bluuebunny/crossref_metadata_2025 huggingface dataset:
INACCESSIBLE CONTINUOUSLY STABLE STRATEGIES
Authors: APALOO J.
Published: August 2010

ABSTRACT. The evolutionary stability concepts continuously stable strategies (CSS) and evolutionarily stable neighborhood invader strategies (ESNIS) share two properties in common. First, they are both evolutionarily stable strategies (ESS). Secondly, given any strategy in the close neighborhood of the CSS or ESNIS, there are some strategies that are closer to the CSS or ESNIS that can invade it. An ESNIS is a CSS but the converse is not true in general. We examine evolutionary adaptive dynamics in the neighborhood of a CSS that is not an ESNIS. We show that if an evolutionary game possesses a CSS which is not an ESNIS, the succession of strategies mediated by natural selection become arbitrarily close to the CSS but the precise value of the CSS cannot be attained unless the CSS is the first strategy to invade into the environment and is henceforth never perturbed. Thus if evolution does not start with the CSS that is not an ESNIS, we will have a phenomenon of bounded evolutionary succession that does not come to an end. The analysis is applied to a class of monomorphic population evolutionary game models in which species ecological interaction is modeled by the Lotka‐Volterra equations.
THE ECONOMIC VALUE OF ENVIRONMENTAL RESEARCH IN UNDERSTANDING THE RELATIVE CONTRIBUTIONS OF SOURCES OF NUTRIENTS TO COASTAL WATERS
Authors: JIN DI , HOAGLAND PORTER , SOLOW ANDREW
Published: August 2010

ABSTRACT. We model the value of environmental research in the presence of uncertainty about thesources of environmental pollutants and natural processes affecting the level of pollution. The model may be used to estimate the value of environmental research directed at resolving the uncertainty. We illustrate the model using a numerical simulation of a hypothetical case involving nutrient pollution of coastal waters. We show that the ex ante value of research is positively related to the level of uncertainty. There is a diminishing return with respect to the level of research investment. We find that research is more valuable ex post if it leads to unexpected findings.
ON HYPERBOLIC TIME DISCOUNTING IN EXHAUSTIBLE RESOURCE MODELS: AN APPLICATION TO WORLD OIL RESOURCES
Authors: ROWSE JOHN
Published: August 2010

ABSTRACT. Recent research on discounting in long term economic models involves hyperbolic discounting, in which the marginal discount rate shrinks as time passes. To investigate hyperbolic discounting and exhaustible resource allocation, this work develops a discrete‐time world oil model and model solution procedure, then uses the model to examine the consequences of adopting conventional (constant annual) discounting when hyperbolic discounting is appropriate, of adopting one hyperbolic discount rate path when a different hyperbolic path is appropriate, and of adopting hyperbolic discounting when conventional discounting is appropriate. Five conventional and two hyperbolic discount rate paths are considered. One hyperbolic path is that used by Nordhaus and Boyer [2000]; the other is that recommended by Weitzman [2001]. The generality of the findings is also assessed.
A MICRO‐LEVEL ‘CONSUMER APPROACH’ TO SPECIES POPULATION DYNAMICS
Authors: CHRISTIAANS THOMAS , EICHNER THOMAS , PETHIG RÜDIGER
Published: August 2010

ABSTRACT. In this paper we develop a micro ecosystem model whose basic entities are representative organisms which behave as if maximizing their net offspring under constraints. Net offspring is increasing in prey biomass intake, declining in the loss of own biomass to predators and Allee's law applies. The organism's constraint reflects its perception of how scarce its own biomass and the biomass of its prey is. In the short‐run periods prices (scarcity indicators) coordinate and determine all biomass transactions and net offspring which directly translates into population growth functions. We are able to explicitly determine these growth functions for a simple food web when specific parametric net offspring functions are chosen in the micro‐level ecosystem model. For the case of a single species our model is shown to yield the well‐known Verhulst‐Pearl logistic growth function. With two species in predator‐prey relationship, we derive differential equations whose dynamics are completely characterized and turn out to be similar to the predator‐prey model with Michaelis‐Menten type functional response. With two species competing for a single resource we find that coexistence is a knife‐edge feature confirming Tschirhart's [2002] result in a different but related model.
THE INCOMPLETE‐INFORMATION SPLIT‐STREAM FISH WAR: EXAMINING THE IMPLICATIONS OF COMPETING RISKS
Authors: GOLUBTSOV PETER V. , MCKELVEY ROBERT
Published: August 2010

ABSTRACT.. It is now widely recognized that climactic regime shifts, which aperiodically alter a harvested fish stock's biomass and spatial distribution, may lead to distorted fisheries management decisions which negatively impact the fishery, both biologically and economically. This is particularly true for trans‐boundary migratory stocks, where optimal management relies on coordination among independent nation‐states. Unanticipated changes in stock distribution and abundance can upset expectations of national authorities, leading them to sanction inappropriate harvesting levels by their separately managed fleets targeting the same breeding fish stock.

Our theoretical studies are based on a spatially‐distributed stochastic model, which we have called the “split‐stream model,‘ where two separately managed fleets harvest simultaneously at two separate sites. Our key assumption is that competing fleet managers, when harvesting noncooperatively, hold incomplete and asymmetric private information of current stock recruitment and spatial distribution. When subsequently negotiating to coordinate their harvests, they agree that they will share their information and then bargain over partition of the gains from their cooperation. This bargaining process takes into account the fleet's relative competitive strengths, particularly due to private information asymmetries.

In this present article we introduce a more complex information structure than had been assumed in our earlier work (McKelvey and Golubtsov [2002], McKelvey, Miller and Golubtsov [2003], Mckelvey et al. [2004]). Specifically, both stock‐growth and stock‐split parameters vary stochastically and asynchronously. Thus, when harvesting noncooperatively, each fleet may possess private knowledge which is unavailable to the other. We examine the interplay of the harvesting game's information structure with other fishery characteristics, such as the fleets' economics and operating characteristics and their attitudes toward risk, to determine the implications of such structure for the outcome of the harvesting game. All of these changes are made to capture new conceptual phenomena and expand the range of applicability of the model.
ALTERNATIVE METHODS TO ANALYZE THE RANK ORDERED DATA: A CASE OF INVASIVE SPECIES CONTROL
Authors: PAUDEL KRISHNA P. , DUNN MICHAEL A. , BHANDARI DOLESWAR , VLOSKY RICHARD P. , GUIDRY KURT M.
Published: August 2010

ABSTRACT. Data collected regarding homeowner preferences for various Formosan Subterranean termite control methods were analyzed using ordered probit and exploded logit models. Ordered probit model for first, second and fourth preferences had similar variables significant, although the first preference model had many significant variables. The most important variable, in terms of significance, across all preferences was the perception that a respondent thinks that termite existence is a problem in their neighborhood. The results from the exploded logit model indicated that a control option with liquid treatment option and more visits by a pest control agency is a less preferred treatment option.

This paper was presented at the 2004 Research Modeling Association World Conference on Natural Resource Modeling in Melbourne, Australia.
THE FOREST ROTATION PROBLEM WITH STOCHASTIC HARVEST AND AMENITY VALUE
Authors: ALVAREZ LUIS H.R. , KOSKELA ERKKI
Published: August 2010

ABSTRACT.We present a general approach to study optimal rotation policy with amenity valuationunder stochastic forest stand value. We state a set of weak conditions under which a unique optimal harvesting threshold exists and derive the value of the optimal policy. We characterize the impact of forest stand value volatility on both the total and the marginal expected cumulative present value of the revenues accrued from amenities. We also illustrate our results numerically and find that depending on the precise characteristics of amenity valuation higher forest stand value volatility may accelerate the rotation policy by decreasing the optimal harvesting threshold.
A METHOD FOR SIMPLIFYING LARGE ECOSYSTEM MODELS
Authors: LAWRIE JOCK
Published: August 2010

Abstract Simplifying large ecosystem models is essential if we are to understand the underlying causes of observed behaviors. However, such understanding is often employed to achieve simplification. This paper introduces two model simplification methods that can be applied without requiring intimate prior knowledge of the system. Their utility is measured by the resulting values of given model diagnostics relative to those of the large model. The first method is a simple automated procedure for nondimensionalizing large ecosystem models, which identifies and eliminates terms that have little effect on model diagnostics. Some of its limitations are then addressed by the rate elimination method, which measures the relative importance of model terms using least‐squares regression. The methods are applied to a model of the nitrogen cycle in Port Phillip Bay, Victoria, Australia. The rate elimination method provided more insights into the causal relationships built into the model than the nondimensionalizing method. It also allowed the reduction of the model's dimension. Thus it is a useful first step in model simplification.
INTERTEMPORAL INVESTMENTS INTO SYNFUELS
Authors: WIRL FRANZ
Published: August 2010

Abstract This paper considers the interactions of consumers demanding energy services provided by fossil fuels delivered by a cartel and a synfuel industry (competitive, cartelized or run by a consumer cartel, say International Energy Agency [IEA]). The emphasis of this paper is to account for the necessarily sluggish build up capacities instead of the instantaneous unconstrained availability assumed in the backstop literature and to investigate intertemporal and subgame perfect equilibria (in Markov strategies).
TREATMENT VERSUS PREVENTION OF NITROGEN FERTILIZER POLLUTION: AN INTER‐SECTORAL EXTERNALITY POLICY MODEL
Authors: FISHMAN YARON , BECKER NIR , SHECHTER MORDECHAI
Published: August 2010

Abstract This article presents an economic, hydrological, dynamic optimization model, which describes the negative external effects of nitrogen fertilizers on groundwater quality. The relative merits of treatment versus prevention of nitrogen pollution were analyzed. A dynamical water and nitrogen flow between land surface, the unsaturated zone, and groundwater was employed. A specific treatment technology, which gives rise to a discontinuous cost function, was also used. Applying the model to the coastal aquifer in Israel, our results showed that in a joint (agricultural and domestic) water source area that supplies a relatively small quantity of drinking water, it is more efficient to combine a policy that imposes restrictions on the use of nitrogen with a drinking‐water treatment process. However, when a relatively large quantity of drinking water is involved, imposing restrictions on the use of nitrogen only is more efficient. The paper, thus, is useful to planners of fast growing urban population centers with regard to regulation and can be used to calculate and evaluate specific policies.
OUTPUT VERSUS INPUT CONTROLS UNDER UNCERTAINTY: THE CASE OF A FISHERY
Authors: YAMAZAKI SATOSHI , KOMPAS TOM , GRAFTON R. QUENTIN
Published: August 2010

Abstract The paper compares the management outcomes with a total allowable catch (TAC) and a total allowable effort (TAE) in a fishery under uncertainty. Using a dynamic programming model with multiple uncertainties and estimated growth, harvest, and effort functions from one of the world's largest fisheries, the relative economic and biological benefits of a TAC and TAE are compared and contrasted in a stochastic environment. This approach provides a decision and modeling framework to compare instruments and achieve desired management goals. A key finding is that neither instrument is always preferred in a world of uncertainty and that regulator's risk aversion and weighting in terms of expected net profits and biomass, and the trade‐offs in terms of expected values and variance determine instrument choice.
OPTIMAL CHOICE BETWEEN EVEN‐ AND UNEVEN‐AGED FORESTRY
Authors: TAHVONEN OLLI
Published: August 2010

Abstract Existing optimal rotation models include even‐aged management exogenously into the model structure. As an economic model, this Faustmann framework is restrictive, and a more general model should not include any such preconditions. Even‐aged management should follow endogenously as an optimal solution if it proves out to be superior to other systems, such as uneven‐aged management. Without such a general model, the economically optimal choice between even‐aged and uneven‐aged forestry remains somewhat arbitrary. This study specifies such a model and shows how even‐aged management follows endogenously and reveals what factors work in favor of each management alternative. Numerical analysis shows that even‐ and uneven‐aged systems may represent locally optimal solutions and may yield equal economic outcomes. Instead of the usual comparative statics results of the Faustmann model, changes in the rate of discount, timber price, or planting cost may imply that the optimal solution shifts from even‐ to uneven‐aged management.
Novel Glycoside Hydrolases Identified by Screening a Chinese Holstein Dairy Cow Rumen-Derived Metagenome Library
Authors: Zhao Shengguo , Wang Jiaqi , Bu Dengpan , Liu Kailang , Zhu Yaxin , Dong Zhiyang , Yu Zhongtang
Published: August 2010

One clone encoding glycoside hydrolases was identified through functional screening of a rumen bacterial artificial chromosome (BAC) library. Of the 68 open reading frames (ORFs) predicted, one ORF encodes a novel endo-β-1,4-xylanase with two catalytic domains of family GH43 and two cellulose-binding modules (CBMs) of family IV. Partial characterization showed that this endo-xylanase has a greater specific activity than a number of other xylanases over a wide temperature range at neutral pH and could be useful in some industrial applications.
Denitrification Response Patterns during the Transition to Anoxic Respiration and Posttranscriptional Effects of Suboptimal pH on Nitrogen Oxide Reductase in
Paracoccus denitrificans
Authors: Bergaust Linda , Mao Yuejian , Bakken Lars R. , Frostegård Åsa
Published: August 2010

Denitrification in soil is a major source of atmospheric N
2
O. Soil pH appears to exert a strong control on the N
2
O/N
2
product ratio (high ratios at low pH), but the reasons for this are not well understood. To explore the possible mechanisms involved, we conducted an in-depth investigation of the regulation of denitrification in the model organism
Paracoccus denitrificans
during transition to anoxia both at pH 7 and when challenged with pHs ranging from 6 to 7.5. The kinetics of gas transformations (O
2
, NO, N
2
O, and N
2
) were monitored using a robotic incubation system. Combined with quantification of gene transcription, this yields high-resolution data for direct response patterns to single factors.
P. denitrificans
demonstrated robustly balanced transitions from O
2
to nitric oxide-based respiration, with NO concentrations in the low nanomolar range and marginal N
2
O production at an optimal pH of 7. Transcription of
nosZ
(encoding N
2
O reductase) preceded that of
nirS
and
norB
(encoding nitrite and NO reductase, respectively) by 5 to 7 h, which was confirmed by observed reduction of externally supplied N
2
O. Reduction of N
2
O was severely inhibited by suboptimal pH. The relative transcription rates of
nosZ
versus
nirS
and
norB
were unaffected by pH, and low pH had a moderate effect on the N
2
O reductase activity in cells with a denitrification proteome assembled at pH 7. We thus concluded that the inhibition occurred during protein synthesis/assembly rather than transcription. The study shed new light on the regulation of the environmentally essential N
2
O reductase and the important role of pH in N
2
O emission.
Bovine Norovirus: Carbohydrate Ligand, Environmental Contamination, and Potential Cross-Species Transmission via Oysters
Authors: Zakhour Maha , Maalouf Haifa , Di Bartolo Ilaria , Haugarreau Larissa , Le Guyader Françoise S. , Ruvoën-Clouet Nathalie , Le Saux Jean-Claude , Ruggeri Franco Maria , Pommepuy Monique , Le Pendu Jacques
Published: August 2010

Noroviruses (NoV) are major agents of acute gastroenteritis in humans and the primary pathogens of shellfish-related outbreaks. Previous studies showed that some human strains bind to oyster tissues through carbohydrate ligands that are similar to their human receptors. Thus, based on presentation of shared norovirus carbohydrate ligands, oysters could selectively concentrate animal strains with increased ability to overcome species barriers. In comparison with human GI and GII strains, bovine GIII NoV strains, although frequently detected in bovine feces and waters of two estuaries of Brittany, were seldom detected in oysters grown in these estuaries. Characterization of the carbohydrate ligand from a new GIII strain indicated recognition of the alpha-galactosidase (α-Gal) epitope not expressed by humans, similar to the GIII.2 Newbury2 strain. This ligand was not detectable on oyster tissues, suggesting that oysters may not be able to accumulate substantial amounts of GIII strains due to the lack of shared carbohydrate ligand and that they should be unable to contribute to select GIII strains with an increased ability to recognize humans.
Phylogenetic Groups and Pathogenicity Island Markers in Fecal
Escherichia coli
Isolates from Asymptomatic Humans in China
Authors: Li Bin , Sun Jing-yong , Han Li-zhong , Huang Xin-hong , Fu Qiang , Ni Yu-xing
Published: August 2010

The study of phylogenetic groups and pathogenicity island (PAI) markers in commensal
Escherichia coli
strains from asymptomatic Chinese people showed that group A strains are the most common and that nearly half of all fecal strains which were randomly selected harbor PAIs.
Differential Involvement of the Five RNA Helicases in Adaptation of
Bacillus cereus
ATCC 14579 to Low Growth Temperatures
Authors: Pandiani Franck , Brillard Julien , Bornard Isabelle , Michaud Caroline , Chamot Stéphanie , Nguyen-the Christophe , Broussolle Véronique
Published: August 2010

Bacillus cereus
ATCC 14579 possesses five RNA helicase-encoding genes overexpressed under cold growth conditions. Out of the five corresponding mutants, only the
ΔcshA
,
ΔcshB
, and
ΔcshC
strains were cold sensitive. Growth of the
ΔcshA
strain was also reduced at 30°C but not at 37°C. The cold phenotype was restored with the
cshA
gene for the
ΔcshA
strain and partially for the
ΔcshB
strain but not for the
ΔcshC
strain, suggesting different functions at low temperature.
Genotype and Antibiotic Resistance Analyses of
Campylobacter
Isolates from Ceca and Carcasses of Slaughtered Broiler Flocks
Authors: Wirz Simone E. , Overesch Gudrun , Kuhnert Peter , Korczak Bożena M.
Published: August 2010

To obtain genetic information about
Campylobacter jejuni
and
Campylobacter coli
from broilers and carcasses at slaughterhouses, we analyzed and compared 340 isolates that were collected in 2008 from the cecum right after slaughter or from the neck skin after processing. We performed
rpoB
sequence-based identification, multilocus sequence typing (MLST), and
flaB
sequence-based typing; we additionally analyzed mutations within the 23S rRNA and
gyrA
genes that confer resistance to macrolide and quinolone antibiotics, respectively. The
rpoB
-based identification resulted in a distribution of 72.0%
C. jejuni
and 28.0%
C. coli
. The MLST analysis revealed that there were 59 known sequence types (STs) and 6 newly defined STs. Most of the STs were grouped into 4 clonal complexes (CC) that are typical for poultry (CC21, CC45, CC257, and CC828), and these represented 61.8% of all of the investigated isolates. The analysis of 95 isolates from the cecum and from the corresponding carcass neck skin covered 44 different STs, and 54.7% of the pairs had matching genotypes. The data indicate that cross-contamination from various sources during slaughter may occur, although the majority of
Campylobacter
contamination on carcasses appeared to originate from the slaughtered flock itself. Mutations in the 23S rRNA gene were found in 3.1% of
C. coli
isolates, although no mutations were found in
C. jejuni
isolates. Mutations in the
gyrA
gene were observed in 18.9% of
C. jejuni
and 26.8% of
C. coli
isolates, which included two
C. coli
strains that carried mutations conferring resistance to both classes of antibiotics. A relationship between specific genotypes and antibiotic resistance/susceptibility was observed.
Hydrogen Cycling by the Unicellular Marine Diazotroph
Crocosphaera watsonii
Strain WH8501
Authors: Wilson Samuel T. , Tozzi Sasha , Foster Rachel A. , Ilikchyan Irina , Kolber Zbigniew S. , Zehr Jonathan P. , Karl David M.
Published: August 2010

The hydrogen (H
2
) cycle associated with the dinitrogen (N
2
) fixation process was studied in laboratory cultures of the marine cyanobacterium
Crocosphaera watsonii
. The rates of H
2
production and acetylene (C
2
H
2
) reduction were continuously measured over the diel cycle with simultaneous measurements of fast repetition rate fluorometry and dissolved oxygen. The maximum rate of H
2
production was coincident with the maximum rates of C
2
H
2
reduction. Theoretical stoichiometry for N
2
fixation predicts an equimolar ratio of H
2
produced to N
2
fixed. However, the maximum rate of net H
2
production observed was 0.09 nmol H
2
μg chlorophyll
a
(chl
a
)
−1
h
−1
compared to the N
2
fixation rate of 5.5 nmol N
2
μg chl
a
−1
h
−1
, with an H
2
production/N
2
fixation ratio of 0.02. The 50-fold discrepancy between expected and observed rates of H
2
production was hypothesized to be a result of H
2
reassimilation by uptake hydrogenase. This was confirmed by the addition of carbon monoxide (CO), a potent inhibitor of hydrogenase, which increased net H
2
production rates ∼40-fold to a maximum rate of 3.5 nmol H
2
μg chl
a
−1
h
−1
. We conclude that the reassimilation of H
2
by
C. watsonii
is highly efficient (>98%) and hypothesize that the tight coupling between H
2
production and consumption is a consequence of fixing N
2
at nighttime using a finite pool of respiratory carbon and electrons acquired from daytime solar energy capture. The H
2
cycle provides unique insight into N
2
fixation and associated metabolic processes in
C. watsonii
.
The Transcriptional Regulator Nrg1p Controls Candida albicans Biofilm Formation and Dispersion
Authors: Uppuluri Priya , Pierce Christopher G. , Thomas Derek P. , Bubeck Sarah S. , Saville Stephen P. , Lopez-Ribot Jose L.
Published: August 2010

The ability of
Candida albicans
to reversibly switch morphologies is important for biofilm formation and dispersion. In this pathogen, Nrg1p functions as a key negative regulator of the yeast-to-hypha morphogenetic transition. We have previously described a genetically engineered
C. albicans
tet-NRG1
strain in which
NRG1
expression levels can be manipulated by the presence or absence of doxycycline (DOX). Here, we have used this strain to ascertain the role of Nrg1p in regulating the different stages of the
C. albicans
biofilm developmental cycle. In an
in vitro
model of biofilm formation, the
C. albicans
tet-NRG1
strain was able to form mature biofilms only when DOX was present in the medium, but not in the absence of DOX, when high levels of
NRG1
expression blocked the yeast-to-hypha transition. However, in a biofilm cell retention assay in which biofilms were developed with mixtures of
C. albicans
tet-NRG1
and SC5314 strains,
tet-NRG1
yeast cells were still incorporated into the mixed biofilms, in which an intricate network of hyphae of the wild-type strain provided for biofilm structural integrity and adhesive interactions. Also, utilizing an
in vitro
biofilm model under conditions of flow, we demonstrated that
C. albicans
Nrg1p exerts an exquisite control of the dispersal process, as overexpression of
NRG1
leads to increases in dispersion of yeast cells from the biofilms. Our results demonstrate that manipulation of
NRG1
gene expression has a profound influence on biofilm formation and biofilm dispersal, thus identifying Nrg1p as a key regulator of the
C. albicans
biofilm life cycle.
In Vitro
Analysis of the
Staphylococcus aureus
Lipoteichoic Acid Synthase Enzyme Using Fluorescently Labeled Lipids
Authors: Karatsa-Dodgson Maria , Wörmann Mirka E. , Gründling Angelika
Published: August 2010

Lipoteichoic acid (LTA) is an important cell wall component of Gram-positive bacteria. The key enzyme responsible for polyglycerolphosphate lipoteichoic acid synthesis in the Gram-positive pathogen
Staphylococcus aureus
is the membrane-embedded lipoteichoic acid synthase enzyme, LtaS. It is presumed that LtaS hydrolyzes the glycerolphosphate head group of the membrane lipid phosphatidylglycerol (PG) and catalyzes the formation of the polyglycerolphosphate LTA backbone chain. Here we describe an
in vitro
assay for this new class of enzyme using PG with a fluorescently labeled fatty acid chain (NBD-PG) as the substrate and the recombinant soluble C-terminal enzymatic domain of LtaS (eLtaS). Thin-layer chromatography and mass spectrometry analysis of the lipid reaction products revealed that eLtaS is sufficient to cleave the glycerolphosphate head group from NBD-PG, resulting in the formation of NBD-diacylglycerol. An excess of soluble glycerolphosphate could not compete with the hydrolysis of the fluorescently labeled PG lipid substrate, in contrast to the addition of unlabeled PG. This indicates that the enzyme recognizes and binds other parts of the lipid substrate, besides the glycerolphosphate head group. Furthermore, eLtaS activity was Mn
2+
ion dependent; Mg
2+
and Ca
2+
supported only weak enzyme activity. Addition of Zn
2+
or EDTA inhibited enzyme activity even in the presence of Mn
2+
. The pH optimum of the enzyme was 6.5, characteristic for an enzyme that functions extracellularly. Lastly, we show that the
in vitro
assay can be used to study the enzyme activities of other members of the lipoteichoic acid synthase enzyme family.
Elucidation of β-Oxidation Pathways in
Ralstonia eutropha
H16 by Examination of Global Gene Expression
Authors: Brigham Christopher J. , Budde Charles F. , Holder Jason W. , Zeng Qiandong , Mahan Alison E. , Rha ChoKyun , Sinskey Anthony J.
Published: August 2010

Ralstonia eutropha
H16 is capable of growth and polyhydroxyalkanoate production on plant oils and fatty acids. However, little is known about the triacylglycerol and fatty acid degradation pathways of this bacterium. We compare whole-cell gene expression levels of
R. eutropha
H16 during growth and polyhydroxyalkanoate production on trioleate and fructose. Trioleate is a triacylglycerol that serves as a model for plant oils. Among the genes of note, two potential fatty acid β-oxidation operons and two putative lipase genes were shown to be upregulated in trioleate cultures. The genes of the glyoxylate bypass also exhibit increased expression during growth on trioleate. We observed that single β-oxidation operon deletion mutants of
R. eutropha
could grow using palm oil or crude palm kernel oil as the sole carbon source, regardless of which operon was present in the genome, but a double mutant was unable to grow under these conditions. A lipase deletion mutant did not exhibit a growth defect in emulsified oil cultures but did exhibit a phenotype in cultures containing nonemulsified oil. Mutants of the glyoxylate shunt gene for isocitrate lyase were able to grow in the presence of oils, while a malate synthase (
aceB
) deletion mutant grew more slowly than wild type. Gene expression under polyhydroxyalkanoate storage conditions was also examined. Many findings of this analysis confirm results from previous studies by our group and others. This work represents the first examination of global gene expression involving triacylglycerol and fatty acid catabolism genes in
R. eutropha
.
Comparative Genome Biology of a Serogroup B Carriage and Disease Strain Supports a Polygenic Nature of Meningococcal Virulence
Authors: Joseph Biju , Schneiker-Bekel Susanne , Schramm-Glück Anja , Blom Jochen , Claus Heike , Linke Burkhard , Schwarz Roland F. , Becker Anke , Goesmann Alexander , Frosch Matthias , Schoen Christoph
Published: August 2010

Neisseria meningitidisserogroup B strains are responsible for most meningococcal cases in the industrialized countries, and strains belonging to the clonal complex ST-41/44 are among the most prevalent serogroup B strains in carriage and disease. Here, we report the first genome and transcriptome comparison of a serogroup B carriage strain from the clonal complex ST-41/44 to the serogroup B disease strain MC58 from the clonal complex ST-32. Both genomes are highly colinear, with only three major genome rearrangements that are associated with the integration of mobile genetic elements. They further differ in about 10% of their gene content, with the highest variability in gene presence as well as gene sequence found for proteins involved in host cell interactions, including Opc, NadA, TonB-dependent receptors, RTX toxin, and two-partner secretion system proteins. Whereas housekeeping genes coding for metabolic functions were highly conserved, there were considerable differences in their expression pattern upon adhesion to human nasopharyngeal cells between both strains, including differences in energy metabolism and stress response. In line with these genomic and transcriptomic differences, both strains also showed marked differences in theirin vitroinfectivity and in serum resistance. Taken together, these data support the concept of a polygenic nature of meningococcal virulence comprising differences in the repertoire of adhesins as well as in the regulation of metabolic genes and suggest a prominent role for immune selection and genetic drift in shaping the meningococcal genome.
Metabolic Network Analysis of
Pseudomonas aeruginosa
during Chronic Cystic Fibrosis Lung Infection
Authors: Oberhardt Matthew A. , Goldberg Joanna B. , Hogardt Michael , Papin Jason A.
Published: August 2010

System-level modeling is beginning to be used to decipher high throughput data in the context of disease. In this study, we present an integration of expression microarray data with a genome-scale metabolic reconstruction of
P
seudomonas
aeruginosa
in the context of a chronic cystic fibrosis (CF) lung infection. A genome-scale reconstruction of
P. aeruginosa
metabolism was tailored to represent the metabolic states of two clonally related lineages of
P. aeruginosa
isolated from the lungs of a CF patient at different points over a 44-month time course, giving a mechanistic glimpse into how the bacterial metabolism adapts over time in the CF lung. Metabolic capacities were analyzed to determine how tradeoffs between growth and other important cellular processes shift during disease progression. Genes whose knockouts were either significantly growth reducing or lethal
in silico
were also identified for each time point and serve as hypotheses for future drug targeting efforts specific to the stages of disease progression.
Essential role of ER-α-dependent NO production in resveratrol-mediated inhibition of restenosis
Authors: Khandelwal Alok R. , Hebert Valeria Y. , Dugas Tammy R.
Published: August 2010

Resveratrol (Resv), a red wine polyphenol, is known to exhibit vascular protective effects and reduce vascular smooth muscle cell mitogenesis. Vascular smooth muscle cell proliferation is a critical factor in the pathogenesis of restenosis, the renarrowing of vessels that often occurs after angioplasty and/or stent implantation. Although Resv has been shown to be an estrogen receptor (ER) modulator, the role of the ER in Resv-mediated protection against restenosis has not yet been elucidated in vivo. Therefore, with the use of a mouse carotid artery injury model, our objective was to determine the role of ER in modulating Resv-mediated effects on neointimal hyperplasia. Female wild-type and ER-α−/−mice were administered a high-fat diet ± Resv for 2 wk. A carotid artery endothelial denudation procedure was conducted, and the mice were administered a high-fat diet ± Resv for an additional 2 wk. Resv-treated wild-type mice exhibited a dramatic decrease in restenosis, with an increased arterial nitric oxide (NO) synthase (NOS) activity and NO production. However, in the ER-α−/−mice, Resv failed to afford protection and failed to increase NO production, apparently because of a decreased availability of the NOS cofactor tetrahydrobiopterin. To verify the role of NO in Resv-mediated effects, mice were coadministered Resv plus a nonselective NOS inhibitor, NG-nitro-l-arginine methyl ester (l-NAME). Cotreatment with l-NAME significantly attenuated the antirestenotic properties of Resv. These data thus suggest that Resv inhibits vascular proliferative responses after injury, predominately through an ER-α-dependent increase in NO production.
Roles for soluble guanylate cyclase and a thiol oxidation-elicited subunit dimerization of protein kinase G in pulmonary artery relaxation to hydrogen peroxide
Authors: Neo Boon Hwa , Kandhi Sharath , Wolin Michael S.
Published: August 2010

We have previously provided evidence that hydrogen peroxide (H2O2) stimulates soluble guanylate cyclase (sGC) under conditions where it relaxes isolated endothelium-removed bovine pulmonary arteries (BPAs). Since it was recently reported that H2O2induces coronary vasorelaxation associated with a nitric oxide/cGMP-independent thiol oxidation/subunit dimerization-elicited activation of protein kinase G (PKG), we investigated whether this mechanism participates in the relaxation of BPAs to H2O2. BPAs precontracted with serotonin (incubated under hypoxia to lower endogenous H2O2) were exposed to increasing concentrations of H2O2. It was observed that 0.1–1 mM H2O2caused increased PKG dimerization and relaxation. These responses were associated with increased phosphorylation of vasodilator-stimulated phosphoprotein (VASP) at the serine-239 site known to be mediated by PKG. Treatment of BPAs with 1 mM DTT attenuated PKG dimerization, VASP phosphorylation, and relaxation to H2O2. An organoid culture of BPAs for 48 h with 10 μM 1H-[1,2,4]oxadiazolo[4,3-a]quinoxalin-1-one (ODQ), a heme oxidant inhibitor of sGC activation, depleted sGC expression by 85%, associated with a 67% attenuation of VASP phosphorylation and 48% inhibition of relaxation elicited by 100 μM H2O2. Thus both a sGC activation/cGMP-dependent and a thiol oxidation subunit dimerization/cGMP-independent activation of PKG appear to contribute to the relaxation of BPAs elicited by H2O2.
Disruption of adenylyl cyclase type V does not rescue the phenotype of cardiac-specific overexpression of Gαqprotein-induced cardiomyopathy
Authors: Timofeyev Valeriy , Porter Cliff A. , Tuteja Dipika , Qiu Hong , Li Ning , Tang Tong , Singapuri Anil , Han Pyung-Lim , Lopez Javier E. , Hammond H. Kirk , Chiamvimonvat Nipavan
Published: August 2010

Adenylyl cyclase (AC) is the principal effector molecule in the β-adrenergic receptor pathway. ACVand ACVIare the two predominant isoforms in mammalian cardiac myocytes. The disparate roles among AC isoforms in cardiac hypertrophy and progression to heart failure have been under intense investigation. Specifically, the salutary effects resulting from the disruption of ACVhave been established in multiple models of cardiomyopathy. It has been proposed that a continual activation of ACVthrough elevated levels of protein kinase C could play an integral role in mediating a hypertrophic response leading to progressive heart failure. Elevated protein kinase C is a common finding in heart failure and was demonstrated in murine cardiomyopathy from cardiac-specific overexpression of Gαqprotein. Here we assessed whether the disruption of ACVexpression can improve cardiac function, limit electrophysiological remodeling, or improve survival in the Gαqmouse model of heart failure. We directly tested the effects of gene-targeted disruption of ACVin transgenic mice with cardiac-specific overexpression of Gαqprotein using multiple techniques to assess the survival, cardiac function, as well as structural and electrical remodeling. Surprisingly, in contrast to other models of cardiomyopathy, ACVdisruption did not improve survival or cardiac function, limit cardiac chamber dilation, halt hypertrophy, or prevent electrical remodeling in Gαqtransgenic mice. In conclusion, unlike other established models of cardiomyopathy, disrupting ACVexpression in the Gαqmouse model is insufficient to overcome several parallel pathophysiological processes leading to progressive heart failure.
Dense-body aggregates as plastic structures supporting tension in smooth muscle cells
Authors: Zhang Jie , Herrera Ana M. , Paré Peter D. , Seow Chun Y.
Published: August 2010

The wall of hollow organs of vertebrates is a unique structure able to generate active tension and maintain a nearly constant passive stiffness over a large volume range. These properties are predominantly attributable to the smooth muscle cells that line the organ wall. Although smooth muscle is known to possess plasticity (i.e., the ability to adapt to large changes in cell length through structural remodeling of contractile apparatus and cytoskeleton), the detailed structural basis for the plasticity is largely unknown. Dense bodies, one of the most prominent structures in smooth muscle cells, have been regarded as the anchoring sites for actin filaments, similar to the Z-disks in striated muscle. Here, we show that the dense bodies and intermediate filaments formed cable-like structures inside airway smooth muscle cells and were able to adjust the cable length according to cell length and tension. Stretching the muscle cell bundle in the relaxed state caused the cables to straighten, indicating that these intracellular structures were connected to the extracellular matrix and could support passive tension. These plastic structures may be responsible for the ability of smooth muscle to maintain a nearly constant tensile stiffness over a large length range. The finding suggests that the structural plasticity of hollow organs may originate from the dense-body cables within the smooth muscle cells.
Rho kinase modulates postnatal adaptation of the pulmonary circulation through separate effects on pulmonary artery endothelial and smooth muscle cells
Authors: Alvira Cristina M. , Sukovich David J. , Lyu Shu-Chen , Cornfield David N.
Published: August 2010

At birth, pulmonary vasodilation occurs concomitant with the onset of air-breathing life. Whether and how Rho kinase (ROCK) modulates the perinatal pulmonary vascular tone remains incompletely understood. To more fully characterize the separate and interactive effects of ROCK signaling, we hypothesized that ROCK has discrete effects on both pulmonary artery (PA): 1) endothelial cell (PAEC) nitric oxide (NO) production and contractile state; and 2) smooth muscle cell tone independent of endothelial NO synthase (eNOS) activity. To test these hypotheses, NO production and endothelial barrier function were determined in fetal PAEC under baseline hypoxia and following exposure to normoxia with and without treatment with Y-27632, a specific pharmacological inhibitor of ROCK. In acutely instrumented, late-gestation ovine fetuses, eNOS was inhibited by nitro-l-arginine infusion into the left PA (LPA). Subsequently, fetal lambs were mechanically ventilated (MV) with 100% oxygen in the absence (control period) and presence of Y-27632. In PAEC, treatment with Y-27632 had no effect on cytosolic calcium but did increase normoxia-induced NO production. Moreover, acute normoxia increased PAEC barrier function, an effect that was potentiated by Y-27632. In fetal lambs, MV during the control period had no effect on LPA flow. In contrast, MV after Y-27632 increased LPA flow and fetal arterial Po2(PaO2) and decreased PA pressure. In conclusion, ROCK activity modulates vascular tone in the perinatal pulmonary circulation via combined effects on PAEC NO production, barrier function, and smooth muscle tone. ROCK inhibition may represent a novel treatment strategy for neonatal pulmonary vascular disease.
Anti-Sinicism: Roots in Pre-industrial Colonial Southern Africa
Authors: Harris Karen L.
Published: August 2010

With the Chinese presence on the African continent being perceived and portrayed as a new global phenomenon there has been a concomitant, albeit sporadic and nuanced, emergence of an aversion to things Chinese, gradually permeating popular consciousness. In a postcolonial world these anti-Sinitic or Sino-phobic sentiments are crudely reminiscent of the late nineteenth century colonial cries of the “yellow peril”, which culminated in acts of exclusion and extreme prohibition that singled out and targeted the Chinese in the various colonies across the Atlantic and Pacific including South Africa. This article, however, proposes to trace the genesis of some of anti-Sinicism to a pre-industrial period by considering developments in colonial Southern Africa. It will show how in the early Dutch settler and British colonial periods at the Cape, when the number of Chinese present in the region was miniscule, negative feelings towards the Chinese as the “other” were already apparent and evident in the reactions to them prior to the arrival of the large numbers which came to America, Australasia and Africa from the mid-nineteenth century onwards.
A Silent Invasion? African Views on the Growing Chinese Presence in Africa: The Case of Equatorial Guinea
Authors: Esteban Mario
Published: August 2010

The literature on African perceptions of the Chinese presence in Africa tends to present two different perspectives on this issue. The works based on opinion polls typically emphasize the positive nature of African views on China, whereas the qualitatively grounded research often point to the presence of both positive and negative perceptions in African discourses on China. Due to the traditional friendship between Beijing and Malabo, the capital of Equatorial Guinea, the Equatoguinean people seemingly have a positive image of China, but the recent fast mounting Chinese presence in the country has started to raise mixed feelings among the bulk of the population. The local political and economic privileged classes who have benefitted most from the growing Chinese presence in Equatorial Guinea tend to be more supportive of this new phenomenon, whereas a minor group of small entrepreneurs and the main opposition parties are firmly critical of China. The present paper intends to shed some light on these contradictory views through a systematic study of the Equatoguinean people’s attitudes towards China and the Chinese, which elucidate three independent variables as the basis of judgment: (1) the nature of the traditional relationship between Africa and China, (2) occupation, and (3) political affiliation.
Chinese Migrants and Society in Mali: Local Constructions of Globalization
Authors: Bourdarias Françoise
Published: August 2010

In this contribution, I shall consider the social perceptions of politics and economy related to the interdependences between Chinese migrants and local population in Mali. Such representations give a particular shape to a large number of identity constructions. In each specific context, the spaces and groups to which Malian and Chinese residents refer, highlight social representations of the two nation-states and societies, of their present relationships. Individual and collective strategies should then be analysed from a point of view stressing the links between economic rationalities and political constructions.
Chinese Farms in Zambia: From Socialist to “Agro-Imperialist” Engagement?
Authors: Hairong Yan , Sautman Barry
Published: August 2010

Participation by Chinese in Zambia’s agriculture has involved three modes of engagement. Two of these, agro-socialist cooperation until the late 1980s and agro-capitalist “win-win,” since the 1990s, can be examined. The third one, an “agro-imperialist” mode, is not an experience, but a speculation, one possible future based on the Chinese state’s potential to allow firms from China to join in the large-scale, export-oriented “land grabs” by big transnational firms that have occurred since food crises in the developing world in the late 2000s. This paper analyzes all three modes of Chinese engagement, but necessarily concentrates on the second, present-day mode, agro-capitalism. We argue that the present Chinese engagement with Zambian agriculture makes small-scale positive contributions to the domestic food market in Zambia. At the same time, its agro-capitalist production involves the exploitation of farm workers that is typically at the core of commercial farming regardless of the national origins of farm owners. We also contend that while Chinese in Zambia and Africa are not carrying out agro-imperialism, they will likely do so if Chinese leaders decide that this practice represents an international standard.
Strife for Independence in an Autocratic Regime: The Egyptian Judges' Club 2000-2007
Authors: Bentlage Björn
Published: August 2010

This article describes and examines a conflict between the Egyptian Judges' Club and the regime in the years 2000-2007. Due to the Club's special status, this conflict illustrates several developments in today's Egypt: It relates to the state of the judiciary, professional syndicates, national elections and overall state politics. The judges' strife for independence serves as an example of the ways and means of representation, contestation and control in an authoritarian regime.
Nijhoff in America: Booksellers from the Netherlands and the Development of American Research Libraries – Part I
Authors: Edelman Hendrik
Published: August 2010

American libraries began to be developed in the middle of the nineteenth century and were among the world's most prominent a century later. The remarkable history of the major libraries in North America, their European models and their strong and innovative leadership is reported here in more or less chronological sequence from the earliest efforts to about 1970, when the unprecedented growth came to an end. The building of the international library collections could not have been achieved without the enterprising efforts of many booksellers in England and on the European continent. Among those who made significant contributions, were three booksellers from the Netherlands: Frederik Muller, Martinus Nijhoff and Swets & Zeitlinger. This article describes their role, but concentrates on Martinus Nijhoff, publisher and bookseller of The Hague, who had by far the longest successful tenure in supplying American libraries with European books and periodicals. Between 1853 and 1971, three generations of the Nijhoff family – Martinus, Wouter and Wouter Pzn –, with their staff members, built one of the leading international publishing and bookselling houses in the Netherlands. Their legacy is permanently embedded in the collections of the great North American libraries.