bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular Identification of Adenoviruses in Clinical Samples by Analyzing a Partial Hexon Genomic Region
Authors: Casas I. , Avellon A. , Mosquera M. , Jabado O. , Echevarria J. E. , Campos R. H. , Rewers M. , Perez-Breña P. , Lipkin W. I. , Palacios G.
Published: December 2005

Here we present a system for adenovirus detection and genotyping based on PCR amplification and phylogenetic analysis of a conserved hexon gene fragment. The system was validated using 157 sequences (86 previously typed and 71 clinical samples) and correctly identified species and serotype in 100% and 84% of sequences, respectively. Known associations between specific serotypes and clinical syndromes are verified. Possible new associations are described to allow further independent testing.
Clinical Significance of Mites in Urine
Authors: Dini Leigh A. , Frean John A.
Published: December 2005

We report a case where a mite egg found in urine caused diagnostic confusion. The possibility of gut or bladder mite infection should be entertained only after repeated identification of mites in urine or stool samples from a symptomatic patient with no other cause for the symptoms and where the possibilities of contamination and spurious infection have been excluded.
An improved model for predicting the efficiency of hydraulic propeller turbines
Authors: Manness Jessica , Doering Jay
Published: December 2005

Field performance testing of hydraulic turbines is undertaken to define the head-power-discharge relationship that identifies the peak operating point of the turbine. This relationship is essential for the efficient operation of a hydraulic turbine. Unfortunately, in some cases it is not feasible to field test turbines because of time, budgetary, or other constraints. Gordon (2001) proposed a method of predicting and (or) simulating the performance curve for several types of turbines. However, a limited data set was available for the development of his model for certain types of turbines. Moreover, his model did not include a precise method of developing performance curves for rerunnered turbines. Manitoba Hydro operates a large network of hydroelectric turbines, which are subject to periodic field performance testing. This provided a large data set with which to refine the model proposed by Gordon (2001). Furthermore, since these data include rerunnered units, this provides an opportunity to refine the effects of rerunnering. Analysis shows that the accuracy of the refined model is within 2% of the performance test results for an "old" turbine, while for a newer turbine or a rerunnered turbine the error is within 1%. For both an old turbine and a rerunnered turbine, this indicates an accuracy improvement of 3% over the original method proposed by Gordon (2001).Key words: hydraulic turbine, efficiency, simulation modeling
Volume of fluid model for an open channel flow problem
Authors: Ramamurthy A S , Qu Junying , Vo Diep
Published: December 2005

In the past, the solutions to open flow problems were generally found on the basis of experimental data or through the development of theoretical expressions using simplified assumptions. The volume of fluid (VOF) turbulence model can be applied to obtain the flow parameters such as pressure head distributions, velocity distributions, and water surface profiles for flow in open channels. The free overfall in a rectangular open channel that serves as a discharge measuring structure is selected to apply to the VOF model. The predictions of the proposed VOF model are validated using existing experimental data for both subcritical and supercritical flow approach conditions. Based on the path followed by a fluid particle leaving the brink section, the equations for the nappe profiles in supercritical flows are obtained in terms of the end depth. The VOF turbulence model developed is used to predict the characteristics of a free overfall in a rectangular open channel.Key words: turbulence model, VOF model, numerical simulation, overfall characteristics, open channel flow.
Impact response of the fiber-matrix bond in concrete
Authors: Bindiganavile V , Banthia N
Published: December 2005

Fiber reinforced concrete (FRC) is a heterogeneous material comprising of distinct components: fiber, matrix, and fiber-matrix interface. Many applications require an enhanced resistance to impact loading from FRC. While designing for impact, the fiber-matrix interaction is by far the most critical. In the study reported here, three polymeric fibers and one steel fiber were investigated to examine the influence of fiber material, geometry, orientation, and the matrix strength under static and impact loading. Results show bond stiffening under impact loading. This was evident through higher peak loads, lower corresponding values of crack opening and a transition in the failure mode of some polymeric fibers from pull-out to fracture. Higher matrix strength resulted in a stiffer bond for all fiber types. Inclined loading produced better results for steel fibers. Under high crack opening rates, the bond stiffening in deformed polymeric fibers brought it closer in performance to the steel fiber.Key words: bond–COD response, impact loading, steel fiber, polymeric fiber, pull-out test, rate effects.
Influence of road surface roughness on dynamic impact factor of bridge by full-scale dynamic testing
Authors: Park Young Suk , Shin Dong Ku , Chung Tae Ju
Published: December 2005

Effects of road surface roughness on the dynamic impact factor of bridge are investigated through full-scale field loading tests under controlled traffic conditions. The dynamic time histories of displacements are obtained for twenty-five bridges on Korean highways. The impact factors of the bridges are evaluated by using the measured displacements. The road surface profiles of the twenty-five bridges are also measured at every 10 to 30 cm interval in the span direction. By using the measured road surface profiles, the international roughness index (IRI) and the roughness coefficients of the bridges are evaluated. The linear regression and correlation analyses are performed to obtain the coherences between the IRI and the roughness coefficient and between the IRI and the impact factor. The sample correlation coefficients between the impact factor and the IRI and between the impact factor and the roughness coefficient are calculated to be 0.61 and 0.62, respectively, showing a strong coherence between the road surface roughness and the impact factor.Key words: bridge, impact factor, road surface roughness, international roughness index, roughness coefficient.
A molecular view of cytotoxic T lymphocyte induced killing
Authors: Bleackley R Chris
Published: December 2005

Cytotoxic T lymphocytes (CTLs) search out and destroy pathogenic cells, such as those infected with viruses. The biochemistry laboratory at the University of Alberta (Edmonton, Alta.) studies the molecular mechanisms used by these effectors, and this review covers research on this topic primarily from this group. Research there began with the discovery of the granzyme genes and the realization that granzyme B (GrB) had an unusual substrate specificity. Cleavage at aspartate residues gave us the clue that caspases, key regulators of apoptosis, were important substrates. However, it is now clear that mitochondria are also important in controlling granzyme-induced apoptosis. This led to the discovery that the proapoptotic member of the Bcl2 family, Bid, is also activated by GrB. Cleaved Bid then translocates to the mitochondria, resulting in the release of antagonists of inhibitors of apoptosis proteins. The evolution of our understanding of the molecular basis of CTL killing is presented.Key words: cytotoxic T Lymphocyte, granzyme, apoptosis, mitochondria, caspase.
Pathways for compartmentalizing protein synthesis in eukaryotic cells: the template-partitioning model
Authors: Nicchitta Christopher V , Lerner Rachel S , Stephens Samuel B , Dodd Rebecca D , Pyhtila Brook
Published: December 2005

mRNAs encoding signal sequences are translated on endoplasmic reticulum (ER) - bound ribosomes, whereas mRNAs encoding cytosolic proteins are translated on cytosolic ribosomes. The partitioning of mRNAs to the ER occurs by positive selection; cytosolic ribosomes engaged in the translation of signal-sequence-bearing proteins are engaged by the signal-recognition particle (SRP) pathway and subsequently trafficked to the ER. Studies have demonstrated that, in addition to the SRP pathway, mRNAs encoding cytosolic proteins can also be partitioned to the ER, suggesting that RNA partitioning in the eukaryotic cell is a complex process requiring the activity of multiple RNA-partitioning pathways. In this review, key findings on this topic are discussed, and the template-partitioning model, describing a hypothetical mechanism for RNA partitioning in the eukaryotic cell, is proposed.Key words: mRNA, ribosome, endoplasmic reticulum, translation, protein synthesis, signal sequence, RNA localization.
The role of mRNA and protein sorting in seed storage protein synthesis, transport, and deposition
Authors: Crofts Andrew J , Washida Haruhiko , Okita Thomas W , Satoh Mio , Ogawa Masahiro , Kumamaru Toshihiro , Satoh Hikaru
Published: December 2005

Rice synthesizes and accumulates high levels of 2 distinct classes of seed storage proteins and sorts them to separate intracellular compartments, making it an ideal model system for studying the mechanisms of storage protein synthesis, transport, and deposition. In rice, RNA localization dictates the initial site of storage protein synthesis on specific subdomains of the cortical endoplasmic reticulum (ER), and there is a direct relation between the RNA localization site and the final destination of the encoded protein within the endomembrane system. Current data support the existence of 3 parallel RNA localization pathways leading from the nucleus to the actively synthesizing cortical ER. Additional pathways may exist for the synthesis of cytoplasmic and nuclear-encoded proteins targeted to organelles, the latter located in a stratified arrangement in developing endosperm cells. The study of rice mutants, which accumulate unprocessed glutelin precursors, indicates that these multiple pathways prevent nonproductive interactions between different classes of storage proteins that would otherwise disrupt protein sorting. Indeed, it appears that the prevention of disruptive interactions between different classes of storage proteins plays a key role in their biosynthesis in rice. In addition to highlighting the unique features of the plant endomembrane system and describing the relation between RNA and protein localization, this minireview will attempt to address a number of questions raised by recent studies on these processes.Key words: mRNA localization, protein localization, endomembrane system, seed storage proteins, rice.
Wound-induced contractile ring: a model for cytokinesis
Authors: Darenfed Hassina , Mandato Craig A
Published: December 2005

The actomyosin-based contractile ring is required for several biological processes, such as wound healing and cytokinesis of animal cells. Despite progress in defining the roles of this structure in both wound closure and cell division, we still do not fully understand how an actomyosin ring is spatially and temporally assembled, nor do we understand the molecular mechanism of its contraction. Recent results have demonstrated that microtubule-dependent local assembly of F-actin and myosin-II is present in wound closure and is similar to that in cytokinesis in animal cells. Furthermore, signalling factors such as small Rho GTPases have been shown to be involved in the regulation of actin dynamics during both processes. In this review we address recent findings in an attempt to better understand the dynamics of actomyosin contractile rings during wound healing as compared with the final step of animal cell division.Key words: actomyosin ring, microtubules, cytokinesis, wound healing.
Modeling the metabolic adaptations of the biomass under rapid growth and starvation conditions in the activated sludge process
Authors: Lavallée B , Lessard P , Vanrolleghem P A
Published: December 2005

For wastewater treatment, the activated sludge models (ASMs) 1, 2, and 3 of the International Water Association (IWA) are accepted as industrial standard. However, many authors have observed that the kinetic parameters of these models depend on the type of substrate, process configuration, and sludge age. Some publications showed that the kinetic parameters of ASMs could be influenced by regulation of enzyme production. Therefore, an engineer aiming to make some modifications to a specific system is not able to predict the response of the real system after the modifications and choose the right configuration or modifications with the same set of parameters. On the other hand, cybernetic models are proposed for modeling cell growth and focus, among other things, on regulation of enzyme production, that is to say on induction. Thus, the objective of this paper is to present an activated sludge model that mimics the enzymatic induction of active biomass within the framework of ASMs. In the proposed model, process rates are modulated according to the environmental conditions and cell history. The model is fitted on the basis of data found in the literature. All data collected from short and long transient experiments were fitted with the same set of parameters, which was not possible with other models. The proposed model gives a more realistic picture of active biomass and of its specific activity under highly varying process conditions, but further research is required to support the model with experimental data. Key words: activated sludge models (ASMs), activity, biomass, enzymes, induction, model, parameter, rate, regulation, sludge, transient.
Aqueous phase arsenic in weathered shale enriched in native arsenic
Authors: Muloin Tracy , Dudas Marvin J
Published: December 2005

Soils and geologic deposits derived from marine shale often contain elevated levels of arsenic. The source of arsenic is iron sulfide minerals. Oxidative weathering breaks down the iron sulfide minerals and potentially releases undesirable levels of arsenic into the surrounding pore water. Equilibration experiments on a weathered marine shale containing naturally elevated levels of native arsenic and on a mixture of weathered shale and calcareous till were conducted under aerobic conditions to determine how much arsenic was released into pore water and the mechanism responsible for limiting soluble arsenic concentrations. Aqueous phase arsenic released from the shale was less than 10 µg/L for aerobic conditions. Soluble arsenic concentrations were low considering the high total As concentrations in the shale (30 µg As/g shale). Over 4 times as much solution arsenic was released from the higher pH shale–till mixture compared to the acid shale alone. Adsorption and desorption was the mechanism that controlled the concentration of aqueous phase arsenic. Key words: soluble arsenate, groundwater, solution chemistry, adsorption, background concentration.
Using nitrogen limitation to induce polyphosphate metabolism in engineered bioreactors
Authors: Harper, Jr. W F , Moore T L , Russell T L , Turnbull J A
Published: December 2005

Efforts to study enhanced biological phosphorus removal (EBPR) can be hampered by the initial start-up of the culture. A nitrogen limitation was used to select for polyphosphate-accumulating organisms (PAOs) in a mixed culture that did not previously exhibit EBPR characteristics or storage product accumulation. During nitrogen-limiting conditions, accumulation of polyhydroxyalkanoate (PHA) and carbohydrate (CH) was observed, and then the characteristics of polyphosphate metabolism were observed. When the anaerobic–aerobic reactor was operated with an influent COD/N ratio of 25, the PHA and glycogen content increased quickly. During this period, PHA ranged from 13% to 30%, and CH ranged from 10% to 18%, and after 12 d anaerobic P release was observed. Polyphosphate metabolism persisted even after the nitrogen limitation was removed. Storage product accumulation may have contributed to lower effluent total suspended solids (TSS), but it had virtually no effect on sludge volume index (SVI) or capillary suction time (CST). Key words: enhanced biological phosphorus removal, microbial storage products, nutrient limitation.
Haemophilus paragallinarumsecretes metalloproteases
Authors: Rivero-García P C , Cruz C Vázquez , Alonso P Sánchez , Vaca S , Negrete-Abascal E
Published: December 2005

Haemophilus paragallinarum secretes metalloproteases into different culture media lacking serum. Secreted proteins, concentrated by precipitation with 70% ammonium sulphate ((NH4)2SO4) or methanol, displayed proteolytic activity at >100 kDa molecular mass in 10% polyacrylamide gels co-polymerized with porcine gelatin (0.1%). They were active in a broad pH range (4–9); pH 7.5 being the optimum. Protease activity was inhibited by 20 mmol EDTA/L and reactivated by calcium. The proteolytic activity was heat-stable at 40, 50, and 60 °C, but its activity diminished at 70 °C or higher. Secreted proteins partially degraded chicken immunoglobulin G (IgG) and cross-reacted with a polyclonal serum against a high molecular mass protease secreted by Actinobacillus pleuropneumoniae. Extracellular proteases could play a role in infectious coryza caused by H. paragallinarum.Key words: pathogenicity, secreted protein, infectious coryza.
Modification of thiamine pyrophosphate dependent enzyme activity by oxythiamine inSaccharomyces cerevisiaecells
Authors: Tylicki Adam , Czerniecki Jan , Dobrzyn Pawel , Matanowska Agnieszka , Olechno Anna , Strumilo Slawomir
Published: December 2005

Oxythiamine is an antivitamin derivative of thiamine that after phosphorylation to oxythiamine pyro phos phate can bind to the active centres of thiamine-dependent enzymes. In the present study, the effect of oxythiamine on the viability of Saccharomyces cerevisiae and the activity of thiamine pyrophosphate dependent enzymes in yeast cells has been investigated. We observed a decrease in pyruvate decarboxylase specific activity on both a control and an oxythiamine medium after the first 6 h of culture. The cytosolic enzymes transketolase and pyruvate decarboxylase decreased their specific activity in the presence of oxythiamine but only during the beginning of the cultivation. However, after 12 h of cultivation, oxythiamine-treated cells showed higher specific activity of cytosolic enzymes. More over, it was established by SDS–PAGE that the high specific activity of pyruvate decarboxylase was followed by an increase in the amount of the enzyme protein. In contrast, the mitochondrial enzymes, pyruvate dehydrogenase and 2-oxoglutarate dehydrogenase complexes, were inhibited by oxythiamine during the entire experiment. Our results suggest that the observed strong decrease in growth rate and viability of yeast on medium with oxythiamine may be due to stronger in hibition of mitochondrial pyruvate dehydrogenase than of cytosolic enzymes.Key words: pyruvate dehydrogenase, 2-oxoglutarate dehydrogenase, transketolase, pyruvate decarboxylase, activity, oxythiamine, inhibition.
Characteristics of adjacent family 6 acetylxylan esterases fromFibrobacter succinogenesand the interaction with the Xyn10E xylanase in hydrolysis of acetylated xylan
Authors: Kam Dong Keun , Jun Hyun-Sik , Ha Jong K , Inglis G Douglas , Forsberg Cecil W
Published: December 2005

Acetylxylan esterase genes axe6A and axe6B located adjacent to one another on a Fibrobacter succinogenes chromosome have been separately cloned and their properties characterized. The corresponding esterases contained an N-terminal carbohydrate esterase family 6 catalytic domain (CD) and a C-terminal family 6 carbohydrate-binding module (CBM). The amino acid sequences of the CDs and CBMs were found to exhibit 52% and 40% amino acid similarity, respectively. The CDs of the two esterases exhibited the highest similarity to CDs of acetylxylan esterases: AxeA from the ruminal fungi Orpinomyces sp. and BnaA from Neocallimastix patriciarum. Axe6A and Axe6B were optimally active at neutral pH and had low Kmvalues of 0.084 and 0.056 mmol·L–1, respectively. Axe6A and Axe6B were shown to bind to insoluble cellulose and xylan and to soluble arabinoxylan. Axe6A deacetylated acetylated xylan at the same initial rate in the presence and absence of added Xyn10E xylanase from F. succinogenes, but the action of the xylanase on acetylated xylan was dependent upon the initial activity of Axe6A. The capacity of acetylxylan esterases to bind to plant cell wall polymers and to independently deacetylate xylan enabling xylanase to release xylooligo saccharides, documents the central role these enzymes have to improve access of F. succinogenes to cellulose.Key words: Fibrobacter succinogenes S85, acetylxylan esterase, xylanase, synergy.
Study ofTrichoderma viridemetabolism under conditions of the restriction of oxidative processes
Authors: Chovanec Peter , Kaliňák Michal , Liptaj Tibor , Pronayová Naďa , Jakubík Tibor , Hudecová Daniela , Varečka Ľudovít
Published: December 2005

Trichoderma viride was capable of growth and conidiation in the presence of high concentrations of the uncoupler 3,3′,4′,5-tetrachlorosalicylanilide (up to 100 µmol·L–1) and of the respiration inhibitor mucidin (up to 100 µmol·L–1) in both submerged and surface cultivation. When vegetative mycelia were cultivated on the solid Czapek-Dox medium with yeast autolysate under an anaerobic and CO2-containing atmosphere, the growth was observed only rarely but the microorganism survived as long as 3 months under these conditions. Major products of metabolism of both aerobic and anaerobic submerged mycelia were identified by means of1H-NMR measurements. Major products excreted to the medium under aerobic conditions were succinic and citric acids. Major metabolites present in the submerged mycelia were γ-aminobutyric (and glutamic) acid and alanine. Under anaerobic conditions, citric acid was not excreted into the medium but ethanol appeared. Its production could not be increased upon increasing the sugar concentration. The appearance of secondary metabolites was found to be modified by oxygen availability during the mycelial growth. Results suggest that the vegetative form of T. viride is capable of fermentative metabolism characterized by the production of ethanol and succinate and that the excretion of carboxylic acids is developmentally regulated and modified by oxygen availability.Key words: Trichoderma, mycelia, anaerobiosis, citrate, succinate, ethanol, GABA.
Production of acylated homoserine lactones byAeromonasandPseudomonasstrains isolated from municipal activated sludge
Authors: Morgan-Sagastume Fernando , Boon Nico , Dobbelaere Sofie , Defoirdt Tom , Verstraete Willy
Published: December 2005

Up to now, the production and role of N-acyl homoserine lactones (AHLs) in activated sludge have been poorly understood. In this study, cross-feeding assays with the reporter strains Agrobacterium tumefaciens NTL4 and Chromobacterium violaceum CV026 were used to investigate AHL signal production by municipal activated sludge samples. AHL signal production was consistently detected from municipal activated sludge when different samples were incubated on nutrient media. From one municipal activated sludge sample, 10 strains producing AHL-like auto inducers were isolated by an overlay technique. 16S rDNA-based phylogenetic analysis showed that eight of the isolates belonged to Aeromonas spp. and two to Pseudomonas spp. Box-PCR indicated that six of these Aeromonas isolates were different strains and the two Pseudomonas strains were identical. The production of AHL or AHL-like compounds by these strains was confirmed by thin layer chromatography and biosensor overlays. The six different Aeromonas strains were found to produce the same set of AHLs, including N-hexanoyl-L-homoserine lactone. These results may indicate the possible presence of AHLs in municipal activated sludge. The potential roles of AHL in this eco system are briefly discussed.Key words: municipal activated sludge, acylated homoserine lactones, Aeromonas spp., bioaggregates, Pseudomonas spp., AHL biosensors.
Bacterial diversity in water samples from uranium wastes as demonstrated by 16S rDNA and ribosomal intergenic spacer amplification retrievals
Authors: Radeva Galina , Selenska-Pobell Sonja
Published: December 2005

Bacterial diversity was assessed in water samples collected from several uranium mining wastes in Ger many and in the United States by using 16S rDNA and ribosomal intergenic spacer amplification retrievals. The results obtained using the 16S rDNA retrieval showed that the samples collected from the uranium mill tailings of Schlema/Alberoda, Germany, were predominated by Nitrospina-like bacteria, whereas those from the mill tailings of Shiprock, New Mexico, USA, were predominated by γ-Pseudomonas and Frauteria spp. Additional smaller populations of the Cytophaga–Flavobacterium–Bacteroides group and α- and δ-Proteobacteria were identified in the Shiprock samples as well. Proteobacteria and Cytophaga–Flavobacterium–Bacteroides were also found in the third uranium mill tailings studied, Gittersee/Coschütz, Germany, but the groups of the predominant clones were rather small. Most of the clones of the Gittersee/Coschütz samples represented individual sequences, which indicates a high level of bacterial diversity. The samples from the fourth uranium waste studied, Steinsee Deponie B1, Germany, were predominantly occupied by Acinetobacter spp. The ribosomal intergenic spacer amplification retrieval provided results complementary to those obtained by the 16S rDNA analyses. For instance, in the Shiprock samples, an additional predominant bacterial group was identified and affiliated with Nitrosomonas sp., whereas in the Gittersee/Coschütz samples, anammox populations were identified that were not retrieved by the applied 16S rDNA approach.Key words: bacterial diversity, 16S rDNA, ribosomal intergenic spacer amplification (RISA), uranium wastes.
Phylogenetic analysis of several Thermus strains from Rehai of Tengchong, Yunnan, China
Authors: Lin Lianbing , Zhang Jie , Wei Yunlin , Chen Chaoyin , Peng Qian
Published: December 2005

Several Thermus strains were isolated from 10 hot springs of the Rehai geothermal area in Tengchong, Yunnan province. The diversity of Thermus strains was examined by sequencing the 16S rRNA genes and comparing their sequences. Phylogenetic analysis showed that the 16S rDNA sequences from the Rehai geothermal isolates form four branches in the phylogenetic tree and had greater than 95.9% similarity in the phylogroup. Secondary structure comparison also indicated that the 16S rRNA from the Rehai geothermal isolates have unique secondary structure characteristics in helix 6, helix 9, and helix 10 (reference to Escherichia coli). This research is the first attempt to reveal the diversity of Thermus strains that are distributed in the Rehai geothermal area.Key words: Thermus, diversity, phylogenetic analysis, RNA secondary structure.
Participation of the Entner–Doudoroff pathway inEscherichia colistrains with an inactive phosphotransferase system (PTS–Glc+) in gluconate and glucose batch cultures
Authors: Ponce Elizabeth , García Mauricio , Muñoz Ma. Enriqueta
Published: December 2005

The activity of the enzymes of the central metabolic pathways has been the subject of intensive analysis; however, the Entner–Doudoroff (ED) pathway has only recently begun to attract attention. The metabolic response to edd gene knockout in Escherichia coli JM101 and PTS–Glc+was investigated in gluconate and glucose batch cultures and compared with other pyruvate kinase and PTS mutants previously constructed. Even though the specific growth rates between the strain carrying the edd gene knockout and its parent JM101 and PTS–Glc+edd and its parent PTS–Glc+were very similar, reproducible changes in the specific consumption rates and biomass yields were obtained when grown on glucose. These results support the participation of the ED pathway not only on gluconate metabolism but on other metabolic and biochemical processes in E. coli. Despite that gluconate is a non-PTS carbohydrate, the PTS–Glc+and derived strains showed important reductions in the specific growth and gluconate consumption rates. Moreover, the overall activity of the ED pathway on gluconate resulted in important increments in PTS–Glc+and PTS-Glc+pykF mutants. Additional results obtained with the pykA pykF mutant indicate the important contribution of the pyruvate kinase enzymes to pyruvate synthesis and energy production in both carbon sources.Key words: Escherichia coli, gluconate metabolism, Entner-Doudoroff pathway, PT system, pyruvate kinase isoenzymes.
Models of contractile units and their assembly in smooth muscle
Authors: Ali Farah , Paré Peter D , Seow Chun Y
Published: December 2005

It is believed that the contractile filaments in smooth muscle are organized into arrays of contractile units (similar to the sarcomeric structure in striated muscle), and that such an organization is crucial for transforming the mechanical activities of actomyosin interaction into cell shortening and force generation. Details of the filament organization, however, are still poorly understood. Several models of contractile filament architecture are discussed here. To account for the linear relationship observed between the force generated by a smooth muscle and the muscle length at the plateau of an isotonic contraction, a model of contractile unit is proposed. The model consists of 2 dense bodies with actin (thin) filaments attached, and a myosin (thick) filament lying between the parallel thin filaments. In addition, the thick filament is assumed to span the whole contractile unit length, from dense body to dense body, so that when the contractile unit shortens, the amount of overlap between the thick and thin filaments (i.e., the distance between the dense bodies) decreases in exact proportion to the amount of shortening. Assembly of the contractile units into functional contractile apparatus is assumed to involve a group of cells that form a mechanical syncytium. The contractile apparatus is assumed malleable in that the number of contractile units in series and in parallel can be altered to accommodate strains on the muscle and to maintain the muscle's optimal mechanical function.Key words: contraction model, ultrastructure, length adaptation, plasticity.
A maturational model for the study of airway smooth muscle adaptation to mechanical oscillation
Authors: Wang Lu , Chitano Pasquale , Murphy Thomas M
Published: December 2005

It has been shown that mechanical stretches imposed on airway smooth muscle (ASM) by deep inspiration reduce the subsequent contractile response of the ASM. This passive maneuver of lengthening and retraction of the muscle is beneficial in normal subjects to counteract bronchospasm. However, it is detrimental to hyperresponsive airways because it triggers further bronchoconstriction. Although the exact mechanisms for this contrary response by normal and hyperresponsive airways are unclear, it has been suggested that the phenomenon is related to changes in ASM adaptability to mechanical oscillation. Healthy immature airways of both human and animal exhibit hyperresponsiveness, but whether the adaptative properties of hyperresponsive airway differ from normal is still unknown. In this article, we review the phenomenon of ASM adaptation to mechanical oscillation and its relevance and implication to airway hyperresponsiveness. We demonstrate that the age-specific expression of ASM adaptation is prominent using an established maturational animal model developed in our laboratory. Our data on immature ASM showed potentiated contractile force shortly after a length oscillation compared with the maximum force generated before oscillation. Several potential mechanisms such as myogenic response, changes in actin polymerization, or changes in the quantity of the cytoskeletal regulatory proteins plectin and vimentin, which may underlie this age-specific force potentiation, are discussed. We suggest a working model of the structure of smooth muscle associated with force transmission, which may help to elucidate the mechanisms responsible for the age-specific expression of smooth muscle adaptation. It is important to study the maturational profile of ASM adaptation as it could contribute to juvenile hyperresponsiveness.Key words: ASM adaptation, maturation, bronchoprotection, airway hyperresponsiveness.
Airway smooth muscle excitation-contraction coupling and airway hyperresponsiveness
Authors: Hirota Simon , Helli Peter B , Catalli Adriana , Chew Allyson , Janssen Luke J
Published: December 2005

The primary complaints from patients with asthma pertain to function of airway smooth muscle (ASM) function including shortness of breath, wheezing, and coughing. Thus, it is imperative to better understand the mechanisms underlying excitation-contraction coupling in ASM. Here, we review the various signaling pathways underlying contraction in ASM, and then examine how these are altered in asthma and airway hyperresponsiveness (a hallmark feature of asthma). Throughout, we highlight how studies of vascular smooth muscle have helped or hindered progress in understanding ASM physiology and pathophysiology.Key words: airway smooth muscle, vascular smooth muscle, excitation-contraction coupling, calcium, Rho-kinase.
Plasma membrane calcium pumps in smooth muscle: from fictional molecules to novel inhibitors
Authors: Pande Jyoti , Grover Ashok K
Published: December 2005

Plasma membrane Ca2+pumps (PMCA pumps) are Ca2+-Mg2+ATPases that expel Ca2+from the cytosol to extracellular space and are pivotal to cell survival and function. PMCA pumps are encoded by the genes PMCA1, -2, -3, and -4. Alternative splicing results in a large number of isoforms that differ in their kinetics and activation by calmodulin and protein kinases A and C. Expression by 4 genes and a multifactorial regulation provide redundancy to allow for animal survival despite genetic defects. Heterozygous mice with ablation of any of the PMCA genes survive and only the homozygous mice with PMCA1 ablation are embryolethal. Some PMCA isoforms may also be involved in other cell functions. Biochemical and biophysical studies of PMCA pumps have been limited by their low levels of expression. Delineation of the exact physiological roles of PMCA pumps has been difficult since most cells also express sarco/endoplasmic reticulum Ca2+pumps and a Na+-Ca2+-exchanger, both of which can lower cytosolic Ca2+. A major limitation in the field has been the lack of specific inhibitors of PMCA pumps. More recently, a class of inhibitors named caloxins have emerged, and these may aid in delineating the roles of PMCA pumps.Key words: ATPases, hypertension, caloxin, protein kinase A, protein kinase C, calmodulin.
Functional differences of Na+/Ca2+exchanger expression in Ca2+transport system of smooth muscle of guinea pig stomach
Authors: Sakai Yasushi , Kinoshita Hiroki , Saitou Keiichirou , Homma Ikuo , Nobe Koji , Iwamoto Takahiro
Published: December 2005

The plasma membrane ATP-dependent Ca2+pump and the Na+/Ca2+exchanger (NCX) are the major means of Ca2+extrusion in smooth muscle. However, little is known regarding distribution and function of the NCX in guinea pig gastric smooth muscle. The expression pattern and distribution of NCX isoforms suggest a role as a regulator of Ca2+transport in cells. Na+pump inhibition and the consequent to removal of K+caused gradual contraction in fundus. In contrast, the response was significantly less in antrum. Western blotting analysis revealed that NCX1 and NCX2 are the predominant NCX isoforms expressed in stomach, the former was expressed strongly in antrum, whereas the latter displayed greater expression in fundus. Isolated plasma membrane fractions derived from gastric fundus smooth muscle were also investigated to clarify the relationship between NCX protein expression and function. Na+-dependent Ca2+uptake increased directly with Ca2+concentration. Ca2+uptake in Na+-loaded vesicles was markedly elevated in comparison with K+-loaded vesicles. Additionally, Ca2+uptake by the Na+- or K+-loaded vesicles was substantially higher in the presence of A23187 than in its absence. The result can be explained based on the assumption that Na+gradients facilitate downhill movement of Ca2+. Na+-dependent Ca2+uptake was abolished by the monovalent cationic ionophore, monensin. NaCl enhanced Ca2+efflux from vesicles, and this efflux was significantly inhibited by gramicidin. Results documented evidence that NCX2 isoform functionally contributes to Ca2+extrusion and maintenance of contraction-relaxation cycle in gastric fundus smooth muscle.Key words: stomach, smooth muscle, Na+/Ca2+exchanger (NCX), NCX2.
Adenoviral mediated anti-sense CD38 attenuates TNF-α-induced changes in calcium homeostasis of human airway smooth muscle cells
Authors: Kang Bit Na , Deshpande Deepak A , Tirumurugaan K G , Panettieri Reynold A , Walseth Timothy F , Kannan Mathur S
Published: December 2005

CD38 is a membrane-bound protein involved in the synthesis and degradation of cyclic-ADP-ribose (cADPR). cADPR mobilizes calcium from intracellular stores in airway smooth muscle cells. To determine the role of CD38/cADPR signaling in calcium regulation in human airway smooth muscle (HASM) cells, we downregulated CD38 expression using a recombinant replication-defective adenovirus with anti-sense human CD38 (Ad-asCD38). CD38 expression was determined by RT-PCR and real-time quantitative PCR, and ADP-ribosyl cyclase (cyclase) activity was determined by competitive binding assay. In HASM cells infected with Ad-asCD38, TNF-α-induced, augmented-CD38 expression and cyclase activity were significantly lower than in TNF-α-treated cells. The net intracellular calcium responses to 10 nmol/L bradykinin were measured in HASM cells by fluorescence imaging. In cells infected with Ad-asCD38 in the presence of TNF-α, the net intracellular Ca2+ responses were significantly lower than in cells treated with TNF-α in the presence of the control vector (p < 0.001). These results provide evidence for the feasibility of using adenoviral vectors for gene transfer to down regulate gene expression, and confirm the role of CD38 in calcium homeostatis in ASM cells.Key words: cyclic ADP-Ribose, cytokine, smooth muscle.
Smooth muscle length adaptation and actin filament length: a network model of the cytoskeletal dysregulation
Authors: Fredberg Jeffrey J , Silveira Paulo S.P
Published: December 2005

Length adaptation of the airway smooth muscle cell is attributable to cytoskeletal remodeling. It has been proposed that dysregulated actin filaments may become longer in asthma, and that such elongation would prevent a parallel-to-series transition of contractile units, thus precluding the well-known beneficial effects of deep inspirations and tidal breathing. To test the potential effect that actin filament elongation could have in overall muscle mechanics, we present an extremely simple model. The cytoskeleton is represented as a 2-D network of links (contractile filaments) connecting nodes (adhesion plaques). Such a network evolves in discrete time steps by forming and dissolving links in a stochastic fashion. Links are formed by idealized contractile units whose properties are either those from normal or elongated actin filaments. Oscillations were then imposed on the network to evaluate both the effects of breathing and length adaptation. In response to length oscillation, a network with longer actin filaments showed smaller decreases of force, smaller increases in compliance, and higher shortening velocities. Taken together, these changes correspond to a network that is refractory to the effects of breathing and therefore approximates an asthmatic scenario. Thus, an extremely simple model seems to capture some relatively complex mechanics of airway smooth muscle, supporting the idea that dysregulation of actin filament length may contribute to excessive airway narrowing.Key words: asthma, actin filaments, series-to-parallel transition, mechanics, length adaptation.
The association of caveolae, actin, and the dystrophin–glycoprotein complex: a role in smooth muscle phenotype and function?
Authors: Halayko Andrew J , Stelmack Gerald L
Published: December 2005

Smooth muscle cells exhibit phenotypic and mechanical plasticity. During maturation, signalling pathways controlling actin dynamics modulate contractile apparatus-associated gene transcription and contractile apparatus remodelling resulting from length change. Differentiated myocytes accumulate abundant caveolae that evolve from the structural association of lipid rafts with caveolin-1, a protein with domains that confer unique functional properties. Caveolae and caveolin-1 modulate and participate in receptor-mediated signalling, and thus contribute to functional diversity of phenotypically similar myocytes. In mature smooth muscle, caveolae are partitioned into discrete linear domains aligned with structural proteins that tether actin to the extracellular matrix. Caveolin-1 binds with β-dystroglycan, a subunit of the dystrophin glycoprotein complex (DGC), and with filamin, an actin binding protein that organizes cortical actin, to which integrins and focal adhesion complexes are anchored. The DGC is linked to the actin cytoskeleton by a dystrophin subunit and is a receptor for extracellular laminin. Thus, caveolae and caveolin-associated signalling proteins and receptors are linked via structural proteins to a dynamic filamentous actin network. Despite development of transgenic models to investigate caveolins and membrane-associated actin-linking proteins in skeletal and cardiac muscle function, only superficial understanding of this association in smooth muscle phenotype and function has emerged.Key words: caveolin, dystroglycan, filamin, mechanical plasticity, G-protein-coupled receptors.
Do a male garter snake's energy stores limit his reproductive effort?
Authors: Shine Richard , Mason Robert T
Published: December 2005

The storage and utilization of energy plays a critical role in reproductive output for females of many species, including snakes. However, links between energy and reproductive effort in males are less clear. Studies at a communal den of red-sided garter snakes (Thamnophis sirtalis parietalis (Say, 1823)) in Manitoba suggest that energy is critical to reproduction for males as well as females. Males vary substantially in body condition (mass relative to body length) at the time they emerge from winter inactivity. The energy to be expended in courtship is stored in the muscles rather than the "conventional" sites for energy storage in snakes (abdominal fat bodies or liver). A male's reproductive effort (the duration of his residency at courting aggregations near the den) was linked to his energy stores and to the rate of depletion of those stores. Male snakes that emerged from hibernation in better condition, and that lost mass slowly thereafter, remained in courting aggregations near the den for longer periods than did males that emerged in poor condition (i.e., with less energy resources) and (or) lost mass more rapidly. In outdoor arenas, males that engaged in courtship lost mass more rapidly than did males with no courtship opportunities. These data suggest that courtship is energetically expensive for male garter snakes and that the amount of effort that a male invests in reproduction is determined by his energy stores.
Rodent seed predation and GUDs: effect of burning and topography
Authors: Reed A W , Kaufman G A , Kaufman D W
Published: December 2005

We examined the relationships between seed predation and the habitat into which a seed falls, abundance of rodents within that habitat, and foraging pattern of rodents within that habitat. Using seed plots, we assessed seed predation in burned and unburned tallgrass prairies at biweekly intervals between May and September in 2001 and 2002. Significantly more seed was removed from plots in burned than unburned prairies. Rodent abundance did not differ between burned prairie and unburned prairie, although the abundance of omnivorous–granivorous rodents (herbivores excluded) was greater in burned than unburned prairie. Proportion of seed removed in burned and unburned prairies was independent of both total rodent abundance and abundance of omnivorous–granivorous rodents. We also measured giving-up density (GUD) of rodents in burned and unburned prairies during the spring and summer of 2002. GUDs did not differ significantly in burned and unburned prairies. However, rodents had a higher GUD in uplands than in limestone breaks or lowland habitats. Our results suggest that rodent foraging in tallgrass prairie is affected by microhabitat and that rodent abundance is not sufficient to predict seed predation.
Hunting success of wintering Swainson's hawks: environmental effects on timing and choice of foraging method
Authors: Sarasola J H , Negro J J
Published: December 2005

We examined the predatory behavior of Swainson's hawks (Buteo swainsoni Bonaparte, 1838) wintering in the Argentine pampas. Aerial and ground foraging were the main hunting methods employed by hawks in this region. The overall hunting success of hawks preying on insects was 50% and age-related differences in hunting success were not significant. The Swainson's hawks, however, hunted more successfully in the air (65% of prey capture attempts) than on the ground (42%). Aerial hunting while soaring was the most successful hunting method based on the number of prey captured per energy unit. Based on the analysis of prey consumed by hawks during the study period, grasshopper species with poor flight capabilities were available in the air as a consequence of the vertical air motion. With regards to daily activity patterns, the time that a hawk spent using each hunting method was not proportional to the cost ratio associated with each method. Hawks foraged in the air only during midday hours when weather conditions permitted the formation of thermals. Thus, the use of soaring flights and the availability of prey in the air were constrained by the physical environment, and hawks could only exploit airborne food sources during limited periods of the day.
Factors associated with nest- and roost-burrow selection by burrowing owls (Athene cunicularia) on the Canadian prairies
Authors: Poulin Ray G , Todd L Danielle , Dohms Kimberly M , Brigham R Mark , Wellicome Troy I
Published: December 2005

We examined nest- and roost-burrow characteristics from a declining population of burrowing owls (Athene cunicularia (Molina, 1782)) in Saskatchewan. Between 1992 and 2003, 84% of the 584 nests we found were in grassland pastures, even though these pastures constituted only 7% of the potentially available nesting area within our study area. In contrast, less than 3% of nests were in crop fields, despite these fields comprising 90% of the potentially available area. Within grassland pastures, owls selected nest burrows in areas with a higher density of burrows within 75 m (11.1 burrows/ha) compared with non-nest burrows of similar dimensions (5.6 burrows/ha). Richardson's ground squirrels (Spermophilus richardsonii (Sabine, 1822)) and badgers (Taxidea taxus (Schreber, 1777)) are the primary excavators of suitable nesting burrows in prairie Canada. In our study area, burrowing owls chose to nest and roost in badger-sized burrows, selecting those with taller tunnel entrances and soil mounds relative to unused burrows. We suggest that management for burrowing owl nesting habitat in Canada should consider the owls' avoidance of crop fields and their preference for grassland pastures. Managers should also consider the owls' apparent preference for nesting in areas of high burrow densities and their selection of badger-sized burrows for nesting and roosting.