bluuebunny/crossref_metadata_2025 huggingface dataset:
Development of molecular markers and linkage maps for the Carthamus species C. tinctorius and C. oxyacanthus
Authors: Mayerhofer Reinhold , Archibald Catherine , Bowles Victoria , Good Allen G.
Published: May 2010

A set of SSR and RFLP markers for safflower ( Carthamus tinctorius ) and jeweled distaff thistle ( C. oxyacanthus ) was generated from cDNA and genomic libraries and by mining public and proprietary sequence databases. In total, 1412 PCR-based markers and 75 RFLP markers were screened and polymorphic loci were mapped in an intraspecific F2 population of C. tinctorius and an interspecific BC1 population of C. tinctorius × C. oxyacanthus. The two populations shared one common parent and the resulting linkage maps could be compared for synteny. The level of polymorphism was low in both populations and only 8.2% and 13.7% of the analyzed markers could be mapped in the intraspecific and interspecific maps, respectively. The two maps showed significant colinearity of markers in several regions and an apparent translocation or inversion event on one linkage group. Noticeable segregation distortion was found on one linkage group of the C. tinctorius map and dense clustering of loci occurred on several linkage groups of the C. oxyacanthus map. The two maps represent the first major linkage analysis of Carthamus species. The molecular tools will be useful for a variety of genetic and genomic applications in safflower and its related species and have been used in our laboratory to map a flower color gene in C. tinctorius.
A new source of cytoplasmic male sterility found in wild beet and its relationship to other CMS types
Authors: Kawanishi Yuki , Shinada Hiroshi , Matsunaga Muneyuki , Masaki Yusuke , Mikami Tetsuo , Kubo Tomohiko
Published: May 2010

We found a number of male-sterile plants in a wild beet ( Beta vulgaris L. subsp. maritima) accession line, FR4-31. The inheritance study of the male sterility indicated the trait to be of the cytoplasmic type. The mitochondrial genome of FR4-31 proved to lack the male-sterility-associated genes preSatp6 and orf129, which are characteristic of the Owen CMS and I-12CMS(3) cytoplasms of beets, respectively. Instead, the truncated cox2 gene involved in G CMS originating from wild beets was present in the FR4-31 mitochondrial genome. In Southern hybridization using four mitochondrial gene probes, the FR4-31 cytoplasm showed patterns similar to those typical of the G cytoplasm. It is thus likely that the FR4-31 cytoplasm has a different CMS mechanism from both Owen CMS and I-12CMS(3), and that the FR4-31 and G cytoplasms resemble each other closely. A restriction map of the FR4-31 mitochondrial DNA was generated and aligned with those published for the Owen and normal fertile cytoplasms. The FR4-31 mitochondrial genome was revealed to differ extensively in arrangement from the Owen and normal genomes, and the male-sterile Owen and FR4-31 genomes seem to be derived independently from an ancestral genome.
Mitochondrial genome analysis of the predatory mitePhytoseiulus persimilisand a revisit of theMetaseiulus occidentalismitochondrial genome
Authors: Dermauw Wannes , Vanholme Bartel , Tirry Luc , Van Leeuwen Thomas
Published: May 2010

In this study we sequenced and analysed the complete mitochondrial (mt) genome of the Chilean predatory mite Phytoseiulus persimilis Athias-Henriot (Chelicerata: Acari: Mesostigmata: Phytoseiidae: Amblyseiinae). The 16 199 bp genome (79.8% AT) contains the standard set of 13 protein-coding and 24 RNA genes. Compared with the ancestral arthropod mtDNA pattern, the gene order is extremely reshuffled (35 genes changed position) and represents a novel arrangement within the arthropods. This is probably related to the presence of several large noncoding regions in the genome. In contrast with the mt genome of the closely related species Metaseiulus occidentalis (Phytoseiidae: Typhlodrominae) — which was reported to be unusually large (24 961 bp), to lack nad6 and nad3 protein-coding genes, and to contain 22 tRNAs without T-arms — the genome of P. persimilis has all the features of a standard metazoan mt genome. Consequently, we performed additional experiments on the M. occidentalis mt genome. Our preliminary restriction digests and Southern hybridization data revealed that this genome is smaller than previously reported. In addition, we cloned nad3 in M. occidentalis and positioned this gene between nad4L and 12S-rRNA on the mt genome. Finally, we report that at least 15 of the 22 tRNAs in the M. occidentalis mt genome can be folded into canonical cloverleaf structures similar to their counterparts in P. persimilis.
Selection criteria for scoring amplified fragment length polymorphisms (AFLPs) positively affect the reliability of population genetic parameter estimates
Authors: Herrmann Doris , Poncet Bénédicte N. , Manel Stéphanie , Rioux Delphine , Gielly Ludovic , Taberlet Pierre , Gugerli Felix
Published: May 2010

A reliable data set is a fundamental prerequisite for consistent results and conclusions in population genetic studies. However, marker scoring of genetic fingerprints such as amplified fragment length polymorphisms (AFLPs) is a highly subjective procedure, inducing inconsistencies owing to personal or laboratory-specific criteria. We applied two alternative marker selection algorithms, the newly developed script scanAFLP and the recently published AFLPScore, to a large AFLP genome scan to test how population genetic parameters and error rates were affected. These results were confronted with replicated random selections of marker subsets. We show that the newly developed marker selection criteria reduced the mismatch error rate and had a notable influence on estimates of genetic diversity and differentiation. Both effects are likely to influence biological inference. For example, genetic diversity (HS) was 29% lower while genetic differentiation (FST) was 8% higher when applying scanAFLP compared with AFLPScore. Likewise, random selections of markers resulted in substantial deviations of population genetic parameters compared with the data sets including specific selection criteria. These randomly selected marker sets showed surprisingly low variance among replicates. We conclude that stringent marker selection and phenotype calling reduces noise in the data set while retaining patterns of population genetic structure.
GISH characterization of Erianthus arundinaceus chromosomes in three generations of sugarcane intergeneric hybrids
Authors: Piperidis Nathalie , Chen Jian-wen , Deng Hai-hua , Wang Li-Ping , Jackson Phillip , Piperidis George
Published: May 2010

Within Erianthus , a genus close to Saccharum , the species E. arundinaceus has the potential to contribute valuable traits to sugarcane, including adaptation to biotic and abiotic stresses and ratooning ability. Sugarcane breeders have tried for a long time to use Erianthus species in their breeding programs but until recently were constrained by a lack of fertile Saccharum × Erianthus hybrids. We report here for the first time the chromosome composition of fertile Saccharum officinarum  × E. arundinaceus F1, BC1 (F1 × sugarcane cultivar), and BC2 (BC1 × sugarcane cultivar) hybrids. The F1 and BC2 resulted from n + n chromosome transmission, while the BC1 resulted from 2n + n transmission. In the BC1 clones, the number of E. arundinaceus chromosomes ranged from 21 to 30, and in the BC2 clones, the number ranged from 14 to 15, revealing cases of chromosome loss. No recombination events between Saccharum and Erianthus chromosomes were observed in either the BC1 or BC2 clones. The implications of these results for introgression of genes from E. arundinaceus in sugarcane breeding programs are discussed. We propose a strategy to identify the agronomic value of chromosomes from E. arundinaceus and to conduct targeted breeding based on this information.
Genetic control and QTL analysis of cotyledon bleaching resistance in green field pea (Pisum sativumL.)
Authors: Ubayasena Lasantha , Bett Kirstin , Tar’an Bunyamin , Vijayan Perumal , Warkentin Thomas
Published: May 2010

Resistance to bleaching is an important factor for quality grading of Canadian green field pea and an important selection criterion in green pea improvement. This research was conducted to determine the genetic control of bleaching resistance in green peas using 90 recombinant inbred lines (RILs) derived from a cross between cultivars Orb and CDC Striker. These lines were evaluated under field conditions for two years in two locations in Saskatchewan, Canada. Harvested whole seeds and cotyledons were evaluated for greenness using the Hunter Lab colorimeter before and after exposure to a high light intensity accelerated bleaching treatment. The RILs were genotyped using amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) molecular markers. Heritability estimates for whole seed and cotyledon greenness were moderate (0.72 and 0.69, respectively) and increased when assessed after exposing whole seeds and cotyledons to accelerated bleaching conditions (0.83 and 0.82, respectively). The genetic linkage map constructed based on a total of 224 AFLP and SSR markers spanned over 890 cM of the pea genome. Multiple QTL mapping detected major QTLs on LG IV and LG V as well as location- and year-specific QTLs on LG II and LG III associated with green cotyledon bleaching resistance in field pea. The results demonstrated the importance of the seed coat in protecting the cotyledons from bleaching.
A synteny map and disease resistance gene comparison between barley and the model monocotBrachypodium distachyon
Authors: Drader Tom , Kleinhofs Andris
Published: May 2010

Grass species have coevolved with current economically important crop pathogens over millions of years. During this time, speciation of current domestic crops has occurred, resulting in related yet divergent genomes. Here, we present a synteny map between the crop species Hordeum vulgare and the recently sequenced Brachypodium distachyon genome, focusing on regions known to harbor important barley disease resistance genes. The resistance genes have orthologous genes in Brachypodium that show conservation of the form and likely the function of the genes. The level of colinearity between the genomes is highly dependent on the region of interest and, at the DNA level or protein level, the gene of interest. The stem rust resistance gene Rpg1 has an ortholog with a high level of identity at the amino acid level, while the stem rust resistance gene Rpg5 has two orthologs with a high level of identity, one corresponding to the NBS-LRR domain and the other to the serine/threonine protein kinase domain, on different contigs. Interestingly, the predicted product of the Brachypodium Rpg1 ortholog contained a WD40 domain at the C-terminal end. The stem rust resistance gene rpg4 (actin depolymerizing factor 2) also has an ortholog with a high level of identity, in which one of the three residues indicated by allele sequencing in barley cultivars to be important in disease resistance is conserved. The syntenous region of the seedling spot blotch resistance locus, Rcs5, has a high level of colinearity that may prove useful in efforts to identify and clone this gene. A synteny map and orthologous resistance gene comparisons are presented.
Innovative design approach of precast–prestressed girder bridges using ultra high performance concrete
Authors: Almansour H. , Lounis Z.
Published: May 2010

The construction of new bridges and the maintenance and renewal of aging highway bridge network using ultra high performance concrete can lead to the construction of long life bridges that will require minimum maintenance resulting in low life cycle costs. Ultra high performance concrete (UHPC) is a newly developed concrete material that provides very high strength and very low permeability to aggressive agents such as chlorides from de-icing salts or seawater. Ultra high performance concrete could enable major improvements over conventional high performance concrete (HPC) bridges in terms of structural efficiency, durability, and cost-effectiveness over the long term. A simplified design approach of concrete slab on UHPC girders bridge using the Canadian Highway Bridge Design code and the current recommendations for UHPC design is proposed. An illustrative example demonstrates that the use of UHPC in precast–prestressed concrete girders yields a more efficient design of the superstructure where considerable reduction in the number of girders and girder size when compared to conventional HPC girders bridge with the same span length. Hence, UHPC results in a significant reduction in concrete volume and then weight of the superstructure, which in turn leads to significant reduction in the dead load on the substructure, especially for the case of aging bridges, thus improving their performance.
Three-dimensional numerical modeling of unconfined and confined wall-jet flow with two different turbulence models
Authors: Khosronejad Ali , Rennie C. D.
Published: May 2010

Wall-jet flow is an important flow field in hydraulic engineering, and its applications include flow from the bottom outlet of dams and sluice gates. An in-house three-dimensional (3-D) finite-volume Reynolds-averaged-Navier-Stokes (RANS) numerical model predicts the hydrodynamic characteristics of wall jets with square and rectangular source geometry. Either the low-turbulence Reynolds number k–ω or the standard k–ε turbulence closure models are applied. The calculated results for velocity profile and bed shear stress in both longitudinal and vertical directions compare favourably with both the published experimental results and the FLUENT®finite volume model. The two closure models are compared with the k–ω model, displaying 4% greater average accuracy than the k–ε model. Finally, the influence of lateral confinement of the receiving channel on wall-jet hydrodynamics is investigated, with decreased longitudinal deceleration and decreased bed shear stress observed in a confined jet. This has important implications for sediment transport in the receiving channels downstream of sluice gates.
Estimation of speed differentials on rural highways using hierarchical linear regression models
Authors: Park Peter Y. , Miranda-Moreno Luis F. , Saccomanno Frank F.
Published: May 2010

Large speed differentials between highway segments are associated with an increase in the number of accidents. Traditional speed differential measures, derived from single-level linear regression models, suffer from serious deficiencies, namely underestimating the speed differential (due to intracorrelated data) and inflating the adequacy of the model’s explanation (due to aggregate data). High-quality speed differential predictions are highly desirable right from the initial design phase, but the estimation process is not straightforward, and decision makers must recognize that speed differential predictions are subject to considerable uncertainty. This paper compares four models: two single-level models, a conventional multilevel model, and a Bayes multilevel model. The results show empirically that multilevel models increase the accuracy and precision of estimates of speed differentials, possibly with fewer data. The paper introduces a new, easy to interpret speed consistency measure that simply represents the probability that a vehicle exceeds a certain speed differential. This measure is calculated using a multilevel model and takes into account the uncertainty in the estimates of speed differentials. Overall, we show that a multilevel modeling approach can improve the quality of decision making that makes use of speed differential information in road design and road safety.
National Centers for Environmental Prediction – National Center for Atmospheric Research (NCEP–NCAR) reanalyses data for hydrologic modelling on a basin scale
Authors: Solaiman Tarana A. , Simonovic Slobodan P.
Published: May 2010

This paper evaluates the National Centers for Environmental Prediction – National Center for Atmospheric Research (NCEP–NCAR) reanalyses hydroclimatic data as an initial check for assessment of hydrologic impacts of climate change at the basin scale. A reanalysis dataset for daily precipitation, maximum temperature, and minimum temperature from the NCEP–NCAR global (NNGR) and regional (North American Regional Reanalysis or NARR) reanalysis project has been used as input into the semidistributed hydrologic model (Hydrologic Engineering Center Hydraulic Modeling System or HEC–HMS) for the period 1980–2005. An extensive analysis has been performed for assessing the performance of the reanalysis data generated flows compared with the observed inputs during May–November. The stream flows generated from the NARR dataset show encouraging results in simulating summertime low flows with less variability and fewer errors. The results indicate that NNGR results are less accurate and highly variable. This study suggests that NARR can be adequately used as an alternative in data-scarce regions.
Experimental evaluation of remaining strength of crossarms in Gulfport transmission line wood structures
Authors: Pandey M. D. , Ho V. , McCarthy F. , Woodward S. B.
Published: May 2010

Electrical transmission lines in Canada and elsewhere widely utilize wood structures to support electrical conductors. The Gulfport structure is one of the largest wooden structures used in Canada’s electricity transmission networks. Continuous exposure of crossarms to wide-ranging temperature, moisture, and load conditions makes them vulnerable to internal decay and failure under adverse weather conditions, such as windstorms and snowstorms. These failures can result in forced outages and customer disruptions with significant economic losses, and therefore the electrical utility industry has taken a keen interest in developing condition-assessment methods to support cost-effective replacement of aged wood crossarms. At present, there is no dataset available regarding the remaining strength of wood pole crossarms exposed to the aboveground environment for 30–40 years of service life in Canada. This paper presents a comprehensive experimental study focussed on evaluating the remaining strength distribution in a sample of crossarms removed from service. The experimental data presented in the paper are essential to assess remaining life and develop guidelines for condition assessment of crossarms.
CSPα: the neuroprotective J proteinThis paper is one of a selection of papers published in this special issue entitled “Canadian Society of Biochemistry, Molecular & Cellular Biology 52nd Annual Meeting — Protein Folding: Principles and Diseases” and has undergone the Journal's usual peer review process.
Authors: Johnson Jadah N. , Ahrendt Eva , Braun Janice E.A.
Published: May 2010

Cysteine string protein (CSPα, also called DnaJC5) is unique among J proteins. Similar to other J proteins, CSPα interacts with and activates the ATPase of Hsc70s (heat shock proteins of 70 kDa), thereby harnessing the ATPase activity for conformational work on client proteins. In contrast to other J proteins, CSPα is anchored to synaptic vesicles, as well as to exocrine, endocrine and neuroendocrine secretory granules, and has been shown to have an essential anti-neurodegenerative role. CSPα-null organisms exhibit progressive neurodegeneration, behavioural deficits, and premature death, most likely due to the progressive misfolding of one or more client proteins. Here we highlight recent advances in our understanding of the critical role that CSPα plays in governing exocytotic secretory functions.
Membrane catalysis of peptide–receptor bindingThis paper is one of a selection of papers published in this special issue entitled “Canadian Society of Biochemistry, Molecular & Cellular Biology 52nd Annual Meeting — Protein Folding: Principles and Diseases” and has undergone the Journal's usual peer review process.
Authors: Langelaan David N. , Rainey Jan K.
Published: May 2010

The membrane catalysis hypothesis states that a peptide ligand activates its target receptor after an initial interaction with the surrounding membrane. Upon membrane binding and interaction, the ligand is structured such that receptor binding and activation is encouraged. As evidence for this hypothesis, there are numerous studies concerning the conformation that peptides adopt in membrane mimetic environments. This mini-review analyzes the features of ligand peptides with an available high-resolution membrane-induced structure and a characterized membrane-binding region. At the peptide–membrane interface, both amphipathic helices and turn structures are commonly formed in peptide ligands and both hydrophobic and electrostatic interactions can be responsible for membrane binding. Apelin is the ligand to the G-protein coupled receptor (GPCR) named APJ, with various important physiological effects, which we have recently characterized both in solution and bound to anionic micelles. The structural changes that apelin undergoes when binding to micelles provide strong evidence for membrane catalysis of apelin–APJ interactions.
Interpretation of biomolecular NMR spin relaxation parametersThis paper is one of a selection of papers published in this special issue entitled “Canadian Society of Biochemistry, Molecular & Cellular Biology 52nd Annual Meeting — Protein Folding: Principles and Diseases” and has undergone the Journal's usual peer review process.
Authors: Reddy Tyler , Rainey Jan K.
Published: May 2010

Biomolecular nuclear magnetic resonance (NMR) spin relaxation experiments provide exquisite information on the picosecond to nanosecond timescale motions of bond vectors. Spin–lattice (T1) and spin–spin (T2) relaxation times and the steady-state nuclear Overhauser effect (NOE) are the first set of parameters extracted from typical 15N or 13C NMR relaxation experiments. Therefore, verifying that T1, T2, and NOE are consistent with theoretical predictions is an important step before carrying out the more detailed model-free and reduced spectral density mapping analyses commonly employed. In this mini-review, we discuss the essential motional parameters used to describe biomolecular dynamics in the context of a variety of examples of folded and intrinsically disordered proteins and peptides in aqueous and membrane mimetic environments. Estimates of these parameters can be used as input for an online interface, introduced herein, allowing plotting of trends of T1, T2, and NOE with magnetic field strength. The plots may serve as a first-check to the spectroscopist preparing to embark on a detailed NMR relaxation analysis.
Deletion of a terminal residue disrupts oligomerization of a transmembrane α-helixThis paper is one of a selection of papers published in this special issue entitled “Canadian Society of Biochemistry, Molecular & Cellular Biology 52nd Annual Meeting — Protein Folding: Principles and Diseases” and has undergone the Journal's usual peer review process.
Authors: Ng Derek P. , Deber Charles M.
Published: May 2010

In studies of the structural biology of membrane proteins, the success of strategies based on the “divide and conquer” approach, where peptides are used to model the individual transmembrane (TM) α-helices of membrane proteins, depends on the correct identification of the membrane-embedded TM α-helix amino acid sequence within the full-length protein. In the present work, we examine the effects of excluding or including TM boundary residues on the intrinsic properties of a Lys-tagged TM2 α-helix of myelin proteolipid protein (PLP), of parent sequence KKKK-66AFQYVIYGTASFFFLYGALLLAEG89-KKKK along with analogs containing an additional wild type Phe-90, Phe-90 and Tyr-91, and of a hydrophobic mutant Leu-90. Using protein gel electrophoresis, circular dichroism, and fluorescence resonance energy transfer in the membrane-mimetic detergent sodium dodecylsulfate (SDS), we demonstrate that the removal of a single amino acid from the C-terminus of this TM segment is enough to change its intrinsic properties, with TM2 66–89 displaying only a monomeric form, but with dimers arising for the other 3 peptides. A novel use of trifluoroethanol (TFE) as a maximal helix-supporting solvent demonstrated that peptides containing residues at positions 90 and (or) 90–91 displayed significantly increased helical content vs. the TM2 parent peptide. The findings suggest that deletion of critical C-terminal residue(s) tends to reposition the helix terminus toward the membrane–aqueous interface. Our overall results emphasize the potential influence of boundary residues on TM properties when using peptides as models for TM α-helices, and may implicate a role for these residues in membrane protein folding and assembly.
Mechanisms of the Hsp70 chaperone systemThis paper is one of a selection of papers published in this special issue entitled “Canadian Society of Biochemistry, Molecular & Cellular Biology 52nd Annual Meeting — Protein Folding: Principles and Diseases” and has undergone the Journal's usual peer review process.
Authors: Young Jason C.
Published: May 2010

Molecular chaperones of the Hsp70 family have diverse functions in cells. They assist the folding of newly synthesized and stress-denatured proteins, as well as the import of proteins into organelles, and the dissociation of aggregated proteins. The well-conserved Hsp70 chaperones are ATP dependent: binding and hydrolysis of ATP regulates their interactions with unfolded polypeptide substrates, and ATPase cycling is necessary for their function. All cellular functions of Hsp70 chaperones use the same mechanism of ATP-driven polypeptide binding and release. The Hsp40 co-chaperones stimulate ATP hydrolysis by Hsp70 and the type 1 Hsp40 proteins are conserved from Escherichia coli to humans. Various nucleotide exchange factors also promote the Hsp70 ATPase cycle. Recent advances have added to our understanding of the Hsp70 mechanism at a molecular level.
Electrostatics in the stability and misfolding of the prion protein: salt bridges, self energy, and solvationThis paper is one of a selection of papers published in this special issue entitled “Canadian Society of Biochemistry, Molecular & Cellular Biology 52nd Annual Meeting — Protein Folding: Principles and Diseases” and has undergone the Journal's usual peer review process.
Authors: Guest Will C. , Cashman Neil R. , Plotkin Steven S.
Published: May 2010

Using a recently developed mesoscopic theory of protein dielectrics, we have calculated the salt bridge energies, total residue electrostatic potential energies, and transfer energies into a low dielectric amyloid-like phase for 12 species and mutants of the prion protein. Salt bridges and self energies play key roles in stabilizing secondary and tertiary structural elements of the prion protein. The total electrostatic potential energy of each residue was found to be invariably stabilizing. Residues frequently found to be mutated in familial prion disease were among those with the largest electrostatic energies. The large barrier to charged group desolvation imposes regional constraints on involvement of the prion protein in an amyloid aggregate, resulting in an electrostatic amyloid recruitment profile that favours regions of sequence between α helix 1 and β strand 2, the middles of helices 2 and 3, and the region N-terminal to α helix 1. We found that the stabilization due to salt bridges is minimal among the proteins studied for disease-susceptible human mutants of prion protein.
Evaluation of the role of enzymatic and nonenzymatic antioxidant systems in the radiation resistance ofDeinococcus
Authors: Shashidhar Ravindranath , Kumar Sanjukta A. , Misra Hari S. , Bandekar Jayant R.
Published: May 2010

Antioxidant enzymes and antioxidant metabolites appear to have different roles in the oxidative stress resistance responses of radiation-resistant bacteria belonging to the Deinococcus – Thermus group. Twelve distinct strains belonging to 7 Deinococcus species were characterized for their responses to hydrogen peroxide, ciprofloxacin, and ionizing radiation. The levels of catalase and peroxidase activities in these strains showed a positive correlation with resistance to hydrogen peroxide and ciprofloxacin. However, the levels of these enzymes and carotenoids did not appear to contribute significantly to radiation resistance. Our findings support the idea that enzymatic defense systems are not sufficient to account for the extreme radiation resistance of Deinococcus species. Consistent with previously published reports, the Deinococcus strains had high intracellular manganese/iron ratios. No significant correlation was found between intracellular manganese/iron ratios and radiation resistance within different Deinococcus species, suggesting that other components are involved in conferring radiation resistance.
Anti-Escherichia coliO157:H7 activity of free fatty acids under varying pH
Authors: Yang Jinli , Hou Xianzhi , Mir Priya S. , McAllister Tim A.
Published: May 2010

Following screening of 4 strains of Escherichia coli O157:H7 (E32511, E318N, H4420N, and R508N) for acid tolerance, strain H4420N was selected for further study into the influence of pH on bactericidal activity of 6 fatty acids (capric, lauric, palmitic, oleic, linoleic, and linolenic). Strain H4420N was cultured for 6 h in Luria–Bertani broth amended with individual fatty acids at 20 mmol/L, with pH adjusted to 7.0, 4.3, or 2.5. None of the fatty acids exhibited bactericidal activity at pH 7.0 (p >0.05). At pH 4.3, only capric, lauric, and linoleic acids reduced viability of H4420N (p < 0.05). At pH 2.5, oleic (C18:1) and linolenic (C18:3) acids had modest effects on H4420N viability, whereas capric (C10:0), lauric (C12:0), and linoleic (C18:2) acids resulted in a reduction ≥5 log10colony-forming units (CFU)/mL (p < 0.05). Capric and lauric acids were examined further at pH 2.5 over a range of concentrations (0.15–20 mmol/L). After 10 min of exposure, 5 log10 CFU/mL reductions (p < 0.05) were achieved by lauric acid at 2.5 mmol/L and by capric acid at 0.31 mmol/L. Acid stress increased the sensitivity of acid-tolerant E. coli O157:H7 strain H4420N to fatty acids. Including sources of these fatty acids in diets for cattle might impair the ability of this zoonotic pathogen to survive passage through the stomach, possibly reducing the potential for its colonization in the lower gut.
Comparison of effectiveness of wood decay fungi maintained by annual subculture on agar and stored in sterile water for 18 years
Authors: Richter Dana L. , Kangas Laura C. , Smith Jill K. , Laks Peter E.
Published: May 2010

Fourteen isolates of basidiomycete decay fungi (12 species) were maintained for 18 years on agar slants transferred annually and alsostored as mycelium-agar cores under cold sterile water without subculture. Isolates stored by each method were evaluated for decay effectiveness using a standard laboratory accelerated soil-block decay test. Effectiveness was measured by mean percent mass loss of wood blocks. There was no significant difference (p ≤ 0.05) in decay effectiveness between storage methods for 12 of the fungus isolates tested. For the 2 fungi that showed a significant difference in the amount of decay with respect to storage method, 1 fungus ( Fomitopsis lilacinogilva ) produced more decay by the strain maintained as an agar slant, while the other fungus ( Trametes versicolor ) produced more decay by the strain stored in sterile water. Results suggested that storage under sterile water is an easy and effective method to store isolates of decay fungi for long periods, but as with any microbial storage method, careful monitoring of isolates upon revival is necessary.
The activity of silver against Escherichia coli biofilm is increased by a lipopeptide biosurfactant
Authors: Rivardo Fabrizio , Martinotti Maria Giovanna , Turner Raymond Joseph , Ceri Howard
Published: May 2010

Biological contamination of surfaces, both in industry and in health care, plays an important role as a potential vector of disease transmission. Metals have been described to be effective antibiofilm agents, and the efficacy of silver ions as a disinfectant has been known for centuries. The activity of AgNO3 combined with the lipopeptide biosurfactant V9T14 has been studied against a preformed Escherichia coli biofilm on the Calgary Biofilm Device. Results indicated that the activity of silver can be synergistically enhanced by the presence of V9T14, both allowing for a reduction in the quantity of silver used and for greater antimicrobial activity. The concentration of silver needed to obtain this reduction in the silver–biosurfactant solution was from 129- to 258-fold less than the concentration of silver alone. To our knowledge, this is the first time that a synergistic interaction between a lipopeptide biosurfactant and silver has been observed.
Improving the culturability of freshwater bacteria using FW70, a low-nutrient solid medium amended with sodium pyruvate
Authors: Imazaki Iori , Kobori Youichi
Published: May 2010

Bacterial culture based on the use of plate media is an effective method for investigating bacterial populations in the environment. To improve the culturability of bacteria from freshwater lakes, we developed a new medium, FW70, which contains sodium pyruvate, casamino acids, and lake water and is solidified using gellan gum. To test the importance of these components, we prepared a series of media in which one or more of the components was absent. Water was sampled 31 times from 3 Japanese lakes and was passed through a membrane filter (pore size = 0.45 µm) to remove fast-growing microbes before the water was spread onto the plates. In most cases, significantly larger numbers of bacterial colonies were detected on FW70 than on other media. Furthermore, to test the practicality of FW70, we compared it with standard nutrient agar and R2A agar. In all cases, the culturability was significantly greater on FW70 than on standard nutrient agar or R2A agar. Some isolates recovered by means of FW70 belonged to bacteria that had not previously been classified. These results suggest that FW70 improves the culturability of freshwater bacteria and can be used for the isolation of novel bacteria as a result of the filtration step.
Dietary response of Barn Owls (Tyto alba) to large variations in populations of common voles (Microtus arvalis) and European water voles (Arvicola terrestris)
Authors: Bernard Nadine , Michelat Dominique , Raoul Francis , Quéré Jean-Pierre , Delattre Pierre , Giraudoux Patrick
Published: May 2010

The diet of the Barn Owl ( Tyto alba (Scopoli, 1769)) was studied over an 8-year period in the Jura mountains of France, during two population surges of its main rodent prey (common voles, Microtus arvalis (Pallas, 1778), and European water voles, Arvicola terrestris (L.,1758)), allowing us to test whether T. alba is an opportunistic predator as is often cited in the literature or exhibits more complex patterns of prey selection as is reported in arid environments. Small mammals were sampled by trapping and index methods. We observed (i) significant correlations between the proportions of A. terrestris, M. arvalis, and woodland rodents in the diet and their respective densities in the field; (ii) interactions between populations of A. terrestris and M. arvalis, indicating that the proportion of each species in diet was affected by the density of the other; (iii) proportions of red-toothed shrews (genus Sorex (L., 1758)) in the diet did not correlate with their abundance in the field, indicating that those species were likely to be preyed upon when others were no longer available. This confirms that T. alba is generally opportunistic; however, prey selection of a focal species (e.g., Sorex spp., grassland species) can be affected by the density or availability of the other prey species.
REVERSIBLE GEODESICS FOR (α, β)-METRICS
Authors: MASCA IOANA MONICA , SABAU VASILE SORIN , SHIMADA HIDEO
Published: May 2010

A Finsler space is said to have reversible geodesics if for any of its oriented geodesic paths, the same path traversed in the opposite sense is also a geodesic. In [6] the conditions for a Randers space to have reversible geodesics have been found. The main goal of this paper is to find conditions for a Finsler space endowed with an (α, β)-metric to be with reversible geodesics or strictly reversible geodesics, respectively.

Moreover, we obtain some new classes of (α, β)-metrics with reversible geodesics and show how new Finsler metrics with reversible geodesics can be constructed by means of a Randers change.
BRAID MONODROMY OF SOME BRIESKORN–PHAM SINGULARITIES
Authors: LÖNNE MICHAEL
Published: May 2010

For germs of isolated hypersurface singularities Lyashko and Looijenga introduced a map LL on the complement of the bifurcation set. It takes values in the space of simple polynomials of degree equal to the Milnor number μ of the singularity, and thus induces a map LL* from the fundamental group to the braid group on μ strands.

For the case of curve singularities given by a polynomial x3 + yℓ+1 we give a uniform description of the image LL* and derive a presentation of the discriminant knot group, i.e. for the fundamental group of the complement to the discriminant divisor.
POHOŽAEV IDENTITIES FROM DOMAIN DEFORMATION
Authors: XU QINGHUA , LU YING , WANG LIHE
Published: May 2010

This paper presents a unified approach to a class of identities which was first proved by Pohožaev. These identities have generalizations to Schrödinger's equation, the wave equation, the p-Laplace equation and the biharmonic equation. We also show that the systems can be proved under our unified approach.
DEFECT–DEFECT INTERACTION IN SINGLE-WALLED CARBON NANOTUBES UNDER TORSIONAL LOADING
Authors: HUQ ABUL M. A. , BHUIYAN ABUHANIF K. , LIAO KIN , GOH KHENG LIM
Published: May 2010

This paper presents an analysis of interactions between a pair of Stone–Wales (SW) defects in a single-walled carbon nanotube (SWCNT) that has been subjected to an external torque. Defect pairs, representing the different combinations of SW defect of A (SW-A) and B (SW-B) modes, were incorporated in SWCNT models of different chirality and diameter and solved using molecular mechanics. Defect–defect interaction was investigated by evaluating the C–C steric interactions in the defect that possesses the highest potential energy, E, as a function of inter-defect distance, D. This study reveals that the deformation of the C–C bond is attributed to bond stretching and bending. In the SW-B defects, there is an additional contributor arising from the dihedral angular deformation. The magnitude of E depends on the type of defect but the profile of the E versus D curve depends on the orientation of the defects. The largest indifference length, D0, beyond which two defects cease to interact, is approximately 30 Å. When the angular displacement of the tube increases two-fold, E increases, but the profile of the E versus D curve is not affected. The sense of rotation affects the magnitude of E but not the profile of the E versus D curve.
SYNTHESIS OF AMORPHOUS/NANOCRYSTALLINE Ni–Ti POWDERS BY USING LOW ENERGY MECHANICAL ALLOYING
Authors: VERDIAN M. M. , SALEHI M. , RAEISSI K.
Published: May 2010

An amorphous/nanocrystalline 50 Ni –50 Ti powder was produced from elemental Ti and Ni powders by solid state synthesis utilizing low energy mechanical alloying with times up to 100 h. The morphology, microstructure, and phase composition of the milling products were evaluated by using scanning electron microscopy and X-ray diffraction analysis. The results indicated that there was no chemical reaction between the elements during the milling process, which led to the direct formation of an amorphous/nanocrystalline structure without any intermediate phase (intermetallic and/or solid solution phase) formation. It seems that the second kind of amorphization process proposed by Weeber and Bakker is governed. It was shown that the formation of amorphous phase was started after 80 h and developed during the milling for 100 h.
REPLY TO "COMMENT ON 'FALSIFICATION OF THE ATMOSPHERIC CO2GREENHOUSE EFFECTS WITHIN THE FRAME OF PHYSICS' BY JOSHUA B. HALPERN, CHRISTOPHER M. COLOSE, CHRIS HO-STUART, JOEL D. SHORE, ARTHUR P. SMITH, JÖRG ZIMMERMANN"
Authors: GERLICH GERHARD , TSCHEUSCHNER RALF D.
Published: May 2010

It is shown that the notorious claim by Halpern et al. recently repeated in their comment that the method, logic, and conclusions of our "Falsification Of The CO2Greenhouse Effects Within The Frame Of Physics" would be in error has no foundation. Since Halpern et al. communicate our arguments incorrectly, their comment is scientifically vacuous. In particular, it is not true that we are "trying to apply the Clausius statement of the Second Law of Thermodynamics to only one side of a heat transfer process rather than the entire process" and that we are "systematically ignoring most non-radiative heat flows applicable to Earth's surface and atmosphere". Rather, our falsification paper discusses the violation of fundamental physical and mathematical principles in 14 examples of common pseudo-derivations of fictitious greenhouse effects that are all based on simplistic pictures of radiative transfer and their obscure relation to thermodynamics, including but not limited to those descriptions (a) that define a "Perpetuum Mobile Of The 2nd Kind", (b) that rely on incorrectly calculated averages of global temperatures, (c) that refer to incorrectly normalized spectra of electromagnetic radiation. Halpern et al. completely missed an exceptional chance to formulate a scientifically well-founded antithesis. They do not even define a greenhouse effect that they wish to defend. We take the opportunity to clarify some misunderstandings, which are communicated in the current discussion on the non-measurable, i.e., physically non-existing influence of the trace gas CO2on the climates of the Earth.
KNOTS, LINKS AND SPUN DYNAMICAL SYSTEMS
Authors: CHEN W. , BANKS S. P.
Published: May 2010

In this paper we consider spun dynamical systems and show that we can obtain a system on S3 × S1 which contains any finite set of knotted and linked surfaces which are invariant surfaces for the flow.
ON THE ANISOTROPIC POTENTIALS OF MANEV–SCHWARZSCHILD TYPE
Authors: VALLS CLÁUDIA
Published: May 2010

In this paper, we study the two-body problem that describes the motion of two-point masses in an anisotropic space under the influence of a Newtonian force-law with two relativistic correction terms. We will show that the set of initial conditions leading to collisions and ejections and leading to escapes and captures have positive measure. Using the infinity manifold, we study capture and escape solutions in the zero-energy case. We also show that the flow on the zero energy manifold of a two-body problem given by the sum of the Newtonian potential and three anisotropic perturbations (corresponding to three relativistic correction terms) is chaotic.
CAUCHY PROBLEM FOR VISCOUS SHALLOW WATER EQUATIONS WITH A TERM OF CAPILLARITY
Authors: HASPOT BORIS
Published: May 2010

In this paper, we consider the compressible Navier–Stokes equation with density-dependent viscosity coefficients and a term of capillarity introduced formally by van der Waals in Ref. 51. This model includes at the same time the barotropic Navier–Stokes equations with variable viscosity coefficients, shallow-water system and the model introduced by Rohde in Ref. 46.

We first study the well-posedness of the model in critical regularity spaces with respect to the scaling of the associated equations. In a functional setting as close as possible to the physical energy spaces, we prove global existence of solutions close to a stable equilibrium, and local in time existence of solutions with general initial data. Uniqueness is also obtained.
SEMI-ANALYTICAL SOLUTION OF TWO-DIMENSIONAL ELASTICITY PROBLEMS BY FINITE DIFFERENCE–DISTRIBUTED TRANSFER FUNCTION METHOD
Authors: YANG YAUBIN , YANG BINGEN
Published: May 2010

A semi-analytical solution method, called the Finite Difference–Distributed Transfer Function Method, is developed for static and dynamic problems of two-dimensional elastic bodies composed of multiple rectangular subregions. In the development, the original two-dimensional elasticity problem is first reduced into a one-dimensional boundary-value problem by finite difference; the exact solution of the reduced problem is then obtained by using the distributed transfer functions of the elastic continuum. The proposed technique, which combines the simplicity of finite difference and the closed form of analytical solutions, is capable of handling arbitrary boundary conditions, delivers highly accurate solutions for static and dynamic problems, and is computationally efficient. The proposed method is illustrated on a square region and an L-shaped region.
DESIGN FORCE TRANSMITTED BY ISOLATION SYSTEM COMPOSED OF LEAD-RUBBER BEARINGS AND VISCOUS DAMPERS
Authors: HWANG J. S. , HUNG C. F. , HUANG Y. N. , WANG S. J.
Published: May 2010

In seismic isolation design of structures located at soft soil sites or near field areas, viscous dampers (VD) are often included as part of the isolation system to minimize its maximum displacement. Due to the 90° phase angle existing between the force and displacement of the VD, the maximum force transmitted by the isolation system cannot be calculated by simply combining the forces of the isolation bearings, such as lead-rubber bearings (LRB) or high damping rubber bearings (HDRB), and VD in association with the design displacement. Conforming to the code-specified equivalent lateral response procedure for isolation design, this paper presents a formula for determining the seismic design force of the combined LRB and VD isolation system, taking into account the phase angle between the combined force of the LRB and VD and the displacement of the isolation system. The numerical results have shown that the maximum responses of the isolation system predicted by the proposed formula are conservative and comparable with those from the inelastic dynamic response history analysis.
A VEHICLE–BRIDGE LINEAR INTERACTION MODEL AND ITS VALIDATION
Authors: ZHANG N. , XIA H. , GUO W. W. , DE ROECK G.
Published: May 2010

A linear wheel–rail interaction model for the vehicle–bridge coupling system is presented in this paper. The vehicle subsystem is modeled by the rigid-body dynamics method, the bridge subsystem by both the direct stiffness method and superposition method, and the wheel–rail interaction by the "corresponding assumption" and simplified Kalker creep theory. Based on the above modeling for the wheel–rail interaction system, linear simultaneous equations are established and solved. As a case study, the response of the Pioneer train traversing a 24 m simply–supported girder bridge is calculated. The proposed analysis procedure is validated through comparison of the calculated results with the measured ones. Also, some vibration characteristics of the system are discussed.
FREE VIBRATION AND BUCKLING ANALYSIS OF HIGHLY SKEWED PLATES BY LEAST SQUARES-BASED FINITE DIFFERENCE METHOD
Authors: WU W. X. , SHU C. , WANG C. M. , XIANG Y.
Published: May 2010

It is well-known that stress singularities occur at the obtuse corners of skew plates, especially when the skew angles are large. Owing to the stress singularities, accurate bending results, vibration frequencies and buckling loads of highly skewed plates are difficult to obtain accurately. In this paper, the mesh-free least squares-based finite difference (LSFD) method is proposed for solving the free vibration and buckling problems of highly skewed plates. As such vibration and buckling results are scarce in the open literature, the method was verified by comparing the LSFD solutions with existing ones having a skew angle θ ≤ 70°, or by carrying out convergence studies. The vibration and buckling results for plates with very large skew angle (θ = 80°) are presented for the first time. The close agreement observed in the comparison studies and the good convergence behavior of the LSFD solutions provide the confidence that these vibration and buckling results predicted by the LSFD method are of good accuracy.