to the development of nasopharyngeal carcinoma. We report here that antibodies to gp350/220, which inhibit EBV infection of B cells, enhance infection of epithelial cells. The effect is not mediated by Fc receptor binding but is further enhanced by antibody cross-linking, which may patch gp350/220 in the virus envelope. Saliva from EBV-seropositive individuals has similar effects that can be reversed by depletion of antibody. The results are consistent with a model in which gp350/220 interferes with the access of other important players to the epithelial cell surface. The results may have implications for the development of nasopharyngeal carcinoma in high-risk populations in which elevated titers of antibody to EBV lytic cycle proteins are prognostic.
Mobilization of Full-Length Semliki Forest Virus Replicon by Retrovirus Particles
Authors: Piver Eric , Collin Christine , Renault Noémie , Bru Thierry , Pagès Jean-Christophe
Published: September 2006

Conciliating biosafety with efficient gene transfer remains a constant concern in the development of retroviral vectors. Semliki Forest virus (SFV) replicons allow important retroviral vector production with interesting features. It is noteworthy that retroviruses have the ability to package Ψ
+
and, to some extent, Ψ
−
cellular RNAs. Therefore, it was important to study the retroviral transfer of highly abundant SFV genomes expressing retroviral proteins. Here, we show that full-length SFV-vector replicons, with or without Ψ, are efficiently packaged into retrovirus particles. Mechanistically, our data suggest that SFV packaging is the sum of its retroviral nucleocapsid-dependent recruitment together with a passive hijacking of membrane-anchored SFV replicon. A direct consequence of this phenomenon is the formation of particles harboring autonomous replicative abilities and contaminating vector preparations. Importantly, we confirm that retroviral SFV mobilization is not an exclusive feature of murine gamma retroviruses, since it is also observed using lentivectors.
Complementation of Human Immunodeficiency Virus Type 1 Replication by Intracellular Selection of
Escherichia coli
\batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(tRNA_{3}^{Lys}\) \end{document} Supplied in
trans
Authors: McCulley Anna , Morrow Casey D.
Published: September 2006

Human immunodeficiency virus type 1 (HIV-1) exclusively selects
tRNA
3

Lys

as the primer for the initiation of reverse transcription, even though both
tRNA
3

Lys

and
tRNA
1,2

Lys

are found in HIV-1 virions. Alteration of the HIV-1 primer-binding site (PBS) to be complementary to alternate tRNAs results in the use of those tRNAs for replication, indicating that primer complementarity with the PBS is an important determinant of primer selection. In previous studies, we have exploited this fact to develop a system in which yeast (
Saccharomyces cerevisiae
) tRNA
Phe
is provided in
trans
to complement the replication of HIV-1 with a PBS complementary to yeast tRNA
Phe
. Recent studies have demonstrated that the presence of lysyl-tRNA synthetase in HIV-1 virions might account for the preference for the selection of
tRNA
3

Lys

in HIV-1 replication. To establish a complementation system more reflective of HIV-1 primer selection, we have altered the HIV-1 PBS to be complementary to the
Escherichia coli tRNA
3

Lys

, which shares near identity with mammalian
tRNA
3

Lys

except in the 3′-terminal 18-nucleotide sequence that binds to the PBS.
E. coli tRNA
3

Lys

expressed from a plasmid was aminoacylated in mammalian cells. Cotransfection of cells with a plasmid that encodes
E. coli tRNA
3

Lys

and a plasmid encoding an HIV-1 provirus with a PBS complementary to
E. coli tRNA
3

Lys

resulted in the production of infectious virus. A comparison of the two complementation systems revealed that higher levels of intracellular
E. coli tRNA
3

Lys

than of yeast tRNA
Phe
were needed to achieve equal levels of infectious virus, indicating that there was no preferential selection of
E. coli tRNA
3

Lys

. To examine the specificity of tRNA
Lys
selection,
E. coli tRNA
3

Lys

was modified to
tRNA
1,2

Lys

. This tRNA was also aminoacylated when expressed in mammalian cells and complemented the infectivity of HIV-1 at levels similar to those seen for
E. coli tRNA
3

Lys

. Additional mutations in the anticodon of
E. coli tRNA
3

Lys

were constructed; these mutations did not significantly correlate with the capacity of the tRNA primer to complement infectivity of HIV-1, even though they had a drastic effect on the aminoacylation of the tRNAs. The results of these studies demonstrate that
E. coli tRNA
3

Lys

provided in
trans
can complement HIV-1 genomes with the PBS altered to
E. coli tRNA
3

Lys

. However, the capacity of
tRNA
3

Lys

to interact with lysyl-tRNA synthetase does not entirely explain the enhanced preference for selection of
tRNA
3

Lys

for the replication of HIV-1.
A Full-Genome Phylogenetic Analysis of Varicella-Zoster Virus Reveals a Novel Origin of Replication-Based Genotyping Scheme and Evidence of Recombination between Major Circulating Clades
Authors: Peters Geoffrey A. , Tyler Shaun D. , Grose Charles , Severini Alberto , Gray Michael J. , Upton Chris , Tipples Graham A.
Published: September 2006

Varicella-zoster virus (VZV) is a remarkably stable virus that until recently was thought to exhibit near-universal genetic homogeneity among circulating wild-type strains. In recent years, the expanding knowledge of VZV genetics has led to a number of groups proposing sequence-based typing schemes, but no study has yet examined the relationships between VZV genotypes at a full-genome level. A central hypothesis of this study is that VZV has coevolved with humankind. In this study, 11 additional full VZV genomic sequences are presented, bringing the current number of complete genomic sequences publicly available to 18. The full-genome alignment contained strains representing four distinct clades, but the possibility exists that a fifth clade comprised of African and Asian-like isolates was not represented. A consolidated VZV genotyping scheme employing the origin-associated region between reiteration region R4 and open reading frames (ORFs) 63 and 70 is described, one which accurately categorizes strains into one of four clades related to the geographic origin of the isolates. The full-genome alignment also provided evidence for recombination having occurred between the major circulating VZV clades. One Canadian clinical isolate was primarily Asian-like in origin, with most of the genome showing strong sequence identity to the Japanese-like clade B, with the exceptions being two putative recombination regions, located in ORFs 14 to 17 and ORFs 22 to 26, which showed clear similarity to the European/North American clade A. The very low rate of single-nucleotide polymorphisms scattered across the genome made full-genome sequencing the only definitive method for identifying specific VZV recombination events.
Inhibition of Hendra Virus Fusion
Authors: Porotto M. , Doctor L. , Carta P. , Fornabaio M. , Greengard O. , Kellogg G. E. , Moscona A.
Published: September 2006

Hendra virus (HeV) is a recently identified paramyxovirus that is fatal in humans and could be used as an agent of bioterrorism. The HeV receptor-binding protein (G) is required in order for the fusion protein (F) to mediate fusion, and analysis of the triggering/activation of HeV F by G should lead to strategies for interfering with this key step in viral entry. HeV F, once triggered by the receptor-bound G, by analogy with other paramyxovirus F proteins, undergoes multistep conformational changes leading to a six-helix bundle (6HB) structure that accomplishes fusion of the viral and cellular membranes. The ectodomain of paramyxovirus F proteins contains two conserved heptad repeat regions (HRN and HRC) near the fusion peptide and the transmembrane domains, respectively. Peptides derived from the HRN and HRC regions of F are proposed to inhibit fusion by preventing F, after the initial triggering step, from forming the 6HB structure that is required for fusion. HeV peptides have previously been found to be effective at inhibiting HeV fusion. However, we found that a human parainfluenza virus 3 F-peptide is more effective at inhibiting HeV fusion than the comparable HeV-derived peptide.
Resistance to Alpha/Beta Interferon Is a Determinant of West Nile Virus Replication Fitness and Virulence
Authors: Keller Brian C. , Fredericksen Brenda L. , Samuel Melanie A. , Mock Richard E. , Mason Peter W. , Diamond Michael S. , Gale Michael
Published: September 2006

The
emergence of West Nile virus (WNV) in the Western Hemisphere is marked
by the spread of pathogenic lineage I strains, which differ from
typically avirulent lineage II strains. To begin to understand the
virus-host interactions that may influence the phenotypic properties of
divergent lineage I and II viruses, we compared the genetic,
pathogenic, and alpha/beta interferon
(IFN-α/β)-regulatory properties of a lineage II isolate
from Madagascar (MAD78) with those of a new lineage I isolate from
Texas (TX02). Full genome sequence analysis revealed that MAD78
clustered, albeit distantly, with other lineage II strains, while TX02
clustered with emergent North American isolates, more specifically with
other Texas strains. Compared to TX02, MAD78 replicated at low levels
in cultured human cells, was highly sensitive to the antiviral actions
of IFN in vitro, and demonstrated a completely avirulent phenotype in
wild-type mice. In contrast to TX02 and other pathogenic forms of WNV,
MAD78 was defective in its ability to disrupt IFN-induced JAK-STAT
signaling, including the activation of Tyk2 and downstream
phosphorylation and nuclear translocation of STAT1 and STAT2. However,
replication of MAD78 was rescued in cells with a nonfunctional
IFN-α/β receptor (IFNAR). Consistent with this finding,
the virulence of MAD78 was unmasked upon infection of mice lacking
IFNAR. Thus, control of the innate host response and IFN actions is a
key feature of WNV pathogenesis and replication
fitness.
Complete-Genome Phylogenetic Approach to Varicella-Zoster Virus Evolution: Genetic Divergence and Evidence for Recombination
Authors: Norberg Peter , Liljeqvist Jan-Åke , Bergström Tomas , Sammons Scott , Schmid D. Scott , Loparev Vladimir N.
Published: September 2006

Recent studies of varicella-zoster virus (VZV) DNA sequence variation, involving large numbers of globally distributed clinical isolates, suggest that this virus has diverged into at least three distinct genotypes designated European (E), Japanese (J), and mosaic (M). In the present study, we determined and analyzed the complete genomic sequences of two M VZV strains and compared them to the sequences of three E strains and two J strains retrieved from GenBank (including the Oka vaccine preparation, V-Oka). Except for a few polymorphic tandem repeat regions, the whole genome, representing approximately 125,000 nucleotides, is highly conserved, presenting a genetic similarity between the E and J genotypes of approximately 99.85%. These analyses revealed that VZV strains distinctly segregate into at least four genotypes (E, J, M1, and M2) in phylogenetic trees supported by high bootstrap values. Separate analyses of informative sites revealed that the tree topology was dependent on the region of the VZV genome used to determine the phylogeny; collectively, these results indicate the observed strain variation is likely to have resulted, at least in part, from interstrain recombination. Recombination analyses suggest that strains belonging to the M1 and M2 genotypes are mosaic recombinant strains that originated from ancestral isolates belonging to the E and J genotypes through recombination on multiple occasions. Furthermore, evidence of more recent recombination events between M1 and M2 strains is present in six segments of the VZV genome. As such, interstrain recombination in dually infected cells seems to figure prominently in the evolutionary history of VZV, a feature it has in common with other herpesviruses. In addition, we report here six novel genomic targets located in open reading frames 51 to 58 suitable for genotyping of clinical VZV isolates.
Revealing Domain Structure through Linker-Scanning Analysis of the Murine Leukemia Virus (MuLV) RNase H and MuLV and Human Immunodeficiency Virus Type 1 Integrase Proteins
Authors: Puglia Jennifer , Wang Tan , Smith-Snyder Christine , Cote Marie , Scher Michael , Pelletier Joelle N. , John Sinu , Jonsson Colleen B. , Roth Monica J.
Published: September 2006

Linker-scanning libraries were generated within the 3′ terminus of the Moloney murine leukemia virus (M-MuLV)
pol
gene encoding the connection-RNase H domains of reverse transcriptase (RT) as well as the structurally related M-MuLV and human immunodeficiency virus type 1 (HIV-1) integrase (IN) proteins. Mutations within the M-MuLV proviral vectors were Tn
7
based and resulted in 15-bp insertions. Mutations within an HIV-1 IN bacterial expression vector were based on Tn
5
and resulted in 57-bp insertions. The effects of the insertions were examined in vivo (M-MuLV) and in vitro (HIV-1). A total of 178 individual M-MuLV constructs were analyzed; 40 in-frame insertions within RT connection-RNase H, 108 in-frame insertions within IN, 13 insertions encoding stop codons within RNase H, and 17 insertions encoding stop codons within IN. For HIV-1 IN, 56 mutants were analyzed. In both M-MuLV and HIV-1 IN, regions are identified which functionally tolerate multiple-linker insertions. For MuLV, these correspond to the RT-IN proteolytic junction, the junction between the IN core and C terminus, and the C terminus of IN. For HIV-1 IN, in addition to the junction between the IN core and C terminus and the C terminus of IN, insertions between the N terminus and core domains maintained integration and disintegration activity. Of the 40 in-frame insertions within the M-MuLV RT connection-RNase H domains, only the three C-terminal insertions mapping to the RT-IN proteolytic junction were viable. These results correlate with deletion studies mapping the domain and subdomain boundaries of RT and IN. Importantly, these genetic footprints provide a means to identify nonessential regions within RT and IN for targeted gene therapy applications.
High Frequency of Genetic Recombination Is a Common Feature of Primate Lentivirus Replication
Authors: Chen Jianbo , Powell Douglas , Hu Wei-Shau
Published: September 2006

Recent studies indicate that human immunodeficiency virus type 1 (HIV-1) recombines at exceedingly high rates, approximately 1 order of magnitude more frequently than simple gammaretroviruses such as murine leukemia virus and spleen necrosis virus. We hypothesize that this high frequency of genetic recombination is a common feature of primate lentiviruses. Alternatively, it is possible that HIV-1 is unique among primate lentiviruses in possessing high recombination rates. Among other primate lentiviruses, only the molecular mechanisms of HIV-2 replication have been extensively studied. There are reported differences between the replication mechanisms of HIV-1 and those of HIV-2, such as preferences for RNA packaging in
cis
and properties of reverse transcriptase and RNase H activities. These biological disparities could lead to differences in recombination rates between the two viruses. Currently, HIV-1 is the only primate lentivirus in which recombination rates have been measured. To test our hypothesis, we established recombination systems to measure the recombination rates of two other primate lentiviruses, HIV-2 and simian immunodeficiency virus from African green monkeys (SIVagm), in one round of viral replication. We determined that, for markers separated by 588, 288, and 90 bp, HIV-2 recombined at rates of 7.4%, 5.5%, and 2.4%, respectively, whereas SIVagm recombined at rates of 7.8%, 5.6%, and 2.7%, respectively. These high recombination rates are within the same range as the previously measured HIV-1 recombination rates. Taken together, our results indicate that HIV-1, HIV-2, and SIVagm all possess high recombination frequencies; hence, the high recombination potential is most likely a common feature of primate lentivirus replication.
Optimization of Feline Immunodeficiency Virus Vectors for RNA Interference
Authors: Harper Scott Q. , Staber Patrick D. , Beck Christine R. , Fineberg Sarah K. , Stein Colleen , Ochoa Dalyz , Davidson Beverly L.
Published: September 2006

RNA interference (RNAi) occurs naturally in plant and animal cells as a means for modulating gene expression. This process has been experimentally manipulated to achieve targeted gene silencing in cells, tissues, and animals, using a variety of vector systems. Here, we tested the hypothesis that vectors based on feline immunodeficiency virus (FIV) could be used for coexpression of reporter constructs and RNAi expression cassettes. We found, unexpectedly, in our initial constructs that placement of RNAi expression cassettes downstream from a polymerase II (pol II)-expressed reporter gene inhibited reporter expression but not vector titer. Through a series of intermediate vector constructs, we found that placement of the RNAi expression cassette relative to the Rev response element and the pol II expression cassette was critical for efficient RNAi and reporter gene expression. These results suggested that steric factors, including RNA structure and recruitment of competing transcriptional machinery, may affect gene expression from FIV vectors. In a second series of studies, we show that target sequence silencing can be achieved in cells transduced by FIV vectors coexpressing reporter genes and 3′ untranslated region resident microRNAs. The optimized FIV-based RNAi expression vectors will find broad use given the extensive tropism of pseudotyped FIV vectors for many cell types in vitro and in vivo.
Evaluation of the Lytic Origins of Replication of Kaposi's Sarcoma-Associated Virus/Human Herpesvirus 8 in the Context of the Viral Genome
Authors: Xu Yiyang , Rodriguez-Huete Alicia , Pari Gregory S.
Published: September 2006

The lytic origins of DNA replication for human herpesvirus 8 (HHV8), oriLyt-L and oriLyt-R, are located between open reading frames K4.2 and K5 and ORF69 and vFLIP, respectively. These lytic origins were elucidated using a transient replication assay. Although this assay is a powerful tool for identifying many herpesvirus lytic origins, it is limited in its ability to evaluate the activity of replication origins in the context of the viral genome. To this end, we investigated the ability of a recombinant HHV8 bacterial artificial chromosome (BAC) to replicate in the absence of oriLyt-R, oriLyt-L, or both oriLyt regions. We generated the HHV8 BAC recombinants (BAC36-ΔOri-R, BAC36-ΔOri-L, and BAC36-ΔOri-RL), which removed one or all of the identified lytic origins. An evaluation of these recombinant BACs revealed that oriLyt-L was sufficient to propagate the viral genome, whereas oriLyt-R alone failed to direct the amplification of viral DNA.
Major Histocompatibility Complex Class II Molecules Promote Human Immunodeficiency Virus Type 1 Assembly and Budding to Late Endosomal/Multivesicular Body Compartments
Authors: Finzi Andrés , Brunet Alexandre , Xiao Yong , Thibodeau Jacques , Cohen Éric A.
Published: September 2006

Human immunodeficiency virus type 1 (HIV-1) assembly, budding, and release occur mostly at the plasma membrane in T lymphocytes as well as in established nonlymphoid cell lines, while in macrophages these processes occur primarily in intracellular compartments that harbor late endosomal/multivesicular body (LE/MVB) markers, including human leukocyte antigen DR (HLA-DR). Major histocompatibility complex class II molecules (MHC-II), which are expressed in macrophages and activated T cells, have been previously reported to induce the formation of multilaminar and multivesicular endocytic MHC-II-like structures analogous to MVB upon their expression in HEK 293 cells. Here, we have examined the role of MHC-II in HIV-1 Gag targeting as well as in virus assembly and release. Expression of HLA-DR in nonlymphoid cell lines induced a relocation of Gag to intracellular compartments that harbored LE/MVB markers and increased the accumulation of viral particles assembling intracellularly. Consequently, viral production and release from the cell surface was found to be substantially decreased in HLA-DR-expressing cells. This process was specific, since it was not observed with HLA-DR molecules lacking their cytoplasmic tails, nor with structurally related but functionally distinct MHC-II molecules such as HLA-DM or HLA-DO. Importantly, virus released intracellularly in HLA-DR-expressing cells retained infectivity. Overall, these results suggest a role of MHC-II molecules in promoting HIV-1 assembly and budding to LE/MVB and raise the possibility that this activity might be part of a normal pathway of virus production in cell types physiologically expressing MHC-II molecules, such as macrophages.
ICP22 Is Required for Wild-Type Composition and Infectivity of Herpes Simplex Virus Type 1 Virions
Authors: Orlando Joseph S. , Balliet John W. , Kushnir Anna S. , Astor Todd L. , Kosz-Vnenchak Magdalena , Rice Stephen A. , Knipe David M. , Schaffer Priscilla A.
Published: September 2006

The immediate-early regulatory protein ICP22 is required for efficient replication of herpes simplex virus type 1 in some cell types (permissive) but not in others (restrictive). In mice infected via the ocular route, the pathogenesis of an ICP22−virus, 22/n199, was altered relative to that of wild-type virus. Specifically, tear film titers of 22/n199-infected mice were significantly reduced at 3 h postinfection relative to those of mice infected with wild-type virus. Further, 22/n199 virus titers were below the level of detection in trigeminal ganglia (TG) during the first 9 days postinfection. On day 30 postinfection, TG from 22/n199-infected mice contained reduced viral genome loads and exhibited reduced expression of latency-associated transcripts and reduced reactivation efficiency relative to TG from wild-type virus-infected mice. Notably, the first detectable alteration in the pathogenesis of 22/n199 in these tests occurred in the eye prior to the onset of nascent virus production. Thus, ICP22−virions appeared to be degraded, cleared, or adsorbed more rapidly than wild-type virions, implying potential differences in the composition of the two virion types. Analysis of the protein composition of purified extracellular virions indicated that ICP22 is not a virion component and that 22/n199 virions sediment at a reduced density relative to wild-type virions. Although similar to wild-type virions morphologically, 22/n199 virions contain reduced amounts of two γ2late proteins, US11 and gC, and increased amounts of two immediate-early proteins, ICP0 and ICP4, as well as protein species not detected in wild-type virions. Although ICP22−viruses replicate to near-wild-type levels in permissive cells, the virions produced in these cells are biochemically and physically different from wild-type virions. These virion-specific differences in ICP22−viruses add a new level of complexity to the functional analysis of this immediate-early viral regulatory protein.
Invasion of Host Cells by JC Virus Identifies a Novel Role for Caveolae in EndosomalSorting of Noncaveolar Ligands
Authors: Querbes W. , O'Hara B. A. , Williams G. , Atwood W. J.
Published: September 2006

Invasion
of glial cells by the human polyomavirus, JC virus (JCV), leads to a
rapidly progressing and uniformly fatal demyelinating disease known as
progressive multifocal leukoencephalopathy. The endocytic trafficking
steps used by JCV to invade cells and initiate infection are not known.
We demonstrated that JCV infection was inhibited by dominant defective
and constitutively active Rab5-GTPase mutants that acted at distinct
steps in endosomal sorting. We also found that labeled JCV colocalized
with labeled cholera toxin B and with caveolin-1 (cav-1) on early
endosomes following internalization by clathrin-dependent endocytosis.
JCV entry and infection were both inhibited by dominant defective
mutants of eps15 and Rab5-GTPase. Expression of a dominant-negative
scaffolding mutant of cav-1 did not inhibit entry or infection by JCV.
A single-cell knockdown experiment using cav-1 shRNA did not inhibit
JCV entry but interfered with a downstream trafficking event important
for infection. These data show that JCV enters cells by
clathrin-dependent endocytosis, is transported immediately to early
endosomes, and is then sorted to a caveolin-1-positive endosomal
compartment. This latter step is dependent on Rab5-GTPase, cholesterol,
caveolin-1, and pH. This is the first example of a ligand that enters
cells by clathrin-dependent endocytosis and is then sorted from early
endosomes to caveosomes, indicating that caveolae-derived vesicles play
a more important role than previously realized in sorting cargo from
early
endosomes.
Vaccinia Virus F9 Virion Membrane Protein Is Required for Entry but Not Virus Assembly, in Contrast to the Related L1 Protein
Authors: Brown Erica , Senkevich Tatiana G. , Moss Bernard
Published: September 2006

All sequenced poxviruses encode orthologs of the vaccinia virus L1 and F9 proteins, which are structurally similar and share about 20% amino acid identity. We found that F9 further resembles L1 as both proteins are membrane components of the mature virion with similar topologies and induce neutralizing antibodies. In addition, a recombinant vaccinia virus that inducibly expresses F9, like a previously described L1 mutant, had a conditional-lethal phenotype: plaque formation and replication of infectious virus were dependent on added inducer. However, only immature virus particles are made when L1 is repressed, whereas normal-looking intracellular and extracellular virions formed in the absence of F9. Except for the lack of F9, the polypeptide components of such virions were indistinguishable from those of wild-type virus. These F9-deficient virions bound to cells, but their cores did not penetrate into the cytoplasm. Furthermore, cells infected with F9-negative virions did not fuse after a brief low-pH treatment, as did cells infected with virus made in the presence of inducer. In these respects, the phenotype associated with F9 deficiency was identical to that produced by the lack of individual components of a previously described poxvirus entry/fusion complex. Moreover, F9 interacted with proteins of that complex, supporting a related role. Thus, despite the structural relationships of L1 and F9, the two proteins have distinct functions in assembly and entry, respectively.
Gas Permeability of Porous Substances
Authors: Medek Jiří , Kovář Lukáš , Weishauptová Zuzana
Published: September 2006

A dependence of the amount of gas passed Q on the input pressure Pin has been derived for turbulent flow in a model material with an artificially prepared porous texture. For the ratio Q/∆P, where ∆P is the pressure gradient equal to the difference of an input Pin and output Pout pressures, the dependence on Pin is linear with a positive slope value, while for Q/∆P2 for the pressure gradient expressed by Pin2 - Pout2 it is linear as well, but with a negative slope value, which contradicts the experimental results. The ratio Q/∆P has been introduced as a quantity determining the permeability. The dependence of permeability on the path length of the flow L satisfied the power function Q/∆P = CL-b, where the constant C corresponds to the value (Q/∆P)(1) for L = 1, C is characteristic of a given system. Helium has been chosen as a standard gas for studying gas permeability in real porous systems.
The Effect of Gold Oxide on Electrooxidation of Aliphatic Amines
Authors: Łuczak Teresa
Published: September 2006

The electrooxidation of aliphatic amines ranging from ethylamine to butylamine at the gold electrode in contact with an alkaline electrolyte solution has been described. The adsorptive behaviour of substrate molecules was identified by changes in the differential capacitance of the double layer at the electrode/solution interface. Subsequent stages of the oxidation process are proposed.
Corrosion of concrete reinforcement and electrochemical factors in concrete patch repair
Authors: Zhang Jieying , Mailvaganam Noël P
Published: September 2006

Corrosion of concrete reinforcement at a patch repair is a complex problem, and current knowledge of its mechanism is quite limited. This review examined the correlation between two corrosion mechanisms, macrocell and microcell corrosion, from fundamental electrochemical principles. It was found that both mechanisms could play significant roles in inducing corrosion damage, contrary to the prevailing opinion that macrocell corrosion is the main deterioration mechanism in patch repair. This has practical implications that need to be considered for an effective and durable repair. A review of the studies done to date also enabled the identification of the key factors in patch repair controlling the corrosion characteristics. Corrosion could occur at different locations in the vicinity of the patch — substrate, interface, or patch area — depending on the respective electrochemical environments induced by the repair material properties and treatments, as well as the in-service exposure and mechanical loading. The review indicates that much of the needed research should focus on identification of corrosion mechanisms to effect successful patch repair in reinforced concrete structures.Key words: patch repair, substrate, corrosion, macrocell corrosion, microcell corrosion.
CO2 sequestration using calcium-silicate concrete
Authors: Shao Yixin , Mirza M Saeed , Wu Xiaorong
Published: September 2006

The potential for using calcium silicate concrete to sequester CO2 and simultaneously develop strong and durable concrete building products is studied. It is the calcium compounds in cement that react with CO2 through the early-age carbonation curing, forming geologically stable calcium carbonates. Both type 10 and type 30 Portland cements were investigated as CO2 binders in concretes with 0%, 25%, 50%, and 75% quartz aggregates and lightweight aggregates. The sequestration took place in a chamber under 0.5 MPa pressure at ambient temperature for a duration of 2 h; a 100% concentration of CO2 was used to simulate the recovered CO2 from flue gas. The CO2 uptake was quantified by direct mass gain and by infrared-based carbon analyzer, and the performance of the carbonated concrete was evaluated by its strength. A CO2 uptake of 9%16% by binder mass was achieved in 2 h. The X-ray diffraction spectra showed the presence of strong calcite peaks and a total absence of Ca(OH)2. The 2 h carbonation strength exceeded the 7 d hydration strength. The calcium silicate concrete approach is shown to be feasible for CO2 sequestration and would result in technical, environmental, and economical benefits.Key words: CO2 sequestration, concrete, carbonation curing, calcium carbonates, strength.
Effect of second-order forces on seismic response
Authors: Humar J , Mahgoub M , Ghorbanie-Asl M
Published: September 2006

In a building structure subjected to seismic forces, the gravity loads acting through the lateral displacements lead to additional shears and moments. This is generally referred to as the P–Δ effect; it tends to reduce the capacity of the structure to resist the seismic forces and may lead to instability. It has been suggested that an increase in structural strength, in stiffness, or in both would mitigate the P–Δ effect and ensure stability of the structure. It is shown here that instability results when the P–Δ effect causes the stiffness of the structure to become negative in the post-yield range, in which case increasing the strength, the stiffness, or both does not ensure stability. In a single-storey structure, stability can be ensured if there is sufficient strain hardening that the post-yield stiffness is positive even in the presence of the P–Δ effect. For a multistorey building the vulnerability of the structure to P–Δ instability can be judged by obtaining a pushover curve. It is shown that as long as the maximum displacement produced by the design earthquake lies in the region of positive slope of the pushover curve, the structure will remain stable.Key words: seismic response, P–Δ effect, dynamic instability, stability coefficient, amplification factor, pushover analysis, nonlinear analysis.
Privatisation of fixed-rail transit systems: a case study of Malaysia's STAR and PUTRA
Authors: Abdul-Aziz Abdul-Rashid
Published: September 2006

Since the early 1980s, many public utilities have been privatised under Malaysia's privatisation programme. A few, however, have since prematurely returned to government hands, among them the two light-rail transit systems in the capital city of Kuala Lumpur, STAR and PUTRA. This paper chronicles the pre- and post-privatisation events of both facilities before attempting to provide rational explanation behind their untimely surrender to the public domain. Based on publicly available material, this paper argues that neither the quality of government negotiators nor the length of time devoted to negotiating could be attributed to the bailout. Nor is there hint that political favouritism and corruption were at play. More than likely, despite the copious incentives provided to the two concession companies, the two projects proved financially unviable.Key words: build–operate–transfer (BOT), Malaysia, privatisation, light-rail transit system.
Fatigue damage analysis in asphalt concrete mixtures using the dissipated energy approach
Authors: Ghuzlan Khalid A , Carpenter Samuel H
Published: September 2006

An asphalt concrete damage–energy fatigue approach based on the concept of change in dissipated energy is presented in this paper. The damage–energy based fatigue approach is simple and based on a sound theoretical background. The central concept of the energy approach is the energy fatigue curve, which is based on two key elements, namely the plateau value (PV) and the number of load cycles to true failure (Ntf). The plateau value represents the constant value of the percentage of dissipated energy that produces damage to the material under cyclic loading. Failure is defined as the number of load cycles at which this percentage of dissipated energy begins to increase rapidly, indicating instability. Flexural fatigue testing was used to test hundreds of asphalt concrete beams, mainly under controlled-strain testing conditions. It was found that PV is highly dependent on the initial loading conditions, stress, strain, and dissipated energy. As a result, it can be used conveniently in pavement design. The number of load cycles to 50% reduction in initial stiffness was found to be highly correlated with the new failure point (Ntf). Using the dissipated energy concepts in fatigue analysis makes it possible to account for damage accumulation in a straightforward manner.Key words: fatigue of asphalt concrete, dissipated energy, damage, energy ratio.
An experimental study into local scour in a channel caused by a 90° bend
Authors: Sui Jueyi , Fang Daxian , Karney Bryan W
Published: September 2006

Based on a series of experiments, this paper explores the influence of a 90° change in flow direction on local scouring. The influence on local scour patterns due to hydraulic parameters such as the Froude number, the slope of the protection wall, the width of the protection apron along the outside wall of the downstream section, and the grain size of the channel bed material is examined. Protection-wall slopes ranging from 1:0.5 to 1:4 (vertical to horizontal) were investigated, as were different widths of the protection apron; the goal was to ascertain the role of these variables in local scour patterns in the vicinity of the bend. The factors affecting local scour depth are related through empirical equations to key hydraulic variables, the slope of the protection wall, and the width of the protection apron.Key words: bent flume, channel erosion, Froude number, scour depth, slope of protection wall (SPW), width of protection apron (WPA).
Durability design of infrastructure and some related issues
Authors: Mirza Saeed
Published: September 2006

The life cycle performance of any infrastructure should be taken into consideration in its design, its construction, its maintenance, its operation, and when needed, its rehabilitation. The protection of infrastructure must be holistic, taking into account long-term socioeconomic and environmental considerations and the impact of the global climate change. Fulfilling the requirements of the ultimate and serviceability limit states over the service life of the facility requires an understanding of the use of the system, the deterioration response of the materials and their components when subjected to aggressive environments, and how this deterioration can be prevented or significantly delayed by preventive, remedial, and routine maintenance. The composition, microstructure, macrostructure, and various modes of deterioration of materials used in construction (steel, wood, concrete) are reviewed, along with possible remedial measures. The development of concrete as a construction material, its durability, and the relevant durability provisions in the various Canadian Standards Association standards are reviewed briefly. Current European practice and the 1990 Comité Euro-International du béton Design Guide for Durable Concrete Structures are evaluated. The engineer's responsibility for durable performance of a facility and the importance of durability audits are also examined.Key words: aggressive environment, construction materials, deterioration, durability, durability audits, life cycle performance, macrostructure, microstructure, socioeconomic and environmental considerations, sustainability.
Aerated stabilization basin design and operating practices in the Canadian pulp and paper industry
Authors: Mahmood Talat , Paice Michael
Published: September 2006

Aerated stabilization basins (ASBs) currently account for about one third of the pulp and paper industry's secondary treatment capacity. We surveyed mills with ASBs to analyze design and operating practices. Of the 19 mills that responded, 15 were kraft, reflecting the industry's overall use of ASBs. Biochemical oxygen demand (BOD) and total suspended solids (TSS) loading to the ASBs varied considerably and were factors in biotreatment performance. Problems identified with some ASBs included excessive solids accumulation resulting in the need for frequent dredging, high TSS discharge, and difficulty with nutrient management. Most ASBs have either two or three cells. An important parameter identified for these cells is the benthal settling area. Too small an area results in a higher dredging frequency, with limited nutrient feedback. In general, ASB systems that used the most intensive mixing and aeration in the upstream cells tended to have a smaller benthal settling area, resulting in the need to dredge more frequently. Ideally, some benthal settling should be designed into the upstream cells to allow nutrient feedback where it is needed most. Key words: aeration tanks, lagoons, basins, aeration, benthic deposits, design, operations, biological treatment, primary treatment, tertiary treatment, nutrients, aerated stabilization basin (ASB).
Comparison of on-site and upstream greenhouse gas emissions from Canadian municipal wastewater treatment facilities
Authors: Sahely Halla R , MacLean Heather L , Monteith Hugh D , Bagley David M
Published: September 2006

Canada's ratification of the Kyoto Protocol has focused attention on the importance of accurately estimating emissions of greenhouse gases (GHG) from all sectors. An inventory of emissions of greenhouse gases from Canadian municipal wastewater treatment plants was prepared using a life-cycle approach. Both on-site emissions at the treatment facility due to the biological processes used and fossil fuels consumed for energy and heat and upstream emissions related to off-site production and transmission of fuels and the off-site production of electricity for the plant were included. For the year 2000, the on-site methane (CH4) emission rate from Canadian municipal wastewater treatment facilities was estimated at 1600 Mg/year. The total on-site emission rate of carbon dioxide (CO2) was estimated at 669 100 Mg/year, but the estimated total CO2 equivalent emissions rose to 1 048 500 Mg/year once upstream emissions were included. Clear abatement strategies related to more efficient energy use and energy recovery can be identified once accurate GHG emissions inventories are in place.Key words: municipal wastewater treatment, life-cycle approach, greenhouse gas emissions, anaerobic processes.
Proposed water management and control device for water losses problem in Jordan
Authors: Beithou N
Published: September 2006

Jordan is considered to be one of the most water-scarce countries in the world, where the water shortage problem has become of a permanent nature. All efforts are focused on managing water usage, saving existing water, and creating new water resources. In this paper, a water management and control device (WMCD) is proposed to solve the problem of floating storage tanks in areas which are not suited for the indirect water supply systems. The WMCD aims to manage the existing water in the storage tanks and automatically control the storage tanks filling operation with minimum energy and no water losses. The water management and control device consists of valves, sensors, and controllers; it uses a programmable logic control (PLC) to control the overall filling operation and to monitor the water level in the storage tanks. It satisfies its purpose by giving consumers the chance to manage their available water resources as they observe the level of water in their storage tanks continuously, and it controls the filling operation by means of water and pressure sensors, thus saving water and energy. Key words: water management, water control, storage tanks, control devices, Jordan, water losses.
Acetylene blockage technique as a tool to determine denitrification potential of a biomass fixed on an organic media treating wastewater
Authors: Gilbert Y , Bihan Y Le , Lessard P
Published: September 2006

Biofiltration on organic media is used in many wastewater applications. However, no tools are available to survey the microorganisms' activity inside the process. The acetylene blockage technique was adapted to evaluate the potential denitrifiers' activity. The objectives of this work were to adapt and verify the applicability of the method by evaluating its sensitivity and variability. A closed cell was built and installed in an open network where pure gaseous nitrogen and acetylene had been successively injected at fixed rate on filtering media samples. N2O produced by the denitrifying biomass was monitored during the test. Assays were realized in replicates, with different quantities of filtering media, to observe the sensitivity and the variability of the method. Potential denitrifying activity and quantity of biomass correlation shows that the adapted method was sensitive for 50 to 150 g (wet basis) of filtering media. Moreover, when under an acetylene atmosphere, the coefficients of variation observed for the tests varied between 10% and 32% when under anoxic conditions. This work shows that the technique as adapted could be used as a tool to survey the potential activity of denitrifiers fixed on an organic media.Key words: denitrification, biofilter, acetylene, nitrous oxide, organic media, potential activity.
Synthesis and thermolysis rate constants of diastereomeric oxadiazoline sources of acetoxy(methoxy)carbene — Reaction of acetoxy(methoxy)carbene with isocyanates
Authors: Sokol Wojciech , Warkentin John
Published: September 2006

Oxidation of the methoxycarbonylhydrazone of p-methoxyacetophenone affords both the cis- and trans-2-acetoxy-2-methoxy-5-(p-methoxyphenyl)-5-methyl-Δ3-1,3,4-oxadiazolines (also known as corresponding 2,5-dihydro-1,3,4-oxadiazoles) as well as methyl 1-acetoxy-1-(p-methoxyphenylethyl)diazenecarboxylate. The three isomers were separated and identified by spectroscopic means. Methyl 1-acetoxy-1-(p-methoxyphenylethyl)diazenecarboxylate is the major product from oxidation in dichloromethane. Oxidation in acetic acid did not afford the oxadiazolines but gave the diazenecarboxylate and, in addition, 1-(p-methoxyphenyl)ethyl acetate. Attempts to isomerize the diazenecar boxylate to the oxadiazolines by acid catalysis were not successful. Thermolysis of the oxadiazolines at 50.4 °C occurred with approximately the same rate constant (ca. 3.6 × 10–5 s–1) to afford acetoxy(methoxy)carbene, which rearranges to methyl pyruvate by acetyl transfer. The carbene, which reacts with relatively unhindered isocyanates to transfer the methoxy carbonyl group to carbon and the acetyl group to nitrogen, can be considered an acyl anion equivalent in that reaction.Key words: acetoxy(methoxy)carbene, diazene, oxadiazoline, isocyanate, (acetylamino)oxoacetate.
Protein mass measurement combined with mass spectrometric sequencing of protein digests for detection and characterization of protein modifications1
Authors: Ji Chengjie , Wang Zhengping , Li Liang
Published: September 2006

A method for the characterization of modifications of low molecular weight proteins (<20 kDa) extracted from a microorganism based on the use of multiple separation tools and mass spectrometric techniques is described. In this method, intact proteins from cell extracts are first separated and fractionated by liquid chromatography (LC). Individual fractions are then analyzed by matrix-assisted laser desorption ionization (MALDI) mass spectrometry (MS) to provide intact protein mass information. The fractions are further characterized by using trypsin digestion and LC electrospray ionization (ESI) MS/MS analysis of the resultant peptides to identify the proteins. Gel electrophoresis of a fraction is also carried out to estimate the molecular masses of the proteins. The gel bands are identified by in-gel digestion and peptide mass mapping and sequencing using MALDI-MS and MALDI-MS/MS. The combined information generated from these experiments is interpreted for detecting and characterizing modified proteins. This method has been developed and applied to the analysis of posttranslational modifications (PTMs) of low-mass proteins (5–20 kDa) extracted from a relatively well-characterized microorganism, Escherichia coli. Using this method, not only previously reported PTMs involving acetylation, methylation, oxidation, and the removal of signal peptides, but also two novel PTMs, namely loss of N-terminal Met-Thr-Met (MTM) and hydroxylation of arginine, were identified. It is envisaged that this method should be applicable to other relatively simple microorganisms for the discovery of new PTMs.Key words: top-down proteomics, protein modification, HPLC, gel electrophoresis, tandem mass spectrometry.