bluuebunny/crossref_metadata_2025 huggingface dataset:
The Role of the Coordinating Center in the Obesity Prevention at the Worksite Consortium
Authors: Stevens Victor J. , Donald Judy
Published: April 2008

This paper describes the role of the Coordinating Center for a seven‐project consortium funded through a common request for applications. The seven studies are focusing on prevention and treatment of obesity at worksites. These projects are being conducted at different types of work sites that have diverse employee populations. The Center's functions include identifying opportunities for collaboration, encouraging communication among the project investigators, facilitating the adoption of common measures, combining data from two or more projects to achieve greater statistical power, and pooling data on measures such as physical activity, work productivity, health care use, and return on investment. To these ends, the Coordinating Center helped to develop a committee structure within the consortium, established a communications and data transmission web site, and arranged conference calls, committee meetings, and paper writing groups. The development and implementation of these functions are described in this paper.
Rashba spin splitting of the minibands of coupled InAs∕GaAs pyramid quantum dots
Authors: Zhang Xiu-Wen , Xu Qiang , Fan Wei-Jun , Luo Jun-Wei , Li Shu-Shen , Xia Jian-Bai
Published: April 2008

The Rashba spin splitting of the minibands of coupled InAs∕GaAs pyramid quantum dots is investigated using the k⋅p method and valence force field model. The Rashba splitting of the two dimensional miniband in the lateral directions is found due to the structure inversion asymmetry in the vertical direction while the miniband in the vertical direction has no Rashba spin splitting. As the space between dots increases, the Rashba coefficients decrease and the conduction-band effective mass increases. This Rashba spin splitting of the minibands will significantly affect the spin transport properties between quantum dots.
Saturation mutagenesis of putative catalytic residues of benzoylformate decarboxylase provides a challenge to the accepted mechanism
Authors: Yep Alejandra , Kenyon George L. , McLeish Michael J.
Published: April 2008

Benzoylformate decarboxylase from
Pseudomonas putida
(
Pp
BFDC) is a thiamin diphosphate-dependent enzyme that carries out the nonoxidative decarboxylation of aromatic 2-keto acids. The x-ray structure of
Pp
BFDC suggested that Ser-26, His-70, and His-281 would play important roles in its catalytic mechanism, and the S26A, H70A, and H281A variants all exhibited greatly impaired catalytic activity. Based on stopped-flow studies with the alanine mutants, it was proposed that the histidine residues acted as acid-base catalysts, whereas Ser-26 was involved in substrate binding and played a significant, albeit less well defined, role in catalysis. While developing a saturation mutagenesis protocol to examine residues involved in
Pp
BFDC substrate specificity, we tested the procedure on His-281. To our surprise, we found that His-281, which is thought to be necessary for protonation of the carbanion/enamine intermediate, could be replaced by phenyl alanine with only a 5-fold decrease in
k
cat
. Even more surprising were our subsequent observations (
i
) that His-70 could be replaced by threonine or leucine with approximately a 30-fold decrease in
k
cat
/
K
m
compared with a 4,000-fold decrease for the H70A variant and (
ii
) that Ser-26, which forms hydrogen bonds with the substrate carboxylate, could be replaced by threonine, leucine, or methionine without significant loss of activity. These results call into question the assigned roles for Ser-26, His-70, and His-281. Further, they demonstrate the danger in assigning catalytic function based solely on results with alanine mutants and show that saturation mutagenesis is a valuable tool in assessing the role and relative importance of putative catalytic residues.
The catalytic scaffold of the haloalkanoic acid dehalogenase enzyme superfamily acts as a mold for the trigonal bipyramidal transition state
Authors: Lu Zhibing , Dunaway-Mariano Debra , Allen Karen N.
Published: April 2008

The evolution of new catalytic activities and specificities within an enzyme superfamily requires the exploration of sequence space for adaptation to a new substrate with retention of those elements required to stabilize key intermediates/transition states. Here, we propose that core residues in the large enzyme family, the haloalkanoic acid dehalogenase enzyme superfamily (HADSF) form a “mold” in which the trigonal bipyramidal transition states formed during phosphoryl transfer are stabilized by electrostatic forces. The vanadate complex of the hexose phosphate phosphatase BT4131 from
Bacteroides thetaiotaomicron
VPI-5482 (HPP) determined at 1.00 Å resolution via X-ray crystallography assumes a trigonal bipyramidal coordination geometry with the nucleophilic Asp-8 and one oxygen ligand at the apical position. Remarkably, the tungstate in the complex determined to 1.03 Å resolution assumes the same coordination geometry. The contribution of the general acid/base residue Asp-10 in the stabilization of the trigonal bipyramidal species via hydrogen-bond formation with the apical oxygen atom is evidenced by the 1.52 Å structure of the D10A mutant bound to vanadate. This structure shows a collapse of the trigonal bipyramidal geometry with displacement of the water molecule formerly occupying the apical position. Furthermore, the 1.07 Å resolution structure of the D10A mutant complexed with tungstate shows the tungstate to be in a typical “phosphate-like” tetrahedral configuration. The analysis of 12 liganded HADSF structures deposited in the protein data bank (PDB) identified stringently conserved elements that stabilize the trigonal bipyramidal transition states by engaging in favorable electrostatic interactions with the axial and equatorial atoms of the transferring phosphoryl group.
Molecular assembly for high-performance bivalent nucleic acid inhibitor
Authors: Kim Youngmi , Cao Zehui , Tan Weihong
Published: April 2008

It is theorized that multivalent interaction can result in better affinity and selectivity than monovalent interaction in the design of high-performance ligands. Accordingly, biomolecular engineers are increasingly taking advantage of multivalent interactions to fabricate novel molecular assemblies, resulting in new functions for ligands or enhanced performance of existing ligands. Substantial efforts have been expended in using small molecules or epitopes of antibodies for designing multifunctional or better-performing ligands. However, few attempts to use nucleic acid aptamers as functional domains have been reported. In this study, we explore the design of bivalent nucleic acid ligands by using thrombin and its aptamers as the model by which to evaluate its functions. By assembling two thrombin-binding aptamers with optimized design parameters, this assembly has resulted in the successful development of a nucleic acid-based high-performance bivalent protein inhibitor. Our experimentation proved (
i
) that the simultaneous binding of two aptamers after linkage achieved 16.6-fold better inhibition efficiency than binding of the monovalent ligand and (
ii
) that such an improvement originated from changes in the kinetics of the binding interactions, with a
k
off
rate ≈1/50 as fast. In addition, the newly generated aptamer assembly is an excellent anticoagulant reagent when tested with different samples. Because this optimized ligand design offers a simple and noninvasive means of accomplishing higher performance from known functional aptamers, it holds promise as a potent antithrombin agent in the treatment of various diseases related to abnormal thrombin activities.
Bacterial addiction module toxin Doc inhibits translation elongation through its association with the 30S ribosomal subunit
Authors: Liu Mohan , Zhang Yonglong , Inouye Masayori , Woychik Nancy A.
Published: April 2008

Bacterial toxin–antitoxin (TA) systems (or “addiction modules”) typically facilitate cell survival during intervals of stress by inducing a state of reversible growth arrest. However, upon prolonged stress, TA toxin action leads to cell death. TA systems have also been implicated in several clinically important phenomena: biofilm formation, bacterial persistence during antibiotic treatment, and bacterial pathogenesis. TA systems harbored by pathogens also serve as attractive antibiotic targets. To date, the mechanism of action of the majority of known TA toxins has not yet been elucidated. We determined the mode of action of the Doc toxin of the Phd-Doc TA system. Doc expression resulted in rapid cell growth arrest and marked inhibition of translation without significant perturbation of transcription or replication. However, Doc did not cleave mRNA as do other addiction-module toxins whose activities result in translation inhibition. Instead, Doc induction mimicked the effects of treatment with the aminoglycoside antibiotic hygromycin B (HygB): Both Doc and HygB interacted with 30S ribosomal subunits, stabilized polysomes, and resulted in a significant increase in mRNA half-life. HygB also competed with ribosome-bound Doc, whereas HygB-resistant mutants suppressed Doc toxicity, suggesting that the Doc-binding site includes that of HygB (i.e., helix 44 region of 16S rRNA containing the A, P, and E sites). Overall, our results illuminate an intracellular target and mechanism of TA toxin action drawn from aminoglycoside antibiotics: Doc toxicity is the result of inhibition of translation elongation, possibly at the translocation step, through its interaction with the 30S ribosomal subunit.
Fine structure mapping of a gene-rich region of wheat carrying
Ph1
, a suppressor of crossing over between homoeologous chromosomes
Authors: Sidhu Gaganpreet K. , Rustgi Sachin , Shafqat Mustafa N. , von Wettstein Diter , Gill Kulvinder S.
Published: April 2008

The wheat gene-rich region (GRR) 5L0.5 contains many important genes, including
Ph1
, the principal regulator of chromosome pairing. Comparative marker analysis identified 32 genes for the GRR controlling important agronomic traits. Detailed characterization of this region was accomplished by first physically localizing 213 wheat group 5L-specific markers, using group 5 nulli-tetrasomics, three
Ph1
gene deletion/insertion mutants, and nine terminal deletion lines with their breakpoints around the 5L0.5 region. The
Ph1
gene was localized to a much smaller region within the GRR (
Ph1
gene region). Of the 61 markers that mapped in the four subregions of the GRR, 9 mapped in the
Ph1
gene region. High stringency sequence comparison (
e
< 1 ×10
−25
) of 157 group 5L-specific wheat ESTs identified orthologs for 80% sequences in rice and 71% in
Arabidopsis
. Rice orthologs were present on all rice chromosomes, although most (34%) were on rice chromosome 9 (R9). No single collinear region was identified in
Arabidopsis
even for a smaller region, such as the
Ph1
gene region. Seven of the nine
Ph1
gene region markers mapped within a 450-kb region on R9 with the same gene order. Detailed domain/motif analysis of the 91 putative genes present in the 450-kb region identified 26 candidates for the
Ph1
gene, including genes involved in chromatin reorganization, microtubule attachment, acetyltransferases, methyltransferases, DNA binding, and meiosis/anther specific proteins. Five of these genes shared common domains/motifs with the meiosis specific genes
Zip1
,
Scp1
,
Cor1
,
RAD50
,
RAD51
, and
RAD57
. Wheat and
Arabidopsis
homologs for these rice genes were identified.
Physics analysis of the ITER ECW system for optimized performance
Authors: Ramponi G. , Farina D. , Henderson M.A. , Poli E. , Sauter O. , Saibene G. , Zohm H. , Zucca C.
Published: April 2008

A predictive analysis of the capabilities of the ITER electron cyclotron wave system is presented in this work. Modifications of both the upper launcher and the equatorial launcher aimed at increasing the potentialities of the system are identified and discussed. A modification of the upper launcher has already been incorporated in the updated front steering design called the extended physics launcher. By adopting different deposition ranges for the upper and lower steering mirrors, this design offers the flexibility to drive current from the radial region required for the stabilization of neoclassical tearing modes (NTM) up to that required for sawtooth control, allowing a synergy with the equatorial launcher. Here a comparison of the performance of the new design of the upper launcher with those of a dropped upper launcher is performed, showing that better performance for both NTM stabilization and sawtooth control may be obtained by lowering the upper port location. An analysis of the EC current driven by the equatorial launcher is also presented, showing that adding to the present design the possibility to drive counter-current in addition to the existing co-current capability would increase the flexibility of the system. The behaviour of all launchers at reduced magnetic fields is also discussed.
Nuclear analyses for the ITER ECRH launcher
Authors: Serikov A. , Fischer U. , Heidinger R. , Spaeh P. , Stickel S. , Tsige-Tamirat H.
Published: April 2008

Computational results of the nuclear analyses for the ECRH launcher integrated into the ITER upper port are presented. The purpose of the analyses was to provide the proof for the launcher design that the nuclear requirements specified in the ITER project can be met. The aim was achieved on the basis of 3D neutronics radiation transport calculations using the Monte Carlo code MCNP. In the course of the analyses an adequate shielding configuration against neutron and gamma radiation was developed keeping the necessary empty space for mm-waves propagation in accordance with the ECRH physics guidelines. Different variants of the shielding configuration for the extended performance front steering launcher (EPL) were compared in terms of nuclear response functions in the critical positions. Neutron damage (dpa), nuclear heating, helium production rate, neutron and gamma fluxes have been calculated under the conditions of ITER operation. It has been shown that the radiation shielding criteria are satisfied and the supposed shutdown dose rates are below the ITER nuclear design limits.
Domain annotation of trimeric autotransporter adhesins—daTAA
Authors: Szczesny Pawel , Lupas Andrei
Published: April 2008

Motivation: Trimeric autotransporter adhesins (TAAs), such as Yersinia YadA, Neisseria NadA, Moraxella UspAs, Haemophilus Hia and Bartonella BadA, are important pathogenicity factors of proteobacteria. Their high sequence diversity and distinct mosaic-like structure lead to difficulties in the annotation of their sequences. These stem from the large number of short repeats, the presence of compositionally unusual coiled-coils, fuzzy domain boundaries and regions of seemingly low sequence complexity.

Results: We have developed a workflow, named daTAA, for the accurate domain annotation of TAAs. Its core consists of manually curated alignments and of knowledge-based rules that enhance assignments made by sequence similarity. Compared to general domain annotation servers such as PFAM, daTAA captures more domains and provides more sensitive domain detection, as well as integrated and detailed coiled-coil assignments.

Availability: The daTAA server is freely accessible at http://toolkit.tuebingen.mpg.de/dataa

Contact:  andrei.lupas@tuebingen.mpg.de

Supplementary information: Supplementary data are available at Bioinformatics online.
Development of a method to reduce the spread of the ascidian Didemnum vexillum with aquaculture transfers
Authors: Denny C. M.
Published: April 2008

Denny, C. M. 2008. Development of a method to reduce the spread of the ascidian Didemnum vexillum with aquaculture transfers. – ICES Journal of marine Science, 65: 805–810. The colonial ascidian Didemnum vexillum was discovered in Shakespeare Bay (New Zealand) in 2001 and now poses a serious threat to the aquaculture industry. I assess several techniques to eliminate Didemnum from Greenshell™ seed-mussels (Perna canaliculus) in order to reduce the spread of the pest species with aquaculture transfers. Simple approaches based on fresh-water immersion proved ineffective or impractical in controlling Didemnum, so different chemical treatments were evaluated. Initial trials were conducted using acetic acid at concentrations ranging from 0.1 to 10% for a range of exposure times. However, at concentrations or exposure times tolerated by seed-mussels, Didemnum colonies survived with, on average, ∼80% mortality. These results led to the testing of other chemicals, and sodium hypochlorite (bleach) was identified as a potential candidate. It was determined that dipping Didemnum in a 0.5% solution of bleach for 2 min was a 100% effective method of treatment that also left seed-mussels relatively unaffected.
Multiple assessments of introduced seaweeds in the Northwest Atlantic
Authors: Mathieson Arthur C. , Pederson Judith R. , Neefus Christopher D. , Dawes Clinton J. , Bray Troy L.
Published: April 2008

Mathieson, A. C., Pederson, J. R., Neefus, C. D., Dawes, C. J., and Bray, T. L. 2008. Multiple assessments of introduced seaweeds in the Northwest Atlantic. – ICES Journal of Marine Science, 65: 730–741. Historical and recent floristic studies, rapid assessment surveys, and molecular investigations were used to evaluate the occurrence of 20 seaweeds introduced to the Northwest Atlantic, including 2 green, 4 brown, and 14 red algae. Based on floristic comparisons of Mount Desert Island and Casco Bay, ME, from the late 1800s to the early 1900s, some initial records of seaweed introductions were documented, as well as increased numbers of non-indigenous taxa. Detailed floristic studies in southern ME and NH from the mid-1960s to 2007 have revealed expansive patterns for two Asiatic taxa (Codium fragile subsp. tomentosoides and Neosiphonia harveyi). Rapid assessment surveys conducted between the Bay of Fundy and Long Island, NY, during four summers (2002, 2004, 2005, and 2007) revealed seven introduced species and a recent expansion of the Asiatic red alga Grateloupia turuturu into the Gulf of Maine. Molecular evaluations confirmed the presence of several cryptic introduced species of Porphyra from Asia. A synopsis of the dates of introduction, probable vectors, and sources of these 20 introduced taxa in the Northwest Atlantic is given, as well as comparisons of numbers of non-indigenous taxa from other geographies.
Golden hamsters are nocturnal in captivity but diurnal in nature
Authors: Gattermann Rolf , Johnston Robert E , Yigit Nuri , Fritzsche Peter , Larimer Samantha , Özkurt Sakir , Neumann Karsten , Song Zhimin , Colak Ercüment , Johnston Joan , McPhee M. Elsbeth
Published: April 2008

Daily activity rhythms are nearly universal among animals and their specific pattern is an adaptation of each species to its ecological niche. Owing to the extremely consistent nocturnal patterns of activity shown by golden hamsters (
Mesocricetus auratus
) in the laboratory, this species is a prime model for studying the mechanisms controlling circadian rhythms. In contrast to laboratory data, we discovered that female hamsters in the wild were almost exclusively diurnal. These results raise many questions about the ecological variables that shape the activity patterns in golden hamsters and the differences between laboratory and field results.
Anterior-to-posterior wave of buccal expansion in suction feeding fishes is critical for optimizing fluid flow velocity profile
Authors: Bishop Kristin L , Wainwright Peter C , Holzman Roi
Published: April 2008

In fishes that employ suction feeding, coordinating the timing of peak flow velocity with mouth opening is likely to be an important feature of prey capture success because this will allow the highest forces to be exerted on prey items when the jaws are fully extended and the flow field is at its largest. Although it has long been known that kinematics of buccal expansion in feeding fishes are characterized by an anterior-to-posterior wave of expansion, this pattern has not been incorporated in most previous computational models of suction feeding. As a consequence, these models have failed to correctly predict the timing of peak flow velocity, which according to the currently available empirical data should occur around the time of peak gape. In this study, we use a simple fluid dynamic model to demonstrate that the inclusion of an anterior-to-posterior wave of buccal expansion can correctly reproduce the empirically determined flow velocity profile, although only under very constrained conditions, whereas models that do not allow this wave of expansion inevitably predict peak velocity earlier in the strike, when the gape is less than half of its maximum. The conditions that are required to produce a realistic velocity profile are as follows: (i) a relatively long time lag between mouth opening and expansion of the more posterior parts of the mouth, (ii) a short anterior portion of the mouth relative to more posterior sections, and (iii) a pattern of movement that begins slowly and then rapidly accelerates. Greater maximum velocities were generated in simulations without the anterior-to-posterior wave of expansion, suggesting a trade-off between maximizing fluid speed and coordination of peak fluid speed with peak gape.
Existence of solutions to the convection problem in a pseudomeasure-type space
Authors: Ferreira Lucas C.F , Villamizar Roa Elder Jesús
Published: April 2008

We study the well-posedness of a convection problem in a pseudomeasure-type space PM

a

, without assuming that the gravitational field is bounded. Considering the PM

a

space with right homogeneity, the existence of self-similar solutions is proved. Finally, an analysis about asymptotic stability is made.
On the thermodynamics of degradation
Authors: Bryant M.D , Khonsari M.M , Ling F.F
Published: April 2008

The science base that underlies modelling and analysis of machine reliability has remained substantially unchanged for decades. Therefore, it is not surprising that a significant gap exists between available machinery technology and science to capture degradation dynamics for prediction of failure. Further, there is a lack of a systematic technique for the development of accelerated failure testing of machinery components. This article develops a thermodynamic characterization of degradation dynamics, which employs entropy, a measure of thermodynamic disorder, as the fundamental measure of degradation; this relates entropy generation to irreversible degradation and shows that components of material degradation can be related to the production of corresponding thermodynamic entropy by the irreversible dissipative processes that characterize the degradation. A theorem that relates entropy generation to irreversible degradation, via generalized thermodynamic forces and degradation forces, is constructed. This theorem provides the basis of a structured method for formulating degradation models consistent with the laws of thermodynamics. Applications of the theorem to problems involving sliding wear and fretting wear, caused by effects of friction and associated with tribological components, are presented.
Velocity profile in the Knudsen layer according to the Boltzmann equation
Authors: Lilley Charles R , Sader John E
Published: April 2008

Flow of a dilute gas near a solid surface exhibits non-continuum effects that are manifested in the Knudsen layer. The non-Newtonian nature of the flow in this region has been the subject of a number of recent studies suggesting that the so-called ‘effective viscosity’ at a solid surface is half that of the standard dynamic viscosity. Using the Boltzmann equation with a diffusely reflecting surface and hard sphere molecules, Lilley & Sader discovered that the flow exhibits a striking power-law dependence on distance from the solid surface where the velocity gradient is singular. Importantly, these findings (i) contradict these recent claims and (ii) are not predicted by existing high-order hydrodynamic flow models. Here, we examine the applicability of these findings to surfaces with arbitrary thermal accommodation and molecules that are more realistic than hard spheres. This study demonstrates that the velocity gradient singularity and power-law dependence arise naturally from the Boltzmann equation, regardless of the degree of thermal accommodation. These results are expected to be of particular value in the development of hydrodynamic models beyond the Boltzmann equation and in the design and characterization of nanoscale flows.
Limitations of Boltzmann's kinetic equation
Authors: Woods L.C
Published: April 2008

It is often assumed that Boltzmann's kinetic equation (BKE) for the evolution of the velocity distribution function
f
(

r

, 

w

, 
t
) in a gas is valid regardless of the magnitude of the Knudsen number defined by
ϵ
≡
τ
d ln 
ϕ
/d
t
, where
ϕ
is a macroscopic variable like the fluid velocity

v

or temperature
T
, and
τ
is the collision interval. Almost all accounts of transport theory based on BKE are limited to terms in
O
(
ϵ
)≪1, although there are treatments in which terms in
O
(
ϵ
2
) are obtained, classic examples being due to Burnett and Grad. The
mathematical
limitations that arise are discussed, for example, by Kreuzer and Cercignani. However, as we shall show, the
physical
limitation to BKE is that it is
not
valid for the terms of order higher than
ϵ
because the assumption of ‘molecular chaos’, which is the basis of Boltzmann's collision integral, is an approximation that applies only up to first order in
ϵ
.

Another difficulty with Boltzmann's collision integral is that it is defined at a point, so that the varying ambient conditions upon which transport depends must be found by Taylor series expansions along particle trajectories. This fails in a strong-field magnetoplasma where, in a single collision interval, the trajectories are almost infinitely repeating gyrations; we shall illustrate this by deriving a dominant
O
(
ϵ
2
) transport equation for a magnetoplasma that
cannot
be found from Boltzmann's equation.

A further problem that sometimes arises in BKE occurs when an external force is present, the equilibrium state being constrained by the stringent Maxwell–Boltzmann conditions. Unless this is removed by a transformation of coordinates, confusion between convection and diffusion is probable. A mathematical theory for transport in tokamaks, termed
neoclassical transport
, is shown to be invalid, one of several errors being the retention of an electric field component in the drift kinetic equation.
Breeding synchrony in colonial birds: from local stress to global harmony
Authors: Jovani Roger , Grimm Volker
Published: April 2008

Why and how birds in colonies often breed in striking synchrony is an unsolved question. In colonies, conspecific birds often destroy eggs and kill chicks, either intentionally or not. We propose that social tranquillity at the time of laying can be achieved if a bird's stress level is partly determined by the agitation of its neighbours. Moreover, we propose that this local process, together with environmental cues, can synchronize breeding between neighbours and through a whole colony. We tested our hypotheses using a generic individual-based model where the breeding predisposition of females was updated daily depending on an increase in the photoperiod (positively) and the stress level of neighbours: negatively if they were agitated, and positively otherwise. A female laid her eggs when her stress level fell to a critical value. Even giving only a low relevance to the neighbour's stress level was enough to synchronize the laying date of neighbours and also of a huge colony. Moreover, females bred in a safer environment, which is known from field studies to increase fitness. Our study highlights the power of local adaptive (individual) behaviour to create global (colony) patterns. We argue that collective patterns such as breeding synchrony in colonial birds could have simple adaptive individual-level explanations.
Macrophysiology for a changing world
Authors: Chown Steven L , Gaston Kevin J
Published: April 2008

The Millennium Ecosystem Assessment (MA) has identified climate change, habitat destruction, invasive species, overexploitation and pollution as the major drivers of biodiversity loss and sources of concern for human well-being. Understanding how these drivers operate and interact and how they might be mitigated are among the most pressing questions facing humanity. Here, we show how macrophysiology—the investigation of variation in physiological traits over large geographical, temporal and phylogenetic scales—can contribute significantly to answering these questions. We do so by demonstrating, for each of the MA drivers, how a macrophysiological approach can or has helped elucidate the impacts of these drivers and their interactions. Moreover, we illustrate that a large-scale physiological perspective can provide insights into previously unrecognized threats to diversity, such as the erosion of physiological variation and stress tolerance, which are a consequence of the removal of large species and individuals from the biosphere. In so doing we demonstrate that environmental physiologists have much to offer the scientific quest to resolve major environmental problems.
Early nutrition and phenotypic development: ‘catch-up’ growth leads to elevated metabolic rate in adulthood
Authors: Criscuolo François , Monaghan Pat , Nasir Lubna , Metcalfe Neil B
Published: April 2008

Resting metabolic rate (RMR) is responsible for up to 50% of total energy expenditure, and so should be under strong selection pressure, yet it shows extensive intraspecific variation and a low heritability. Environmental conditions during growth are thought to have long-term effects through ‘metabolic programming’. Here we investigate whether nutritional conditions early in life can alter RMR in adulthood, and whether this is due to growth acceleration or the change in diet quality that prompts it. We manipulated dietary protein levels during the main growth period of zebra finches (Taeniopygia guttata) such that an episode of poor nutrition occurred with and without growth acceleration. This produced different growth trajectories but a similar adult body mass. Only the diet that induced growth acceleration resulted in a significant (19%) elevation of RMR at adulthood, despite all the birds having been on the same diet after the first month. This is the first study to show that dietary-induced differences in growth trajectories can have a long-term effect on adult metabolic rate. It suggests that modification of metabolic efficiency may be one of the mechanisms mediating the observed long-term costs of accelerated growth, and indicates links between early nutrition and the metabolic syndrome.
Mapping the spawning grounds of North Sea cod (
Gadus morhua
) by direct and indirect means
Authors: Fox Clive J , Taylor Martin , Dickey-Collas Mark , Fossum Petter , Kraus Gerd , Rohlf Norbert , Munk Peter , van Damme Cindy J.G , Bolle Loes J , Maxwell David L , Wright Peter J
Published: April 2008

Despite recent evidence for sub-stock structuring, North Sea cod are assessed as a single unit. As a consequence, knowledge of sub-stock trends is poor. In particular, there are no recent evaluations of which spawning grounds are active. Here we report results from the first ichthyoplankton survey to cover the whole North Sea. Also, this survey, conducted in 2004, was the first to make extensive use of DNA-based molecular methods to unambiguously identify early developmental stage cod eggs. We compare the findings from the plankton survey with estimated egg production inferred from the distribution of mature cod in contemporaneous trawl surveys. Results from both approaches were in general agreement and showed hot spots of egg production around the southern and eastern edges of the Dogger Bank, in the German Bight, the Moray Firth and to the east of the Shetlands. These areas broadly coincide with known spawning locations from the period 1940 to 1970. We were, however, unable to directly detect significant numbers of cod eggs at the historic spawning ground off Flamborough (northeast coast of England). The results demonstrate that most of the major spawning grounds of cod in the North Sea are still active but that some localized populations may have been reduced to the point where it is now difficult to detect the presence of eggs in the plankton.
Identification and Regulation of TPS04/GES, anArabidopsisGeranyllinalool Synthase Catalyzing the First Step in the Formation of the Insect-Induced Volatile C16-Homoterpene TMTT
Authors: Herde Marco , Gärtner Katrin , Köllner Tobias G. , Fode Benjamin , Boland Wilhelm , Gershenzon Jonathan , Gatz Christiane , Tholl Dorothea
Published: April 2008

Volatile secondary metabolites emitted by plants contribute to plant–plant, plant–fungus, and plant–insect interactions. The C16-homoterpene TMTT (for 4,8,12-trimethyltrideca-1,3,7,11-tetraene) is emitted after herbivore attack by a wide variety of plant species, including Arabidopsis thaliana, and is assumed to play a role in attracting predators or parasitoids of herbivores. TMTT has been suggested to be formed as a degradation product of the diterpene alcohol (E,E)-geranyllinalool. Here, we report the identification of Terpene Synthase 04 (TPS04; At1g61120) as a geranyllinalool synthase (GES). Recombinant TPS04/GES protein expressed in Escherichia coli catalyzes the formation of (E,E)-geranyllinalool from the substrate geranylgeranyl diphosphate. Transgenic Arabidopsis lines carrying T-DNA insertions in the TPS04 locus are deficient in (E,E)-geranyllinalool and TMTT synthesis, a phenotype that can be complemented by expressing the GES gene under the control of a heterologous promoter. GES transcription is upregulated under conditions that induce (E,E)-geranyllinalool and TMTT synthesis, including infestation of plants with larvae of the moth Plutella xylostella and treatment with the fungal peptide alamethicin or the octadecanoid mimic coronalon. Induction requires jasmonic acid but is independent from salicylic acid or ethylene. This study paves the ground to address the contribution of TMTT in ecological interactions and to elucidate the signaling network that regulates TMTT synthesis.
Thylakoid Membrane Remodeling during State Transitions inArabidopsis
Authors: Chuartzman Silvia G. , Nevo Reinat , Shimoni Eyal , Charuvi Dana , Kiss Vladimir , Ohad Itzhak , Brumfeld Vlad , Reich Ziv
Published: April 2008

Adaptability of oxygenic photosynthetic organisms to fluctuations in light spectral composition and intensity is conferred by state transitions, short-term regulatory processes that enable the photosynthetic apparatus to rapidly adjust to variations in light quality. In green algae and higher plants, these processes are accompanied by reversible structural rearrangements in the thylakoid membranes. We studied these structural changes in the thylakoid membranes of Arabidopsis thaliana chloroplasts using atomic force microscopy, scanning and transmission electron microscopy, and confocal imaging. Based on our results and on the recently determined three-dimensional structure of higher-plant thylakoids trapped in one of the two major light-adapted states, we propose a model for the transitions in membrane architecture. The model suggests that reorganization of the membranes involves fission and fusion events that occur at the interface between the appressed (granal) and nonappressed (stroma lamellar) domains of the thylakoid membranes. Vertical and lateral displacements of the grana layers presumably follow these localized events, eventually leading to macroscopic rearrangements of the entire membrane network.
Effects of stand tree species composition and diversity on abundance of predatory arthropods
Authors: Vehviläinen Harri , Koricheva Julia , Ruohomäki Kai
Published: April 2008

Diverse plant communities are predicted to have higher abundance of predators as compared to species‐poor ones. In this study we explored whether this prediction holds true for the abundance of predatory arthropods in forest ecosystems, which have been poorly studied in this respect. We collected ground‐dwelling arthropods using pitfall traps from six long‐term forest diversity experiments in Finland, Sweden and UK. The effects of tree species diversity on abundance of five main groups of predatory arthropods (ants, spiders, carabids, staphylinids and opilionids) were examined by means of meta‐analysis. Overall, the diversity of tree species did not affect abundances of predators with the exception of staphylinids, which were more abundant in mixed stands than in monocultures. However, the effects of stand diversity on predator abundance became apparent when analyses were conducted on tree species basis. Preference for stands containing particular tree species was clear in the case of opilionids, carabids and staphylinids, and these preferences overruled the effects of tree species diversity in comparisons between monocultures and mixed stands containing the same tree species. Tree species diversity effects on predator abundance were furthermore mediated by the tree age, plot size and planting density used in the experiment. Overall, our results show that predator abundance does not increase uniformly with increase in tree species diversity, but rather suggest that predators have distinct preferences for stands composed of particular tree species and that these species preferences may overrule the effects of diversity.
The interacting effects of herbivore exclosures and seed addition in a wet meadow
Authors: Fraser L. H. , Madson E. B.
Published: April 2008

Seed limitation may prevent successful restoration of native plant communities. Seed addition is a common restoration practice but the role of small mammals in affecting seedling recruitment is not well understood. The purpose of this investigation was to test the relative effect of seed introduction in combination with small mammal and bird exclosures in an Ohio wet meadow. We ask whether the ambient population of Microtus pennsylvanicus (1) alters species composition (e.g. forb/grass/sedge, invasive, non‐native); (2) influences plant diversity; and (3) reduces the effect of increasing local plant richness through seed introductions. We established a 2×2 factorial design including a seed addition treatment (0 and 20 seed species added) and an exclosure treatment (open and fenced to exclude all mammalian and bird herbivores and granivores). Seeds from twenty native species were selected to represent a broad range of plant life forms typically found in temperate eastern North American wet meadow communities. All species were obligate or facultative wetland species with forbs, grasses and sedges represented. We found that forb species increased inside exclosures, especially in the seed addition treatment. We also found that relative biomass of invasive species was reduced in exclosures and with seed addition. Species richness increased with seed addition; however, exclosures significantly increased species richness and diversity, particularly of those species that were experimentally introduced by seed. Our results support the seed limitation hypotheses. It is also evident that seed and seedling predation are important factors that can control wet meadow community composition and diversity.
Adaptive consequences and heritable basis of asynchronous hatching inNicrophorus vespilloides
Authors: Smiseth Per T. , Hwang Wenbe , Steiger Sandra , Müller Josef K.
Published: April 2008

Asynchronous hatching is an important component of animal reproductive strategies, yet it has been studied almost exclusively in altricial birds. In this study, we provide evidence on the adaptive consequences and the heritable basis of asynchronous hatching in an insect, the burying beetleNicrophorus vespilloides. Parents of this species breed on carcasses of small vertebrates and provide food in the form of predigested carrion for their offspring. We found that the size of the carcass used for breeding had a significant effect on hatching skew towards the earlier part of the hatching period, suggesting that female parents adjust hatching skew facultatively to the amount of resources available for breeding. Using a full sibling breeding design, we also found that parent family had a significant effect on both hatching skew and hatching spread, suggesting that there is a heritable basis to asynchronous hatching. Finally, we found that hatching spread affected offspring survivorship, providing evidence that asynchronous hatching patterns have adaptive consequences inN. vespilloides. Our study provides valuable new insights into the evolution and ecological significance of asynchronous hatching by providing evidence on the adaptive consequences and the heritable basis of asynchronous hatching in a non‐avian species.
Life history plasticity to combined time and biotic constraints in Lestes damselflies from vernal and temporary ponds
Authors: De Block Marjan , McPeek Mark A. , Stoks Robby
Published: April 2008

Little is known about the ecological correlates and macro‐evolution of life history plasticity to time constraints. Here, we compared age and mass at emergence and their plasticity toward combinations of time constraints (delayed larval development), food level and predation risk (caged dragonfly larvae) by rearing two temporary‐pond Lestes damselflies (L. congener and L. forcipatus) and the derived vernal‐pond L. dryas from the eggs until adult emergence in outdoor tubs. Life history plasticity under time constraints, low food and predation risk was as predicted by optimality models. Delayed larvae in all three species accelerated development and showed a lower fat content and a substantially elevated mortality rate. At low food, all species emerged later at a smaller mass. Also under predation risk adults of all species emerged later, and (at high food) at a smaller mass. Unexpectedly, delayed larvae did not show a smaller life history response to predation risk imposed by dragonfly larvae. Compared to the two temporary‐pond Lestes studied, the derived species that invaded more ephemeral vernal ponds showed a faster development rate and a lower deceleration of development to low food. It also showed a lower acceleration of development to time constraints, possibly reflecting that it reached development rates near to its physiological maximum. Unexpectedly, the vernal‐pond Lestes did not slow its development less under predation risk. Our results stress the importance of evaluating ecological and evolutionary correlates of life history plasticity under as realistic conditions as possible.
Habitat, topographical, and geographical components structuring shrubsteppe bird communities
Authors: Knick Steven T. , Rotenberry John T. , Leu Matthias
Published: April 2008

Landscapes available to birds to select for breeding locations are arrayed along multiple dimensions. Identifying the primary gradients structuring shrubsteppe bird communities in the western United States is important because widespread habitat loss and alteration are shifting the environmental template on which these birds depend. We integrated field habitat surveys, GIS coverages, and bird counts from 61 Breeding Bird Survey routes located in shrubsteppe habitats across a >800 000 km2 region to determine the gradients of habitat, topography, and geography underlying bird communities. A small set of habitat features dominated the primary environmental gradients in a canonical ordination; the 13 species in the shrubsteppe bird community were closely packed along the first two axes. Using hierarchical variance partitioning, we identified habitat as the most important pure (31% explained variation) or shared component. Topography (9%) and geography (4%) were minor components but each shared a larger contribution with habitat (habitat‐topography 21%; habitat‐geography 22%) in explaining the organization of the bird community. In a second tier partition of habitat structure, pure composition (% land cover) was more important (45%) than configuration (patch size and edge) (7%); the two components shared 27% of the explained variation in the bird community axes. Local (9%), community (14%), and landscape (10%) levels contributed equally. Adjacent organizational levels had a larger shared contribution (local‐community 26%; community‐landscape 27%) than more separated local‐landscape levels (21%). Extensive conversion of shrubsteppe habitats to agriculture, exotic annual grasslands, or pinyon (Pinus spp.)–juniper (Juniperus spp.) woodlands is occurring along the primary axes of habitat structure. Because the shrubsteppe bird community was organized along short gradients dominated by habitat features, relatively small shifts in their available environment will exert a strong influence on these bird populations in the absence of buffering by alternative gradients.
Cryptococcus neoformans inhibits nitric oxide synthesis caused by CpG‐oligodeoxynucleotide‐stimulated macrophages in a fashion independent of capsular polysaccharides
Authors: Xiao Gang , Miyazato Akiko , Inden Ken , Nakamura Kiwamu , Shiratori Kohei , Nakagawa Kiyotaka , Miyazawa Teruo , Suzuki Kazuo , Kaku Mitsuo , Kawakami Kazuyoshi
Published: April 2008

Cryptococcus neoformans is eradicated by macrophages via production of NO. Unmethylated CpG‐ODN protect mice from infection with this fungal pathogen by inducing IFN‐γ. The present study was designed to elucidate the effect of C. neoformans on the synthesis of NO by alveolar macrophages. For this purpose, MH‐S, an alveolar macrophage cell line, was stimulated with CpG‐ODN in the presence of IFN‐γ. A highly virulent strain of C. neoformans with thick capsule suppressed the production of NO. Capsular polysaccharides were not essential for this suppression, because there was no difference between acapsular mutant (Cap67) and its parent strain. Physical or close interaction of Cap67 with MH‐S was necessary, as shown by the loss of such effect when direct contact was interfered by nitrocellulose membrane. Similar effects were observed by disrupted as well as intact Cap67. Whereas the inhibitory effect of intact Cap67 was completely abrogated by heat treatment, disrupted Cap67 did not receive such influence. Finally, disrupted Cap67 did not show any inhibitory effect on the TLR9‐mediated activation of NF‐κB in a luciferase reporter assay with HEK293T cells, although the TLR4‐mediated activation was suppressed. These results revealed that C. neoformans suppressed the synthesis of NO by CpG‐ODN and IFN‐γ‐stimulated macrophages in a fashion independent of capsular polysaccharides, although the precise mechanism remains to be elucidated.