bluuebunny/crossref_metadata_2025 huggingface dataset:
Structural factors underlying the species barrier and susceptibility to infection in prion diseaseThis 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: Sweeting B. , Khan M. Qasim , Chakrabartty A. , Pai E. F.
Published: May 2010

The term prion disease describes a group of fatal neurodegenerative diseases that are believed to be caused by the pathogenic misfolding of a host cell protein, PrP. Susceptibility to prion disease differs between species and incubation periods before symptom onset can change dramatically when infectious prion strains are transmitted between species. This effect is referred to as the species or transmission barrier. Prion strains represent different structures of PrPScand the conformational selection model proposes that the source of theses barriers is the preferential incorporation of PrP from a given species into only a subset of PrPScstructures of another species. The basis of this preferential incorporation is predicted to reside in subtle structural differences in PrP from varying species. The overall fold of PrP is highly conserved among species, but small differences in the amino acid sequence give rise to structural variability. In particular, the loop between the second β-strand and the second α-helix has shown structural variability between species, with loop mobility correlating with resistance to prion disease. Single amino acid polymorphisms in PrP within a species can also affect prion susceptibility, but do not appear to drastically alter the biophysical properties of the native form. These polymorphisms affect the propensity of self-association, in recombinant PrP, to form β-sheet enriched, oligomeric, and amyloid-like forms. These results indicate that the major factor in determining susceptibility to prion disease is the ability of PrP to adopt these misfolded forms by promoting conformational change and self association.
New insights into the biogenesis of nuclear RNA polymerases?This 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: Cloutier Philippe , Coulombe Benoit
Published: May 2010

More than 30 years of research on nuclear RNA polymerases (RNAP I, II, and III) has uncovered numerous factors that regulate the activity of these enzymes during the transcription reaction. However, very little is known about the machinery that regulates the fate of RNAPs before or after transcription. In particular, the mechanisms of biogenesis of the 3 nuclear RNAPs, which comprise both common and specific subunits, remains mostly uncharacterized and the proteins involved are yet to be discovered. Using protein affinity purification coupled to mass spectrometry (AP–MS), we recently unraveled a high-density interaction network formed by nuclear RNAP subunits from the soluble fraction of human cell extracts. Validation of the dataset using a machine learning approach trained to minimize the rate of false positives and false negatives yielded a high-confidence dataset and uncovered novel interactors that regulate the RNAP II transcription machinery, including a set of proteins we named the RNAP II-associated proteins (RPAPs). One of the RPAPs, RPAP3, is part of an 11-subunit complex we termed the RPAP3/R2TP/prefoldin-like complex. Here, we review the literature on the subunits of this complex, which points to a role in nuclear RNAP biogenesis.
Acid stress response in enteropathogenic gammaproteobacteria: an aptitude for survivalThis 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: Zhao Boyu , Houry Walid A.
Published: May 2010

Enteric bacteria such as Escherichia coli have acquired a wide array of acid stress response systems to counteract the extreme acidity encountered when invading the host’s digestive or urinary tracts. These acid stress response systems are both enzyme and chaperone based. The 3 main enzyme-based acid resistance pathways are glutamate-, arginine-, and lysine-decarboxylase pathways. They are under a complex regulatory network allowing the bacteria to fine tune its response to the external environment. HdeA and HdeB are the main chaperones involved in acid stress response. The decarboxylase systems are also found in Vibrio cholera, Vibrio vulnifus, Shigella flexneri, and Salmonella typhimurium, although some differences exist in their functional mechanism and regulation.
Structures and ice-binding faces of the alanine-rich type I antifreeze proteinsThis 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: Patel Shruti N. , Graether Steffen P.
Published: May 2010

Antifreeze proteins (AFPs) protect cold-blooded organisms from the damage caused by freezing through their ability to inhibit ice growth. The type I AFP family, found in several fish species, contains proteins that have a high alanine content (>60% of the sequence) and structures that are almost all α-helical. We examine the structure of the type I AFP isoforms HPLC6 from winter flounder, shorthorn sculpin 3, and the winter flounder hyperactive type I AFP. The HPLC6 isoform structure consists of a single α-helix that is 37 residues long, whereas the shorthorn sculpin 3 isoform consists of two helical regions separated by a kink. The high-resolution structure of the hyperactive type I AFP has yet to be determined, but circular dichroism data and analytical ultracentrifugation suggest that the 195 residue protein is a side-by-side dimer of two α-helices. The alanine-rich ice-binding faces of HPLC6 and hyperactive type I AFP are discussed, and we propose that the ice-binding face of the shorthorn sculpin 3 AFP contains Ala14, Ala19, and Ala25. We also propose that the denaturation of hyperactive type I AFP at room temperature is explained by the stabilization of the dimerization interface through hydrogen bonds.
Charge, hydrophobicity, and confined water: putting past simulations into a simple theoretical frameworkThis 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: England Jeremy L. , Pande Vijay S.
Published: May 2010

Water permeates all life, and mediates forces that are essential to the process of macromolecular self-assembly. Predicting these forces in a given biological context is challenging, since water organizes itself differently next to charged and hydrophobic surfaces, both of which are typically at play on the nanoscale in vivo. In this work, we present a simple statistical mechanical model for the forces water mediates between different confining surfaces, and demonstrate that the model qualitatively unifies a wide range of phenomena known in the simulation literature, including several cases of protein folding under confinement.
The utility and application of real-time PCR and FISH in the detection of single-copy gene targets inEscherichia coliO157:H7 andSalmonellaTyphimurium
Authors: Haffar Merriam , Gilbride Kimberley A.
Published: May 2010

The ultimate specificity in molecular-based assays for pathogen detection relies on the design of the primers and probes. Their ability to hybridize to DNA sequences found only in pathogens can be realized by designing primers and probes that are complementary to pathogen-specific virulence genes. This study evaluates the detection and enumeration strengths of real-time PCR (qPCR) and fluorescent in situ hybridization (FISH) for selected waterborne pathogens and their ultimate applicability within a monitoring framework. Detection limits calculated in the qPCR assay were 150 tir (intimin protein receptor) gene copies for Escherichia coli O157:H7 and 2 × 103invA (inner membrane invasive protein) gene copies for Salmonella enterica serovar Typhimurium. Detection limits were, however, at least 100-fold less sensitive in wastewater extracts, partly because of the inhibitory effect of the wastewater itself. Fluorescent signals from hybridized whole target cells were below the detection limit of the FISH assay. While this research demonstrates the potential detection strength of qPCR, it highlights the need for strong dependable primer and probe sets among PCR and FISH methodologies as well as the need for further signal amplification with DNA-targeted FISH for single-copy gene targets within environmental samples.
Effect of recombinant Panton–Valentine leukocidin in vitro on apoptosis and cytokine production of human alveolar macrophages
Authors: Wu Benquan , Zhang Wenxian , Huang Jing , Liu Hui , Zhang Tiantuo
Published: May 2010

Panton–Valentine leukocidin (PVL) is associated with rare cases of necrotizing pneumonia that occur in otherwise healthy individuals. Human alveolar macrophages (HAMs) are major effector cells in host defense against infections. However, the impact of PVL on HAMs is uncertain. We evaluated the role of PVL in cytotoxicity and production of inflammatory cytokines secreted by HAMs. HAMs were purified from bronchoalveolar lavage fluid. Recombinant PVL (rPVL) was used in the study to interfere with HAM apoptosis and cytokine production in vitro. Hoechst 33342 fluorescence staining, transmission electron microscopy examination, and flow cytometry indicated that rPVL (10 nmol/L) treatment resulted in HAMs with markedly apoptotic characteristics, and HAMs treated with rPVL at 100 nmol/L showed clear indication of necrosis. A treatment of rPVL at 10 nmol/L elicited the secretion of IL-10 by HAMs relative to untreated control cells, but there was a slight decrease in the constitutive secretion of tumor necrosis factor (TNF)-α. Our results indicate that PVL-treated samples decreased HAM viability, leading to apoptosis at low concentrations and necrosis at high concentrations. In addition, PVL-treated cells released increased amounts of IL-10 and decreased amounts of TNF-α under apoptosis-inducing concentrations. Therefore, we speculated that PVL could play a negative role in HAM function at lower concentrations.
Utility of a Luminex-based assay for multiplexed, rapid species identification of Candida isolates from an ongoing candidemia surveillance
Authors: Deak Eszter , Etienne Kizee A. , Lockhart Shawn R. , Gade Lalitha , Chiller Tom , Balajee S. Arunmozhi
Published: May 2010

A Candida -specific Luminex-based assay with 11 probes was employed for multiplexed, rapid identification of 1182 Candida sp. isolates that were received as part of an ongoing population-based surveillance. All the Candida isolates were previously identified by a combination of methods, including phenotype and sequence analysis. Results showed that the Luminex assay was an attractive alternative to reference methods, as it is rapid, yields correct species identification, and is user friendly.
The characterization and diversity of bacterial endophytes of grapevine
Authors: West E. R. , Cother E. J. , Steel C. C. , Ash G. J.
Published: May 2010

The diversity of culturable and nonculturable bacterial endophytes of grapevine ( Vitis vinifera L.) was examined using a combination of cultivation and molecular methods. Entire grapevines were sampled to characterize bacterial diversity from different locations throughout the vine. Gas chromatography of fatty acid methyl esters (FAMEs) was used to identify culturable isolates prior to subsequent further microbiological characterization, whilst denaturing gradient gel electrophoresis (DGGE) was used to profile the ribosomal DNA of the bacterial endophyte community extracted from grapevines. Gas chromatography of FAMEs identified 75% of culturable bacterial endophytes to genus level (similarity index >0.3). Many isolates were identified as Bacillus spp., Pseudomonas spp., and Curtobacterium spp. Additionally, actinomycetes are reported for the first time as endophytes of grapevines, with a number of isolates identified as Streptomyces spp. DGGE was successfully used to identify major bands present in samples and indicated a degree of homogeneity of bacterial endophyte community profiles within the grapevines sampled. The major bacterial bands were sequenced and used in identification. Comparison with bacterial markers produced from cultured bacterial endophytes suggested that bacteria in the DGGE profiles were not the species most commonly cultured. Additional research demonstrated similarities between epiphytic and endophytic populations and examined potential entry vectors. Endophyte entry was demonstrated in both field-grown and potted grapevines (‘Chardonnay’) using a rifampicin-resistant Bacillus cereus mutant. The possibility of grapevine epiphytes becoming endophytes, if the opportunity arises, was supported by comparison of gas chromatography of FAMEs from epiphytic and endophytic populations. This research adds grapevine bacterial endophyte communities to those that have been characterized by a multifaceted approach.
Characterization of arsenic-resistant bacteria from the rhizosphere of arsenic hyperaccumulatorPteris vittata
Authors: Huang Anhui , Teplitski Max , Rathinasabapathi Bala , Ma Lena
Published: May 2010

Arsenic hyperaccumulator fern Pteris vittata L. produces large amounts of root exudates that are hypothesized to solubilize arsenic and maintain a unique rhizosphere microbial community. Total heterotrophic counts on rich or defined media supplemented with up to 400 mmol/L of arsenate showed a diverse arsenate-resistant microbial community from the rhizosphere of P. vittata growing in arsenic-contaminated sites. Twelve bacterial isolates tolerating 400 mmol/L of arsenate in liquid culture were identified. Selected bacterial isolates belonging to different genera were tested for their resistance to osmotic and oxidative stresses. Results showed that growth was generally better under osmotic stress generated by arsenic than under that generated by NaCl or PEG 6000, demonstrating that arsenic detoxification metabolism also cross-protected bacterial isolates from arsenic-induced osmotic stress. After 32 h of growth, all arsenate at 1 mmol/L was reduced to arsenite by strains Naxibacter sp. AH4, Mesorhizobium sp. AH5, and Pseudomonas sp. AH21, but arsenite at 1 mmol/L remained unchanged. Sensitivity to hydrogen peroxide was similar to that in broad-host pathogen Salmonella enterica sv. Typhimurium wild type, except strain AH4. The results suggested that these arsenic-resistant bacteria are metabolically adapted to arsenic-induced osmotic or oxidative stresses in addition to the specific bacterial system to exclude cellular arsenic. Both these adaptations contribute to the high arsenic resistance in the bacterial isolates.
Validation of a partialrpoBgene sequence as a tool for phylogenetic identification of aeromonads isolated from environmental sources
Authors: Lamy Brigitte , Laurent Fréderic , Kodjo Angeli
Published: May 2010

A collection of 50 aeromonads isolated from environmental sources were studied, together with all known Aeromonas nomenspecies, by phenotypic, amplified 16S rDNA restriction analysis (16S rDNA RFLP) and by partial sequence alignment of both 16S rDNA and rpoB genes. Although most of the type strain showed a unique phenotypic pattern, a database constructed on type strain phenotype allowed the identification of only 24% of the isolates. Analysis of 16S rDNA RFLP and the rpoB sequence were almost concordant in identifying environmental isolates at the species level, except for strains belonging to Aeromonas caviae spp., which were not differentiated from Aeromonas aquariorum , nor Aeromonas hydrophila susbsp. dhakensis by 16S rDNA RFLP. In addition, rpoB gene analysis clustered separately a group of isolates found in snails within the A. hydrophila species. In contrast to 16S rDNA RFLP and rpoB, the partial 16S rDNA sequence analysis was weak in resolving species identity. Part of these results, phenotypic and phylogenetic data, showed that Aeromonas molluscorum and Aeromonas sharmana are distant from all other Aeromonas species and that the type species of A. hydrophila subsp. anaerogenes is similar to A. caviae and should be considered synonymous.
Differentially expressed genes after hyper- and hypo-salt stress in the halophilic archaeonMethanohalophilus portucalensis
Authors: Shih Chao-Jen , Lai Mei-Chin
Published: May 2010

Methanohalophilus portucalensis FDF1 can grow over a range of external NaCl concentrations, from 1.2 to 2.9 mol/L. Differential gene expression in response to long-term hyper-salt stress (3.1 mol/L of NaCl) and hypo-salt stress (0.9 mol/L of NaCl) were compared by differential display RT-PCR. Fourteen differentially expressed genes responding to long-term hyper- or hypo-salt stress were detected, cloned, and sequenced. Several of the differentially expressed genes were related to the unique energy-acquiring methanogenesis pathway in this organism, including the transmembrane protein MttP, cobalamin biosynthesis protein, methenyl-H4MPT cyclohydrolase and monomethylamine methyltransferase. One signal transduction histidine kinase was identified from the hyper-salt stress cultures. Moreover, 3 known stress-response gene homologues — the DNA mismatch repair protein, MutS, the universal stress protein, UspA, and a member of the protein-disaggregating multichaperone system, ClpB — were also detected. The transcriptional analysis of these long-term salt stress response and adaptation-related genes for cells immediately after salt stress indicated that the expression of the energy metabolism genes was arrested during hyper-salt shock, while the chaperone clpB gene was stimulated by both hypo- and hyper-salt shock.
Escherichia coliserogroup O2 and O28ac O-antigen gene cluster sequences and detection of pathogenicE. coliO2 and O28ac by PCR
Authors: Fratamico Pina M. , Yan Xianghe , Liu Yanhong , DebRoy Chitrita , Byrne Brian , Monaghan Aine , Fanning Seamus , Bolton Declan
Published: May 2010

The O-antigen gene clusters of Escherichia coli serogroups O2 and O28ac were sequenced, and PCR assays were developed to identify strains belonging to these 2 serogroups. Sixteen and 8 open reading frames were mapped to these loci in E. coli O2:H4 U 9-41 and E. coli O28ac:H25 96-3286, respectively. The wzx (O-antigen flippase) and wzy (O-antigen polymerase) genes in the E. coli O2 and O28ac O-antigen gene clusters were selected as targets for PCR assays for their identification. PCR assays targeting the wzx and wzy genes were specific for these serogroups, with one exception. Escherichia coli serogroup O42 strains gave positive results with wzx and wzy PCR assays targeting E. coli O28ac, and antiserum raised against O42 cross-reacted with serogroup O28ac strains. The O-antigen gene cluster of a strain of E. coli serogroup O42 was sequenced, and there were only 3 nt differences between the O-antigen gene clusters of the O28ac and O42 strains. Multiplex PCR assays targeting the O2 wzx gene, the stx1, stx2, hly, eae, and saa genes, and the O28ac wzx, ial, ipaC, and ipaH genes were developed for detecting Shiga toxin-producing E. coli O2 strains and enteroinvasive E. coli O28ac strains, respectively. The O2 and O28ac wzx and wzy genes can be used as diagnostic markers in PCR assays for rapid identification of these serogroups as an alternative to serotyping, and the multiplex PCR assays targeting serogroup-specific genes in combination with virulence genes can be used to identify and to detect pathogenic serogroup O2 and O28ac strains.
Chemical composition of lipopolysaccharides isolated from various endophytic nitrogen-fixing bacteria of the genus Herbaspirillum
Authors: Serrato R. V. , Sassaki G. L. , Cruz L. M. , Carlson R. W. , Muszyński A. , Monteiro R. A. , Pedrosa F. O. , Souza E. M. , Iacomini M.
Published: May 2010

Bacteria from the genus Herbaspirillum are endophytes responsible for nitrogen fixation in gramineous plants of economic importance such as maize, sugarcane, sorghum, rice, and wheat. Some species are known to produce plant growth substances. In contrast, Herbaspirillum rubrisubalbicans strains are known to be mild plant pathogens. The molecular communication between the plant and the microbes might involve lipopolysaccharides present in the outer membrane of these gram-negative bacteria. Phenol–water extraction was used to obtain lipopolysaccharides from 7 strains of Herbaspirillum seropedicae (SmR1, Z67, Z78, ZA95, and M2) and H. rubrisubalbicans (M1 and M4). The electrophoretic profiles and chemical composition of the lipopolysaccharides obtained in the phenol and aqueous extracts were shown herein.
The effect of silver nanoparticles on phytopathogenic spores of Fusarium culmorum
Authors: Kasprowicz Marek Jan , Kozioł Magdalena , Gorczyca Anna
Published: May 2010

The aim of the present experiment was to investigate the influence of silver nanoparticles on Fusarium culmorum (W.G. Smith) Sacc. (FC) spores. The silver nanoparticles were produced by the high-voltage arc discharge method. To test the effect of silver nanoparticles on FC spores, 3 parameters were tested. One of these parameters was the vegetative mycelial growth in 2 experiments. The first involved the growth of FC spores on potato dextrose agar (PDA) medium after contact with 0.12–10 ppm of silver nanoparticles, and the second the growth of spores after contact with 0.12–2.5 ppm solutions of silver, but with culturing on 3 types of media (PDA, nutrient-poor PDA, and agar) instead. The next parameter was the formation of spores after the mycelia were cultured. The last parameter was spore germination in a 2.5 ppm solution of silver nanoparticles. A significant reduction in mycelial growth was observed for spores incubated with silver nanoparticles. This relationship was dependent on the incubation time and type of growth medium, but did not depend significantly on the concentration of silver nanoparticles up to 2.5 ppm. The sporulation test showed that, relative to control samples, the number of spores formed by mycelia increased in the culture after contact with silver nanoparticles, especially on the nutrient-poor PDA medium. The 24 h incubation of FC spores with a 2.5 ppm solution of silver nanoparticles greatly reduced the number of germinating fragments and sprout length relative to the control.
Growth inhibition of adherent Pseudomonas aeruginosa by an N-butanoyl-l-homoserine lactone analog
Authors: Khalilzadeh Pouneh , Lajoie Barbora , El Hage Salomé , Furiga Aurélie , Baziard Geneviève , Berge Mathieu , Roques Christine
Published: May 2010

The discovery of quorum sensing (QS) communication systems regulating bacterial virulence has afforded a novel opportunity for controlling infectious bacteria by interfering with QS. Pseudomonas aeruginosa is an example of an opportunistic human pathogen for which N-acyl homoserine lactone (AHL)-related compounds have been described as potent inhibitors of biofilm formation and virulence factors, given their similarity to the natural QS autoinducers (AHLs). Our purpose was to design potent analogs of N-butanoyl-l-homoserine lactone (C4-HSL) and to screen them for biological activity. Eleven original compounds characterized by the modification of the lactone moiety were screened for their ability to impair biofilm formation. Among them, compound 11 was able to modify the growth kinetics and to restrict the number of adherent cells when added from the early stages of biofilm formation (i.e., adhesion and microcolony formation) in a dose-dependent manner. To demonstrate antagonism with C4-HSL, we showed that the inhibition of biofilm formation by compound 11 was impaired when C4-HSL was added. Structure–activity relationships are discussed with respect to the results obtained.
Comparison of the automated Phoenix with the Vitek 2 for the identification of Streptococcus pneumoniaePortions of this study were presented at the 2007 American Society of Microbiology 107th General Meeting in Toronto, Ontario, Canada.
Authors: Mittman Scott A. , Huard Richard C. , Della-Latta Phyllis , Whittier Susan
Published: May 2010

Rapid and accurate identification of Streptococcus pneumoniae is a critical component in the optimal management of infected patients. The performance of the BD Phoenix Automated Microbiology System (BD Diagnostic Systems, Sparks, Md.) was evaluated for identification of S. pneumoniae (n = 311) and was compared to the Vitek 2 (bioMérieux, Marcy l’Étoile, France). Strains with discordant identification between methods were resolved with 16S rRNA gene sequencing as the gold standard. The Phoenix and the Vitek 2 correctly identified 96.8% (n = 301) and 95.2% (n = 296) of S. pneumoniae strains, respectively. Overall, there was no statistically significant difference in the performance of the 2 automated systems for the identification of S. pneumoniae in this study. The Vitek 2 mean time-to-results for all streptococcal identification was 1.5 h faster than that for the Phoenix. We conclude that the automated Phoenix and the Vitek 2 systems are comparable in their ability to identify S. pneumoniae and are preferable to the use of routine biochemical assays, which have delayed time-to-results and are not dependably accurate.
Chlamydia pneumoniaeinfection suppressesStaphylococcusenterotoxin B-induced proliferation associated with down-expression of CD25 in lymphocytes
Authors: Hirai Itaru , Utsumi Maki , Yamaguchi Hiroyuki , Yamamoto Yoshimasa
Published: May 2010

Chlamydia pneumoniae ( Chlamydophila pneumoniae ) infects lymphocytes and modulates their immune functions; this is critical in the development of chronic inflammatory diseases associated with this pathogen. Therefore, to clarify this immune modulation due to C. pneumoniae infection, the effect of this infection on the proliferation of human peripheral blood lymphocytes was examined. Lymphocytes were proliferated by stimulation with Staphylococcus aureus enterotoxin B, and the cell number was increased up to 3 times the unstimulated lymphocyte number. Further, induction of CD25 expression was observed in 55.8% of lymphocytes. Infection with C. pneumoniae suppressed the proliferation of almost half the lymphocytes induced by stimulation with S. aureus enterotoxin B, and CD25 induction was inhibited in 64.7% of lymphocytes. Inhibition of CD25 expression was observed in both infected and uninfected lymphocytes in culture. However, the expression of VLA4 was not affected by C. pneumoniae infection. Furthermore, inhibition was observed only by infection with viable C. pneumoniae and not by the heat-killed bacteria. These results suggest that C. pneumoniae affects lymphocyte function by inhibiting proliferation and CD25 expression in response to immunological stimulation, possibly via humoral mediator(s).
Influence of incubation temperature on morphology and locomotion performance of Leatherback (Dermochelys coriacea) hatchlings
Authors: Mickelson L. E. , Downie J. R.
Published: May 2010

The journey of Leatherback ( Dermochelys coriacea (Vandelli, 1761)) hatchlings from nest to the sea is a vulnerable life-history stage. Studies have shown that nest incubation temperatures influence hatchling morphology and locomotor performance, which may affect hatchling fitness. We obtained incubation temperature profiles from 16 Leatherback nests in Tobago, West Indies, during the 2008 nesting season (March–June). There was significant variation among mean nest incubation temperatures, which had a significant influence on hatchling morphology. Using principal components analysis, we determined the morphological traits that explained the most variation among hatchlings, which allowed investigation of the relationship between hatchling morphology and terrestrial locomotion speed. Hatchlings with a narrower carapace width and longer flipper reach (produced at lower incubation temperatures) had significantly faster terrestrial speed and total run time than those with opposite characteristics (produced at higher incubation temperatures). Our results demonstrate that lower incubation temperatures produce hatchlings with traits that are significantly advantageous to terrestrial locomotion. These findings suggest that nest incubation temperature is important in determining hatchling fitness, as nest incubation temperature significantly influences hatchling morphology and locomotor capabilities. This study supplements related findings in Green Turtles ( Chelonia mydas (L., 1758)), but also illustrates some unique features in Leatherbacks.
Relative growth, life-history phases, and sexual maturity of American lobster (Homarus americanus)
Authors: Émond Kim , Sainte-Marie Bernard , Gendron Louise
Published: May 2010

Previous studies of relative growth in crustaceans have focused primarily on body parts representing sexual characters for the purpose of determining size at onset of sexual maturity. We have revisited the relative growth of abdomen and crusher claw in American lobster ( Homarus americanus H. Milne Edwards, 1837) in a general life-history perspective using a broad spectrum of lobster sizes (6–160 mm cephalothorax length (CL)). Growth phases were recognized by inflections in scatterplots of a body-part measurement against CL. The abdomen is characterized by three growth phases in the male and female, whereas the crusher claw has at least three growth phases in the male and at least two in the female. Additionally, we explored relative growth of gonopod and vas deferens for males of 35–150 mm CL. Both organs exhibit a synchronous change from strong to weak positive growth allometry. The growth phases can be associated with major life-history events including the transition from a cryptic to an overt lifestyle and the onset of physiological, functional, and morphometric maturity. The onset of morphometric maturation inferred from relative growth of abdomen and crusher claw precedes functional maturity in females and follows it in males.
Mitochondrial DNA genetic structure transcends natural boundaries in Great Lakes populations of woodland deer mice (Peromyscus maniculatus gracilis)
Authors: Taylor Zachary S. , Hoffman Susan M.G.
Published: May 2010

The landscape of the Great Lakes region has been fragmented since the lakes formed starting about 20 000 years ago. Small mammals, such as deer mice ( Peromyscus maniculatus (Wagner, 1845)), inhabiting the region therefore face barriers to migration and gene flow, which could complicate ongoing range shifts related to climate change. We analyzed DNA sequences for 481 base pairs of the mitochondrial D-loop to compare mouse genetic structure with the fragmented landscape and geological history of the region. Phylogenetic analyses reveal two distinct lineages of mice in the Great Lakes region. The spatial distribution of these two groups is not congruent with the fragmentation of the landscape; rather, a western group is found from Minnesota through the western Upper Peninsula of Michigan, whereas an eastern group spans southern Ontario and the rest of northern Michigan. The genetic data suggest that the eastern clade colonized Michigan through Ontario from a source shared with southern Appalachian mice, but are less informative for the western clade. Together, these findings suggest that the Great Lakes are relatively porous barriers in the long term but may still have implications for the response of small-mammal communities to climate change.
Ontogeny of swimming movements in bronze corydoras (Corydoras aeneus)
Authors: Mauguit Q. , Olivier D. , Vandewalle N. , Vandewalle P.
Published: May 2010

Fish larvae experience fundamental morphological, physiological, and physical changes from hatching to adulthood. All of these changes have an effect on the locomotor movements observed in the larvae. We describe the development of swimming movements in larval bronze corydoras ( Corydoras aeneus (Gill, 1858); Ostariophysi, Siluriformes) during their ontogeny. Swimming movements of adults and larvae, aged 0–512 h posthatching, were recorded at 500 frames/s. Movements were analyzed by digitizing points along the fish midline. Movements are described by direct (swimming speed and amplitude of landmarks) and indirect (r2meanand CV of r2as movement coordination indices; Strouhal number as an efficiency index) parameters. The increase in swimming speed correlated with improvement of movement coordination in both larvae and adults, as well as with an increase in swimming efficiency in larvae. Directly after hatching, swimming movements were coordinated but were not efficient. Efficiency increased rapidly with fish growth up to 8 mm total fish length and disappearance of the yolk sac. These events were coupled with reduction of the maximal lateral amplitude observed along the whole body during swimming. The anguilliform swimming mode was used at hatching, but a transition to the carangiform mode was observed at approximately 17 mm total fish length.
Altitudinal migration in American Dippers (Cinclus mexicanus): Do migrants produce higher quality offspring?
Authors: Mackas R. H. , Green D. J. , Whitehorne I. B.J. , Fairhurst E. N. , Middleton H. A. , Morrissey C. A.
Published: May 2010

Breeding at high elevations can favour life-history strategies in which parents shift to investing in higher quality rather than higher numbers of offspring. In American Dippers ( Cinclus mexicanus Swainson, 1827), altitudinal migrants produce fewer fledglings than sedentary individuals (residents) that breed at lower elevations. We examined whether migrants compensate for their lower fecundity by providing their offspring with a higher quality diet and (or) more food, and producing higher quality offspring. Nestling diet was assessed using observations and stable isotope analysis of feathers grown during the nestling period. Nestling quality was assessed using a condition index (residuals from a mass–tarsus regression) and postfledging survival. We found that migrants fed their offspring less fish, and despite having higher feeding rates, had lower energetic provisioning rates than residents. Migrants also produced offspring that were in worse condition and had lower postfledging survival. This study found no evidence that altitudinal migration is associated with a trade-off favouring the production of smaller numbers of higher quality young. Instead our data provide support for the hypothesis that altitudinal migration in American Dippers is an outcome of competition for limited nest sites at lower elevations that forces some individuals to move to higher elevations to breed.
Population subdivision of house mice (Mus musculus) in an agrarian landscape: consequences for control
Authors: León V. A. , Fraschina J. , Busch M.
Published: May 2010

In Argentinean agroecosystems, house mice ( Mus musculus L., 1758) show a discontinuous distribution, with high abundances in farms but scarce abundance in crop fields. In our study area, the abundance of M. musculus could be affected by their movements among farms. We hypothesize that (1) M. musculus do not move among farms versus (2) M. musculus do move among farms. Furthermore, based on our second hypothesis, M. musculus move actively (hypothesis 2.1) or passively by human transport (hypothesis 2.2). Based on hypothesis 1, we predict that genetic subdivision will exist among farms and that genetic divergence will be independent of geographic distance. Based on hypothesis 2.1, genetic differentiation will be correlated with geographic distance. Based on hypothesis 2.2, genetic subdivision will be absent, or genetic differentiation will be related to human movements. We examined genetic variation among farms (n = 15) using five microsatellite loci and tracked the movements of 36 individuals from five farms with fluorescent powders. Populations of M. musculus showed genetic differentiation at both farm and shed scales. Genetic and geographic distances were significantly correlated. There was no evidence of passive movements of M. musculus. The movements of 36 M. musculus within farms, tracked with fluorescent powder, were short. According to these results, hypothesis 2.1 is favoured.
Scale and selection of habitat and resources: Tibetan argali (Ovis ammon hodgsoni) in high-altitude rangelands
Authors: Singh N. J. , Yoccoz N. G. , Lecomte N. , Côté S. D. , Fox J. L.
Published: May 2010

Processes of habitat selection occur at multiple spatiotemporal scales, where large-scale selection is often determined by predation risk and landscape features, and finer scale selection by resource abundance and quality. To determine whether this hierarchy exists in relatively homogenous systems, we investigated patterns of habitat (landscape topography) and resource (feeding patch and plant group) selection by a medium-sized ungulate, the Tibetan argali ( Ovis ammon hodgsoni Blyth, 1840), in the high-altitude rangelands of the Indian Trans-Himalaya. We ran ecological niche factor analyses to explore habitat selection, bias-reduced logistic regression to analyze the selection of feeding patches, fuzzy correspondence analysis for vegetation categories, and microhistological analyses for the selection of plant groups. For springs and summers of 2005–2007, argali preferred an intermediate range of altitude, slope, and forage abundance. Selection of feeding patch was mainly determined by forage quality, not biomass, selecting graminoids and forbs, in particular. The avoidance of habitat with high forage abundance could indicate a trade-off between forage quality and quantity; a pattern consistent at the feeding-patch scale. Our results provide evidence that the hierarchical pattern of habitat selection probably also occurs in relatively homogeneous systems.
Is there a role for stripes of adults and colour of larvae in determining the avoidance of the Colorado potato beetle by the American toad?
Authors: Boiteau G. , McCarthy P. C.
Published: May 2010

It has been suggested that the stripes on the elytra of the adult Colorado potato beetle ( Leptinotarsa decemlineata (Say, 1824); Coleoptera: Chrysomelidae) and the red colouration of the larvae are aposematic characters warning predators of their distastefulness as prey. The role of stripes and red colour in determining the avoidance behaviour of the American Toad ( Bufo americanus Holbrook, 1836 = Anaxyrus americanus (Holbrook, 1836); Anura: Bufonidae) for the Colorado potato beetle was investigated in a series of laboratory tests. The behaviour of toads exposed to wild Colorado potato beetles was compared with that of toads exposed to genetic mutant Colorado potato beetles without elytral stripes. Tests confirmed the distastefulness of adult and larval stages and demonstrated the development of prey avoidance (cessation of feeding in spite of hunger) combined or not to behavioural displays where the toad plants down, crouches, and turns away or shows wincing, prey dropping, and mouth gaping after snapping at the beetle. However, toads showed the same response to mutant adult beetles without stripes and to mutant larval beetles without the red colour as to wild adult beetles with stripes and to wild red larvae. Results indicate that the stripes and the red colouration of the Colorado potato beetle do not constitute aposematic characters for the toad.
Ambient light alters temporal-updating behaviour during mate choice in a Neotropical frog
Authors: Baugh Alexander T. , Ryan Michael J.
Published: May 2010

It is well known that animal decision-making can be influenced by environmental variables, such as the risk of predation. During the breeding season, nocturnal amphibians encounter a range of environmental conditions at breeding aggregations, including variable ambient light conditions. For nocturnal frogs, illumination is expected to minimize conspicuous movement that might increase predator detection. Previous work has shown that female Physalaemus pustulosus (Cope, 1864) (= Engystomops pustulosus (Cope, 1864)) are sensitive to variation in light levels during mate choice. Here we use an acoustic playback design in which stimuli are adjusted for intensity and complexity during female phonotaxis to show that choosiness is influenced by light level. Frogs were more likely to commit to an initial mate choice despite a dynamic reduction in mate attractiveness under dim light conditions compared with darkness. These results suggest that females are trading off the attractiveness of potential mates with the perceived costs of executing mate choice by committing to an initial decision and thereby reducing assessment time and movement. The dynamic playback design used here provides an approach that could be applied in other systems in which context-dependent decision-making is thought to be important.
Temperature fluctuations affect offspring sex but not morphological, behavioral, or immunological traits in the Northern Painted Turtle (Chrysemys picta)
Authors: Paitz Ryan T. , Clairardin Sandrine G. , Griffin Adam M. , Holgersson Mikael C.N. , Bowden Rachel M.
Published: May 2010

Evolutionary theory predicts that when phenotypic variation arises during development that differently influences the fitness of each sex, selection should favor the maternal ability to match offspring phenotype to the sex that incurs a fitness benefit from that phenotype. In reptiles with temperature-dependent sex determination, the temperatures experienced during incubation can influence numerous phenotypic parameters, including sex. To mimic more naturalistic conditions, this experiment examined how variation in temperature fluctuations affects offspring sex as well as a suite of phenotypic parameters having putative fitness consequences in the Northern Painted Turtle ( Chrysemys picta (Schneider, 1783)). We also characterized variation in natural nest temperatures, including the daily temperature range, related to the vegetation cover surrounding the nest. We found that temperature fluctuations did not affect hatchling morphology, immune response, or behavior, but did significantly affect offspring sex ratios. Thermal profiles of natural nests were related to the amount of surrounding vegetation. Results suggest that nest-site choice by females could influence the sex of their offspring, but we found no evidence that variation in temperature fluctuations adaptively matches offspring sex and phenotype.
Wolf body mass, skull morphology, and mitochondrial DNA haplotypes in the Riding Mountain National Park region of Manitoba, Canada
Authors: Stronen Astrid V. , Forbes Graham J. , Sallows Tim , Goulet Gloria , Musiani Marco , Paquet Paul C.
Published: May 2010

Two types of wolves, gray ( Canis lupus L., 1758) and eastern ( Canis lupus lycaon Schreber, 1775 or Canis lycaon ) or Great Lakes wolves, representing Old World (OW) and New World (NW) mitochondrial DNA (mtDNA) haplotypes, have been reported in eastern Canada and the Great Lakes region. Both haplotypes were found in Duck Mountain Provincial Park and Forest, Manitoba. Only OW haplotypes have been reported from the isolated Riding Mountain National Park (RMNP), 30 km to the south. Wolves with NW haplotypes hybridize with C. lupus and coyotes ( Canis latrans Say, 1823) and could mediate gene flow between canids. We examined available data on wolf body mass, skull morphology, and mtDNA from the RMNP region, as well as mtDNA from Manitoba and Saskatchewan, to assess the occurrence of NW haplotypes in wolves and possible canid hybridization. Mean body mass of female (n = 54) and male (n = 42) RMNP wolves during 1985–1987 was higher than that of females (n = 12) and males (n = 8) during 1999–2004. Thirteen skull measures from 29 wolf skulls did not suggest significant differences between RMNP and Duck Mountain wolves. Nineteen of 20 RMNP samples had OW haplotypes, whereas one clustered together with NW haplotypes.
ON COMPLEX RANDERS METRICS
Authors: CHEN BIN , SHEN YIBING
Published: May 2010

A characteristic for a complex Randers metric to be a complex Berwald metric is obtained. The formula of the holomorphic curvature for complex Randers metrics is given. It is shown that a complex Berwald Randers metric with isotropic holomorphic curvature must be either usually Kählerian or locally Minkowskian. The Deicke and Brickell theorems in complex Finsler geometry are also proved.
A PLANAR ALGEBRA CONSTRUCTION OF THE HAAGERUP SUBFACTOR
Authors: PETERS EMILY
Published: May 2010

Most known examples of subfactors occur in families, coming from algebraic objects such as groups, quantum groups and rational conformal field theories. The Haagerup subfactor is the smallest index finite depth subfactor which does not occur in one of these families. In this paper we construct the planar algebra associated to the Haagerup subfactor, which provides a new proof of the existence of the Haagerup subfactor. Our technique is to find the Haagerup planar algebra as a singly generated subfactor planar algebra, that is contained inside a graph planar algebra.
COMMENT ON "FALSIFICATION OF THE ATMOSPHERICCO2GREENHOUSE EFFECTS WITHIN THE FRAME OF PHYSICS"
Authors: HALPERN JOSHUA B. , COLOSE CHRISTOPHER M. , HO-STUART CHRIS , SHORE JOEL D. , SMITH ARTHUR P. , ZIMMERMANN JÖRG
Published: May 2010

In this journal, Gerhard Gerlich and Ralf D. Tscheuschner claim to have falsified the existence of an atmospheric greenhouse effect.1Here, we show that their methods, logic, and conclusions are in error. Their most significant errors include 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 systematically ignoring most non-radiative heat flows applicable to the Earth's surface and atmosphere. They claim that radiative heat transfer from a colder atmosphere to a warmer surface is forbidden, ignoring the larger transfer in the other direction which makes the complete process allowed. Further, by ignoring heat capacity and non-radiative heat flows, they claim that radiative balance requires that the surface cool by 100 K or more at night, an obvious absurdity induced by an unphysical assumption. This comment concentrates on these two major points, while also taking note of some of Gerlich and Tscheuschner's other errors and misunderstandings.
THE DYNAMICS OF EMBODIED COGNITION
Authors: HOTTON SCOTT , YOSHIMI JEFF
Published: May 2010

Historically cognition was understood as the result of processes occurring solely in the brain. Recently, however, cognitive scientists and philosophers studying "embodied" or "situated" cognition have begun emphasizing the role of the body and environment in which brains are situated, i.e. they view the brain as an "open system". However, these theorists frequently rely on dynamical systems which are traditionally viewed as closed systems. We address this tension by extending the framework of dynamical systems theory. We show how structures which appear in the state space of an embodied agent differ from those that appear in closed systems, and we show how these structures can be used to model representational processes in embodied agents. We focus on neural networks as models of embodied cognition.
CODIMENSION ONE BIFURCATION OF EQUIVARIANT NEURAL NETWORK MODEL WITH DELAY
Authors: ZHANG CHUNRUI , ZHENG BAODONG
Published: May 2010

In this paper, we consider double zero singularity of a symmetric BAM neural network model with a time delay. Based on the normal form approach and the center manifold theory, we obtain the normal form on the centre manifold with double zero singularity. Some numerical simulations support our analysis results.