bluuebunny/crossref_metadata_2025 huggingface dataset:
Weights in the Balance: Jasmonic Acid and Salicylic Acid Signaling in Root-Biotroph Interactions
Authors: Gutjahr Caroline , Paszkowski Uta
Published: June 2009

Work on the interaction of aerial plant parts with pathogens has identified the signaling molecules jasmonic acid (JA) and salicylic acid (SA) as important players in induced defense of the plant against invading organisms. Much less is known about the role of JA and SA signaling in root infection. Recent progress has been made in research on plant interactions with biotrophic mutualists and parasites that exclusively associate with roots, namely arbuscular mycorrhizal and rhizobial symbioses on one hand and nematode and parasitic plant interactions on the other hand. Here, we review these recent advances relating JA and SA signaling to specific stages of root colonization and discuss how both signaling molecules contribute to a balance between compatibility and defense in mutualistic as well as parasitic biotroph-root interactions.
Ralstonia solanacearum Encounters an Oxidative Environment During Tomato Infection
Authors: Flores-Cruz Zomary , Allen Caitilyn
Published: June 2009

Ralstonia solanacearum genes that are induced during tomato infection suggested that this pathogen encounters reactive oxygen species (ROS) during bacterial wilt pathogenesis. The genomes of R. solanacearum contain multiple redundant ROS-scavenging enzymes, indirect evidence that this pathogen experiences intense oxidative stress during its life cycle. Over 9% of the bacterium's plant-induced genes were also upregulated by hydrogen peroxide in culture, suggesting that oxidative stress may be linked to life in the plant host. Tomato leaves infected by R. solanacearum contained hydrogen peroxide, and concentrations of this ROS increased as pathogen populations increased. Mutagenesis of a plant-induced predicted peroxidase gene, bcp, resulted in an R. solanacearum strain with reduced ability to detoxify ROS in culture. The bcp mutant caused slightly delayed bacterial wilt disease onset in tomato. Moreover, its virulence was significantly reduced on tobacco plants engineered to overproduce hydrogen peroxide, demonstrating that Bcp is necessary for detoxification of plant-derived hydrogen peroxide and providing evidence that host ROS can limit the success of this pathogen. These results reveal that R. solanacearum is exposed to ROS during pathogenesis and that it has evolved a redundant and efficient oxidative stress response to adapt to the host environment and cause disease.
Molecular Characterization and Functional Analysis of MgNLP, the Sole NPP1 Domain–Containing Protein, from the Fungal Wheat Leaf Pathogen Mycosphaerella graminicola
Authors: Motteram Juliet , Küfner Isabell , Deller Siân , Brunner Frédéric , Hammond-Kosack Kim E. , Nürnberger Thorsten , Rudd Jason J.
Published: June 2009

Analysis of the fully sequenced genome of the wheat leaf-specific fungal pathogen Mycosphaerella graminicola identified only a single gene encoding a member of the necrosis- and ethylene-inducing peptide 1 (Nep1)-like protein family (NLP). NLP proteins have frequently been shown to trigger cell death and the activation of defense signaling reactions in dicotyledonous plants. However, complete loss-of-function reverse genetics analyses for their importance in the virulence of eukaryotic plant pathogens are generally lacking. Real-time quantitative polymerase chain reaction on MgNLP demonstrated the gene to be specifically expressed in planta. Peak expression was observed during the immediate presymptomatic phase of colonization of a susceptible host genotype. This was followed by a dramatic decrease during disease lesion formation which, in this system, exhibits characteristics of host programmed cell death (PCD). No comparable peak in transcript levels was seen during an incompatible interaction with a host genotype exhibiting gene-for-gene–based disease resistance. Heterologously expressed MgNLP protein induced necrotic cell death and the activation of defense-related genes when infiltrated into Arabidopsis leaves but not in leaves of a susceptible wheat genotype. MgNLP infiltration also failed to stimulate wheat mitogen-activated protein kinase activities. Finally, targeted deletion of M. graminicola MgNLP caused no detectable reduction in plant pathogenicity or virulence, suggesting that this protein is not a major virulence determinant during fungal infection of its host plant. To our knowledge, this represents the first complete loss-of-function analysis of NLP in a eukaryotic plant pathogen and we discuss our findings in the context of possible functions for NLP in pathogens which only infect monocotyledonous plants.
Absence of Symbiotic Leghemoglobins Alters Bacteroid and Plant Cell Differentiation During Development of Lotus japonicus Root Nodules
Authors: Ott Thomas , Sullivan John , James Euan K. , Flemetakis Emmanouil , Günther Catrin , Gibon Yves , Ronson Clive , Udvardi Michael
Published: June 2009

During development of legume root nodules, rhizobia and their host plant cells undergo profound differentiation, which is underpinned by massive changes in gene expression in both symbiotic partners. Oxygen concentrations in infected and surrounding uninfected cells drop precipitously during nodule development. To assess what effects this has on plant and bacterial cell differentiation and gene expression, we used a leghemoglobin-RNA-interference (LbRNAi) line of Lotus japonicus, which is devoid of leghemoglobins and has elevated levels of free-oxygen in its nodules. Bacteroids in LbRNAi nodules showed altered ultrastructure indicating changes in bacterial differentiation. Transcript analysis of 189 plant and 192 bacterial genes uncovered many genes in both the plant and bacteria that were differentially regulated during nodulation of LbRNAi plants compared with the wild type (containing Lb and able to fix nitrogen). These included fix and nif genes of the bacteria, which are involved in microaerobic respiration and nitrogen fixation, respectively, and plant genes involved in primary and secondary metabolism. Metabolite analysis revealed decreased levels of many amino acids in nodules of LbRNAi plants, consistent with the defect in symbiotic nitrogen fixation of this line.
Fusarium oxysporum Ste12 Controls Invasive Growth and Virulence Downstream of the Fmk1 MAPK Cascade
Authors: Rispail Nicolas , Di Pietro Antonio
Published: June 2009

A conserved mitogen-activated protein kinase (MAPK) cascade homologous to the yeast Fus3/Kss1 mating/filamentation pathway regulates virulence in fungal plant pathogens. In the soilborne fungus Fusarium oxysporum, the MAPK Fmk1 is required for infection and development of vascular wilt disease on tomato plants. Knockout mutants lacking Fmk1 are deficient in multiple virulence-related functions, including root adhesion and penetration, invasive growth, secretion of pectinolytic enzymes, and vegetative hyphal fusion. The transcription factors mediating these different outputs downstream of the MAPK cascade are currently unknown. In this study, we have analyzed the role of ste12 which encodes an orthologue of the yeast homeodomain transcription factor Ste12p. F. oxysporum mutants lacking the ste12 gene were impaired in invasive growth on tomato and apple fruit tissue and in penetration of cellophane membranes. However, ste12 was not required for adhesion to tomato roots, secretion of pectinolytic enzymes, and vegetative hyphal fusion, suggesting that these Fmk1-dependent functions are mediated by other downstream MAPK targets. The Δste12 strains displayed dramatically reduced virulence on tomato plants, similar to the Δfmk1 mutant. These results indicate that invasive growth is the major virulence function controlled by the Fmk1 MAPK cascade and depends critically on the transcription factor Ste12.
Multiple R-Like Genes Are Negatively Regulated by BON1 and BON3 in Arabidopsis
Authors: Li Yongqing , Pennington Britney O. , Hua Jian
Published: June 2009

The Arabidopsis thaliana genome contains more than 200 rapidly evolved resistance (R)-like genes coding for nucleotide binding leucine-rich repeat (NB-LRR) and their related proteins. A dozen of them are shown to play key roles in plant responses to biotic attacks, and they need to be repressed in the absence of biotic stresses to prevent activation of defense responses that are usually detrimental to plant growth and development. Here, we show that the Arabidopsis BON1 and BON3 genes, two members of the evolutionarily conserved copine, are negative regulators of several R-like genes. At least four such genes of the Toll-interleukin-1 receptor-like (TIR)-NB-LRR or TIR-NB type were identified through their activities in triggering cell death in the absence of the BON1 and BON3 function and their natural variations between two Arabidopsis accessions, Col-0 and Ws-2. These so-named lesion cell death (LCD) genes contribute quantitatively to the phenotypes of enhanced defense response and cell death in the bon1bon3 mutant. Further, their activation in the bon1bon3 mutants appears to be through different regulatory modes, and BON1 and BON3 may repress the transcript accumulation or protein activities of these R-like genes.
Regulatory Interactions Between Quorum-Sensing, Auxin, Cytokinin, and the Hrp Regulon in Relation to Gall Formation and Epiphytic Fitness of Pantoea agglomerans pv. gypsophilae
Authors: Chalupowicz Laura , Barash Isaac , Panijel Mary , Sessa Guido , Manulis-Sasson Shulamit
Published: June 2009

Gall formation by Pantoea agglomerans pv. gypsophilae is controlled by hrp/hrc genes, phytohormones, and the quorum-sensing (QS) regulatory system. The interactions between these three components were investigated. Disruption of the QS genes pagI and pagR and deletion of both substantially reduced the transcription levels of the hrp regulatory genes hrpXY, hrpS, and hrpL, as determined by quantitative reverse-transcriptase polymerase chain reaction. Expression of hrpL in planta was inhibited by addition of 20 μM or higher concentrations of the QS signal C4-HSL. The pagR and hrpL mutants caused an equivalent reduction of 1.3 orders in bacterial multiplication on bean leaves, suggesting possible mediation of the QS effect on epiphytic fitness of P. agglomerans pv. gypsophilae by the hrp regulatory system. indole-3-acetic acid (IAA) and cytokinin significantly affected the expression of the QS and hrp regulatory genes. Transcription of pagI, pagR, hrpL, and hrpS in planta was substantially reduced in iaaH mutant (disrupted in IAA biosynthesis via the indole-3-acetamide pathway) and etz mutant (disrupted in cytokinin biosynthesis). In contrast, the ipdC mutant (disrupted in IAA biosynthesis via the indole-3-pyruvate pathway) substantially increased expression of pagI, pagR, hrpL, and hrpS. Results presented suggest the involvement of IAA and cytokinins in regulation of the QS system and hrp regulatory genes.
NADPH Oxidase-Mediated Reactive Oxygen Species Production: Subcellular Localization and Reassessment of Its Role in Plant Defense
Authors: Lherminier Jeannine , Elmayan Taline , Fromentin Jérôme , Elaraqui Khadija Tantaoui , Vesa Simona , Morel Johanne , Verrier Jean-Louis , Cailleteau Bernard , Blein Jean-Pierre , Simon-Plas Françoise
Published: June 2009

Chemiluminescence detection of reactive oxygen species (ROS) triggered in tobacco BY-2 cells by the fungal elicitor cryptogein was previously demonstrated to be abolished in cells transformed with an antisense construct of the plasma membrane NADPH oxidase, NtrbohD. Here, using electron microscopy, it has been confirmed that the first hydrogen peroxide production occurring a few minutes after challenge of tobacco cells with cryptogein is plasma membrane located and NtrbohD mediated. Furthermore, the presence of NtrbohD in detergent-resistant membrane fractions could be associated with the presence of NtrbohD-mediated hydrogen peroxide patches along the plasma membrane. Comparison of the subcellular localization of ROS in wild-type tobacco and in plants transformed with antisense constructs of NtrbohD revealed that this enzyme is also responsible for the hydrogen peroxide production occurring at the plasma membrane after infiltration of tobacco leaves with cryptogein. Finally, the reactivity of wild-type and transformed plants to the elicitor and their resistance against the pathogenic oomycete Phytophthora parasitica were examined. NtrbohD-mediated hydrogen peroxide production does not seem determinant for either hypersensitive response development or the establishment of acquired resistance but it is most likely involved in the signaling pathways associated with the protection of the plant cell.
Assessing Heterogeneity in the Relationship Between Wheat Yield and Fusarium Head Blight Intensity Using Random-Coefficient Mixed Models
Authors: Madden L. V. , Paul P. A.
Published: June 2009

Seventy-seven studies reporting Fusarium head blight disease index (Y; mean percentage of diseased spikelets per spike) and wheat yield (W; MT/ha) were analyzed to determine the relationship between W and Y, and to assess the degree of variation for the relationship among studies. A linear random-coefficient model—comprising a population-average intercept and slope, a random residual term, and random effects of study on the intercept and slope (best linear unbiased predictors; BLUPs)—was successfully fitted to the data using maximum likelihood. From the predicted random effects, study-specific intercepts and slopes were obtained, and both population-average and subject-specific predictions of yield were determined. The estimated population-average intercept (expected yield when disease symptoms were not present) was 4.10 MT/ha, and the population-average slope was 0.038 MT/ha per unit increase of disease index. Wheat class had a significant effect on the intercept but not on the slope, with soft-red winter wheat having, on average, 0.85 MT/ha higher yield than spring wheat. Based on the estimates of the among-study variances, there was high variation in the effects of study on the intercept, but substantially lower variation in the effects of study on the slope. Thus, although one cannot predict with accuracy the actual wheat yield in a field or plot based on disease index using population-average results, one can predict with accuracy the decline in yield at a given level of disease index using the population-average slope. Through the modeling results, predicted relative yield (as a percentage of yield when disease is not present) can be determined, as well as predicted disease index at which a prespecified level of yield (or yield loss) is expected to occur. The predicted reduction in yield on a percentage scale was greater for spring than for soft-red winter wheat, on average, because of the lower estimated intercept in absolute units for spring wheat.
Admixture analysis of stocked brown trout populations using mapped microsatellite DNA markers: indigenous trout persist in introgressed populations
Authors: Hansen Michael M. , Mensberg Karen-Lise D.
Published: June 2009

Admixture between wild and captive populations is an increasing concern in conservation biology. Understanding the extent of admixture and the processes involved requires identification of admixed and non-admixed individuals. This can be achieved by statistical methods employing Bayesian clustering, but resolution is low if genetic differentiation is weak. Here, we analyse stocked brown trout populations represented by historical (1943–1956) and contemporary (2000s) samples, where genetic differentiation between wild populations and stocked trout is weak (pairwiseFSTof 0.047 and 0.053). By analysing a high number of microsatellite DNA markers (50) and making use of linkage map information, we achieve clear identification of admixed and non-admixed trout. Moreover, despite strong population-level admixture by hatchery strain trout in one of the populations (70.8%), non-admixed individuals nevertheless persist (7 out of 53 individuals). These remnants of the indigenous population are characterized by later spawning time than the majority of the admixed individuals. We hypothesize that isolation by time mediated by spawning time differences between wild and hatchery strain trout is a major factor rescuing a part of the indigenous population from introgression.
Tree shrew lavatories: a novel nitrogen sequestration strategy in a tropical pitcher plant
Authors: Clarke Charles M. , Bauer Ulrike , Lee Ch'ien C. , Tuen Andrew A. , Rembold Katja , Moran Jonathan A.
Published: June 2009

Nepenthes pitcher plants are typically carnivorous, producing pitchers with varying combinations of epicuticular wax crystals, viscoelastic fluids and slippery peristomes to trap arthropod prey, especially ants. However, ant densities are low in tropical montane habitats, thereby limiting the potential benefits of the carnivorous syndrome.
Nepenthes lowii
, a montane species from Borneo, produces two types of pitchers that differ greatly in form and function. Pitchers produced by immature plants conform to the ‘typical’
Nepenthes
pattern, catching arthropod prey. However, pitchers produced by mature
N. lowii
plants lack the features associated with carnivory and are instead visited by tree shrews, which defaecate into them after feeding on exudates that accumulate on the pitcher lid. We tested the hypothesis that tree shrew faeces represent a significant nitrogen (N) source for
N. lowii
, finding that it accounts for between 57 and 100 per cent of foliar N in mature
N. lowii
plants. Thus,
N. lowii
employs a diversified N sequestration strategy, gaining access to a N source that is not available to sympatric congeners. The interaction between
N. lowii
and tree shrews appears to be a mutualism based on the exchange of food sources that are scarce in their montane habitat.
Bäcklund transformations and the Atiyah–Ward ansatz for non-commutative anti-self-dual Yang–Mills equations
Authors: Gilson Claire R. , Hamanaka Masashi , Nimmo Jonathan J. C.
Published: June 2009

We present Bäcklund transformations for the non-commutative anti-self-dual Yang–Mills equation where the gauge group isG=GL(2), and use it to generate a series of exact solutions from a simple seed solution. The solutions generated by this approach are represented in terms of quasi-determinants. We also explain the origins of all the ingredients of the Bäcklund transformations within the framework of non-commutative twistor theory. In particular, we show that the generated solutions belong to a non-commutative version of the Atiyah–Ward ansatz.
Global depression in gene expression as a response to rapid thermal changes in vent mussels
Authors: Boutet Isabelle , Tanguy Arnaud , Le Guen Dominique , Piccino Patrice , Hourdez Stéphane , Legendre Pierre , Jollivet Didier
Published: June 2009

Hydrothermal vent mussels belonging to the genusBathymodiolusare distributed worldwide and dominate communities at shallow Atlantic hydrothermal sites. While organisms inhabiting coastal ecosystems are subjected to predictable oscillations of physical and chemical variables owing to tidal cycles, the vent mussels sustain pronounced temperature changes over short periods of time, correlated to the alternation of oxic/anoxic phases. In this context, we focused on the short-term adaptive response of mussels to temperature change at a molecular level. The mRNA expression of 23 genes involved in various cell functions of the vent musselBathymodiolus azoricuswas followed after heat shocks for either 30 or 120 min, at 25 and 30°C over a 48 h recovery period at 5°C. Mussels were genotyped at 10 enzyme loci to explore a relationship between natural genetic variation, gene expression and temperature adaptation. Results indicate that the mussel response to increasing temperature is a depression in gene expression, such a response being genotypically correlated at least for thePgm-1locus. This suggests that an increase in temperature could be a signal triggering anaerobiosis forB. azoricusor this latter alternatively behaves more like a ‘cold’ stenotherm species, an attribute more related to its phylogenetic history, a cold seeps/wood fall origin.
Increasing numbers of bird species result from taxonomic progress, not taxonomic inflation
Authors: Sangster George
Published: June 2009

The impact and significance of modern taxonomy on other fields in biology have been subjects of much debate. It has been proposed that increasing numbers of vertebrate species are largely owing to ‘taxonomic inflation’. According to this hypothesis, newly recognized species result from reinterpretations of species limits based on phylogenetic species concepts (PSCs) rather than from new discoveries. Here, I examine 747 proposals to change the taxonomic rank of birds in the period 1950–2007. The trend to recognize more species of birds started at least two decades before the introduction of PSCs. Most (84.6%) newly recognized species were supported by new taxonomic data. Proposals to recognize more species resulted from application of all six major taxonomic criteria. Many newly recognized species (63.4%) were not based exclusively on PSC-based criteria (diagnosability, monophyly and exclusive coalescence of gene trees). Therefore, this study finds no empirical support for the idea that the increase in species is primarily epistemological rather than data-driven. This study shows that previous claims about the causes and effects of taxonomic inflation lack empirical support. I argue that a more appropriate term for the increase in species is ‘taxonomic progress’.
Where do species' geographic ranges stop and why? Landscape impermeability and the Afrotropical avifauna
Authors: McInnes Lynsey , Purvis Andy , Orme C. David L.
Published: June 2009

Although understanding large-scale spatial variation in species' distributions is a major goal in macroecology, relatively little attention has been paid to the factors limiting species' ranges. An understanding of these factors may improve predictions of species' movements in response to global change. We present a measure of landscape impermeability, defined as the proportion of resident species whose ranges end in an area. We quantify and map impermeability for Afrotropical birds and use multi-model inference to assess support for a wide suite of hypotheses about its potential environmental correlates. Non-spatial analyses emphasize the importance of broad-scale environmental patterns of energy availability and habitat heterogeneity in limiting species' distributions. Conversely, spatial analyses focus attention on small-scale factors of habitat and topographic complexity. These results hold even when only species from the top quartile of range sizes are assessed. All our analyses highlight that range edges are concentrated in heterogeneous habitats. Global change is expected to alter the nature and distribution of such habitats, necessitating range movement by many resident species. Therefore, impermeability provides a simple measure for identifying regions, where continuing global change and human encroachment are likely to cause profound changes in regional diversity patterns.
Identification of non-tuberculous mycobacteria: utility of the GenoType Mycobacterium CM/AS assay compared with HPLC and 16S rRNA gene sequencing
Authors: Lee Andie S. , Jelfs Peter , Sintchenko Vitali , Gilbert Gwendolyn L.
Published: June 2009

Non-tuberculous mycobacteria (NTM) causing clinical disease have become increasingly common and more diverse. A new reverse line probe assay, GenoType Mycobacterium CM/AS (Hain Lifescience), was evaluated for identification of a broad range of NTM. It was compared with phenotypic (HPLC) and molecular (DNA probes, in-house real-time multiplex species-specific PCR, 16S rRNA gene PCR and sequencing) identification techniques, which together provided the reference ‘gold standard’. A total of 131 clinical isolates belonging to 31 Mycobacterium species and 19 controls, including 5 non-Mycobacterium species, was used. Concordant results between the GenoType Mycobacterium assay and the reference identification were obtained in 119/131 clinical isolates (90.8 %). Identification of Mycobacterium abscessus and Mycobacterium lentiflavum by the assay was problematic. The GenoType Mycobacterium assay enables rapid identification of a broad range of potentially clinically significant Mycobacterium species, but some species require further testing to differentiate or confirm ambiguous results.
Comparison of an in-house PCR assay, direct fluorescence assay and the Roche AMPLICOR Chlamydia trachomatis kit for detection of C. trachomatis
Authors: Sachdeva Poonam , Patel Achchhe Lal , Sachdev Divya , Ali Mashook , Mittal Aruna , Saluja Daman
Published: June 2009

To improve the control of Chlamydia trachomatis infection in India, a rapid, specific and cost-effective method is much needed. We developed an in-house PCR assay by targeting a unique genomic sequence encoding a protein from the C. trachomatis phospholipase D endonuclease superfamily that produces an amplified fragment of 368 bp. The specificity of the primers was confirmed using genomic DNA from other sexually transmitted disease-causing and related micro-organisms and from humans. The assay was highly sensitive and could detect as low as 10 fg C. trachomatis DNA. Clinical evaluation of the in-house-developed PCR was carried out using 450 endocervical specimens that were divided in two groups. In group I (n=274), in-house PCR was evaluated against the direct fluorescence assay. The resolved sensitivity of the in-house PCR method was 97.22 % compared with 88 % for the direct fluorescent antibody assay. In group II (n=176), the in-house PCR was compared with the commercial Roche AMPLICOR MWP CT detection kit. The resolved sensitivity of the in-house PCR assay reported here was 93.1 % and the specificity was 97.46 %, making it a cost-effective alternative for routine diagnosis of genital infection by C. trachomatis. The method should facilitate early detection leading to better prevention and treatment of genital infection in India.
Novel sample preparation technique for protein crystal X-ray crystallographic analysis combining microfluidics and acoustic manipulation
Authors: Oberti Stefano , Möller Dirk , Gutmann Sascha , Neild Adrian , Dual Jürg
Published: June 2009

In order to perform X-ray crystallographic analysis, protein crystals are removed from their growing solution by means of a nylon loop, which is then mounted on a goniometer. As this process is repeated for a large number of crystals, there is a need for automation, especially with regard to the placement on the nylon loop. A novel technique involving the use of acoustic radiation forces and a micro-machined fluidic device is introduced here. After insertion into the micro-machined channel, the crystals are positioned in a row along its centre-line by excitation of a high-frequency standing pressure field, and then moved towards an orifice by applying a flow along the channel, which also ensures spatial separation. Once located in a defined orifice, the single crystals can be removed using a nylon loop. X-ray crystallographic analysis showed that application of ultrasound does not influence the diffraction properties of the crystals.
Electron diffraction of ABX
3 perovskites with both layered ordering of A cations and tilting of BX
6 octahedra
Authors: Kishida Kyosuke , Goto Kengo , Inui Haruyuki
Published: June 2009

It is shown that 21 ABX
3 perovskites with tilted BX
6 octahedra and layered ordering of A cations can be generated on the basis of group–subgroup relations. These structures (with 16 different space groups) are classified into ten diffraction types in terms of the conditions for superstructure reflections caused by the ordering of A cations, tilting of BX
6 octahedra and structural absences. SAED (selected-area electron diffraction) allows the distinction of seven of the 21 different perovskites, while additional symmetry analysis by CBED (convergent-beam electron diffraction) is needed for the remaining 14 structures. The space groups of lithium lanthanum titanate pseudomorphs (with discrete chemical compositions) are successfully deduced by electron diffraction experiments.
Transferability and reproducibility in electron-density studies – bond-topological and atomic properties of tripeptides of the type L-alanyl-X-L-alanine
Authors: Grabowsky Simon , Kalinowski Roman , Weber Manuela , Förster Diana , Paulmann Carsten , Luger Peter
Published: June 2009

In the last decade three different data bank approaches have been developed that are intended to make electron-density examinations of large biologically important molecules possible. They rely on Bader's concept of transferability of submolecular fragments with retention of their electronic properties. Therefore, elaborate studies on the quantification of transferability in experiment and theory are still very important. Tripeptides of the type L-alanyl-X-L-alanine (X being any of the 20 naturally encoded amino acids) serve as a model case between amino acids and proteins. The two experimental electron-density determinations (L-alanyl-L-histidinyl-L-alanine and L-alanyl-L-phenylalanyl-L-alanine, highly resolved synchrotron X-ray diffraction data sets) performed in this study and theoretical calculations on all 20 different L-alanyl-X-L-alanine molecules contribute to a better estimation of transferability in the peptide case. As a measure of reproducibility and transferability, standard deviations from averaging over bond-topological and atomic properties of atoms or bonds that are considered equal in their chemical environments were calculated. This way, transferability and reproducibility indices were introduced. It can be shown that experimental transferability indices generally slightly exceed experimental reproducibility indices and that these larger deviations can be attributed to chemical effects such as changes in the geometry (bond lengths and angles), the polarization pattern and the neighboring sphere due to crystal packing. These effects can partly be separated from each other and quantified with the help of gas-phase calculations at optimized and experimental geometries. Thus, the degree of transferability can be quantified in very narrow limits taking into account experimental errors and chemical effects.
Quantitative trait loci for litter size and prenatal loss in a White Duroc × Chinese Erhualian resource population
Authors: Li K. , Ren J. , Xing Y. , Zhang Z. , Ma J. , Guo Y. , Huang L.
Published: June 2009

To detect quantitative trait loci (QTL) for litter size related traits, the total number of born piglets (TNB), the number of born alive piglets (NBA), the number of stillborn piglets (NSB) and the number of mummies (NM) at the first parity were recorded in 299 F2 sows in a White Duroc × Chinese Erhualian intercross resource population. A whole genome scan was performed with 183 microsatellites distributed across 19 porcine chromosomes in the resource population, and the QTL analysis was performed with a least‐squares method. A 5% genome‐wide significant QTL was detected at 88 cM on pig chromosome (SSC) 15 for NBA, which also showed suggestive effect on TNB. In addition, four suggestive QTL were detected on SSC 6, 7, 8 and 15 for TNB, NBA or NSB. Two of the five QTL detected showed accordance with previous reports. No QTL was found for NM.
Platelet‐derived growth factor and transforming growth factor‐β modulate the expression of matrix metalloproteinases and migratory function of human airway smooth muscle cells
Authors: Ito I. , Fixman E. D. , Asai K. , Yoshida M. , Gounni A. S. , Martin J. G. , Hamid Q.
Published: June 2009

Background
Matrix metalloproteinases (MMPs) and tissue inhibitors of metalloproteinase (TIMPs) have been suggested to be involved in the pathogenesis of asthma. Their expression in airway smooth muscle (ASM) cells could be involved in collagen turnover and migration of these cells and thus may contribute to airway remodelling.

Objective
To examine the effect of pro‐fibrotic growth factors TGF‐β and platelet‐derived growth factor (PDGF) on the expression of MMPs/TIMPs in cultured human ASM cells and to examine the role of MMP in the migration of ASM cells.

Methods
ASM cells were stimulated with TGF‐β and/or PDGF. Expression and activity of MMP‐1, MMP‐2, MMP‐3, TIMP‐1 and TIMP‐2 were evaluated by quantitative RT‐PCR, Western blot and zymography. Modified Boyden‐chamber migration assay was performed to investigate the effect of secreted MMP‐3 and TIMP‐1 on ASM‐cell migration.

Results
PDGF strongly up‐regulated the expression of MMP‐1 at mRNA and protein levels. PDGF, when combined with TGF‐β, caused synergistic up‐regulation of MMP‐3. TIMP‐1 was additively up‐regulated by TGF‐β and PDGF. These growth factors had no effect on the expression of MMP‐2 and TIMP‐2. U0126, an extracellular signal‐regulated kinase (ERK) pathway inhibitor, inhibited the up‐regulation of MMP‐1 by PDGF. The synergistic/additive up‐regulation of MMP‐3 and TIMP‐1 was inhibited by U0126 and SB431542, a Smad pathway inhibitor. Supernatant from ASM cells in which MMP‐3 production was knocked down by RNA interference showed a decreased migratory effect on ASM cells, whereas supernatant from cells with suppressed TIMP‐1 expression resulted in increased migration.

Conclusion
Our results suggest that PDGF with/without TGF‐β could facilitate migration of ASM cells by modification of MMP–TIMP balance through the ERK pathway.
Vascular hyporesponsiveness to angiotensin II in rats with CCl4‐induced liver cirrhosis
Authors: Hennenberg M. , Trebicka J. , Kohistani A. Z. , Heller J. , Sauerbruch T.
Published: June 2009

Background Portal hypertension is triggered by vasodilation due to impaired contraction of extrahepatic vessels. Angiotensin II type 1 (AT1) receptor‐induced vasocontraction is mediated by G proteins and may be desensitized by recruitment of β‐arrestin‐2 to the receptor. In this study, we analysed the interaction of AT1receptors with β‐arrestin‐2 in the context of vascular hypocontractility in rats with CCl4‐induced cirrhosis.

Methods Micronodular liver cirrhosis in rats (n = 15) was induced by regular CCl4exposure. Age‐matched rats (n = 15) served as controls. Contractility of aortic rings was measured by myography. Protein expressions and phosphorylations were assessed by Western blot analysis, and AT1receptor interaction with β‐arrestin‐2 by co‐immunoprecipitation.

Results Aortic rings from CCl4rats were hypocontractile to angiotensin II independent of nitric oxide synthases (Nω‐nitro‐l‐arginine methyl ester 200 μM). Expression of the AT1receptor, Gαq/11and the contraction‐mediating effector Rho kinase was similar in aortas from both groups. Expression and AT1receptor binding of β‐arrestin‐2 were up‐regulated in aortas from CCl4rats. Stimulation of isolated aortas with exogenous angiotensin II caused recruitment of β‐arrestin‐2 in aortas from noncirrhotic rats, but no further interaction of AT1receptors with β‐arrestin‐2 was found in aortas from CCl4rats. While angiotensin II stimulation resulted in Rho kinase activation in aortas from noncirrhotic rats but not in aortas from CCl4rats, extracellular signal‐regulated kinase activation in response to angiotensin II was observed in aortas from both groups.

Conclusions Vascular hyporesponsiveness to angiotensin II in CCl4rats is due to enhanced interaction of the AT1receptor with β‐arrestin‐2 and consecutively changed receptor function.
A quartet of cephalopodologists
Authors: Holland Charles Hepworth
Published: June 2009

Joachim Barrande, J. F. Blake, August F. Foerste and Rousseau H. Flower were outstanding palaeontologists who worked on Silurian cephalopods. They make a remarkable quartet, their work spanning the 19th and 20th centuries.
An unusual bit of the hard stuff–Derbyshire chert
Authors: Ford Trevor D.
Published: June 2009

Chert once had a practical use in the pottery industry, but its origins remain obscure.
Radial growth response of four dominant boreal tree species to climate along a latitudinal gradient in the eastern Canadian boreal forest
Authors: HUANG JIANGUO , TARDIF JACQUES C. , BERGERON YVES , DENNELER BERNHARD , BERNINGER FRANK , GIRARDIN MARTIN P.
Published: June 2009

To address the central question of how climate change influences tree growth within the context of global warming, we used dendroclimatological analysis to understand the reactions of four major boreal tree species –Populus tremuloides, Betula papyrifera, Picea mariana, and Pinus banksiana– to climatic variations along a broad latitudinal gradient from 46 to 54°N in the eastern Canadian boreal forest. Tree‐ring chronologies from 34 forested stands distributed at a 1° interval were built, transformed into principal components (PCs), and analyzed through bootstrapped correlation analysis over the period 1950–2003 to identify climate factors limiting the radial growth and the detailed radial growth–climate association along the gradient. All species taken together, previous summer temperature (negative influences), and current January and March–April temperatures (positive influences) showed the most consistent relationships with radial growth across the gradient. Combined with the identified species/site‐specific climate factors, our study suggested that moisture conditions during the year before radial growth played a dominant role in positively regulating P. tremuloides growth, whereas January temperature and growing season moisture conditions positively impacted growth of B. papyrifera. Both P. mariana and P. banksiana were positively affected by the current‐year winter and spring or whole growing season temperatures over the entire range of our corridor. Owing to the impacts of different climate factors on growth, these boreal species showed inconsistent responsiveness to recent warming at the transition zone, where B. papyrifera, P. mariana, and P. banksiana would be the most responsive species, whereas P. tremuloides might be the least. Under continued warming, B. papyrifera stands located north of 49°N, P. tremuloides at northern latitudes, and P. mariana and P. banksiana stands located north of 47°N might benefit from warming winter and spring temperatures to enhance their radial growth in the coming decades, whereas other southern stands might be decreasing in radial growth.
Assimilation exceeds respiration sensitivity to drought: A FLUXNET synthesis
Authors: SCHWALM CHRISTOPHER R. , WILLIAMS CHRISTOPHER A. , SCHAEFER KEVIN , ARNETH ALMUT , BONAL DAMIEN , BUCHMANN NINA , CHEN JIQUAN , LAW BEVERLY E. , LINDROTH ANDERS , LUYSSAERT SEBASTIAAN , REICHSTEIN MARKUS , RICHARDSON ANDREW D.
Published: June 2009

The intensification of the hydrological cycle, with an observed and modeled increase in drought incidence and severity, underscores the need to quantify drought effects on carbon cycling and the terrestrial sink. FLUXNET, a global network of eddy covariance towers, provides dense data streams of meteorological data, and through flux partitioning and gap filling algorithms, estimates of net ecosystem productivity (FNEP), gross ecosystem productivity (P), and ecosystem respiration (R). We analyzed the functional relationship of these three carbon fluxes relative to evaporative fraction (EF), an index of drought and site water status, using monthly data records from 238 micrometeorological tower sites distributed globally across 11 biomes. The analysis was based on relative anomalies of both EF and carbon fluxes and focused on drought episodes by biome and climatic season. Globally P was ≈50% more sensitive to a drought event than R. Network‐wide drought‐induced decreases in carbon flux averaged −16.6 and −9.3 g C m−2 month−1 for P and R, i.e., drought events induced a net decline in the terrestrial sink. However, in evergreen forests and wetlands drought was coincident with an increase in P or R during parts of the growing season. The most robust relationships between carbon flux and EF occurred during climatic spring for FNEP and in climatic summer for P and R. Upscaling flux sensitivities to a global map showed that spatial patterns for all three carbon fluxes were linked to the distribution of croplands. Agricultural areas exhibited the highest sensitivity whereas the tropical region had minimal sensitivity to drought. Combining gridded flux sensitivities with their uncertainties and the spatial grid of FLUXNET revealed that a more robust quantification of carbon flux response to drought requires additional towers in all biomes of Africa and Asia as well as in the cropland, shrubland, savannah, and wetland biomes globally.
A framework for assessing the biodiversity and fishery aspects of marine reserves
Authors: Levin Phillip S. , Kaplan Isaac , Grober‐Dunsmore Rikki , Chittaro Paul M. , Oyamada Seichi , Andrews Kate , Mangel Marc
Published: June 2009

1.  Resource management agencies are often charged with managing natural resources for economic and social goals, while also protecting and conserving biodiversity and ecosystem function. However, this may not always be possible. Ecosystem‐based management is frequently suggested as a way to achieve multiple objectives in resource management and requires that trade‐offs among conflicting objectives be identified and an effective means to utilize these trade‐offs developed.

2.  We examine the relationship between area and species richness in a diverse assemblage of fishes along the US West Coast and then use parameters from this relationship as input for a model that considers trade‐offs between fisheries yield and the number of species protected by different management strategies.

3.
 The species–area relationship (S = cAz) for fishes along the US Pacific coast is well described by the relationship S = 16·18A0·226.

4.  There are nearly linear trade‐offs between diversity and yield when fishing effort is low. However, the trade‐offs become nonlinear as fishing effort increases and imposing MPAs increases both the conservation and fisheries value of the system when the system is overfished.

5.
 Synthesis and applications. Solving conflicts between fisheries and conservation requires attention as to how conservation benefits accrue as fishing effort is reduced. However, scientists often lack quantitative information about the trade‐offs inherent in human activities such as fisheries. The approach we develop here can begin to help frame the questions to be posed and evaluate the likely consequences of different management options.
Trade‐offs between specificity and regional generality in habitat association models: a case study of two species of African vulture
Authors: Bamford Andrew J. , Monadjem Ara , Anderson Mark D. , Anthony Angus , Borello Wendy D. , Bridgeford Marilyn , Bridgeford Peter , Hancock Pete , Howells Bill , Wakelin James , Hardy Ian C.W.
Published: June 2009

1.  The habitat requirements of various species have been evaluated by statistical models. However, recent studies have shown that models are often not transferable between regions, limiting their applicability and ability to inform management decisions. One possible cause is that models tend to reflect dominant landscape features, which vary between regions. Transferability, and thus applicability, may be increased by developing models from multiple regions.

2.
 We addressed this via a case study of two vulture species (white‐backed and lappet‐faced vultures, Gyps africanus and Aegypius tracheliotos) from six biogeographically different regions across southern Africa. Logistic models, developed using an information‐theoretic approach, were used to predict nest occurrence based on explanatory variables derived from a Geographic Information System (GIS), the usual method for species with large ranges. Variables reflected key requirements at different spatial scales: food availability, human disturbance and nesting trees. We developed models using data from single and multiple regions, and tested the cross‐regional transferability. We also collected field data to asses the adequacy of the GIS variables.

3.  There was a significant negative correlation between specificity and regional generality, multi‐region models tending to be more consistently transferable than single‐region models but having a weaker fit within the regions where they were developed. Multi‐region models of nesting habitat were more structurally similar to each other than single‐region models. GIS variables adequately represented the landscape but with differing adequacy between regions. There were no observed fitness benefits to the observed site selection.

4.
 Synthesis and applications. Models of species distribution are not transferable between regions, and use of models to inform management decisions in regions other than that used for model development should be undertaken with caution. Models are often built using GIS predictors only broadly related to the landscape properties of interest and the adequacy of such proxies can vary between regions, leading to models that emphasize dominant landscape features. Models developed from multiple regions partially overcome this problem by identifying predictors that apply across many regions and are more transferable. However, this increased generality trades off against reduced specificity. Models should be constructed with consideration to their intended use.
Changes in coronary heart disease risk profile of adults with intellectual disabilities following a physical activity intervention
Authors: Moss S. J.
Published: June 2009

Background  Regular physical activity is one of the modifiable risk factors for coronary heart disease (CHD). With an increasing age profile and similar patterns of morbidity to the general population, persons with intellectual disabilities (ID) and their caregivers would benefit from data that indicate CHD risk factors. Knowledge of the CHD risk factors and the changes a physical activity intervention may have on theses risk factors will facilitate future intervention programmes.

Methods  A cohort of 100 men and women between the ages of 21 and 73 years with ID living in a community group home in the North‐West Province of South Africa was recruited. A CHD risk profile was compiled by means of a questionnaire and physical assessment that included resting blood pressure, body mass index, non‐fasting glucose and cholesterol and cardiorespiratory fitness. A 12‐week physical activity intervention was then conducted 3 days/week after which the baseline measurements were repeated.

Results  The results indicated that 85% of the participants were inactive, while 67% were overweight and obese. Hypertension (6.1%) and smoking (6.1%) were relatively low in this population with ID. Glucose concentrations above the recommended cut‐off values were observed in 28% of the participants. Total cholesterol concentrations above normal were measured in 23% of the participants. The physical activity intervention reduced inactivity to 50% and resulted in a significant increase in cardiorespiratory fitness and a decrease in percentage body fat in both men and women.

Conclusion  Inactivity is a major risk factor in this population with ID living in a community group setting. The implementation of the physical activity intervention significantly reduced the risk factors for CHD.