bluuebunny/crossref_metadata_2025 huggingface dataset:
Characterization of RNA Elements That Regulate Gag-Pol Ribosomal Frameshifting in Equine Infectious Anemia Virus
Authors: Chen Chaoping , Montelaro Ronald C.
Published: September 2003

Synthesis of Gag-Pol polyproteins of retroviruses requires ribosomes to shift translational reading frame once or twice in a −1 direction to read through the stop codon in the
gag
reading frame. It is generally believed that a slippery sequence and a downstream RNA structure are required for the programmed −1 ribosomal frameshifting. However, the mechanism regulating the Gag-Pol frameshifting remains poorly understood. In this report, we have defined specific mRNA elements required for sufficient ribosomal frameshifting in equine anemia infectious virus (EIAV) by using full-length provirus replication and Gag/Gag-Pol expression systems. The results of these studies revealed that frameshifting efficiency and viral replication were dependent on a characteristic slippery sequence, a five-base-paired GC stretch, and a pseudoknot structure. Heterologous slippery sequences from human immunodeficiency virus type 1 and visna virus were able to substitute for the EIAV slippery sequence in supporting EIAV replication. Disruption of the GC-paired stretch abolished the frameshifting required for viral replication, and disruption of the pseudoknot reduced the frameshifting efficiency by 60%. Our data indicated that maintenance of the essential RNA signals (slippery sequences and structural elements) in this region of the genomic mRNA was critical for sufficient ribosomal frameshifting and EIAV replication, while concomitant alterations in the amino acids translated from the same region of the mRNA could be tolerated during replication. The data further indicated that proviral mutations that reduced frameshifting efficiency by as much as 50% continued to sustain viral replication and that greater reductions in frameshifting efficiency lead to replication defects. These studies define for the first time the RNA sequence and structural determinants of Gag-Pol frameshifting necessary for EIAV replication, reveal novel aspects relative to frameshifting elements described for other retroviruses, and provide new genetic determinants that can be evaluated as potential antiviral targets.
New Inhibitors of Scrapie-Associated Prion Protein Formation in a Library of 2,000 Drugs and Natural Products
Authors: Kocisko David A. , Baron Gerald S. , Rubenstein Richard , Chen Jiancao , Kuizon Salomon , Caughey Byron
Published: September 2003

Transmissible spongiform encephalopathies (TSEs) are fatal, untreatable neurodegenerative diseases associated with the accumulation of a disease-specific form of prion protein (PrP) in the brain. One approach to TSE therapeutics is the inhibition of PrP accumulation. Indeed, many inhibitors of the accumulation of PrP associated with scrapie (PrP
Sc
) in scrapie-infected mouse neuroblastoma cells (ScN
2
a) also have antiscrapie activity in rodents. To expedite the search for potential TSE therapeutic agents, we have developed a high-throughput screening assay for PrP
Sc
inhibitors using ScN
2
a cells in a 96-well format. A library of 2,000 drugs and natural products was screened in ScN
2
a cells infected with scrapie strain RML (Chandler) or 22L. Forty compounds were found to have concentrations causing 50% inhibition (IC
50
s) of PrP
Sc
accumulation of ≤10 μM against both strains. Seventeen had IC
50
s of ≤1 μM against both strains. Several classes of compounds were represented in the 17 most potent inhibitors, including naturally occurring polyphenols (e.g., tannic acid and tea extracts), phenothiazines, antihistamines, statins, and antimalarial compounds. These 17 compounds were also evaluated in a solid-phase cell-free hamster PrP conversion assay. Only the polyphenols inhibited the cell-free reaction, and their IC
50
s were near 100 nM. Several of the new PrP
Sc
inhibitors cross the blood-brain barrier and thus have potential to be effective after TSE infection reaches the brain. The fact that many are either approved human drugs or edible natural products should facilitate their use in animal testing and clinical trials.
Early Transcription from Nonintegrated DNA in Human Immunodeficiency Virus Infection
Authors: Wu Yuntao , Marsh Jon W.
Published: September 2003

Replication of human immunodeficiency virus (HIV) involves obligatory sequential processes. Following viral entry and reverse transcription, the newly synthesized viral DNA integrates into the host chromatin. Integration is mandatory for viral production, yet HIV infection of CD4 T cells in vivo results in high levels of nonintegrated DNA. The biological potential of nonintegrated HIV DNA is unclear; however, prior work has demonstrated a limited transcription of the
nef
gene by nonintegrated HIV in infected quiescent T-cell populations. In a kinetic analysis of HIV infection of metabolically active transformed and primary CD4 T cells, we find an unexpected transient expression of both early and late message by nonintegrated HIV DNA. However, only the early multiply spliced transcript was measurably translated. This restriction of protein expression was due in part to inadequate Rev function, since expression of Rev in
trans
resulted in the expression of the late structural gene
gag
by nonintegrated HIV DNA.
Tacaribe Virus Z Protein Interacts with the L Polymerase Protein To Inhibit Viral RNA Synthesis
Authors: Jácamo Rodrigo , López Nora , Wilda Maximiliano , Franze-Fernández María T.
Published: September 2003

Tacaribe virus (TV) is the prototype of the New World group of arenaviruses. The TV genome encodes four proteins, the nucleoprotein (N), the glycoprotein precursor, the polymerase (L), and a small RING finger protein (Z). Using a reverse genetic system, we recently demonstrated that TV N and L are sufficient to drive transcription and full-cycle RNA replication mediated by TV-like RNAs and that Z is a powerful inhibitor of these processes (N. López, R. Jácamo, and M. T. Franze-Fernández, J. Virol. 65:12241-12251, 2001). In the present study we investigated whether Z might interact with either of the proteins, N and L, required for RNA synthesis. To that end, we used coimmunoprecipitation with monospecific antibodies against the viral proteins and coimmunoprecipitation with serum against glutathione
S
-transferase (GST) and binding to glutathione-Sepharose beads when Z was expressed as a fusion protein with GST. We demonstrated that Z interacted with L but not with N and that Z inhibitory activity was dependent on its ability to bind to L. We also evaluated the contribution of different Z regions to its binding ability and functional activity. We found that integrity of the RING structure is essential for Z binding to L and for Z inhibitory activity. Mutants with deletions at the N and C termini of Z showed that amino acids within the C-terminal region and immediately adjacent to the RING domain N terminus contribute to efficient Z-L interaction and are required for inhibitory activity. The data presented here provide the first evidence of an interaction between Z and L, suggesting that Z interferes with viral RNA synthesis by direct interaction with L. In addition, coimmunoprecipitation studies revealed a previously unreported interaction between N and L.
An Alphavirus Replicon Particle Chimera Derived from Venezuelan Equine Encephalitis and Sindbis Viruses Is a Potent Gene-Based Vaccine Delivery Vector
Authors: Perri Silvia , Greer Catherine E. , Thudium Kent , Doe Barbara , Legg Harold , Liu Hong , Romero Raul E. , Tang Zequn , Bin Qian , Dubensky Thomas W. , Vajdy Michael , Otten Gillis R. , Polo John M.
Published: September 2003

Alphavirus replicon particle-based vaccine vectors derived from Sindbis virus (SIN), Semliki Forest virus, and Venezuelan equine encephalitis virus (VEE) have been shown to induce robust antigen-specific cellular, humoral, and mucosal immune responses in many animal models of infectious disease and cancer. However, since little is known about the relative potencies among these different vectors, we compared the immunogenicity of replicon particle vectors derived from two very different parental alphaviruses, VEE and SIN, expressing a human immunodeficiency virus type 1 p55Gagantigen. Moreover, to explore the potential benefits of combining elements from different alphaviruses, we generated replicon particle chimeras of SIN and VEE. Two distinct strategies were used to produce particles with VEE-p55gagreplicon RNA packaged within SIN envelope glycoproteins and SIN-p55gagreplicon RNA within VEE envelope glycoproteins. Each replicon particle configuration induced Gag-specific CD8+T-cell responses in murine models when administered alone or after priming with DNA. However, Gag-specific responses varied dramatically, with the strongest responses to this particular antigen correlating with the VEE replicon RNA, irrespective of the source of envelope glycoproteins. Comparing the replicons with respect to heterologous gene expression levels and sensitivity to alpha/beta interferon in cultured cells indicated that each might contribute to potency differences. This work shows that combining desirable elements from VEE and SIN into a replicon particle chimera may be a valuable approach toward the goal of developing vaccine vectors with optimal in vivo potency, ease of production, and safety.
Human Immunodeficiency Virus Type 1 Induces Persistent Changes in Mucosal and Blood γδ T Cells despite Suppressive Therapy
Authors: Poles Michael A. , Barsoum Shady , Yu Wenjie , Yu Jian , Sun Patricia , Daly Jeanine , He Tian , Mehandru Saurabh , Talal Andrew , Markowitz Martin , Hurley Arlene , Ho David , Zhang Linqi
Published: September 2003

γδ T cells are primarily found in the gastrointestinal mucosa and play an important role in the first line of defense against viral, bacterial, and fungal pathogens. We sought to examine the impact of human immunodeficiency virus type 1 (HIV-1) infection on mucosal as well as peripheral blood γδ T-cell populations. Our results demonstrate that HIV-1 infection is associated with significant expansion of Vδ1 and contraction of Vδ2 cell populations in both the mucosa and peripheral blood. Such changes were observed during acute HIV-1 infection and persisted throughout the chronic phase, without apparent reversion after treatment with highly active antiretroviral therapy (HAART). Despite an increase in the expression of CCR9 and CD103 mucosal homing receptors on peripheral blood γδ T cells in infected individuals, mucosal and peripheral blood γδ T cells appeared to be distinct populations, as reflected by distinct CDR3 length polymorphisms and sequences in the two compartments. Although the underlying mechanism responsible for triggering the expansion of Vδ1 γδ T cells remains unknown, HIV-1 infection appears to have a dramatic impact on γδ T cells, which could have important implications for HIV-1 pathogenesis.
Identification of the Receptor Binding Domain of the Mouse Mammary Tumor Virus Envelope Protein
Authors: Zhang Yuanming , Rassa John C. , deObaldia Maria Elena , Albritton Lorraine M. , Ross Susan R.
Published: September 2003

Mouse mammary tumor virus
(MMTV) is a betaretrovirus that infects rodent cells and uses mouse transferrin receptor 1 for cell entry. To characterize the interaction of MMTV with its receptor, we aligned the MMTV envelope surface (SU) protein with that of Friend murine leukemia virus (F-MLV) and identified a putative receptor-binding domain (RBD) that included a receptor binding sequence (RBS) of five amino acids and a heparin-binding domain (HBD). Mutation of the HBD reduced virus infectivity, and soluble heparan sulfate blocked infection of cells by wild-type pseudovirus. Interestingly, some but not all MMTV-like elements found in primary and cultured human breast cancer cell lines, termed h-MTVs, had sequence alterations in the putative RBS. Single substitution of one of the amino acids found in an h-MTV RBS variant in the RBD of MMTV, Phe
40
to Ser, did not alter species tropism but abolished both virus binding to cells and infectivity. Neutralizing anti-SU monoclonal antibodies also recognized a glutathione
S
-transferase fusion protein that contained the five-amino-acid RBS region from MMTV. The critical Phe
40
residue is located on a surface of the MMTV RBD model that is distant from and may be structurally more rigid than the region of F-MLV RBD that contains its critical binding site residues. This suggests that, in contrast to other murine retroviruses, binding to its receptor may result in few or no changes in MMTV envelope protein conformation.
Influenza B Virus BM2 Protein Is Transported through the
trans-
Golgi Network as an Integral Membrane Protein
Authors: Watanabe Shinji , Imai Masaki , Ohara Yoshiro , Odagiri Takato
Published: September 2003

A bicistronic mRNA transcribed from the influenza B virus RNA segment 7 encodes two viral proteins, matrix protein M1 and uncharacterized small protein BM2. In the present study, we focused on the cytoplasmic transport and cellular membrane association of BM2. Immunofluorescence studies of virus-infected cells indicated that BM2 accumulated at the Golgi apparatus immediately after synthesis and then was transported to the plasma membrane through the
trans
-Golgi network. Localization of a set of BM2 deletion mutants revealed that the N-terminal half of BM2 (residues 2 to 50) was crucial for its transport; in particular, the deletion of residues 2 to 23, deduced to be a transmembrane domain, resulted in diffused distribution of the protein throughout the entire cell. Sucrose gradient flotation and biochemical analyses of the membrane showed that BM2 was tightly associated with cellular membranes as an integral membrane protein. Oligomerization of BM2 was demonstrated by coprecipitation of differentially epitope-tagged BM2 proteins. Taken together, these results strongly suggest that BM2 is integrated into the plasma membrane at the N-terminal hydrophobic domain as fourth membrane protein, in addition to hemagglutinin, neuraminidase, and NB, of the influenza B virus.
JC Virus-Induced Changes in Cellular Gene Expression in Primary Human Astrocytes
Authors: Radhakrishnan Sujatha , Otte Jessica , Enam Sahnila , Del Valle Luis , Khalili Kamel , Gordon Jennifer
Published: September 2003

Cell-type-specific transcription of the JC virus (JCV) promoter in glial cells initiates a series of events leading to viral replication in the brain and the development of the fatal demyelinating disease progressive multifocal leukoencephalopathy (PML) in patients with neurologic complications due to infection with human immunodeficiency virus type 1. Here we employed an in vitro infection of primary cultures of human astrocytes to compare the transcriptional profile of cellular genes after JCV infection by using an oligonucleotide-based microarray of 12,600 genes. Transcription of nearly 355 genes was enhanced and expression of 130 genes was decreased to various degrees. Many transcripts that were increased upon JCV infection were found to encode proteins with properties that suggest their involvement in cell proliferation, including cyclin A and cyclin B1; signaling pathways, such as transforming growth factor β receptor 1, platelet-derived growth factor receptor and fibroblast growth factor family receptor; and other regulatory events, such as inflammatory responses, including cyclo-oxygenase-2 (Cox-2). Microarray-based data for several cell cycle-regulatory genes were further examined by using Western blot analysis of in vitro infected astrocytes harvested early and late during the infection. Results demonstrate that protein levels of all upregulated genes were found to increase at some point during the infection time course. In parallel, immunohistochemical assessment of cell cycle proteins, including cyclins A, B1, E, and Cdk2, showed positive staining of astrocytes within PML lesions of brain tissue from patients with neuro-AIDS. Microarray analysis was found to be a useful predictor of gene expression in infected cells; however, it may not directly correlate with protein levels during infection with JCV.
Preinfection Treatment of Resistant Mice with CpG Oligodeoxynucleotides Renders Them Susceptible to Friend Retrovirus-Induced Leukemia
Authors: Olbrich Anke R. M. , Schimmer Simone , Dittmer Ulf
Published: September 2003

We recently reported that immunostimulatory oligodeoxynucleotides (CpG oligodeoxynucleotides [CpG-ODN]) were effective in postexposure treatment of retrovirus-induced disease (A. R. M. Olbrich et al., J. Virol. 76:11397-11404, 2002). We now show that the timing of treatment is a critical factor in treatment efficacy. In stark contrast to the success of postexposure treatments, we found that CpG treatment of susceptible mice prior to Friend retrovirus infection accelerated the development of virus-induced erythroleukemia. Furthermore, 70.8% of mice that were resistant to Friend virus-induced leukemia developed disease after inoculation of CpG-ODN before infection. The CpG pretreatment of these mice enhanced viral loads in their spleens and blood compared to controls that received ODN without CpG motifs. The main target cells of Friend virus, erythroid precursor cells and B cells, proliferated after CpG-ODN inoculation and provided an enlarged target cell population for viral infection. Our present findings together with our previous report demonstrate that CpG-ODN treatment of viral infections may be a double-edged sword that can result in an effective therapy but also in an acceleration of disease progression depending on the time point of treatment.
Interaction between Human Respiratory Syncytial Virus (RSV) M2-1 and P Proteins Is Required for Reconstitution of M2-1-Dependent RSV Minigenome Activity
Authors: Mason Stephen W. , Aberg Erika , Lawetz Carol , DeLong Rachel , Whitehead Paul , Liuzzi Michel
Published: September 2003

We have investigated protein-protein interactions among the respiratory syncytial virus (RSV) RNA polymerase subunits using affinity chromatography. Here we demonstrate a novel interaction of P and M2-1 proteins. Phosphorylation of either M2-1 or P appears to be dispensable for this interaction. Internal deletions within P mapped the M2-1-binding domain to a region between residues 100 and 120. Alanine-scanning mutagenesis within this region of P revealed that substitution of any one of the three residues, L101, Y102, and F109, prevented both M2-1 and P binding and expression of an M2-1-dependent luciferase reporter gene. However, these same mutations did not prevent the activity of an M2-1-independent chloramphenicol acetyltransferase minigenome, suggesting that these residues of P specifically affect M2-1-P interaction. On the basis of these observations, it is possible that the interaction between RSV M2-1 and P proteins is important for viral replication.
Development and Use of a Vaccinia Virus Neutralization Assay Based on Flow Cytometric Detection of Green Fluorescent Protein
Authors: Earl Patricia L. , Americo Jeffrey L. , Moss Bernard
Published: September 2003

A rapid and sensitive neutralization assay is required to evaluate alternative smallpox vaccines. Here we describe the development and use of a 96-well plate, semi-automated, flow cytometric assay that uses a recombinant vaccinia virus expressing enhanced green fluorescent protein and which would be applicable to other viruses.
Novel Simian Homologues of Epstein-Barr Virus
Authors: Ehlers Bernhard , Ochs Andreas , Leendertz Fabian , Goltz Michael , Boesch Christophe , Mätz-Rensing Kerstin
Published: September 2003

Thirty different lymphocryptoviruses (LCV), 26 of them novel, were detected in primates by a panherpesvirus PCR assay. Nineteen LCV from chimpanzees, bonobos, gorillas, and other Old World primates were closely related to Epstein-Barr virus (EBV), the type species of the genus
Lymphocryptovirus
. Seven LCV originating from New World primates were related to callitrichine herpesvirus 3 (CalHV-3), the first recognized New World LCV. Importantly, a second LCV from gorillas and three LCV from orangutans and gibbons were only distantly related to EBV and CalHV-3. They were tentatively assigned to a novel genogroup of Old World primate LCV. The work described in the paper may also help identify an as yet unknown human LCV.
Simian Virus 40 T Antigens and J Domains: Analysis of Hsp40 Cochaperone Functions in
Escherichia coli
Authors: Genevaux Pierre , Lang Florence , Schwager Françoise , Vartikar Jai V. , Rundell Kathleen , Pipas James M. , Georgopoulos Costa , Kelley William L.
Published: September 2003

The N-terminal exon of DNA tumor virus T antigens represents a J domain that can direct interaction with the host-encoded Hsp70 chaperones. We have taken advantage of rapid Hsp40 cochaperone assays with
Escherichia coli
to assess simian virus 40 (SV40)-encoded J-domain loss of function. We found a strong correlation between loss of cochaperone function in
E. coli
and defective SV40 growth, suggesting that the major role of the J domain in DNA tumor viruses is to provide cochaperone function. We also report the expression of native SV40 virus T antigens in
E. coli
. Our results show that small t antigen, but not large T antigen (LT) or LT truncation TN125 or TN136, can functionally replace under limited growth conditions DnaJ (Hsp40) function in vivo. In addition, purified small t antigen can efficiently stimulate
E. coli
DnaK's (Hsp70) ATPase in vitro, thus behaving like a bona fide cochaperone. Furthermore, small t amino acids 83 to 174, which are adjacent to the viral J domain, can replace the
E. coli
DnaJ J-domain glycine-phenylalanine-rich domain, immediately adjacent to the J-domain sequences, even in the absence of significant amino acid similarity to their DnaJ counterpart. Taken together, our studies demonstrate that functionally related Hsp40 proteins from mammalian viral systems can be rapidly studied in bacteria and exploited to probe the universally conserved Hsp70 chaperone machine mechanism.
The Gene That Encodes the Herpes Simplex Virus Type 1 Latency-Associated Transcript Influences the Accumulation of Transcripts (Bcl-x
L
and Bcl-x
S
) That Encode Apoptotic Regulatory Proteins
Authors: Peng Weiping , Henderson Gail , Perng Guey-Chuen , Nesburn Anthony B. , Wechsler Steven L. , Jones Clinton
Published: September 2003

The herpes simplex virus type 1 latency-associated transcript (LAT) inhibits apoptosis. We demonstrate here that LAT influences the accumulation of the Bcl-x
L
transcript versus the Bcl-x
S
transcript in Neuro-2A cells. Bcl-x
L
encodes an antiapoptotic protein, whereas Bcl-x
S
encodes a proapoptotic protein. Promoting the accumulation of Bcl-x
L
in neurons may inhibit apoptosis, thus enhancing the latency-reactivation cycle.
Detection of a Gene Cluster That Is Dispensable for Human Herpesvirus 6 Replication and Latency
Authors: Kondo Kazuhiro , Nozaki Hideo , Shimada Kazuya , Yamanishi Koichi
Published: September 2003

The U3-U7 gene cluster of human herpesvirus 6 (HHV-6) was replaced with an enhanced green fluorescent protein-puromycin gene cassette containing the cytomegalovirus major immediate-early promoter. Neither viral replication in T cells nor latency and reactivation in macrophages was impaired. During HHV-6 latency, the cytomegalovirus promoter used the transcription start sites employed in cytomegalovirus latency.
A Lipase Isolated from the Silkworm
Bombyx mori
Shows Antiviral Activity against Nucleopolyhedrovirus
Authors: Ponnuvel Kangayam M. , Nakazawa Hiroshi , Furukawa Seiichi , Asaoka Ai , Ishibashi Jun , Tanaka Hiromitsu , Yamakawa Minoru
Published: September 2003

A protein showing strong antiviral activity against
Bombyx mori
nucleopolyhedrovirus (BmNPV) was purified from the digestive juice of
B. mori
larvae. A homology search of the deduced amino acid sequence of the protein cDNA revealed 56% homology with
Drosophila melanogaster
lipase and 21% homology with human lipase. As lipase activity of the protein was confirmed in vitro, this protein was designated Bmlipase-1. Northern blot analysis showed that the Bmlipase-1 gene is expressed in the midgut but not in other tissues, nor is it activated by BmNPV infection. In addition, the Bmlipase-1 gene was shown not to be expressed in the molting and wandering stages, indicating that the gene is hormonally regulated. Our results suggest that an insect digestive enzyme has potential as a physiological barrier against BmNPV at the initial site of viral infection.
Current velocity and injection of GnRHa affect reproductive behavior and body composition of captively reared offspring of wild chinook salmon (Oncorhynchus tshawytscha)
Authors: Berejikian B A , Fairgrieve W T , Swanson P , Tezak E P
Published: September 2003

Captively reared adult Pacific salmon (Oncorhynchus spp.) released for natural spawning exhibit deficiencies in reproductive behavior. The effects of water current velocity in rearing tanks and gonadotropin-releasing hormone analogue (GnRHa) treatment on reproductive behavior of captively reared chinook salmon (Oncorhynchus tshawytscha) were examined. Treatment of females with GnRHa resulted in a significantly greater degree of nest guarding, earlier (more natural) onset of spawning, and higher frequency of aggression towards males. Current velocity did not significantly affect the female reproductive behaviors examined. Males reared under high current velocities (HV) spawned for the first time 2.4 days earlier, and alpha males reared in HV tanks defended their access to spawning females better than alpha males reared in low velocity (LV) tanks. Males reared in HV tanks had 34% lower protein content at the time of death than fish reared in LV tanks. Females reared in HV tanks had 38% lower lipid content, but the effects of current velocity were nonsignificant when accounting for significant random variation among tanks within treatments. Identifying and modifying environmental conditions that control hormonal changes during final maturation may lead to further improvements in reproductive performance of captively reared salmon.
Implications of life-history invariants for biological reference points used in fishery management
Authors: Williams Erik H , Shertzer Kyle W
Published: September 2003

Fish harvest policies typically rely on biological reference points for measures of a stock's status. We examine three common biological reference points based on fishing mortality rates corresponding to maximum sustainable yield with an age-structured deterministic model. We incorporate invariant life-history relationships into the model to maintain parsimony and focus model parameters on biologically plausible parameter space. A wide range of biological and fishery characteristics were used in the model so that our results pertain to the management of virtually any exploited population. Results indicate that two biological reference points based on spawning biomass are insensitive to life-history parameters, whereas one based on natural mortality is highly sensitive. All three depend largely on the choice of a stockrecruitment function and on steepness, a measure of the population growth rate. For each of the three, values have been previously proposed that were intended to safely apply to all fisheries; our results show that no such universal values exist. We recommend determining stockrecruitment functions a priori, establishing biological reference points on steepness explicitly and eliminating harvest policies based on the natural mortality rate altogether.
Relationships among nutrients, phytoplankton, macrophytes, and fish in prairie wetlands
Authors: Zimmer Kyle D , Hanson Mark A , Butler Malcolm G
Published: September 2003

Phytoplankton abundance and nutrient concentrations in shallow-water ecosystems are influenced by submerged macrophytes, zooplankton, and fish, but few studies have simultaneously assessed the influence of all three variables. We sampled 18 semipermanent prairie wetlands for 5 years to assess influences of minnows, submersed macrophytes, cladocerans, and drainage history on phytoplankton abundance and concentrations of nitrogen (N) and phosphorus (P). Our macrophyte data reflect the abundance of three distinct species assemblages (Chara, Potamogeton, and Myriophyllum assemblages) typical of these wetlands. Partial redundancy analysis showed only the Chara and Potamogeton assemblages and fish to be significantly related to algal abundance, N, and P. Macrophytes and fish together explained 40% of the total variance, but the Chara assemblage explained threefold, and the Potamogeton assemblage twofold, more variance than did presence/absence of fish. However, relationships with N and P differed for the two groups of macrophytes: P showed a strong negative relationship with both plant assemblages, and N showed a weak negative relationship with Chara but no relationship with Potamogetons. Our results indicate that phytoplankton and nutrient concentrations in prairie wetlands are strongly influenced by submersed macrophytes, although influences may depend on plant community composition.
Digestion of pelagic Ctenophora and Cnidaria by fish
Authors: Arai Mary N , Welch David W , Dunsmuir Adrienne L , Jacobs Melinda C , Ladouceur Adrian R
Published: September 2003

The diet of chum salmon (Oncorhynchus keta) can range from a primarily arthropod to a primarily gelatinous composition. Because no data exist for the digestion rates of gelatinous prey in any fish, it has not been possible to convert data on stomach contents to feeding rates. We measured rates of digestion to address this issue. In freely feeding age-0 chum salmon, the ctenophore Pleurobrachia bachei was digested almost completely within 1 h, whereas 70% of shrimp sections of similar mass remained after 5 h at 13°C. To examine the fast progress of digestion at smaller intervals, age-0 and age-1 fish were also force-fed with whole P. bachei or sections of the hydromedusa Aequorea victoria. These data emphasize the necessity of examining fish stomachs very quickly after capture. Although gelatinous organisms have high water and salt content relative to their organic content, given the rapid rates of digestion observed, coelenterates might rival arthropods as energy sources.
Background information for some of the proposed earthquake design provisions for the 2005 edition of the National Building Code of Canada
Authors: DeVall Ronald H
Published: September 2003

There are many changes proposed for the Earthquake Design Provisions of the 2005 edition of the National Building Code of Canada (NBCC). Among them are requirements for complete load paths, separation of stiff nonstructural elements, and the introduction of definitions of irregular structures and special design requirements associated with these irregularities. A new requirement for direction of loading is introduced, along with requirements for elements common to more than one lateral load resisting system. The effects of displacements are emphasized throughout the document, and revised provisions for drift limits are proposed. Revisions to the importance factor that integrate it into the proposed revised format for Part 4, Structural design, of the NBCC are given. Background information is presented.Key words: load path importance factor, irregular structures, direction of loading, special requirements, drift limits.
Effect of foundation rocking on the seismic response of shear walls
Authors: Anderson Donald L
Published: September 2003

Some designers have long known that elastically responding shear-wall or core-wall type high-rise structures will not overturn if the footing size is smaller than that required to resist the elastic forces. Most shear walls are designed and built with a yield hinge mechanism at the base using a relatively high value of the force reduction factor R, and the foundation should be stronger than the yield hinge strength if the wall is to perform as designed. Many walls, however, built with R = 2 are stronger than they need to be because of reasons such as architectural sizing and minimum reinforcement requirements. If for these cases the foundation is to be stronger than the wall, then it will in effect be designed for forces corresponding to an R value of <2. This study looks at the effect on the displacement of a shear-wall type structure if the footing is allowed to rock. The structure is kept elastic and the footing is sized to correspond to R values ranging from 1.0 to 3.5. The analysis uses gap elements to model the foundation soil response so that the footing can lift off the soil. Soil stiffness and strength are modelled for a rock and a firm clay site. The response of 7-, 15-, and 30-storey structures to 11 different acceleration records, modified to match a spectrum given in the 1995 National Building Code of Canada (NBCC) for Vancouver, is determined for the different footing dimensions. The results indicate that a footing sized for an R value of 2 does not result in a significant increase in displacement when compared with the fixed base elastic case. In the next version of the NBCC it is suggested that footings need not be designed for forces corresponding to R < 2.Key words: seismic shear walls, overturning, liftoff, rocking footings.
Determination of seismic design forces by equivalent static load method
Authors: Humar JagMohan , Mahgoub Mohamed A
Published: September 2003

In the proposed 2005 edition of the National Building Code of Canada (NBCC), the seismic hazard will be represented by uniform hazard spectra corresponding to a 2% probability of being exceeded in 50 years. The seismic design base shear for use in an equivalent static load method of design will be obtained from the uniform hazard spectrum for the site corresponding to the first mode period of the building. Because this procedure ignores the effect of higher modes, the base shear so derived must be suitably adjusted. A procedure for deriving the base shear adjustment factors for different types of structural systems is described and the adjustment factor values proposed for the 2005 NBCC are presented. The adjusted base shear will be distributed across the height of the building in accordance with the provisions in the current version of the code. Since the code-specified distribution is primarily based on the first mode vibration shape, it leads to an overestimation of the overturning moments, which should therefore be suitably adjusted. Adjustment factors that must be applied to the overturning moments at the base and across the height are derived for different structural shapes, and the empirical values for use in the 2005 NBCC are presented.Key words: uniform hazard spectrum, seismic design base shear, equivalent static load procedure, higher mode effects, base shear adjustment factors, distribution of base shear, overturning moment adjustment factors.
Overview of seismic provisions of the proposed 2005 edition of the National Building Code of Canada
Authors: Heidebrecht Arthur C
Published: September 2003

The proposed 2005 edition of the National Building Code of Canada (NBCC) will contain very significant changes in the provisions for seismic loading and design. A brief history of the NBCC seismic provisions is presented followed by a discussion of the reasons for introducing such major changes in the next edition of the code. The major changes to the seismic provisions are summarized; this includes updated hazard in spectral format, change in return period (probability of exceedance), period-dependent site factors, delineation of effects of overstrength and ductility, modified period calculation formulae, explicit recognition of higher mode effects, rational treatment of irregularities, triggers for special provisions incorporated directly in classification of structural systems, and placing dynamic analysis as the normal "default" method of analysis for use in seismic design. The impact of these changes on the seismic level of protection is considered by comparing the 2005 NBCC and 1995 NBCC base shear coefficients for a selection of common structural systems located on a range of site conditions in three urban areas having low to high levels of seismic hazard, i.e., Toronto, Montréal, and Vancouver.Key words: seismic, design, loading, code, hazard, buildings, structures, foundations, period, analysis.
Proposed Canadian code provisions for seismic design of elements of structures, nonstructural components, and equipment
Authors: McKevitt W E
Published: September 2003

Proposed code provisions for the seismic design of elements of structures, nonstructural components, and equipment are presented. In these provisions a new format is introduced which gives a consistent treatment for all elements and components, architectural, mechanical, and electrical. For the first time, soil effects are included in the provisions, which also seek to ensure that designers consider the interrelationship of the nonstructural components and differential displacements within the building structure. The proposed force equation is based on a uniform hazard spectrum approach with force modification factors. Specified force levels are based on data from instrumented buildings recorded during recent earthquakes. Updated requirements for connection design specify forces that are consistent with component design forces. New element and component categories are provided in an expanded table of elements of structures, nonstructural components, and equipment. To assess the impact of the proposed provisions on component design at various locations across the country, calculations are presented for typical multistorey buildings in a number of Canadian cities.Key words: seismic design, elements of structures, nonstructural mechanical electrical architectural components.
Integrated three-dimensional computer-aided design and discrete-event simulation models
Authors: Xu Jianfei , AbouRizk S M , Fraser Cam
Published: September 2003

Three-dimensional computer-aided design (3D-CAD) systems that integrate critical path method (CPM) algorithms, commonly referred to as four-dimensional computer-aided design (4D-CAD), have received a high level of interest over the past few years due to the insight they offer into constructability and feasibility analysis. This paper outlines an approach that facilitates this modeling method through integration between a commercial 3D-CAD software package and a discrete-event simulation tool. This approach employs a product-based modeling method that integrates simulation models with CAD drawings to provide real-time analysis and improved model accuracy in modeling construction operations. By integrating with 3D-CAD drawings, the models require much less data entry and provide a much higher degree of accuracy. Additionally, during the course of a project, resource and time consumption data can be collected and used to continually update the model, minimizing the use of assumptions and generalized data. This paper provides a short background and literature review to contextualize the problem statement, describes the product atomic component (PAC) used to integrate 3D-CAD and the simulation model, outlines some of the implementation issues in a simulation context, and presents a prototype system with an example application for an earthmoving project.Key words: 4D-CAD, CPM, product atomic component, simulation modeling, integration, earthmoving.
Harmonizing structural safety levels with life-quality objectives
Authors: Maes M A , Pandey M D , Nathwani J S
Published: September 2003

Life-quality objectives are identified as an essential element in design decision making. Of particular concern is the question of optimal safety levels that are consistent with reasonable expectations of individuals in a present-day society. Using sound principles of decision analysis and utility theory, a lifetime utility function is developed. It is shown to be related to human consumption, life duration including the cumulative effects of mortality and discounting, and the relative amount of time spent on work versus leisure. Questions regarding the acceptability and affordability of changes in life quality can be addressed using the utility functions developed. As an application, design safety levels for the Confederation Bridge are examined and discussed. Life-quality objectives can also be included in a life-cycle cost optimization. This allows us to perform a level IV probabilistic design approach including costs and consequences without having to estimate the value of human life, but instead including the effect of consequences on changes in life quality of individuals at risk. This results in a useful tool to determine optimal limit state design safety levels, as is illustrated in a parametric analysis in the case of a single limit state.Key words: lifetime utility, life-quality index, risk acceptance, limit states design, target reliability levels, risk reduction, minimum life-cycle cost, structural safety.
Artificial neural networks for predicting creep with an example application to structural masonry
Authors: Taha M.M Reda , Noureldin A , El-Sheimy N , Shrive N G
Published: September 2003

Numerous creep models with limited accuracy have been developed within the last few decades to predict creep of concrete and masonry structures. The stochastic nature of creep deformation and its reliance on a large number of interdependent parameters (e.g., the brick and mortar types, the relative humidity, and the history and level of applied loading) make developing a single, general, and yet accurate mathematical model almost impossible. Artificial neural networks (ANNs) have been recently introduced as an efficient artificial intelligence modeling technique for applications incorporating a large number of variables. Artificial neural networks have proven successful in many instances where conventional mathematical modeling techniques were not as accurate or capable. Here, the potential use of ANNs in predicting creep is examined. A new ANN model is applied to the prediction of creep of structural masonry. The ANN developed is able to predict the creep performance with an excellent level of accuracy compared with that of conventional models.Key words: creep, artificial intelligence, neural networks, viscoelastic deformation, masonry structures.
Prediction and mitigation of construction noise in an urban environment
Authors: Gilchrist A , Allouche E N , Cowan D
Published: September 2003

A growing number of construction projects are performed in congested urban areas. Often, the surrounding community finds these projects annoying because of noise, vibration, dust, light, and greenhouse gas emissions. This paper focuses on one type of irritant, noise. Common noise generators on construction sites are identified, and the elements of a generic program for mitigating construction-related noise are outlined. Mitigation strategies including source control, path control, and receiver control are discussed. A deterministic model based on the Monte Carlo simulation technique is used. It is capable of predicting the magnitude and frequency of noise levels generated by construction equipment at receptor locations around a construction site during each construction stage. The utilization of the model as a planning tool for optimizing the composition, geometry, and location of noise barriers around a construction site is demonstrated via a case history, namely the construction of an eight-storey parking garage in London, Ont. The model is validated by comparing its predictions to field measurements undertaken during various construction stages. Predictions agree favourably with field measurements.Key words: construction, noise, mitigation, barriers, modeling, Monte Carlo simulation.
Hydrodynamic analysis of wave interactions with a moored floating breakwater using the element-free Galerkin method
Authors: Lee Jeongwoo , Cho Woncheol
Published: September 2003

This paper deals with a numerical investigation of incident wave interactions with a moored pontoon-type floating breakwater. The element-free Galerkin method, in which only nodal data are required to analyze the problem, is employed to solve the diffraction and radiation boundary value problems addressed by the modified Helmholtz equation. The numerical model includes the hydrodynamic and mooring analyses, and it is validated by previous numerical and experimental results. Using the numerical model, we are able to assess the hydrodynamic performance of a moored pontoon-type floating breakwater in regular waves. Numerical results are presented to show the effects of wave conditions and mooring system configuration. This paper also presents the simple forms of stiffness coefficients of a slack mooring line. The influence of mooring line condition on the performance of a floating breakwater is highlighted. Key words: moored floating breakwater, element-free Galerkin method, mooring line condition.
Development of Canadian asphalt pavement deterioration models to benchmark performance
Authors: Raymond Chris , Tighe Susan , Haas Ralph , Rothenburg Leo
Published: September 2003

The Canadian Long Term Pavement Performance (C-LTPP) study, initiated in 1989, involves 65 sections located at 24 sites constructed with various asphalt overlay rehabilitation treatments. This study investigates the impacts of the various alternative rehabilitation treatments on pavement roughness progression. A series of models are developed for predicting the rate of pavement deterioration occurring for the first 8 years of service. The models examine both within-site factors and between-site factors. Site location is found to be the primary influence on the rate of pavement deterioration. Overlay thickness and the amount of cracking prior to rehabilitation are also determined to influence pavement deterioration at a strong statistical level. Models are provided for benchmarking the performance of pavements across Canada, for comparison with individual project designs, and for estimating the performance of designs with different overlay thickness.Key words: Canadian Long Term Pavement Performance program, roughness, pavement deterioration, site effects, asphalt overlays, benchmark, univariate analysis.
Mapping environmental conditions in the St. Lawrence River onto ice parameters using artificial neural networks to predict ice jams
Authors: Morse Brian , Hessami Masoud , Bourel Céline
Published: September 2003

This paper evaluates the potential of using artificial neural networks to model ice parameters related to ice jams in the St. Lawrence River navigation channel through Lake St. Pierre. The artificial neural networks mapped environmental conditions onto ice parameters through multilayer feed-forward networks. The ice parameters include velocity, thickness, concentration, and unit discharge. The input to the network is based on two meteorological parameters: wind velocity and air temperature. The LevenbergMarquardt algorithm with Bayesian regularization is used to train the feed-forward network. The artificial neural networks adequately modelled the ice parameters. The predicted ice velocity, thickness, and unit discharge were very satisfactory, but ice concentration was not. Methods to improve forecasting (particularly of ice concentration) are suggested.Key words: ice parameters, ice jam, artificial neural network, ADCP, IPS.