bluuebunny/crossref_metadata_2025 huggingface dataset:
Organism impact assessment: risk analysis for post-incursion management
Authors: Campbell Marnie L.
Published: May 2008

Campbell, M. L. 2008. Organism impact assessment: risk analysis for post-incursion management. – ICES Journal of Marine Science, 65: 795–804. Risk analysis is a management tool that is becoming increasingly common in biosecurity because it aids decision-making in the face of uncertainty. A risk analysis model [referred to as an organism impact assessment (OIA)] is described, one that was developed in New Zealand to facilitate the management of incursions of introduced aquatic species in a post-border (after quarantine is breached) scenario. The New Zealand biosecurity risk-management framework assesses ecological, cultural, social, and economic values congruently, ensuring that a transparent and objective framework is established with clearly stated ecological and socio-political imperatives. Using expert heuristics and published and observed data, the present study assesses the likelihood that a target introduced species will have ecological, cultural, social, and economic impacts. The consequences (impact and/or change) of such events are then determined, to establish a relative risk ranking, using consequence matrices to aid assessment of the ecological, cultural, social, and economic value impacts of species unintentionally introduced to New Zealand. To illustrate the risk model, the OIA for the incursion of the fresh-water diatom Didymosphenia geminata is presented. The likelihood and consequences resulting in risk pertaining to the introduction of D. geminata varied across regions, but based on public perception at the initial incursion location, Southland, D. geminata was considered to be an extreme risk across all core values.
Nonlinear interaction model of subsonic jet noise
Authors: Sandham Neil D , Salgado Adriana M
Published: May 2008

Noise generation in a subsonic round jet is studied by a simplified model, in which nonlinear interactions of spatially evolving instability modes lead to the radiation of sound. The spatial mode evolution is computed using linear parabolized stability equations. Nonlinear interactions are found on a mode-by-mode basis and the sound radiation characteristics are determined by solution of the Lilley–Goldstein equation. Since mode interactions are computed explicitly, it is possible to find their relative importance for sound radiation. The method is applied to a single stream jet for which experimental data are available. The model gives Strouhal numbers of 0.45 for the most amplified waves in the jet and 0.19 for the dominant sound radiation. While in near field axisymmetric and the first azimuthal modes are both important, far-field sound is predominantly axisymmetric. These results are in close correspondence with experiment, suggesting that the simplified model is capturing at least some of the important mechanisms of subsonic jet noise.
Something old, something new
Authors: Aref Hassan
Published: May 2008

Some thoughts on the development of theoretical fluid dynamics in this century and some reflections on the developments of the past century were provided as an introduction to a broad-ranging conference. A written synopsis of these remarks is provided here.
Experimental and theoretical progress in pipe flow transition
Authors: Willis A.P , Peixinho J , Kerswell R.R , Mullin T
Published: May 2008

There have been many investigations of the stability of Hagen–Poiseuille flow in the 125 years since Osborne Reynolds' famous experiments on the transition to turbulence in a pipe, and yet the pipe problem remains the focus of attention of much research. Here, we discuss recent results from experimental and numerical investigations obtained in this new century. Progress has been made on three fundamental issues: the threshold amplitude of disturbances required to trigger a transition
to
turbulence from the laminar state; the threshold Reynolds number flow below which a disturbance decays
from
turbulence to the laminar state, with quantitative agreement between experimental and numerical results; and understanding the relevance of recently discovered families of unstable travelling wave solutions to transitional and turbulent pipe flow.
Global responses of terrestrial productivity to contemporary climatic oscillations
Authors: Woodward F.I , Lomas M.R , Quaife T
Published: May 2008

The terrestrial biosphere is subjected to a wide range of natural climatic oscillations. Best known is the El Niño–southern oscillation (ENSO) that exerts globally extensive impacts on crops and natural vegetation. A 50-year time series of ENSO events has been analysed to determine those geographical areas that are reliably impacted by ENSO events. Most areas are impacted by changes in precipitation; however, the Pacific Northwest is warmed by El Niño events. Vegetation gross primary production (GPP) has been simulated for these areas, and tests well against independent satellite observations of the normalized difference vegetation index. Analyses of selected geographical areas indicate that changes in GPP often lead to significant changes in ecosystem structure and dynamics. The Pacific decadal oscillation (PDO) is another climatic oscillation that originates from the Pacific and exerts global impacts that are rather similar to ENSO events. However, the longer period of the PDO provided two phases in the time series with a cool phase from 1951 to 1976 and a warm phase from 1977 to 2002. It was notable that the cool phase of the PDO acted additively with cool ENSO phases to exacerbate drought in the earlier period for the southwest USA. By contrast in India, the cool phase of the PDO appears to reduce the negative impacts of warm ENSO events on crop production.
The evolution of inorganic carbon concentrating mechanisms in photosynthesis
Authors: Raven John A , Cockell Charles S , De La Rocha Christina L
Published: May 2008

Inorganic carbon concentrating mechanisms (CCMs) catalyse the accumulation of CO2around rubisco in all cyanobacteria, most algae and aquatic plants and in C4and crassulacean acid metabolism (CAM) vascular plants. CCMs are polyphyletic (more than one evolutionary origin) and involve active transport of, CO2and/or H+, or an energized biochemical mechanism as in C4and CAM plants. While the CCM in almost all C4plants and many CAM plants is constitutive, many CCMs show acclimatory responses to variations in the supply of not only CO2but also photosynthetically active radiation, nitrogen, phosphorus and iron. The evolution of CCMs is generally considered in the context of decreased CO2availability, with only a secondary role for increasing O2. However, the earliest CCMs may have evolved in oxygenic cyanobacteria before the atmosphere became oxygenated in stromatolites with diffusion barriers around the cells related to UV screening. This would decrease CO2availability to cells and increase the O2concentration within them, inhibiting rubisco and generating reactive oxygen species, including O3.
Phylogenetic and evolutionary relationships of RubisCO and the RubisCO-like proteins and the functional lessons provided by diverse molecular forms
Authors: Tabita F. Robert , Hanson Thomas E , Satagopan Sriram , Witte Brian H , Kreel Nathan E
Published: May 2008

Ribulose 1,5-bisphosphate (RuBP) carboxylase/oxygenase (RubisCO) catalyses the key reaction by which inorganic carbon may be assimilated into organic carbon. Phylogenetic analyses indicate that there are three classes of bona fide RubisCO proteins, forms I, II and III, which all catalyse the same reactions. In addition, there exists another form of RubisCO, form IV, which does not catalyse RuBP carboxylation or oxygenation. Form IV is actually a homologue of RubisCO and is called the RubisCO-like protein (RLP). Both RubisCO and RLP appear to have evolved from an ancestor protein in a methanogenic archaeon, and comprehensive analyses indicate that the different forms (I, II, III and IV) contain various subgroups, with individual sequences derived from representatives of all three kingdoms of life. The diversity of RubisCO molecules, many of which function in distinct milieus, has provided convenient model systems to study the ways in which the active site of this protein has evolved to accommodate necessary molecular adaptations. Such studies have proven useful to help provide a framework for understanding the molecular basis for many important aspects of RubisCO catalysis, including the elucidation of factors or functional groups that impinge on RubisCO carbon dioxide/oxygen substrate discrimination.
To concentrate or ventilate? Carbon acquisition, isotope discrimination and physiological ecology of early land plant life forms
Authors: Meyer Moritz , Seibt Ulli , Griffiths Howard
Published: May 2008

A comparative study has been made of the photosynthetic physiological ecology and carbon isotope discrimination characteristics for modern-day bryophytes and closely related algal groups. Firstly, the extent of bryophyte distribution and diversification as compared with more advanced land plant groups is considered. Secondly, measurements of instantaneous carbon isotope discrimination (Δ), photosynthetic CO2assimilation and electron transport rates were compared during the drying cycles. The extent of surface diffusion limitation (when wetted), internal conductance and water use efficiency (WUE) at optimal tissue water content (TWC) were derived for liverworts and a hornwort from contrasting habitats and with differing degrees of thallus ventilation (as intra-thalline cavities and internal airspaces). We also explore how the operation of a biophysical carbon-concentrating mechanism (CCM) tempers isotope discrimination characteristics in two other hornworts, as well as the green algaeColeochaete orbicularisandChlamydomonas reinhardtii. The magnitude ofΔwas compared for each life form over a drying curve and used to derive the surface liquid-phase conductance (when wetted) and internal conductance (at optimal TWC). The magnitude of external and internal conductances, and WUE, was higher for ventilated, compared with non-ventilated, liverworts and hornworts, but the values were similar within each group, suggesting that both factors have been optimized for each life form. For the hornworts, leakiness of the CCM was highest forMegaceros vincentianusandC. orbicularis(approx. 30%) and, at 5%, lowest inC. reinhardtiigrown under ambient CO2concentrations. Finally, evidence for the operation of a CCM in algae and hornworts is considered in terms of the probable role of the chloroplast pyrenoid, as the origins, structure and function of this enigmatic organelle are explored during the evolution of land plants.
Electrons, life and the evolution of Earth's oxygen cycle
Authors: Falkowski Paul G , Godfrey Linda V
Published: May 2008

The biogeochemical cycles of H, C, N, O and S are coupled via biologically catalysed electron transfer (redox) reactions. The metabolic processes responsible for maintaining these cycles evolved over the firstca2.3 Ga of Earth's history in prokaryotes and, through a sequence of events, led to the production of oxygen via the photobiologically catalysed oxidation of water. However, geochemical evidence suggests that there was a delay of several hundred million years before oxygen accumulated in Earth's atmosphere related to changes in the burial efficiency of organic matter and fundamental alterations in the nitrogen cycle. In the latter case, the presence of free molecular oxygen allowed ammonium to be oxidized to nitrate and subsequently denitrified. The interaction between the oxygen and nitrogen cycles in particular led to a negative feedback, in which increased production of oxygen led to decreased fixed inorganic nitrogen in the oceans. This feedback, which is supported by isotopic analyses of fixed nitrogen in sedimentary rocks from the Late Archaean, continues to the present. However, once sufficient oxygen accumulated in Earth's atmosphere to allow nitrification to out-compete denitrification, a new stable electron ‘market’ emerged in which oxygenic photosynthesis and aerobic respiration ultimately spread via endosymbiotic events and massive lateral gene transfer to eukaryotic host cells, allowing the evolution of complex (i.e. animal) life forms. The resulting network of electron transfers led a gas composition of Earth's atmosphere that is far from thermodynamic equilibrium (i.e. it is an emergent property), yet is relatively stable on geological time scales. The early coevolution of the C, N and O cycles, and the resulting non-equilibrium gaseous by-products can be used as a guide to search for the presence of life on terrestrial planets outside of our Solar System.
The evolution of photosynthesis…again?
Authors: Rothschild Lynn J
Published: May 2008

‘Replaying the tape’ is an intriguing ‘would it happen again?’ exercise. With respect to broad evolutionary innovations, such as photosynthesis, the answers are central to our search for life elsewhere. Photosynthesis permits a large planetary biomass on Earth. Specifically, oxygenic photosynthesis has allowed an oxygenated atmosphere and the evolution of large metabolically demanding creatures, including ourselves. There are at least six prerequisites for the evolution of biological carbon fixation: a carbon-based life form; the presence of inorganic carbon; the availability of reductants; the presence of light; a light-harvesting mechanism to convert the light energy into chemical energy; and carboxylating enzymes. All were present on the early Earth. To provide the evolutionary pressure, organic carbon must be a scarce resource in contrast to inorganic carbon. The probability of evolving a carboxylase is approached by creating an inventory of carbon-fixation enzymes and comparing them, leading to the conclusion that carbon fixation in general is basic to life and has arisen multiple times. Certainly, the evolutionary pressure to evolve new pathways for carbon fixation would have been present early in evolution. From knowledge about planetary systems and extraterrestrial chemistry, if organic carbon-based life occurs elsewhere, photosynthesis—although perhaps not oxygenic photosynthesis—would also have evolved.
A genomic analysis of RNA polymerase II modification and chromatin architecture related to 3′ end RNA polyadenylation
Authors: Lian Zheng , Karpikov Alexander , Lian Jin , Mahajan Milind C. , Hartman Stephen , Gerstein Mark , Snyder Michael , Weissman Sherman M.
Published: May 2008

Genomic analyses have been applied extensively to analyze the process of transcription initiation in mammalian cells, but less to transcript 3′ end formation and transcription termination. We used a novel approach to prepare 3′ end fragments from polyadenylated RNA, and mapped the position of the poly(A) addition site using oligonucleotide arrays tiling 1% of the human genome. This approach revealed more 3′ ends than had been annotated. The distribution of these ends relative to RNA polymerase II (PolII) and di- and trimethylated lysine 4 and lysine 36 of histone H3 was compared. A substantial fraction of unannotated 3′ ends of RNA are intronic and antisense to the embedding gene. Poly(A) ends of annotated messages lie on average 2 kb upstream of the end of PolII binding (termination). Near the termination sites, and in some internal sites, unphosphorylated and C-terminal domain (CTD) serine 2 phosphorylated PolII (POLR2A) accumulate, suggesting pausing of the polymerase and perhaps dephosphorylation prior to release. Lysine 36 trimethylation occurs across transcribed genes, sometimes alternating with stretches of DNA in which lysine 36 dimethylation is more prominent. Lysine 36 methylation decreases at or near the site of polyadenylation, sometimes disappearing before disappearance of phosphorylated RNA PolII or release of PolII from DNA. Our results suggest that transcription termination loss of histone 3 lysine 36 methylation and later release of RNA polymerase. The latter is often associated with polymerase pausing. Overall, our study reveals extensive sites of poly(A) addition and provides insights into the events that occur during 3′ end formation.
Mutation of a Rice Gene Encoding a Phenylalanine Biosynthetic Enzyme Results in Accumulation of Phenylalanine and Tryptophan
Authors: Yamada Tetsuya , Matsuda Fumio , Kasai Koji , Fukuoka Shuichi , Kitamura Keisuke , Tozawa Yuzuru , Miyagawa Hisashi , Wakasa Kyo
Published: May 2008

Two distinct biosynthetic pathways for Phe in plants have been proposed: conversion of prephenate to Phe via phenylpyruvate or arogenate. The reactions catalyzed by prephenate dehydratase (PDT) and arogenate dehydratase (ADT) contribute to these respective pathways. The Mtr1 mutant of rice (Oryza sativa) manifests accumulation of Phe, Trp, and several phenylpropanoids, suggesting a link between the synthesis of Phe and Trp. Here, we show that the Mtr1 mutant gene (mtr1-D) encodes a form of rice PDT with a point mutation in the putative allosteric regulatory region of the protein. Transformed callus lines expressing mtr1-D exhibited all the characteristics of Mtr1 callus tissue. Biochemical analysis revealed that rice PDT possesses both PDT and ADT activities, with a preference for arogenate as substrate, suggesting that it functions primarily as an ADT. The wild-type enzyme is feedback regulated by Phe, whereas the mutant enzyme showed a reduced feedback sensitivity, resulting in Phe accumulation. In addition, these observations indicate that rice PDT is critical for regulating the size of the Phe pool in plant cells. Feeding external Phe to wild-type callus tissue and seedlings resulted in Trp accumulation, demonstrating a connection between Phe accumulation and Trp pool size.
Auxilin Depletion Causes Self‐Assembly of Clathrin into Membraneless Cages In Vivo
Authors: Hirst Jennifer , Sahlender Daniela A. , Li Sam , Lubben Nienke B. , Borner Georg H. H. , Robinson Margaret S.
Published: May 2008

Auxilin is a cofactor for Hsc70‐mediated uncoating of clathrin‐coated vesicles (CCVs). However, small interfering RNA (siRNA) knockdown of the ubiquitous auxilin 2 in HeLa cells only moderately impairs clathrin‐dependent trafficking. In this study, we show that HeLa cells also express auxilin 1, previously thought to be neuron specific, and that both auxilins need to be depleted for inhibition of clathrin‐mediated endocytosis and intracellular sorting. Depleting both auxilins cause an ∼50% reduction in the number of clathrin‐coated pits at the plasma membrane but enhances the association of clathrin and adaptors with intracellular membranes. CCV fractions isolated from auxilin‐depleted cells have an ∼1.5‐fold increase in clathrin content and more than fivefold increase in the amount of AP‐2 adaptor complex and other endocytic machinery, with no concomitant increase in cargo. In addition, the structures isolated from auxilin‐depleted cells are on average smaller than CCVs from control cells and are largely devoid of membrane, indicating that they are not CCVs but membraneless clathrin cages. Similar structures are observed by electron microscopy in intact auxilin‐depleted HeLa cells. Together, these findings indicate that the two auxilins have overlapping functions and that they not only facilitate the uncoating of CCVs but also prevent the formation of nonproductive clathrin cages in the cytosol.
Voluntary exercise‐induced changes in β2‐adrenoceptor signalling in rat ventricular myocytes
Authors: Stones Rachel , Natali Antonio , Billeter Rudolf , Harrison Simon , White Ed
Published: May 2008

Regular exercise is beneficial to cardiovascular health. We tested whether mild voluntary exercise training modifies key myocardial parameters [ventricular mass, intracellular calcium ([Ca2+]i) handling and the response to β‐adrenoceptor (β‐AR) stimulation] in a manner distinct from that reported for beneficial, intensive training and pathological hypertrophic stimuli. Female rats performed voluntary wheel‐running exercise for 6–7 weeks. The mRNA expression of target proteins was measured in left ventricular tissue using real‐time reverse transcriptase‐polymerase chain reaction. Simultaneous measurement of cell shortening and [Ca2+]i transients were made in single left ventricular myocytes and the inotropic response to β1‐ and β2‐AR stimulation was measured. Voluntary exercise training resulted in cardiac hypertrophy, the heart weight to body weight ratio being significantly greater in trained compared with sedentary animals. However, voluntary exercise caused no significant alteration in the size or time course of myocyte shortening and [Ca2+]i transients or in the mRNA levels of key proteins that regulate Ca2+ handling. The positive inotropic response to β1‐AR stimulation and the level of β1‐AR mRNA were unaltered by voluntary exercise but both mRNA levels and inotropic response to β2‐AR stimulation were significantly reduced in trained animals. The β2‐AR inotropic response was restored by exposure to pertussis toxin. We propose that in contrast to pathological stimuli and to beneficial, intense exercise training, modulation of Ca2+ handling is not a major adaptive mechanism in the response to mild voluntary exercise. In addition, and in a reversal of the situation seen in heart failure, voluntary exercise training maintains the β1‐AR response but reduces the β2‐AR response. Therefore, although voluntary exercise induces cardiac hypertrophy, there are distinct differences between its effects on key myocardial regulatory mechanisms and those of hypertrophic stimuli that eventually cause cardiac decompensation.
Dose‐dependent cardiac effect of oestrogen replacement in mice post‐myocardial infarction
Authors: Zhan Enbo , Keimig Thomas , Xu Jiang , Peterson Edward , Ding Jennifer , Wang Fangfei , Yang Xiao‐Ping
Published: May 2008

Hormonal replacement therapy (HRT) has recently been shown to increase the risk of cardiovascular events in women. However, it is not clear whether the adverse effect of HRT is related to dosage and/or the presence of progestin. Using a mouse model of myocardial infarction (MI), we studied the dose‐effect of oestrogen replacement on mortality and cardiac remodelling and dysfunction post‐MI in the absence of progestin. Six‐week‐old females were subjected to ovariectomy (OVX). A pellet containing a low, moderate or high dose of 17β‐oestradiol (E2; 0.42, 4.2 or 18.8 μg day−1) or placebo was implanted subcutaneously on the day of OVX. Myocardial infarction was induced 8 weeks later, and cardiac morphology and function were evaluated 8 weeks after MI. We found that E2 at moderate and high doses adversely affected mortality. A low dose of E2 that restored plasma oestrogen close to physiological levels had no significant effect on mortality but tended to improve cardiac function and remodelling, associated with reduced fibrosis and increased capillary density. At the moderate dose, E2 exacerbated cardiac fibrosis, hypertrophy, dysfunction and dilatation, associated with liver and kidney enlargement and ascites. Protein kinase C and extracellular signal‐regulated kinase were increased by MI but were not affected by E2. In summary, E2 at a low dose tended to be cardioprotective. At increased doses that raised plasma oestrogen far beyond the physiological level, E2 was detrimental to the heart. Our data suggest that dosage should be an important consideration when studying the effect of oestrogen replacement on the heart.
An Approach Based on Process Signature Modeling for Roundness Evaluation of Manufactured Items
Authors: Moroni Giovanni , Pacella Massimo
Published: May 2008

In evaluating the geometrical characteristics of mechanical part, cleverness may be added with the definition of an empirical model representing the “signature” left by the manufacturing process used to make the part. This manufacturing signature is the systematic pattern that characterizes all the features machined with that process. If such a model is available, it may be exploited to enhance geometrical inspection accuracy. In this paper, an approach for geometrical inspection of machined profiles is proposed. This approach consists in computing form deviations by reconstructing the actual profile using a frequency model of process signature. The method has been thoroughly investigated in different simulated scenarios and benefits in terms of improved accuracy are demonstrated. Within the paper, a case study, related to roundness of mechanical parts obtained by turning, is used. The relationships between the number of sampled points and fitting algorithms are also pointed out.
Automatic Detection of Tangential Discontinuities in Point Cloud Data
Authors: Song Hao , Feng Hsi-Yung , OuYang Daoshan
Published: May 2008

A point cloud data set, a dense set of discrete coordinate points scanned or sampled from the surface of a 3D physical object or design model, is emerging as a new representation format for geometric modeling. This paper presents a new method to detect tangential discontinuities in point cloud data. The method introduces an original criterion, named as incompatibility, to quantify the magnitude of shape change in the vicinity of a data point. The introduced criterion is unique since in smooth regions of the underlying surface where shape change around a data point is small, the calculated incompatibilities tend to cluster around small values. At points close to tangential discontinuities, the calculated incompatibilities become relatively large. By modeling the incompatibilities of points in smooth regions following a statistical distribution, the proposed method identifies tangential discontinuities as those points whose incompatibilities are considered outliers with respect to the distribution. As the categorization of outliers is in effect independent of the underlying surface shape and sampling conditions of the data points, a threshold can be automatically determined via a generic procedure and used to identify tangential discontinuities. The effectiveness of the proposed method is demonstrated through many case studies using both simulated and practical point cloud data sets.
An Efficient Sensing Localization Algorithm for Free-Form Surface Digitization
Authors: Huang Yunbao , Qian Xiaoping
Published: May 2008

We present a divide-and-conquer method that efficiently finds a near-optimal distribution of sensing locations for free-form surface digitization. We formulate a next-best-point problem and transform the uncertainty of a B-spline surface into a higher-dimensional B-spline surface. This technique allows the use of the convex hull and subdivision properties of B-spline surfaces in the divide-and-conquer algorithm. It thus greatly reduces the search time for determining the next best sensing location.
An Algorithm for the Fast Simulation of Multicomponent Object Deformation
Authors: Zhou Aifang , Hui Kinchuen
Published: May 2008

In this paper, a fast algorithm for the simulation of deformable objects composed of multiple components made of different materials is introduced. By using the boundary element method and considering individual components and their interfaces separately, a relationship between the unknown and known displacements is established. Based on this expression, a component-based condensation method can be applied. This reduces the size of the matrix to be inverted to depend only on the number of unknown displacements of the components with changing boundary condition. To speed up the construction of the required matrices, a maximal matrix method is proposed. By categorizing the changes in boundary conditions, three fast update strategies on matrix inverse are introduced. Based on the maximal matrix method and the matrix inverse update strategy, we define eight easily formed characteristic matrices, which enhance the computation speed further. The efficiency of the proposed method is demonstrated by a set of experimental results.
Creation of Body Surfaces From Reverse-Engineered Components
Authors: Lecrivain Gregory , Kennedy Ian , Slaouti Arezki
Published: May 2008

In the automotive industry or in similar industries, body panels need to be perfectly smooth for visual and aerodynamic reasons. In some cases, the component is a hand-made body part that will require a suitable CAD model for further development and manufacturing. Such a smooth CAD model can only be produced through reverse-engineering and CAD procedures that will make use of accurate surface reconstruction. This paper describes a reverse-engineering procedure for the production of a suitable CAD mesh from which surface reconstruction can take place. It then analyzes and compares three approaches assessing the continuity and the quality of each set of NURBS patches: automatic, semiautomatic, and completely manual surfacing. Recommendations are made for each method when creating CAD surfaces. Finally, a procedure is suggested to optimize the time and the quality of the final CAD model.
Freeform Deformation Versus B-Spline Representation in Inverse Airfoil Design
Authors: Amoiralis Eleftherios I. , Nikolos Ioannis K.
Published: May 2008

Freeform deformation (FFD) is a well established technique for 3D animation applications, used to deform two—or three-dimensional geometrical entities. Over the past few years, FFD technique has aroused growing interest in several scientific communities. In this work, an extensive bibliographic survey of the FFD technique is initially introduced, in order to explore its capabilities in shape parametrization. Moreover, FFD technique is compared to the classical parametrization technique using B-spline curves, in the context of the airfoil design optimization problem, by performing inverse airfoil design tests, with a differential evolution algorithm to serve as the optimizer. The criterion of the comparison between the two techniques is the achieved accuracy in the approximation of the reference pressure distribution. Experiments are presented, comparing FFD to B-spline techniques under the same flow conditions, for various numbers of design variables. Sensitivity analysis is applied for providing further insight into the differences in the performance of the two techniques.
Planktonic and Sediment-Associated Aerobic Methanotrophs in Two Seep Systems along the North American Margin
Authors: Tavormina Patricia L. , Ussler William , Orphan Victoria J.
Published: May 2008

Methane vents are of significant geochemical and ecological importance. Notable progress has been made toward understanding anaerobic methane oxidation in marine sediments; however, the diversity and distribution of aerobic methanotrophs in the water column are poorly characterized. Both environments play an essential role in regulating methane release from the oceans to the atmosphere. In this study, the diversity of particulate methane monooxygenase (
pmoA
) and 16S rRNA genes from two methane vent environments along the California continental margin was characterized. The
pmoA
phylotypes recovered from methane-rich sediments and the overlying water column differed. Sediments harbored the greatest number of unique
pmoA
phylotypes broadly affiliated with the
Methylococcaceae
family, whereas planktonic
pmoA
phylotypes formed three clades that were distinct from the sediment-hosted methanotrophs and distantly related to established methanotrophic clades. Water column-associated phylotypes were highly similar between field sites, suggesting that planktonic methanotroph diversity is controlled primarily by environmental factors rather than geographical proximity. Analysis of 16S rRNA genes from methane-rich waters did not readily recover known methanotrophic lineages, with only a few phylotypes demonstrating distant relatedness to
Methylococcus
. The development of new
pmo
primers increased the recovery of monooxygenase genes from the water column and led to the discovery of a highly diverged monooxygenase sequence which is phylogenetically intermediate to Amo and pMMO. This sequence potentiates insight into the
amo/pmo
superfamily. Together, these findings lend perspective into the diversity and segregation of aerobic methanotrophs within different methane-rich habitats in the marine environment.
Identification of a Cellobiose Utilization Gene Cluster with Cryptic β-Galactosidase Activity inVibrio fischeri
Authors: Adin Dawn M. , Visick Karen L. , Stabb Eric V.
Published: May 2008

Cellobiose utilization is a variable trait that is often used to differentiate members of the familyVibrionaceae. We investigated howVibrio fischeriES114 utilizes cellobiose and found a cluster of genes required for growth on this β-1,4-linked glucose disaccharide. This cluster includes genes annotated as a phosphotransferase system II (celA,celB, andcelC), a glucokinase (celK), and a glucosidase (celG). Directly downstream ofcelCBGKAiscelI, which encodes a LacI family regulator that repressesceltranscription in the absence of cellobiose. When thecelCBGKAIgene cluster was transferred to cellobiose-negative strains ofVibrioandPhotobacterium, the cluster conferred the ability to utilize cellobiose. Genomic analyses of naturally cellobiose-positiveVibriospecies revealed thatV. salmonicidahas a homolog of thecelCBGKAIcluster, butV. vulnificusdoes not. Moreover, bioinformatic analyses revealed that CelG and CelK share the greatest homology with glucosidases and glucokinases in the phylumFirmicutes. These observations suggest that distinct genes for cellobiose utilization have been acquired by different lineages within the familyVibrionaceae. In addition, the loss of thecelIregulator, but not the structural genes, attenuated the ability ofV. fischerito compete for colonization of its natural host,Euprymna scolopes, suggesting that repression of thecelgene cluster is important in this symbiosis. Finally, we show that theV. fischericellobioase (CelG) preferentially cleaves β-d-glucose linkages but also cleaves β-d-galactose-linked substrates such as 5-bromo-4-chloro-3-indolyl-β-d-galactoside (X-gal), a finding that has important implications for the use oflacZas a marker or reporter gene inV. fischeri.
Preferential Use of an Anode as an Electron Acceptor by an Acidophilic Bacterium in the Presence of Oxygen
Authors: Malki Moustafa , De Lacey Antonio L. , Rodríguez Nuria , Amils Ricardo , Fernandez Victor M.
Published: May 2008

Several anaerobic metal-reducing bacteria have been shown to be able to donate electrons directly to an electrode. This property is of great interest for microbial fuel cell development. To date, microbial fuel cell design requires avoiding O
2
diffusion from the cathodic compartment to the sensitive anodic compartment. Here, we show that
Acidiphilium
sp. strain 3.2 Sup 5 cells that were isolated from an extreme acidic environment are able to colonize graphite felt electrodes. These bacterial electrodes were able to produce high-density electrocatalytic currents, up to 3 A/m
2
at a poised potential of +0.15 V (compared to the value for the reference standard calomel electrode) in the absence of redox mediators, by oxidizing glucose even at saturating air concentrations and very low pHs.
Biosynthetic Intermediate Analysis and Functional Homology Reveal a Saxitoxin Gene Cluster in Cyanobacteria
Authors: Kellmann Ralf , Mihali Troco Kaan , Jeon Young Jae , Pickford Russell , Pomati Francesco , Neilan Brett A.
Published: May 2008

Saxitoxin (STX) and its analogues cause the paralytic shellfish poisoning (PSP) syndrome, which afflicts human health and impacts coastal shellfish economies worldwide. PSP toxins are unique alkaloids, being produced by both prokaryotes and eukaryotes. Here we describe a candidate PSP toxin biosynthesis gene cluster (sxt) fromCylindrospermopsis raciborskiiT3. The saxitoxin biosynthetic pathway is encoded by more than 35 kb, and comparative sequence analysis assigns 30 catalytic functions to 26 proteins. STX biosynthesis is initiated with arginine,S-adenosylmethionine, and acetate by a new type of polyketide synthase, which can putatively perform a methylation of acetate, and a Claisen condensation reaction between propionate and arginine. Further steps involve enzymes catalyzing three heterocyclizations and various tailoring reactions that result in the numerous isoforms of saxitoxin. In the absence of a gene transfer system in these microorganisms, we have revised the description of the known STX biosynthetic pathway, with in silico functional inferences based onsxtopen reading frames combined with liquid chromatography-tandem mass spectrometry analysis of the biosynthetic intermediates. Our results indicate the evolutionary origin for the production of PSP toxins in an ancestral cyanobacterium with genetic contributions from diverse phylogenetic lineages of bacteria and provide a quantum addition to the catalytic collective available for future combinatorial biosyntheses. The distribution of these genes also supports the idea of the involvement of this gene cluster in STX production in various cyanobacteria.
Occurrence and Genetic Diversity of
Bacillus anthracis
Strains Isolated in an Active Wool-Cleaning Factory
Authors: Wattiau Pierre , Klee Silke R. , Fretin David , Van Hessche Mieke , Ménart Marie , Franz Tatjana , Chasseur Camille , Butaye Patrick , Imberechts Hein
Published: May 2008

Culturable microorganisms from various samples taken at an active factory performing wool and goat hair cleaning were isolated and analyzed.
Bacillus anthracis
was found in air filter dust, wastewater, and goat hairs, where it accounted for approximately 1% of the total counts of viable bacteria. Consistent with the countries of origin of the processed material (South Caucasian and Middle Eastern), all
B. anthracis
isolates belonged to the same phylogenetic cluster, as determined by variable-number tandem repeat (VNTR) typing at eight loci. Within this cluster, five closely related VNTR subtypes could be identified, of which two were previously unreported. Additional diversity was observed when more sensitive genetic markers were assayed, demonstrating the multifocal nature of goat hair contamination. Goat hair originating from areas where anthrax is endemic remains a material with high biological risk for modern woolworkers.
Effectiveness of
Bacillus thuringiensis
-Transgenic Chickpeas and the Entomopathogenic Fungus
Metarhizium anisopliae
in Controlling
Helicoverpa armigera
(Lepidoptera: Noctuidae)
Authors: Lawo N. C. , Mahon R. J. , Milner R. J. , Sarmah B. K. , Higgins T. J. V. , Romeis J.
Published: May 2008

The use of genetically modified (Bt) crops expressing lepidopteran-specific Cry proteins derived from the soil bacterium
Bacillus thuringiensis
is an effective method to control the polyphagous pest
Helicoverpa armigera
. As
H. armigera
potentially develops resistance to Cry proteins, Bt crops should be regarded as one tool in integrated pest management. Therefore, they should be compatible with biological control. Bioassays were conducted to understand the interactions between a Cry2Aa-expressing chickpea line, either a susceptible or a Cry2A-resistant
H. armigera
strain, and the entomopathogenic fungus
Metarhizium anisopliae
. In a first concentration-response assay, Cry2A-resistant larvae were more tolerant of
M. anisopliae
than susceptible larvae, while in a second bioassay, the fungus caused similar mortalities in the two strains fed control chickpea leaves. Thus, resistance to Cry2A did not cause any fitness costs that became visible as increased susceptibility to the fungus. On Bt chickpea leaves, susceptible
H. armigera
larvae were more sensitive to
M. anisopliae
than on control leaves. It appeared that sublethal damage induced by the
B. thuringiensis
toxin enhanced the effectiveness of
M. anisopliae
. For Cry2A-resistant larvae, the mortalities caused by the fungus were similar when they were fed either food source. To examine which strain would be more likely to be exposed to the fungus, their movements on control and Bt chickpea plants were compared. Movement did not appear to differ among larvae on Bt or conventional chickpeas, as indicated by the number of leaflets damaged per leaf. The findings suggest that Bt chickpeas and
M. anisopliae
are compatible to control
H. armigera
.
Isolation of Bacteria Whose Growth Is Dependent on High Levels of CO
2
and Implications of Their Potential Diversity
Authors: Ueda Kenji , Tagami Yudai , Kamihara Yuka , Shiratori Hatsumi , Takano Hideaki , Beppu Teruhiko
Published: May 2008

Although some bacteria require an atmosphere with high CO
2
levels for their growth, CO
2
is not generally supplied to conventional screening cultures. Here, we isolated 84 bacterial strains exhibiting high-CO
2
dependence. Their phylogenetic affiliations imply that high-CO
2
culture has potential as an effective method to isolate unknown microorganisms.
Synthesis of the Compatible Solute Ectoine in
Virgibacillus pantothenticus
Is Triggered by High Salinity and Low Growth Temperature
Authors: Kuhlmann Anne U. , Bursy Jan , Gimpel Silvy , Hoffmann Tamara , Bremer Erhard
Published: May 2008

The quantification of the intracellular concentration of ectoine in
Virgibacillus pantothenticus
revealed that the production of this compatible solute is triggered either by an increase in the external salinity or by a reduction in the growth temperature. This finding reflects increased transcription of the ectoine biosynthetic operon (
ectABC
) under both environmental conditions.
Genotypic Characterization and Prevalence of Virulence Factors among Canadian
Escherichia coli
O157:H7 Strains
Authors: Ziebell Kim , Steele Marina , Zhang Yongxiang , Benson Andrew , Taboada Eduardo N. , Laing Chad , McEwen Scott , Ciebin Bruce , Johnson Roger , Gannon Victor
Published: May 2008

In this study, the association between genotypic and selected phenotypic characteristics was examined in a collection of Canadian
Escherichia coli
O157:H7 strains isolated from humans and cattle in the provinces of Alberta, Ontario, Saskatchewan, and Quebec. In a subset of 69 strains selected on the basis of specific phage types (PTs), a strong correlation between the lineage-specific polymorphism assay (LSPA6) genotype and PT was observed with all strains of PTs 4, 14, 21, 31, 33, and 87 belonging to the LSPA6 lineage I (LSPA6-LI) genotype, while those of PTs 23, 45, 67, and 74 belonged to LSPA6 lineage II (LSPA6-LII) genotypes. This correlation was maintained when additional strains of each PT were tested.
E. coli
O157:H7 strains with the LSPA6-LI genotype were much more common in the collection than were the LSPA6-LII or lineage I/II (LSPA6-LI/II)-related genotypes (82.6, 11.2, and 5.8%, respectively). Of the strains tested, proportionately more LSPA6-LI than LSPA6-LII genotype strains were isolated from humans (52.7% versus 19.7%) than from cattle (47.8% versus 80.2%). In addition, 96.7% of the LSPA6-LII strains carried the
stx
2c
variant gene, while only 50.0% of LSPA6-LI/II and 2.7% of LSPA6-LI strains carried this gene. LSPA6-LII strains were also significantly more likely to possess the colicin D gene,
cda
(50.8% versus 23.2%), and have combined resistance to streptomycin, sulfisoxazole, and tetracycline (72.1% versus 0.9%) than were LSPA6-LI strains. The LSPA6 genotype- and PT-related characteristics identified may be important markers of specific ecotypes of
E. coli
O157:H7 that have unique epidemiological and virulence characteristics.
A Monoclonal Antibody toHistoplasma capsulatumAlters the Intracellular Fate of the Fungus in Murine Macrophages
Authors: Shi Li , Albuquerque Priscila C. , Lazar-Molnar Eszter , Wang Xintao , Santambrogio Laura , Gácser Attila , Nosanchuk Joshua D.
Published: May 2008

Monoclonal antibodies (MAbs) to a cell surface histone onHistoplasma capsulatummodify murine infection and decrease the growth ofH. capsulatumwithin macrophages. Without the MAbs,H. capsulatumsurvives within macrophages by modifying the intraphagosomal environment. In the present study, we aimed to analyze the affects of a MAb on macrophage phagosomes. Using transmission electron and fluorescence microscopy, we showed that phagosome activation and maturation are significantly greater whenH. capsulatumyeast are opsonized with MAb. The MAb reduced the ability of the organism to regulate the phagosomal pH. Additionally, increased antigen processing and reduced negative costimulation occur in macrophages that phagocytose yeast cells opsonized with MAb, resulting in more-efficient T-cell activation. The MAb alters the intracellular fate ofH. capsulatumby affecting the ability of the fungus to regulate the milieu of the phagosome.
Histone Acetyltransferase Inhibitor Anacardic Acid Causes Changes in Global Gene Expression during In Vitro
Plasmodium falciparum
Development
Authors: Cui Long , Miao Jun , Furuya Tetsuya , Fan Qi , Li Xinyi , Rathod Pradipsinh K. , Su Xin-zhuan , Cui Liwang
Published: May 2008

To better understand the role of histone lysine acetylation in transcription in
Plasmodium falciparum
, we sought to attenuate histone acetyltransferase (HAT) activity using anacardic acid (AA). We showed that AA reversibly and noncompetitively inhibited the HAT activity of recombinant PfGCN5. To a lesser extent, AA inhibited the PfGCN5 activity in parasite nuclear extracts but did not affect histone deacetylase activity. AA blocked the growth of both chloroquine-sensitive and -resistant strains, with a 50% inhibitory concentration of ∼30 μM. Treatment of the parasites with 20 μM of AA for 12 h had no obvious effect on parasite growth or gross morphology but induced hypoacetylation of histone H3 at K9 and K14, but not H4 at K5, K8, K12, and K16, suggesting inhibition of the PfGCN5 HAT. Microarray analysis showed that this AA treatment resulted in twofold or greater change in the expression of 271 (∼5%) parasite genes in late trophozoites, among which 207 genes were downregulated. Cluster analysis of gene expression indicated that AA mostly downregulated active genes, and this gene pool significantly overlapped with that enriched for H3K9 acetylation. We further demonstrated by chromatin immunoprecipitation and real-time PCR that AA treatment reduced acetylation near the putative promoters of a set of downregulated genes. This study suggests that the parasiticidal effect of AA is at least partially associated with its inhibition of PfGCN5 HAT, resulting in the disturbance of the transcription program in the parasites.