bluuebunny/crossref_metadata_2025 huggingface dataset:
Small-scale temporal and spatial variation in Atlantic cod (Gadus morhua) life history
Authors: McIntyre Tara M , Hutchings Jeffrey A
Published: October 2003

Life histories of Atlantic cod (Gadus morhua) from the Gulf of St. Lawrence south to Georges Bank differ significantly through time and space. Within the Southern Gulf, fecundity per unit body mass differed by more than 40% over short (2 years) and long (4245 years) periods of time. Significant variation in size-specific fecundity is also evident among populations: Southern Gulf cod produce almost 30% more eggs per unit body mass than those on Georges Bank, whereas fecundity of Scotian Shelf cod is almost half that of cod in Sydney Bight. Compared with those on Georges Bank, Southern Gulf cod life histories are characterized by high fecundity, late maturity, high gonadosomatic index, and large eggs. Relative to the influence of body size, neither temporal nor spatial differences in fecundity can be attributed to physiological condition, as reflected by liver weight, hepatosomatic index, and Fulton's K. Delayed maturity and higher reproductive allotment among Southern Gulf cod can be explained as selection responses to slower growth, higher prereproductive mortality, and fewer lifetime reproductive events. Patterns of covariation in heritable, fitness-related traits suggest the existence of adaptive variation and evolutionarily significant units at spatial scales considerably smaller than the species range in the Northwest Atlantic.
The influence of hatchery coho salmon (Oncorhynchus kisutch) on the productivity of wild coho salmon populations in Oregon coastal basins
Authors: Nickelson Thomas
Published: October 2003

To aid in the recovery of depressed wild salmon populations, the operation of hatcheries must be changed to reduce interactions of juvenile hatchery fish with wild fish. Evidence suggests that productivity of wild populations can be reduced by the presence of large numbers of hatchery smolts in lower rivers and estuaries that attract predators. An index of productivity based on the density-independent rate of reproduction of wild coho salmon (Oncorhynchus kisutch) in 12 Oregon coastal river basins and two lake basins was negatively correlated with the average number of hatchery coho salmon smolts released in each basin. The index of productivity was not significantly correlated with the average proportion of hatchery coho salmon in each naturally spawning population or with habitat quality. Alterations to hatchery programs that could encourage recovery of wild populations include (i) avoiding release of large numbers of smolts in areas with high concentrations of wild fish, (ii) decreasing the number of smolts released, and (iii) using a volitional release strategy or a strategy that employs smaller release groups spread temporally.
Potential impact of forest harvesting on lake chemistry in south-central Ontario at current levels of acid deposition
Authors: Watmough S A , Aherne J , Dillon P J
Published: October 2003

The potential impact of harvesting on lake chemistry was assessed for ~1300 lakes in south-central Ontario using a critical loads approach based on the steady-state water chemistry (SSWC) model. The critical load of acidity is currently only exceeded by bulk sulphate deposition in 9% of the lakes if harvesting does not occur. However, the percentage increases to 23%, 56%, and 72% under potential harvesting scenarios that assume wood-only (stem without bark), stem-only, or whole-tree harvesting, respectively. This increase in exceedance of critical load is due to the much lower base cation concentrations in lakes resulting from base cation removals during harvest. For example, only 0.3% of lakes will have Ca2+ concentrations <50 μequiv.·L1 if harvesting does not occur, whereas 52% of lakes will have Ca2+ concentrations <50 μequiv.·L1 if whole-tree harvesting occurs. Harvesting clearly has an enormous potential impact on lake chemistry, which will become more apparent as exchangeable base cation pools in soil decline and acid inputs can no longer be buffered.
Detecting juvenile survival effects of habitat actions: power analysis applied to endangered Snake River springsummer chinook (Oncorhynchus tshawytscha)
Authors: Paulsen Charles M , Fisher Timothy R
Published: October 2003

Using 10 years of parr-to-smolt survival rate estimates for passive integrated transponder (PIT) tagged, endangered wild Snake River chinook (Oncorhynchus tshawytscha) (measured in eight spawning streams), we demonstrate that moderate increases in base-case survival may be detectable quickly, as required by recent U.S. National Marine Fisheries Service regulations. The regulations require that effects of tributary habitat actions on juvenile salmonid survival rates be detectable within 5 to 8 years. Simple log-linear regression models were employed where the natural log of survival is a function of parr size, parent stock abundance, tagging location, and year. The analysis uses beforeafter controlimpact (BACI) statistical techniques. The results suggest that multiplicative survival rate changes of 30% should be detectable within 7 years, and increases of 50% within 3 years. Models with higher information-theoretic weights were more powerful than less plausible models. Models using juvenile survival were substantially more powerful than models using spawnerrecruit data for the same stocks, but the analysis is no substitute for field studies, which are still very rare.
A first-generation map of the turkey genome
Authors: Harry David E , Zaitlin David , Marini Paul J , Reed Kent M
Published: October 2003

A primary linkage map of the domestic turkey (Meleagris gallopavo) was developed by segregation analysis of genetic markers within a backcross family. This reference family includes 84 offspring from one F1sire mated to two dams. Genomic DNA was digested using one of five restriction enzymes, and restriction fragment length polymorphisms were detected on Southern blots using probes prepared from 135 random clones isolated from a whole-embryo cDNA library. DNA sequence was subsequently determined for 114 of these cDNA clones. Sequence comparisons were done using BLAST searches of the GenBank database, and redundant sequences were eliminated. High similarity was found between 23% of the turkey sequences and mRNA sequences reported for the chicken. The current map, based on expressed genes, includes 138 loci, encompassing 113 loci arranged into 22 linkage groups and an additional 25 loci that remain unlinked. The average distance between linked markers is 6 cM and the longest linkage group (17 loci) measures 131 cM. The total map distance contained within linkage groups is 651 cM. The present map provides an important framework for future genome mapping in the turkey.Key words: genetic map, Meleagris gallopavo, expressed sequence tag, RFLP.
Microsatellite variability and heterozygote deficiency in the arcticalpine Alaskan wheatgrass (Elymusalaskanus) complex
Authors: Sun Genlou , Salomon Björn
Published: October 2003

Genetic variation in the allotetraploid grass Elymus alaskanus complex was assessed using microsatellites in seven populations from Canada, Greenland, and the U.S.A. Microsatellite variation was compared with allozyme and RAPD variation. Our results indicated that E. alaskanus was highly homozygous but also highly variable. The polymorphic loci ranged from 50 to 100% with a mean of 78.6%, and the mean number of allele per locus was 3.14. Average expected heterozygosity value (HE, gene diversity) varied across populations and ranged from 0.244 to 0.651 with mean of 0.414. The mean value of HEacross Canadian populations (0.517) was significantly higher than that across populations in Greenland (0.367). The correlation between allozyme and microsatellite gene diversity value (HE) showed a high positive correlation (r = 0.68), but between RAPD and microsatellite showed a low positive correlation (r = 0.08). Populations were highly differentiated, with 38% of variation among populations. Interpopulation genetic distance showed no association with geographic distance between the population sites of origin. A Hardy-Weinberg exact test for all loci and all populations reveals a significant heterozygote deficiency. Possible explanations for heterozygote deficiency are discussed.Key words: Elymus alaskanus, microsatellites, heterozygote deficiency, genetic differentiation, variability.
Analysis and sorting of rye (Secale cerealeL.) chromosomes using flow cytometry
Authors: Kubaláková M , Valárik M , Barto J , Vrána J , Cíhalíková J , Molnár-Láng M , Dolezel J
Published: October 2003

Procedures for chromosome analysis and sorting using flow cytometry (flow cytogenetics) were developed for rye (Secale cereale L.). Suspensions of intact chromosomes were prepared by mechanical homogenization of synchronized root tips after mild fixation with formaldehyde. Histograms of relative fluorescence intensity obtained after the analysis of DAPI-stained chromosomes (flow karyotypes) were characterized and the chromosome content of the DNA peaks was determined. Chromosome 1R could be discriminated on a flow karyotype of S. cereale 'Imperial'. The remaining rye chromosomes (2R7R) could be discriminated and sorted from individual wheatrye addition lines. The analysis of lines with reconstructed karyotypes demonstrated a possibility of sorting translocation chromosomes. Supernumerary B chromosomes could be sorted from an experimental rye population and from S. cereale 'Adams'. Flow-sorted chromosomes were identified by fluorescence in situ hybridization (FISH) with probes for various DNA repeats. Large numbers of chromosomes of a single type sorted onto microscopic slides facilitated detection of rarely occurring chromosome variants by FISH with specific probes. PCR with chromosome-specific primers confirmed the identity of sorted fractions and indicated suitability of sorted chromosomes for physical mapping. The possibility to sort large numbers of chromosomes opens a way for the construction of large-insert chromosome-specific DNA libraries in rye.Key words: chromosome isolation, chromosome sorting, fluorescence in situ hybridization, repetitive DNA sequences, wheat-rye addition lines, B chromosomes, physical mapping.
Alloplasmic male sterile Brassica napus with Enarthrocarpus lyratus cytoplasm: introgression and molecular mapping of an E. lyratus chromosome segment carrying a fertility restoring gene
Authors: Janeja H S , Banga S K , Bhaskar P B , Banga S S
Published: October 2003

A cytoplasmic male sterility (CMS) system for Brassica napus (2n = 38; AACC) was developed by backcross substitution of its nucleus into the cytoplasm of a wild crucifer, Enarthrocarpus lyratus. Male sterility was complete, stable, and expressed in small flowers with rudimentary anthers. Since the B. napus germplasm lines were complete or partial maintainers of male sterility, the required fertility restorer gene (Rfl) was introgressed from the cytoplasm donor species. Inheritance studies carried out on F1 and F2 populations derived from hybridizing cytoplasmic male sterile and male fertile near-isogenic (PNILs) lines of B. napus 'Westar', revealed a monogenic dominant control for fertility restoration. Bulked segregant analysis with 215 RAPD primers helped in the identification of putative primers associated with fertility restoration. Co-segregation analysis of eight such primers with Rfl gene revealed two markers, OPK 15700 and OPZ 061300, which flank the Rfl locus on either side at a distance of 8.2 and 2.5 cM, respectively. These DNA markers will be useful in marker-assisted selection for improving the commercial potential of this newly developed CMS-fertility-restorer system for hybrid seed production programs in rapeseed.Key words: oilseed rape, hybrids, cytoplasmic male sterility, fertility restoration, RAPD mapping.
Construction of a cDNA-based microarray forDrosophila melanogaster: a comparison of gene transcription profiles from SL2 and Kc167 cells
Authors: Neal Scott J , Gibson Meredith L , So Anthony K.-C , Westwood J Timothy
Published: October 2003

We have constructed a DNA microarray that represents approximately 6900 of the estimated 13 598 genes in the Drosophila melanogaster genome. The microarray contains 5756 target cDNAs from the Berkeley Drosophila Genome Project, 1078 cDNAs from the National Institutes of Health Drosophila testis cDNA library, and 546 gene fragments that were amplified from genomic DNA. The methods for DNA amplification and microarray manufacture are presented. Academic researchers can obtain the microarray from the Canadian Drosophila Microarray Centre. To evaluate the utility of these arrays, we compared the gene transcription profiles of two commonly used Drosophila cell lines. Analysis revealed that 5412 spot pairs gave signals consistently above the average background in Kc167 cells, whereas 5636 spot pairs met this criterion in SL2 cells. When the expression profiles of the cell lines were compared, 1437 genes displayed at least a 1.5-fold difference, and 170 genes had a threefold or greater difference between the two cell lines. In each case, with respect to Kc167 when compared with SL2 cells, the number of genes that were upregulated was nearly equal to the number of downregulated genes. This result demonstrates that despite the similar embryonic derivation of both cell lines, their transcriptional profiles are very different.Key words: DNA microarray, Drosophila, transcriptional regulation, SL2, Kc167.
Identification of a major locus conferring resistance to powdery mildew (ErysiphepolygoniDC) in mungbean (VignaradiataL. Wilczek) by QTL analysis
Authors: Humphry M E , Magner T , McIntyre C L , Aitken E A.B , Liu C J
Published: October 2003

A major locus conferring resistance to the causal organism of powdery mildew, Erysiphe polygoni DC, in mungbean (Vigna radiata L. Wilczek) was identified using QTL analysis with a population of 147 recombinant inbred individuals. The population was derived from a cross between 'Berken', a highly susceptible variety, and ATF 3640, a highly resistant line. To test for response to powdery mildew, F7and F8lines were inoculated by dispersing decaying mungbean leaves with residual conidia of E. polygoni amongst the young plants to create an artificial epidemic and assayed in a glasshouse facility. To generate a linkage map, 322 RFLP clones were tested against the two parents and 51 of these were selected to screen the mapping population. The 51 probes generated 52 mapped loci, which were used to construct a linkage map spanning 350 cM of the mungbean genome over 10 linkage groups. Using these markers, a single locus was identified that explained up to a maximum of 86% of the total variation in the resistance response to the pathogen.Key words: mungbean, powdery mildew, Erysiphe polygoni, QTL, molecular markers.
Isolation and characterization of 70 novel microsatellite markers from ostrich (Struthiocamelus) genome
Authors: Tang Bo , Huang Yin Hua , Lin Li , Hu Xiao Xiang , Feng Ji Dong , Yao Ping , Zhang Lao , Li Ning
Published: October 2003

Microsatellite markers are widely used in linkage mapping, parentage testing, population genetic studies, and molecular evolution studies in many agricultural species, while only a limited number of ostrich (Struthio camelus) microsatellites have been isolated. Thus, we constructed a random small-insert genomic library and a microsatellite-enriched library containing CA repeats. Fourteen clones containing CA repeats were isolated from 3462 clones in the non-enriched library by radioactive screening and 248 positive clones were isolated from 300 sequenced clones from the enriched library by PCR screening. After the enrichment procedures, the proportion of clones containing CA repeats was raised to 78.8%, compared with 0.4% in the non-enriched libraries, indicating that the enrichment value approaches 200 fold, which decreased the time and cost of cloning. The number of complete simple CA repeats in these positive clones ranged from 5 to 29. The primers for 94 of these microsatellites were developed and used to detect polymorphisms, of which 61 loci exhibited length polymorphisms in 17 unrelated ostrich individuals. The new polymorphic microsatellite markers we have identified and characterized will contribute to the ostrich genetic map, parentage testing, and comparative genomics between avian species.Key words: ostrich, microsatellite markers, enriched library, polymorphism.
No clustering for linkage map based on low-copy and undermethylated microsatellites
Authors: Zhou Yi , Gwaze David P , Reyes-Valdés M Humberto , Bui Thomas , Williams Claire G
Published: October 2003

Clustering has been reported for conifer genetic maps based on hypomethylated or low-copy molecular markers, resulting in uneven marker distribution. To test this, a framework genetic map was constructed from three types of microsatellites: low-copy, undermethylated, and genomic. These Pinus taeda L. microsatellites were mapped using a three-generation pedigree with 118 progeny. The microsatellites were highly informative; of the 32 markers in intercross configuration, 29 were segregating for three or four alleles in the progeny. The sex-averaged map placed 51 of the 95 markers in 15 linkage groups at LOD > 4.0. No clustering or uneven distribution across the genome was observed. The three types of P. taeda microsatellites were randomly dispersed within each linkage group. The 51 microsatellites covered a map distance of 795 cM, an average distance of 21.8 cM between markers, roughly half of the estimated total map length. The minimum and maximum distances between any two bins was 4.4 and 45.3 cM, respectively. These microsatellites provided anchor points for framework mapping for polymorphism in P. taeda and other closely related hard pines.Key words: simple sequence repeats, genome duplication, conifers, Pinus taeda L. hypomethylation, low-copy kinetic component.
Genome size estimates for two important freshwater molluscs, the zebra mussel (Dreissena polymorpha) and the schistosomiasis vector snail (Biomphalaria glabrata)
Authors: Gregory T Ryan
Published: October 2003

The haploid genome sizes of two important molluscs were assessed by Feulgen image analysis densitometry. The genome size of the zebra mussel (Dreissena polymorpha), a prolific invader of North American lakes, was estimated to be 1C = 1.70 ± 0.03 pg, and that of the freshwater snail Biomphalaria glabrata, the predominant intermediate vector of the human parasite Schistosoma mansoni, was estimated at 0.95 ± 0.01 pg. These estimates will be important in future efforts in molluscan genomics, which at present lags far behind work being carried out with vertebrate and arthropod models. B. glabrata in particular, which has one of the smallest known gastropod genomes, is recommended as a highly suitable target for future genome sequencing.Key words: densitometry, DNA content, DNA sequencing, Feulgen, image analysis, Great Lakes, invading species, molluscs, Schistosoma mansoni.
Experimental procedure for evaluating ground displacement factors in directional drilling
Authors: Lueke Jason S , Ariaratnam Samuel T
Published: October 2003

As the utilization of horizontal directional drilling increases in urban areas, damage resulting from surface heave during pullback is becoming a greater concern for municipalities, regulatory agencies, and contractors alike. The magnitude and extent of surface deformations are influenced by several factors, including borehole pressure, depth of cover, soil density, backream rate, soil composition, annular space, and reamer type and diameter. With any complex system, understanding how these factors relate to each other in the development of surface deformations is beneficial in the planning of future installations. This paper outlines work towards the development of a model to understand how these factors contribute to surface heave during the backream phase of a horizontal, directionally drilled installation. Initial identification and selection of factors to be used are facilitated through the analytical hierarchy procedure (AHP). Using the ranking identified by the AHP, a full factorial experiment was designed and implemented in field conditions, with ground movements measured at various stages along four uniquely designed borepaths. With a better understanding of the factors associated with directionally drilled installations, contractors and engineers may better select tooling and techniques to minimize the magnitude and extent of surface heave.Key words: horizontal directional drilling, analytical hierarchy procedure, data collection, modeling, experimental design, surface heave, trenchless technology.
Seismic repair and rehabilitation of a shear-failure damaged circular bridge column using carbon fiber reinforced plastic jacketing
Authors: Li Yeou-Fong , Sung Yi-Ying
Published: October 2003

In this paper, the analytical and experimental results of tests on a benchmark and a damaged circular bridge column are presented. The benchmark column is a 40% scale reinforced concrete circular bridge column damaged as a result of shear failure during a cyclic-loading test; the benchmark column was then repaired by epoxy and non-shrinkage mortar and rehabilitated by carbon fiber reinforced plastic (CFRP) after the cyclic-loading test. The benchmark bridge column is tested under a cyclic-loading test with constant axial load. The result shows that the column suffered shear failure at low displacement ductility. Non-shrinkage mortar with high-pressure epoxy injection was used to repair the damaged bridge column, and then three-layer CFRP was used to rehabilitate the shear strength of the bridge column. The test result shows that the repaired and rehabilitated column develops significantly improved hys ter etic responses at high displacement ductility. The analytical lateral force  displacement relationship of the bridge columns can accurately predict the experimental result, especially in the nonlinear region.Key words: carbon fiber reinforced plastic, repair and rehabilitation, bridge column.
Experimental investigation of block shear failure in coped steel beams
Authors: Franchuk Cameron R , Driver Robert G , Grondin Gilbert Y
Published: October 2003

Relatively few tests have been conducted to determine the block shear capacity and behaviour of coped steel beam connections. Furthermore, design standards are inconsistent in the way they treat this failure mode and may predict capacities significantly higher than those determined experimentally. To address these issues, 17 full-scale tests were conducted on coped wide-flange beams. Parameters considered in the study include beam end rotation, end and edge distances, and bolt layout. Many of these parameters had not been systematically investigated prior to this research, and the effect of end rotation, i.e., the rotation at the connection due to flexural beam action, had not been examined. It is found that few of these parameters significantly affect the connection capacity, apart from the associated changes in net tension and gross shear areas. Following the laboratory tests, capacity design equations outlined in Canadian, American, European, and Japanese standards were examined. Tests-to-predicted ratios for each standard were calculated and compared. It was found that none of these standards accurately and consistently predict block shear capacity, especially when considering two-line connections.Key words: beams, block shear, bolts, connections, end rotation, rupture, shear, steel, tension, yield.
An effective peak stress formula for concrete confined with carbon fiber reinforced plastics
Authors: Lin Chih-Tsung , Li Yeou-Fong
Published: October 2003

The uniaxial compression test results of three different strengths and three different sizes of concrete cylinders confined with different layers of carbon fiber reinforced plastics (CFRP) are used to develop an effective peak stress formula for predicting the strength of confined concrete. The theory of this peak stress formula was based on the triaxial confined test of soil and rock, and the lateral confinement of the concrete was assumed to be due to the CFRP. The peak stress of the confined concrete can be explicitly expressed as a function of the unconfined concrete strength and the lateral CFRP confined strength. Experiments were done on 108 concrete cylinders, and the test results show the accuracy and effectiveness of this peak stress formulation of confined concrete.Key words: confined concrete, peak stress, carbon fiber reinforced plastics.
Analysis of load in ties in masonry veneer walls
Authors: Yi Junyi , Laird David , McEwen Bill , Shrive Nigel G
Published: October 2003

Masonry is frequently used as a veneer, tied to a backup structural system. In many cases, the structural system is steel studding. Very little research has been conducted to examine the effect of staggering the ties between the veneer and the backup on the load distributions in the ties and studs. This paper describes three-dimensional (3-D) finite element models developed for masonry veneer walls (brick veneer  steel stud) subjected to wind load. Various tie arrangements were analyzed. Shell elements were used to model the brick veneer, and beam elements were used to model the steel studs and ties. Cracking was introduced in a horizontal mortar joint through the use of gap elements (discrete cracking method). The loads in the ties for various tie arrangements were examined. It appears that staggering the ties does not overload them when a full row of ties is provided at the top or at both the top and the bottom. The load distribution in the ties in a staggered arrangement is close to that in the full-tie arrangement.Key words: masonry veneer walls, 3-D, finite element models, brick veneer, steel studs, ties.
The effect of end distance on the moment resistance of timber rivet connections
Authors: Hampson J A , Prion H G.L , Lam F
Published: October 2003

The results of an experimental study on moment connections with timber rivets are reported. The end distance for a four-rivet moment connection is varied in an attempt to determine the effect on the moment capacity and the failure mode. Varying the end distance did not seem to induce the occurrence of a brittle failure mode, but a slight reduction in the strength and stiffness of joint was observed. This was confirmed for specimens made with glued-laminated timber (glulam), laminated-veneer lumber (LVL), and parallel-strand lumber (PSL).Key words: wood, timber, moment, connection, brittle, end distance, glulam and rivet.
Fibre-reinforced polymer composite bars for the concrete deck slab of Wotton Bridge
Authors: El-Salakawy Ehab , Benmokrane Brahim , Desgagné Gérard
Published: October 2003

A new concrete bridge in the Municipality of Wotton, Quebec, Canada, was constructed using fibre-reinforced polymer (FRP) bars as reinforcement for the deck slab. The new bridge is a girder type with four main girders simply supported over a span of 30.60 m. One half of the concrete deck slab was reinforced with carbon and glass FRP bars, and the other half with conventional steel bars. The design of the reinforced concrete deck slab was made according to sections 8 and 16 of the new Canadian Highway Bridge Design Code. The bridge was well instrumented at critical locations for long-term internal temperature and strain data collection using fibre optic sensors. The construction of the bridge was completed and the bridge opened for traffic in October 2001. The bridge was then tested for service performance using standard truckloads. Design, construction details, and the results of the field test and 1 year of remote monitoring are discussed. Under the same real service and environmental conditions, very similar behaviour was obtained from the FRP (glass and carbon) and steel bars.Key words: concrete bridges, deck slabs, FRP bars, field test, fibre optic sensors, remote monitoring, serviceability.
Failure analysis of columnslab connections with stud shear reinforcement
Authors: Guan Hong , Loo Yew-Chaye
Published: October 2003

The design of a flat plate structure is generally governed either by serviceability limits on deflection or punching shear strength of the columnslab connections. To increase the strength of a columnslab connection, a new type of shear reinforcement, referred to as shear stud, is gaining popularity in practice. In this paper, a nonlinear layered finite element method (LFEM) is used to investigate the effectiveness of the shear studs in increasing the punching shear strength of edge and corner columnslab connections. In total, nine large-scale reinforced concrete slabs of a flat plate floor in the vicinity of edge and corner columns, tested previously in the laboratory, are analysed. All the slabs contained stud shear reinforcement (SSR) except a control slab where no SSR was provided. The test variables were the column size and the ratio of stud spacing to slab thickness. The punching shear strengths, loaddeflection responses, and crack patterns predicted by the LFEM are compared with the experimental results. The numerical investigation confirms the accuracy and effectiveness of the LFEM in predicting the strength of columnslab connections with SSR.Key words: columnslab connection, concrete flat plate, punching shear, stud shear reinforcement, finite element analysis.
Décomposition du pseudo-profil et analyse de l'indice de rugosité international (IRI)
Authors: Vaillancourt Michel , Perraton Daniel , Dorchies Pierre , Doré Guy
Published: October 2003

In order to get the most out data from a pseudo-profile and to further develop an international roughness index (IRI) concept, a new interpretation approach of the IRI is presented. It is based on the breakdown of the initial pseudo-profile of a pavement into elementary pseudo-profiles based on various well-defined wavelengths. The underlying hypothesis to this approach is that the IRI calculated on these elementary pseudo-profiles is proportional to the contribution of each one to pavement condition. From this hypothesis, various pseudo-profile analytical techniques are presented. A few definitions and context are presented first. The following approach is then described: (i) filtering technique, (ii) calculation of the IRI for elementary pseudo-profiles, (iii) additional analytical tools. Finally, an application example describes the approach.Key words: IRI, filtering, pseudo-profile, pavement, defect, wavelength, bandwidth, profilometre, evenness.[Journal Translation]
The bacterial receptor protein, transferrin-binding protein B, does not independently facilitate the release of metal ion from human transferrin
Authors: Nemish Ulyana , Yu Rong-Hua , Tari Leslie W , Krewulak Karla , Schryvers Anthony B
Published: October 2003

Pathogenic Gram-negative bacteria of the Pasteurellaceae and Neisseriaceae acquire iron for growth from host transferrin through the action of specific surface receptors. Iron is removed from transferrin by the receptor at the cell surface and is transported across the outer membrane to the periplasm. A periplasmic binding protein-dependent pathway subsequently transports iron into the cell. The transferrin receptor is composed of a largely surface-exposed lipoprotein, transferrin binding protein B, and a TonB-dependent integral outer membrane protein, transferrin binding protein A. To examine the role of transferrin binding protein B in the iron removal process, complexes of recombinant transferrin binding protein B and transferrin were prepared and compared with transferrin in metal-binding and -removal experiments. A polyhistidine-tagged form of recombinant transferrin binding protein B was able to purify a complex with transferrin that was largely monodisperse by dynamic light scattering analysis. Gallium was used instead of iron in the metal-binding studies, since it resulted in increased stability of recombinant transferrin binding protein B in the complex. Difference absorption spectra were used to monitor removal of gallium by nitrilotriacetic acid. Kinetic and equilibrium binding studies indicated that transferrin binds gallium more tightly in the presence of transferrin binding protein B. Thus, transferrin binding protein B does not facilitate metal ion removal and additional components are required for this process.Key words: iron, transport, outer membrane, lipoprotein, glycoprotein.
The product of the bacteriophage lambdaWgene: purification and properties
Authors: Murialdo Helios , Xing Xuekun , Tzamtzis Dimitra , Haddad Abraham , Gold Marvin
Published: October 2003

Gene W is one of the 10 genes that control the morphogenesis of the bacteriophage λ head. The morpho genesis of the phage λ head proceeds through the synthesis of an intermediate assembly called the prohead. This is an empty shell into which the bacteriophage DNA is introduced  packaged  by the phage enzyme DNA terminase. The product of W (gpW) acts after DNA packaging, but before the addition of another phage product, gene product FII, and before the addition of tails. The role of gpW is unknown. The structure of N- and C-tagged gpW has been previously determined by nuclear magnetic resonance (NMR) spectroscopy. Here we report some of the properties of the native protein. The purification of gpW to homogeneity, overproduced by a plasmid derivative, is described. To obtain large amounts of the protein, the ribosome-binding site had to be modified, showing that inefficient translation of the message is the main mechanism limiting W gene expression. The molecular weight of the protein is in close agreement to the value predicted from the DNA sequence of the gene, which suggests that it is not post-transcriptionally modified. It behaves as a monomer in solution. Radioactively labeled gpW is incorporated into phage particles in in vitro complementation, showing that gpW is a structural protein. The stage at which gpW functions and other circumstantial evidence support the idea that six molecules of gpW polymerize on the connector before the incorporation of six molecules of gpFII and before the tail attaches.Key words: bacteriophage morphogenesis, lambda gene W, viral structure.
Purification of bovine cathepsin B: proteomic characterization of the different forms and production of specific antibodies
Authors: Sentandreu M A , Aubry L , Ouali A
Published: October 2003

Cathepsin B (EC 3.4.22.1) has been highly purified (14 225 fold) from bovine kidney by a rapid procedure that included the preparation of an enriched lysosomal extract, a selective fractionation with ammonium sulphate, size-exclusion chromatography, two cation-exchange chromatographies, and anion-exchange chromatography on diethylaminoethylSephacel. After the last purification step, two hydrolytic peaks against Z-Phe-Arg-AMC were separated from each other, a minor peak corresponding to the cathepsin B single-chain form and a major one representing the double-chain form of cathepsin B. The single-chain form showed a molecular mass of 31 kDa on sodium dodecyl sulphate  polyacrylamide gel electrphoresis (PAGE) under reducing conditions, whereas the heavy chain of the double-chain form appeared as a doublet with molecular masses of 23.4 and 25 kDa, respectively. The identity of the different cathepsin B isoforms and the quality of the final enzyme preparation were confirmed by using two types of antibodies, one against a synthetic peptide sequence and one against purified cathepsin B. The proteomic study confirmed the identity of the different SDSPAGE protein bands as cathepsin B isoforms and allowed the comparison and study of some structural differences between them at the level of their primary structures.Key words: cathepsin B, bovine kidney, MALDI-TOF, cathepsin B isoforms, antibodies.
Inactivation and conformational changes of creatine kinase at low concentrations of hexafluoroisopropanol solutions
Authors: Wang Xiao-Yun , Meng Fan-Guo , Zhou Hai-Meng
Published: October 2003

Using the methods of far-ultraviolet circular dichroism (CD) spectra, fluorescence spectra, and enzyme activity assays, the inactivation and conformational changes of creatine kinase (CK) induced by 1,1,1,3,3,3-hexafluoro-2-propanol (hexafluoroisopropanol (HFIP)) of different concentrations were investigated. To avoid the aggregation of CK that occurs with high HFIP, concentrations of 0%5% HFIP were used in this study. The CD spectra showed that HFIP concentrations above 2.5% strongly induced the formation of secondary structures of CK. No marked conformational changes were observed at low concentrations of HFIP (0%2.5%). After incubation with 0.2% HFIP for 10 min, CK lost most of its activity. The kinetic theory of the substrate reaction during irreversible inhibition of enzyme activity described previously by Tsou was applied to study the kinetics of CK inactivation during denaturation by HFIP. The inactivation rate constants for the free enzyme and the substrateenzyme complex were determined by Tsou's method. The results suggested that low concentrations of HFIP had a high potential to induce helices of protein and that the active site of the enzyme was situated in a limited and flexible region of the enzyme molecule that was more susceptible to the denaturant than was the protein as a whole.Key words: creatine kinase, inactivation, conformation, kinetics, hexafluoroisopropanol.
Expression of bovine lactoferrin and lactoferrin N-lobe by recombinant baculovirus and its antimicrobial activity against Prototheca zopfii
Authors: Tanaka Tetsuya , Nakamura Ichiro , Lee Nai-Yuan , Kumura Haruto , Shimazaki Kei-ichi
Published: October 2003

Lactoferrin (LF) is a multifunctional, iron-binding glycoprotein found in secretory fluids of mammals. In this study, DNA encoding bovine lactoferrin (bLF) or the N-terminal half of bLF (bLF N-lobe) was inserted into a baculovirus transfer vector, and a recombinant virus expressing bLF or bLF N-lobe was isolated. An 80-kDa bLF-related protein expressed by the recombinant baculovirus was detected by monoclonal antibodies against bLF N-lobe and the C-terminal half of bLF (bLF C-lobe). A 43-kDa bLF N-lobe-related protein expressed by the recombinant baculovirus was detected by anti-bLF N-lobe monoclonal antibody, but not by anti-bLF C-lobe monoclonal antibody. These proteins were also secreted into the supernatant of insect cell cultures. Recombinant bLF (rbLF) and bLF N-lobe (rbLF N-lobe) were affected by tunicamycin treatment, indicating that rbLF and rbLF N-lobe contain an N-linked glycosylation site. Antimicrobial activity of these recombinant proteins against Prototheca zopfii (a yeast-like fungus that causes bovine mastitis) was evaluated by measuring the optical density of the culture microplate. Prototheca zopfii was sensitive to rbLF and rbLF N-lobe, as well as native bLF. There was no difference in antimicrobial activity between rbLF N-lobe and bLF C-lobe.Key words: lactoferrin, lactoferrin N-lobe, baculovirus, antimicrobial activity, Prototheca zopfii.
β1integrins are distributed in adhesion structures with fibronectin and caveolin and in coated pits
Authors: Boyd Nikhat D , Chan Bosco M. C , Petersen Nils O
Published: October 2003

Integrins are found in adhesion structures, which link the extracelullar matrix to cytoskeletal proteins. Here, we attempt to further define the distribution of β1integrins in the context of their association with matrix proteins and other cell surface molecules relevant to the endocytic process. We find that β1integrins colocalize with fibronectin in fibrillar adhesion structures. A fraction of caveolin is also organized along these adhesion structures. The extracellular matrix protein laminin is not concentrated in these structures. The α4β1integrin exhibits a distinct distribution from other β1integrins after cells have adhered for 1 h to extracellular matrix proteins but is localized in adhesion structures after 24 h of adhesion. There are differences between the fibronectin receptors: α5β1integrins colocalize with adaptor protein-2 in coated pits, while α4β1integrins do not. This parallels our earlier observation that of the two laminin receptors, α1β1and α6β1, only αaβ1integrins colocalize with adaptor protein-2 in coated pits. Calcium chelation or inhibition of mitogen-activated protein kinase kinase, protein kinase C, or src did not affect localization of α1β1and α5β1integrins in coated pits. Likewise, the integrity of coated-pit structures or adhesion structures is not required for integrin and adaptor protein-2 colocalization. This suggests a robust and possibly constitutive interaction between these integrins and coated pits.Key words: adhesion, endocytosis, extracellular matrix, microscopy, confocal, signalling.
Graham's law of effusion in dense systems with nonuniform interactions
Authors: Mohazzabi P , Cumaranatunge L
Published: October 2003

We investigate Graham's law of effusion in a series of molecular dynamics simulations. We show that the law remains valid not only in a dilute gas, but also in fluids dense enough to cause localization, even when various particles of the system interact according to varying interatomic force laws. Although Maxwellian velocity distribution is a sufficient condition for Graham's law of effusion to hold, it is not strictly necessary, in the sense that the law is obeyed even by systems that deviate significantly from Maxwellian. PACS Nos.: 05.20.Dd, 51.10.+y
Adhesion of probiotic lactobacilli to chick intestinal mucus
Authors: Gusils C , Oppezzo O , Pizarro R , González S
Published: October 2003

In the present work, interactions between three Lactobacillus strains (Lactobacillus fermentum CRL1015, Lactobacillus animalis CRL1014, and Lactobacillus fermentum CRL1016) and chicken small intestinal mucus were determined. Three lactobacilli isolated from chicken and selected by their potentially probiotic properties were able to grow in mucus preparations. Three peaks from gel filtration chromatography of intestinal mucus were obtained. The adhesion to three mucus fractions (I, II, and III), especially fraction III, was higher (P < 0.01) in L. fermentum CRL1015 than L. animalis CRL1014. Pretreatment of this fraction with proteases and metaperiodate showed lower (P < 0.01) adhesion values than that of the control, suggesting that a glycoprotein from the mucus acts as a receptor for L. fermentum CRL1015. Highest adhesion values were obtained at pH 7 and 42 °C, and neither the removal of divalent cations with ethylenediaminetetraacetic acid (EDTA) nor the addition of calcium produced significant variation from the adhesion values of the control (P > 0.01). This adhesion was only inhibited by N-acetyl-glucosamine. Salmonella pullorum and Salmonella gallinarum showed high (P < 0.01) values of adhesion to chick intestinal mucus. The results obtained from assays of the inhibition of adherence of Salmonella spp. to mucus, immobilized in polystyrene tissue culture wells, indicated that the pathogen adhesion was not reduced by lactobacilli (P > 0.05) or their spent culture supernatants (P > 0.05), suggesting that these strains did not interfere with the binding sites for Salmonella spp. adhesion to the small intestinal mucus.Key words: mucus, adhesion, Lactobacillus, probiotic, chicken.
Indole can act as an extracellular signal to regulate biofilm formation ofEscherichia coliand other indole-producing bacteria
Authors: Di Martino P , Fursy R , Bret L , Sundararaju B , Phillips R S
Published: October 2003

We demonstrated previously that genetic inactivation of tryptophanase is responsible for a dramatic decrease in biofilm formation in the laboratory strain Escherichia coli S17-1. In the present study, we tested whether the biochemical inhibition of tryptophanase, with the competitive inhibitor oxindolyl-L-alanine, could affect polystyrene colonization by E. coli and other indole-producing bacteria. Oxindolyl-L-alanine inhibits, in a dose-dependent manner, indole production and biofilm formation by strain S17-1 grown in LuriaBertani (LB) medium. Supplementation with indole at physiologically relevant concentrations restores biofilm formation by strain S17-1 in the presence of oxindolyl-L-alanine and by mutant strain E. coli 3714 (S17-1 tnaA::Tn5) in LB medium. Oxindolyl-L-alanine also inhibits the adherence of S17-1 cells to polystyrene for a 3-h incubation time, but mutant strain 3714 cells are unaffected. At 0.5 mg/mL, oxindolyl-L-alanine exhibits inhibitory activity against biofilm formation in LB medium and in synthetic urine for several clinical isolates of E. coli, Klebsiella oxytoca, Citrobacter koseri, Providencia stuartii, and Morganella morganii but has no affect on indole-negative Klebsiella pneumoniae strains. In conclusion, these data suggest that indole, produced by the action of tryptophanase, is involved in polystyrene colonization by several indole-producing bacterial species. Indole may act as a signalling molecule to regulate the expression of adhesion and biofilm-promoting factors.Key words: Escherichia coli, biofilm, indole, tryptophanase, signalling molecule.
Regulation oftoxAby PtxR inPseudomonas aeruginosaPA103
Authors: Carty Nancy L , Rumbaugh Kendra P , Hamood A N
Published: October 2003

Exotoxin A (ETA) production in Pseudomonas aeruginosa requires the regulatory locus regAB. Pseudomonas aeruginosa PA103 produces significantly higher levels of ETA than the prototypic strain PAO1 does, partly because of differences in the regAB locus. Other factors that contribute to this variation are not known. We previously described the P. aeruginosa gene ptxR that positively regulates production of ETA through regAB. ETA production was enhanced but still iron regulated in the PAO1 strain PAO1-XR that carries two copies of ptxR on its chromosome. Here we determine whether ptxR regulation of ETA is different in PA103. In contrast to PAO1-XR, ETA activity produced by PA103-2R, a PA103 strain carrying two copies of ptxR, is enhanced tenfold and partially deregulated in the presence of iron. Real-time PCR transcriptional analysis showed that the copy number of toxA mRNA in PA103-2R is significantly higher than in PA103 in both the presence and absence of iron, yet no similar increase in either regAB or ptxR mRNA copy number was detected. The integrated plasmid together with adjoining DNA was retrieved from the PA103-2R chromosome to determine whether integration-induced DNA changes played a role in this phenotype. Introduction of the retrieved plasmid in PA103 produced a phenotype similar to that of PA103-2R. Sequence analysis of the plasmid revealed the loss of 322 bp within the region 3' of ptxR. A plasmid construct carrying a 4-bp insertion in this same region produced in PA103 a phenotype similar to that of PA103-2R. Our results suggest that the effect of ptxR on toxA expression is different in PA103 than in PAO1 and that this variation in PA103-2R does not occur solely through regAB. Changes within the region 3' of ptxR are critical for the production of the unique PA103-2R phenotype, which occurs in trans and requires intact ptxR, but is not caused by ptxR overexpression.Key words: ptxR, toxA, regulation, Pseudomonas aeruginosa, PA103.
A low molecular weight enterotoxic hemolysin from clinicalEnterobacter cloacae
Authors: Simi S , Carbonell G V , Falcón R M , Gatti M S.V , Joazeiro P P , Darini A L , Yano T
Published: October 2003

Seven of 50 Enterobacter cloacae strains from clinical isolates produced small turbid zones of hemolysis in horse and sheep blood agar plates, and the culture supernatants were also positive for hemolytic activity. The hem o l y sin was partially purified from the culture supernatant of E. cloacae by ultrafiltration (PM-10 membrane) and extraction with acetone. Semipurified hemolysin was stable to heating (100 °C, 30 min) and was soluble in organic solvents (acetone, ethanol, and methanol). The toxin showed no loss of biological activity after treatment with trypsin and was stable to acid treatment at pH 2.0 but not at a pH greater than 7.0. In the rat intestinal loop assay, the hemolysin caused hemorrhagic fluid accumulation and severe histological alterations. These findings indicate that this hemolysin may be a putative virulence factor in E. cloacae infections.Key words: Enterobacter cloacae, hemolysin, enterotoxin.