bluuebunny/crossref_metadata_2025 huggingface dataset:
The effect of environmental conditions on extracellular protease activity in controlled fermentations of Aspergillus niger
Authors: Braaksma Machtelt , Smilde Age K. , van der Werf Mariët J. , Punt Peter J.
Published: September 2009

Proteolytic degradation by host proteases is one of the key issues in the application of filamentous fungi for non-fungal protein production. In this study the influence of several environmental factors on the production of extracellular proteases ofAspergillus nigerwas investigated systematically in controlled batch cultures. Of all factors investigated in a series of initial screening experiments, culture pH and nitrogen concentration in particular strongly affected extracellular protease activities. For instance, at a culture pH of 4, protease activity was higher than at pH 5, and protease activity increased with increasing concentrations of ammonium as nitrogen source. Interestingly, an interdependence was observed for several of the factors studied. These possible interaction effects were investigated further using a full factorial experimental design. Amongst others, the results showed a clear interaction effect between nitrogen source and nitrogen concentration. Based on the observed interactions, the selection of environmental factors to reduce protease activity is not straightforward, as unexpected antagonistic or synergistic effects occur. Furthermore, not only were the effects of the process parameters on maximum protease activity investigated, but five other protease-related phenotypes were studied as well, such as maximum specific protease activity and maximum protease productivity. There were significant differences in the effect of the environmental parameters on the various protease-related phenotypes. For instance, pH significantly affected final levels of protease activity, but not protease productivity. The results obtained in this study are important for the optimization ofA. nigerfor protein production.
Global transcriptional analysis of acid-inducible genes in Streptococcus mutans: multiple two-component systems involved in acid adaptation
Authors: Gong Yongxing , Tian Xiao-Lin , Sutherland Tara , Sisson Gary , Mai Junni , Ling Junqi , Li Yung-Hua
Published: September 2009

Streptococcus mutans in dental biofilms is regularly exposed to cycles of acidic pH during the ingestion of fermentable dietary carbohydrates. The ability of S. mutans to tolerate low pH is crucial for its virulence and pathogenesis in dental caries. To better understand its acid tolerance mechanisms, we performed genome-wide transcriptional analysis of S. mutans in response to an acidic pH signal. The preliminary results showed that adaptation of S. mutans to pH 5.5 induced differential expression of nearly 14 % of the genes in the genome, including 169 upregulated genes and 108 downregulated genes, largely categorized into nine functional groups. One of the most interesting findings was that the genes encoding multiple two-component systems (TCSs), including CiaHR, LevSR, LiaSR, ScnKR, Hk/Rr1037/1038 and ComDE, were upregulated during acid adaptation. Real-time qRT-PCR confirmed the same trend in the expression profiles of these genes at pH 5.5. To determine the roles of these transduction systems in acid adaptation, mutants with a deletion of the histidine-kinase-encoding genes were constructed and assayed for the acid tolerance response (ATR). The results revealed that inactivation of each of these systems resulted in a mutant that was impaired in ATR, since pre-exposure of these mutants to pH 5.5 did not induce the same level of protection against lethal pH levels as the parent did. A competitive fitness assay showed that all the mutants were unable to compete with the parent strain for persistence in dual-strain mixed cultures at acidic pH, although, with the exception of the mutant in liaS, little effect was observed at neutral pH. The evidence from this study suggests that the multiple TCSs are required for S. mutans to orchestrate its signal transduction networks for optimal adaptation to acidic pH.
The Constructionist Approach to Framing: Bringing Culture Back In
Authors: Van Gorp Baldwin
Published: September 2009

This article aims, within the constructionist paradigm, at integrating culture into the framing process. Four characteristics are important for this approach: the distinction between the event, the media content, and the frame; the explicit attention to the reconstruction of frame packages; the relationship between frame packages and cultural phenomena; and the interaction between frame sponsors, key events, media content, schemata, and the stock of frames. An elaborated framing model is presented, and, subsequently, the constructionist approach is compared with priming and agenda setting. Finally, the methodological implications are discussed, in order to develop a strategy to reconstruct frame packages.

L’approche constructionniste au cadrage: ramener la culture

Baldwin Van Gorp

Department of Communication Science, Radboud University Nijmegen, Pays-Bas
Diversity and abundance of insect visitors to flowers of trees and shrubs in a South African savannah
Authors: Mawdsley Jonathan R. , Sithole Hendrik
Published: September 2009

This study presents the results of a landscape‐scale survey for insect floral visitors in the Skukuza Ranger District, Kruger National Park, South Africa. Floral visitors were sampled from flowering trees and shrubs along linear transects spanning the entire district. Six plant species were sampled in the late dry season (Acacia grandicornuta Gerstner, A. nigrescens Oliver, Cassia abbreviata Oliver, Combretum hereroense Schinz, Combretum zeyheri Sonder, Euclea divonorum Hiern), and eleven plant species were sampled during the rainy season (Acacia exuvialis Verdcourt, A. grandicornuta Gerstner, A. nilotica (L.) Willdenow, A. tortilis (Forsskal) Hayne, Dichrostachys cinerea Miquel, Flueggea virosa (Roxburgh) Baillon, Grewia bicolor Jussieu, G. flava De Candolle, G. flavescens Jussieu, G. monticola Sonder, and Peltophorum africanum Sonder). Coleoptera, Hymenoptera and Lepidoptera comprised the majority of floral visitors, while species of Blattodea, Diptera, Hemiptera and Neuroptera also occurred on flowers. Known or likely pollinators include bees (Hymenoptera: Apidae, Halictidae and Megachilidae) and scarab beetles (Coleoptera: Scarabaeidae). These plant species appear to have generalist pollination systems, with the exception of species of Grewia L., which appear to be pollinated primarily by bees. A provisional plant–pollinator food web is presented for the eleven species of trees and shrubs which flower during the rainy season.
Threat of rapid extermination of the lion (Panthera leo leo) in Waza National Park, Northern Cameroon
Authors: Tumenta P. N. , Kok J. S. , Van Rijssel J. C. , Buij R. , Croes B. M. , Funston P. J. , De Iongh H. H. , Udo de Haes H. A.
Published: September 2009

Lion populations in West and Central Africa are small and fragmented. In areas where park management is weak, threats will likely facilitate the extinction of the lion. Wildlife management requires knowledge of the population estimate. The population of lions in Waza National Park (Waza NP) was assessed by individual identification of members in the population. The population was assessed to comprise of 14–21 adult individual lions. The age structure was skewed towards adults; cubs comprised 22% of all lions identified while the sex ratio was 1 : 3. Two out of four collared lions were lost to illegal, retaliatory killings within 1 year; and probably two more males and one more female were also killed during this period. The lion population appears to have declined during the last 5 years with six lions dying per year, which is at a much higher rate than observed in the previous decades. Human‐livestock pressure has increased tremendously in this period, resulting to frequent human‐lion conflicts. To ensure the survival of the lion in Waza NP and in the entire region, management needs to intensify efforts to mitigate the pressure from humans and their livestock.
Confirmation and refinement of a QTL on BTA5 affecting milk production traits in the Fleckvieh dual purpose cattle breed
Authors: Awad A. , Russ I. , Emmerling R. , Förster M. , Medugorac I.
Published: September 2009

We analysed a QTL affecting milk yield (MY), milk protein yield (PY) and milk fat yield (FY) in the dual purpose cattle breed Fleckvieh on BTA5. Twenty‐six microsatellite markers covering 135 cM were selected to analyse nine half‐sib families containing 605 sons in a granddaughter design. We thereby assigned two new markers to the public linkage map using the CRI‐MAP program. Phenotypic records were daughter yield deviations (DYD) originating from the routinely performed genetic evaluations of breeding animals. To determine the position of the QTL, three different approaches were applied: interval mapping (IM), linkage analysis by variance component analysis (LAVC), and combined linkage disequilibrium (LD) and linkage (LDL) analysis. All three methods mapped the QTL in the same marker interval (BM2830‐ETH152) with the greatest test‐statistic value at 118, 119.33 and 119.33 cM respectively. The positive QTL allele simultaneously increases DYD in the first lactation by 272 kg milk, 7.1 kg milk protein and 7.0 kg milk fat. Although the mapping accuracy and the significance of a QTL effect increased from IM over LAVC to LDL, the confidence interval was large (13, 20 and 24 cM for FY, MY and PY respectively) for the positional cloning of the causal gene. The estimated averages of pair wise marker LD with a distance <5 cM were low (0.107) and reflect the large effective population size of the Fleckvieh subpopulation analysed. This low level of LD suggests a need for increase in marker density in following fine mapping steps.
The influence of extracellular matrix and prolactin on global gene expression profiles of primary bovine mammary epithelial cellsin vitro
Authors: Riley L. G. , Gardiner‐Garden M. , Thomson P. C. , Wynn P. C. , Williamson P. , Raadsma H. W. , Sheehy P. A.
Published: September 2009

Anin vitrobovine mammosphere model was characterized for use in lactational biology studies using a functional genomics approach. Primary bovine mammary epithelial cells cultured on a basement membrane, Matrigel, formed three‐dimensional alveoli‐like structures or mammospheres. Gene expression profiling during mammosphere formation by high‐density microarray analysis indicated that mammospheres underwent similar molecular and cellular processes to developing alveoli in the mammary gland. Gene expression profiles indicated that genes involved in milk protein and fat biosynthesis were expressed, however, lactose biosynthesis may have been compromised. Investigation of factors influencing mammosphere formation revealed that extracellular matrix (ECM) was responsible for the initiation of this process and that prolactin (Prl) was necessary for high levels of milk protein expression.CSN3(encoding κ‐casein) was the most highly expressed casein gene, followed byCSN1S1(encoding αS1‐casein) andCSN2(encoding β‐casein). Eighteen Prl‐responsive genes were identified, includingCSN1S1,SOCS2andCSN2,however, expression ofCSN3was not significantly increased by Prl andCSN1S2was not expressed at detectable levels in mammospheres. A number of novel Prl responsive genes were identified, including ECM components and genes involved in differentiation and apoptosis. This mammosphere model is a useful model system for functional genomics studies of certain aspects of dairy cattle lactation.
Sequence polymorphisms in porcine homologs of murine coat colour‐related genes
Authors: Okumura N. , Hayashi T. , Uenishi H. , Fukudome N. , Komatsuda A. , Suzuki A. , Shibata M. , Nii M. , Yamaguchi T. , Kojima‐Shibata C. , Hamasima N. , Awata T.
Published: September 2009

Herein, we report the variability among 57 porcine homologs of murine coat colour‐related genes. We identified single nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) within 44 expressed gene sequences by aligning eight pig complementary DNA (cDNA) samples. The sequence alignment revealed a total of 485 SNPs and 15 InDels. The polymorphisms were then validated by performing matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOF MS) with reference DNA samples obtained from 384 porcine individuals. Of the 384 individuals, three parents of the experimental F2 family were included to detect polymorphisms between them for linkage mapping. We also genotyped previously reported polymorphisms of 12 genes, and one SNP each in three genes that were detected by performing a BLAST search of the Trace database. A total of 211 SNPs and three InDels were successfully genotyped from our porcine DNA panel. We detected SNPs in 33 of the 44 genes among the parents of an experimental F2 family and then constructed a linkage map of the 33 genes for this family. The linkage assignment of each gene to the porcine chromosomes was consistent with the location of the BAC clone in the porcine genome and the corresponding gene sequence. We confirmed complete substitutions of EDNRB and MLPH in the Jinhua and Clawn miniature breeds, respectively. Furthermore, we identified polymorphic alleles exclusive to each pig group: 13 for Jinhua, two for Duroc, three for Meishan, four for the Japanese wild boar, one for the Clawn miniature pig and four for the Potbelly pig.
Evaluation of 16 loci to examine the cross‐species utility of single nucleotide polymorphism arrays
Authors: Sechi T. , Coltman D. W. , Kijas J. W.
Published: September 2009

Large collections of single nucleotide polymorphisms (SNPs) have recently been identified from a number of livestock genomes. This raises the possibility that SNP arrays might be useful for analysis in related species for which few genetic markers are currently available. To address the likely success of such an approach, the aim of this study was to examine the threshold number and position of flanking mutations which act to prevent genotype calls being produced. Sequence diversity was measured across 16 loci containing SNPs known either to work successfully between species or fail between species. In pairwise comparisons between domestic and wild sheep, sequence divergence surrounding working SNP assays was significantly lower than that surrounding non‐functional assays. In addition, the location of flanking mismatches tended to be closer to the target SNP in loci that failed to generate genotype calls across species. The magnitude of sequence divergence observed for both working and non‐functional assays was compared with the divergence separating domestic sheep from European Mouflon, African Barbary, goat and cattle. The results suggest that the utility of SNP arrays for analysis of shared polymorphism will be restricted to closely related pairs of species. Analysis across more divergent species will, however, be successful for other objectives, such as the identification of the ancestral state of SNPs.
A standard panel of microsatellites for Asian seabass(Lates calcarifer)
Authors: Zhu Z. Y. , Wang C. M. , Lo L. C. , Lin G. , Feng F. , Tan J. , Chou R. , Lim H. S. , Orban L. , Yue G. H.
Published: September 2009

Microsatellites are the most popular markers for parentage assignment and population genetic studies. To meet the demand for international comparability for genetic studies of Asian seabass, a standard panel of 28 microsatellites has been selected and characterized using the DNA of 24 individuals from Thailand, Malaysia, Indonesia and Australia. The average allele number of these markers was 10.82 ± 0.71 (range: 6–19), and the expected heterozygosity averaged 0.76 ± 0.02 (range: 0.63–1.00). All microsatellites showed Mendelian inheritance. In addition, eight standard size controls have been developed by cloning a set of microsatellite alleles into a pGEM‐T vector to calibrate allele sizes determined by different laboratories, and are available upon request. Seven multiplex PCRs, each amplifying 3–5 markers, were optimized to accurately and rapidly genotype microsatellites. Parentage assignment using 10 microsatellites in two crosses (10 × 10 and 20 × 20) demonstrated a high power of these markers for revealing parent‐sibling connections. This standard set of microsatellites will standardize genetic diversity studies of Asian seabass, and the multiplex PCR sets will facilitate parentage assignment.
Alternative haematopoietic stem cell sources for transplantation: place of umbilical cord blood
Authors: Smith Angela R. , Wagner John E.
Published: October 2009

Umbilical cord blood has rapidly become a valuable alternative stem cell source for allogeneic haematopoietic stem cell transplantation. Extensive research over the last 20 years has established the safety and efficacy of umbilical cord blood transplantation in both children and adults with a variety of malignant and non‐malignant diseases. This research has clearly shown that this stem cell source has several unique characteristics resulting in distinct advantages and disadvantages when compared to transplantation with unrelated bone marrow or peripheral blood stem cells. This article reviews the most recent literature comparing the outcomes after umbilical cord blood transplantation with other alternative stem cell sources.
Improving outcomes of cord blood transplantation: HLA matching, cell dose and other graft‐ and transplantation‐related factors
Authors: Rocha Vanderson , Gluckman Eliane ,   on behalf of the Eurocord‐Netcord registry and European Blood and Marrow Transplant group
Published: October 2009

The use of unrelated umbilical cord blood (UCB) as an alternative source of haematopoietic stem cells transplantation (HSCT) has been widely used for patients lacking a human leucocyte antigen (HLA) matched donor. One of the disadvantages of using UCB is the limited number of haematopoietic stem cells and, consequently, delayed engraftment and increased risk of early mortality. Many approaches have been investigated in the attempt to improve engraftment and survival. Among those, studies analysing prognostic factors related to patients, disease, donor and transplantation have been performed. Variable factors have been identified, such as factors related to donor choice (HLA, cell dose and others) and transplantation (conditioning and graft‐versus‐host disease prophylaxis regimens). This review will focus on the interactions between HLA, cell dose and other modifiable factors related to the UCB unit selection and transplantation that may improve outcomes after UCB transplantation.
Peroxisome proliferator‐activated receptor γ agonists potentiate the cytotoxic effect of valproic acid in multiple myeloma cells
Authors: Aouali Nassera , Palissot Valérie , El‐Khoury Victoria , Moussay Etienne , Janji Bassam , Pierson Sandrine , Brons Nicolaas H. C. , Kellner Laurent , Bosseler Manon , Van Moer Kris , Berchem Guy
Published: September 2009

The main challenge in using chemotherapy to treat multiple myeloma (MM) is drug resistance. In order to evaluate the anti‐neoplastic properties of a new drug combination in MM, two clinically available drugs, valproic acid (VPA) a histone deacetylase (HDAC) inhibitor and pioglitazone, a peroxisome proliferator‐activated receptor gamma (PPARγ) agonist, were tested in vitro on MM cell lines and MM patient cells. The sensitivity towards VPA alone was observed on several MM cell lines tested and also on primary myeloma cells and peripheral blood mononuclear cells from healthy donors. Importantly, the addition of a PPARγ agonist to the VPA treatment increased the cytotoxic effect of VPA in a synergistic/additive manner on the different MM cell lines and MM patient cells. This effect was observed at the physiological range of VPA used to treat epileptic patients. The mechanisms underlying this increase induced a cell cycle arrest and caspase‐dependent apoptosis. The potentiation of the effect of VPA by pioglitazone was mediated by higher acetylation levels of histones H3 and H4 compared to levels induced by HDAC inhibitors alone. This association reveals a new promising chemotherapeutic combination to be tested in MM.
MS‐1020 is a novel small molecule that selectively inhibits JAK3 activity
Authors: Kim Byung‐Hak , Oh Sei‐Ryang , Yin Chang‐Hong , Lee Sangku , Kim Eun‐Ah , Kim Min‐Seok , Sandoval Claudio , Jayabose Somasundaram , Bach Erika A. , Lee Hyeong‐Kyu , Baeg Gyeong‐Hun
Published: September 2009

In order to identify Janus kinase/signal transducer and activator of transcription (JAK/STAT) signalling inhibitors, a cell‐based high throughput screening was performed using a plant extract library that identified Nb‐(α‐hydroxynaphthoyl)serotonin called MS‐1020 as a novel JAK3 inhibitor. MS‐1020 potently inhibited persistently‐active STAT3 in a cell type‐specific manner. Further examination showed that MS‐1020 selectively blocked constitutively‐active JAK3 and consistently suppressed interleukin‐2‐induced JAK3/STAT5 signalling but not prolactin‐induced JAK2/STAT5 signalling. Furthermore, MS‐1020 affected cell viability only in cancer cells harbouring persistently‐active JAK3/STATs, and in vitro kinase assays showed MS‐1020 binds directly with JAK3, blocking its catalytic activity. Therefore, the present study suggested that this reagent selectively inhibits JAK3 and subsequently leads to a block in STAT signalling. Finally, MS‐1020 decreased cell survival by inducing apoptosis via down‐regulation of anti‐apoptotic gene expression. These results suggest that MS‐1020 may have therapeutic potential in the treatment of cancers harbouring aberrant JAK3 signalling.
Decadal change in wetland–woodland boundaries during the late 20th century reflects climatic trends
Authors: KEITH DAVID A. , RODOREDA SUZETTE , BEDWARD MICHAEL
Published: September 2009

Wetlands are important and restricted habitats for dependent biota and play vital roles in landscape function, hydrology and carbon sequestration. They are also likely to be one of the most sensitive components of the terrestrial biosphere to global climate change. An understanding of relationships between wetland persistence and climate is imperative for predicting, mitigating and adapting to the impacts of future climate change on wetland extent and function. We investigated whether mire wetlands had contracted, expanded or remained stable during 1960–2000. We chose a study area encompassing a regional climatic gradient in southeastern Australia, specifically to avoid confounding effects of water extraction on wetland hydrology and extent. We first characterized trends in climate by examining data from local weather stations, which showed a slight increase in precipitation and marked decline in pan evaporation over the relevant period. Remote sensing of vegetation boundaries showed a marked lateral expansion of mires during 1961–1998, and a corresponding contraction of woodland. The spatial patterns in vegetation change were consistent with the regional climatic gradient and showed a weaker co‐relationship to fire history. Resource exploitation, wildland fires and autogenic mire development failed to explain the observed expansion of mire vegetation in the absence of climate change. We therefore conclude that the extent of mire wetlands is likely to be sensitive to variation in climatic moisture over decadal time scales. Late 20th‐century trends in climatic moisture may be related primarily to reduced irradiance and/or reduced wind speeds. In the 21st century, however, net climatic moisture in this region is projected to decline. As mires are apparently sensitive to hydrological change, we anticipate lateral contraction of mire boundaries in coming decades as projected climatic drying eventuates. This raises concerns about the future hydrological functions, carbon storage capacity and unique biodiversity of these important ecosystems.
Greenhouse gas, upwelling‐favorable winds, and the future of coastal ocean upwelling ecosystems
Authors: BAKUN ANDREW , FIELD DAVID B. , REDONDO‐RODRIGUEZ ANA , WEEKS SCARLA J.
Published: September 2009

Coastal ocean upwelling ecosystems generally represent the most productive large marine ecosystems of the world's oceans, in terms of both primary production rates and tonnages of exploitable fish produced. The Peruvian upwelling system, in particular, stands out as a major factor in world fish production. The Pacific trade winds have traditionally been considered to be the primary driving force for the upwelling system off Peru, but are projected to weaken as climate change proceeds. This leads to concern that the upwelling process in the Peru system, to which its productivity is linked, may likewise weaken. However, other mechanisms involving greenhouse‐associated intensification of thermal low‐pressure cells over the coastal landmasses of upwelling regions suggest general intensification of wind‐driven ocean upwelling in coastal upwelling regions of the world's oceans. But although certain empirical results have supported this expectation, it has not been consistently corroborated in climate model simulations, possibly because the scale of the coastal intensification may be small relative to the scales that are appropriately reflected in the standard models. Here we summarize available evidence for the intensification mechanism and present a proxy test that uses variations in water vapor, the dominant natural greenhouse gas, to offer multiple‐realization empirical evidence for action of the proposed mechanism in the real world situation. While many potential consequences to the future of marine ecosystems would codepend on climate change‐related changes in the thermocline and nutricline structures, an important subset, involving potential increased propensities for hypoxia, noxious gas eruptions, toxic red tide blooms, and/or jellyfish outbreaks, may depend more directly on changes in the upwelling‐favorable wind itself. A prospective role of fisheries in either mitigating or reinforcing this particular class of effects is suggested.
Mathematical modeling of soil carbon turnover in natural Podocarpus forest and Eucalyptus plantation in Ethiopia using compound specific δ13C analysis
Authors: FREIER KORBINIAN P. , GLASER BRUNO , ZECH WOLFGANG
Published: September 2009

Forest soils exhibit huge potential in storing carbon, but may also release large amounts of it if they undergo major changes in land use and environmental conditions. Biogeochemical processes controlling accumulation and release of soil organic carbon (SOC) are not yet sufficiently understood. We investigate the dynamics of SOC depending on its chemical composition below a natural forest (Podocarpus falcatus dominated) and a plantation (Eucalyptus saligna) growing on Nitisols in southern Ethiopia. Soils at the study‐site show a huge shift to less negative δ13C values at a depth of 20–30 cm, indicating a change from C4 savanna to C3 forest during the late Holocene. Total organic carbon (TOC), black carbon (BC), and sugars from microbial (rhamnose, fucose) and plant origin (xylose, arabinose) are subjected to compound‐specific stable isotope analysis. Turnover characteristics are calculated using a numerical advection–diffusion–decomposition model. Our measurements show significant differences in carbon storage (P<0.05) for both sites (Podocarpus 23.5 ± 3.2 kg SOC m−3; Eucalyptus 18.6 ± 2.7 kg SOC m−3). These differences can be explained with an initial loss of 15–26% of TOC about 50 years ago, induced by clearing the natural forest. After canopy closure, the carbon input below Eucalyptus is 15–34% less than below natural forest. At present, mean residence times (MRTs) of the investigated compounds do not differ between both stands. Sugars show the shortest MRTs in the topsoil with 2–7 years (xylose) and 5–13 years (arabinose) and have been affected the most by clear‐cutting. TOC and BC show MRTs of 13–25 years and 20–34 years, respectively. Old C4 carbon below 20 cm has merely been affected by the land use change. Contrary to expectation, our study does not indicate a pronounced recalcitrance of BC.
A cross‐taxonomic index for quantifying the health of farmland biodiversity
Authors: Butler Simon J. , Brooks David , Feber Ruth E. , Storkey Jonathan , Vickery Juliet A. , Norris Ken
Published: September 2009

1. The development of sustainable, multi‐functional agricultural systems involves reconciling the needs of agricultural production with the objectives for environmental protection, including biodiversity conservation. However, the definition of sustainability remains ambiguous and it has proven difficult to identify suitable indicators for monitoring progress towards, and the successful achievement of, sustainability.

2. In this study, we show that a trait‐based approach can be used to assess the detrimental impacts of agricultural change to a broad range of taxonomic groupings and derive a standardised index of farmland biodiversity health, built around an objective of achieving stable or increasing populations in all species associated with agricultural landscapes.

3. To demonstrate its application, we assess the health of UK farmland biodiversity relative to this goal. Our results suggest that the populations of two‐thirds of 333 plant and animal species assessed are unsustainable under current UK agricultural practices.

4. We then explore the potential benefits of an agri‐environment scheme, Entry Level Stewardship (ELS), to farmland biodiversity in the UK under differing levels of risk mitigation delivery. We show that ELS has the potential to make a significant contribution to progress towards sustainability targets but that this potential is severely restricted by current patterns of scheme deployment.

5.
Synthesis and applications: We have developed a cross‐taxonomic sustainability index which can be used to assess both the current health of farmland biodiversity and the impacts of future agricultural changes relative to quantitative biodiversity targets. Although biodiversity conservation is just one of a number of factors that must be considered when defining sustainability, we believe our cross‐taxonomic index has the potential to be a valuable tool for guiding the development of sustainable agricultural systems.
Analysing the spatial heterogeneity of emergent groups to assess ecological restoration
Authors: Pottier Julien , Bédécarrats Alain , Marrs Robert H.
Published: September 2009

1. Effective restoration of ecosystem structure and function needs to be built on a strong conceptual basis. The evaluation of restoration is critical in this respect, as it requires an accurate understanding of vegetation dynamics. This study was, therefore, designed to analyse how initial restoration treatments and spontaneous ecological processes act together to produce spatial heterogeneity of plant species at various scales, taking into account that species might respond differentially to these processes in accordance with their biological attributes.

2. In a model system consisting of a large land settlement located on the banks of the river Rhône (France), 85 geo‐referenced plots were located, and the abundance of all plant species and seven biotic and abiotic environmental factors that have been modified by restoration were recorded. All species were classified into emergent groups (EGs) based on 12 plant traits, and the abundance of each EG was derived for each plot. Spatial variables that explained the spatial autocorrelation of the EGs at four scales were computed. This was performed using a spatial eigenvector mapping technique. The spatial variables were then linked to a range of selected environmental factors.

3. Large‐scale patterning of EGs was explained mainly by the spatial heterogeneity of soil quality and vegetation cover. The attribute combination of the EGs that varied most at this scale suggested that the restoration had influenced vegetation development by inducing harsh physical conditions in some part of the studied area and biotic filtering (through competition) in others.

4. A large amount of the spatial variation of EGs was not explained by the environmental factors providing some evidence for pure spatial autocorrelation effects. At the finest scale, this was linked to poor dispersal abilities of some EGs.

5.
Synthesis and applications. By combining a trait‐based approach with spatially explicit methods, we explained and quantified the role of environmental changes induced by restoration and spontaneous biotic processes in structuring plant communities on different spatial scales within a large land settlement. We discuss how such an approach offers new opportunities for an improved assessment of induced and spontaneous structuring factors for restoring and for monitoring plant communities during ecological restoration.
A prospective study of uric acid by glucose tolerance status and survival: the Rancho Bernardo Study
Authors: Kramer C. K. , Von Mühlen D. , Jassal S. K. , Barrett‐Connor E.
Published: September 2009

Abstract.  Kramer CK, von Mühlen D, Jassal SK, Barrett‐Connor E (University of California, La Jolla, CA; and Hospital de Clinicas de Porto Alegre, RS, Brazil). A prospective study of uric acid by glucose tolerance status and survival: the Rancho Bernardo Study. J Intern Med 2010.

Objectives.  Little is known about uric acid (UA) levels and mortality in the context of glycaemia. We examined whether serum UA levels predict all‐cause and cardiovascular disease (CVD) mortality differentially in older adults by glucose tolerance status.

Design and methods.  Between 1984 and 1987, 2342 community‐dwelling men and women had an oral glucose tolerance test, UA measurement, and assessment of traditional CVD risk factors. We defined glucose tolerance status as normoglycaemia (NG), pre‐diabetes (pre‐DM), and type 2 diabetes mellitus (T2DM). Ninety per cent were followed for vital status up to 23 years. Death certificates were coded using the Ninth International Classification of Diseases.

Results.  Baseline age was 69.5 years; 44.4% were men. At baseline 939 had NG, 957 pre‐DM, and 446 T2DM. The mean UA by glucose tolerance status was 327.1, 362.8, and 374.7 μmol L−1. During follow‐up, there were 1318 deaths 46.8% attributed to CVD. In Cox‐regression analysis, each 119 μmol L−1 (2 mg dL−1) increment in UA levels predicted an increased hazard ratio (HR) for all‐cause deaths independent of age, smoking, body mass index, alcohol, physical activity, diuretic use and estimated glomerular filtration rate in all groups (NG: HR 1.25 95% CI 1.06–1.47, P =0.005; pre‐DM: HR 1.20 95% CI 1.06–1.37, P = 0.04; T2DM: HR 1.20 95% CI 1.01–1.47, P = 0.04). After adjusting for CVD risk factors, the UA association with CVD mortality was significant only in the pre‐DM and T2DM groups.

Conclusion.  All‐cause mortality was independently associated with UA in all groups, but UA predicted CVD mortality only in those with abnormal glucose tolerance.
Recent evolution of host‐associated divergence in the seabird tick Ixodes uriae
Authors: KEMPF FLORENT , BOULINIER THIERRY , DE MEEÛS THIERRY , ARNATHAU CÉLINE , McCOY KAREN D.
Published: September 2009

Ecological interactions are an important source of rapid evolutionary change and thus may generate a significant portion of novel biodiversity. Such changes may be particularly prevalent in parasites, where hosts can induce strong selection for adaptation. To understand the relative frequency at which host‐associated divergences occur, it is essential to examine the evolutionary history of the divergence process, particularly when it is occurring over large geographical scales where both geographical and host‐associated isolation may playa part. In this study, we use population genetics and phylogeography to study the evolutionary history of host‐associated divergence in the seabird tick Ixodes uriae (Acari, Ixodidae). We compare results from microsatellite markers that reflect more ecological timescales with a conserved mitochondrial gene (COIII) that reflects more ancient divergence events. Population structure based on microsatellites showed clear evidence of host‐associated divergence in all colonies examined. However, isolated populations of the same host type did not always group together in overall analyses and the genetic differentiation among sympatric host races was highly variable. In contrast, little host or geographical structure was found for the mitochondrial gene fragment. These results suggest that host race formation in I. uriae is a recent phenomenon, that it may have occurred several times and that local interactions are at different points in the divergence process. Rapid divergence in I. uriae implies a strong interaction with its local host species, an interaction that will alter the ecological dynamics of the system and modify the epidemiological landscape of circulating micropathogens.
Spatial genetic structure in Milicia excelsa (Moraceae) indicates extensive gene dispersal in a low‐density wind‐pollinated tropical tree
Authors: BIZOUX J.‐P. , DAÏNOU K. , BOURLAND N. , HARDY O. J. , HEUERTZ M. , MAHY G. , DOUCET J.‐L.
Published: September 2009

In this study, we analysed spatial genetic structure (SGS) patterns and estimated dispersal distances in Milicia excelsa (Welw.) C.C. Berg (Moraceae), a threatened wind‐pollinated dioecious African tree, with typically low density (∼10 adults/km2). Eight microsatellite markers were used to type 287 individuals in four Cameroonian populations characterized by different habitats and tree densities. Differentiation among populations was very low. Two populations in more open habitat did not display any correlation between genetic relatedness and spatial distance between individuals, whereas significant SGS was detected in two populations situated under continuous forest cover. SGS was weak with a maximum Sp‐statistic of 0.006, a value in the lower quartile of SGS estimates for trees in the literature. Using a stepwise approach with Bayesian clustering methods, we demonstrated that SGS resulted from isolation by distance and not colonization by different gene pools. Indirect estimates of gene dispersal distances ranged from σg = 1 to 7.1 km, one order of magnitude higher than most estimates found in the literature for tropical tree species. This result can largely be explained by life‐history traits of the species. Milicia excelsa exhibits a potentially wide‐ranging wind‐mediated pollen dispersal mechanism as well as very efficient seed dispersal mediated by large frugivorous bats. Estimations of gene flow suggested no major risk of inbreeding because of reduction in population density by exploitation. Different strategy of seed collection may be required for reforestation programmes among populations with different extent of SGS.
It takes two DNA translocases to untangle chromosomes from the division septum
Authors: Wu Ling Juan
Published: September 2009

The DNA translocase function of Bacillus subtilis SpoIIIE is essential for spore development and is important during vegetative growth for moving trapped chromosomal DNA away from division septa. Two papers in this issue of Molecular Microbiology, from the teams of Peter Graumann and William Burkholder, have characterized a second SpoIIIE/FtsK‐like protein in B. subtilis, SftA. This protein lacks any recognizable transmembrane domain possessed by the other characterized members of the family, yet the protein is shown to be associated with the division septum and, like SpoIIIE, is required for clearing DNA from the septum. However, SftA and SpoIIIE act at different stages of septation and together they ensure maximum fidelity in chromosome segregation.
The Bacillus subtilis SftA (YtpS) and SpoIIIE DNA translocases play distinct roles in growing cells to ensure faithful chromosome partitioning
Authors: Biller Steven J. , Burkholder William F.
Published: September 2009

In several bacterial species, the faithful completion of chromosome partitioning is known to be promoted by a conserved family of DNA translocases that includes Escherichia coli FtsK and Bacillus subtilis SpoIIIE. FtsK localizes at nascent division sites during every cell cycle and stimulates chromosome decatenation and the resolution of chromosome dimers formed by recA‐dependent homologous recombination. In contrast, SpoIIIE localizes at sites where cells have divided and trapped chromosomal DNA in the membrane, which happens during spore development and under some conditions when DNA replication is perturbed. SpoIIIE completes chromosome segregation post‐septationally by translocating trapped DNA across the membrane. Unlike E. coli, B. subtilis contains a second uncharacterized FtsK/SpoIIIE‐like protein, SftA (formerly YtpS). We report that SftA plays a role similar to FtsK during each cell cycle but cannot substitute for SpoIIIE in rescuing trapped chromosomes. SftA colocalizes with FtsZ at nascent division sites but not with SpoIIIE at sites of chromosome trapping. SftA mutants divide over unsegregated chromosomes more frequently than wild‐type unless recA is inactivated, suggesting that SftA, like FtsK, stimulates chromosome dimer resolution. Having two FtsK/SpoIIIE paralogues is not conserved among endospore‐forming bacteria, but is highly conserved within several groups of soil‐ and plant‐associated bacteria.
Two NDR kinase–MOB complexes function as distinct modules during septum formation and tip extension in Neurospora crassa
Authors: Maerz Sabine , Dettmann Anne , Ziv Carmit , Liu Yi , Valerius Oliver , Yarden Oded , Seiler Stephan
Published: September 2009

NDR kinases are important for growth and differentiation and require interaction with MOB proteins for activity and function. We characterized the NDR kinases and MOB activators in Neurospora crassa and identified two NDR kinases (COT1 and DBF2) and four MOB proteins (MOB1, MOB2A, MOB2B and MOB3/phocein) that form two functional NDR–MOB protein complexes. The MOB1–DBF2 complex is not only essential for septum formation in vegetative cells and during conidiation, but also functions during sexual fruiting body development and ascosporogenesis. The two MOB2‐type proteins interact with both COT1 isoforms and control polar tip extension and branching by regulating COT1 activity. The conserved region directly preceding the kinase domain of COT1 is sufficient for the formation of COT1–MOB2 heterodimers, but also for kinase homodimerization. An additional N‐terminal extension that is poorly conserved, but present in most fungal NDR kinases, is required for further stabilization of both types of interactions and for stimulating COT1 activity. COT1 lacking this region is degraded in a mob‐2 background. We propose a specific role of MOB3/phocein during vegetative cell fusion, fruiting body development and ascosporogenesis that is unrelated to the three other MOB proteins and NDR kinase signalling.
Ras1 and Ras2 play antagonistic roles in regulating cellular cAMP level, stationary‐phase entry and stress response in Candida albicans
Authors: Zhu Yong , Fang Hao‐Ming , Wang Yan‐Ming , Zeng Gui‐Sheng , Zheng Xin‐De , Wang Yue
Published: September 2009

The GTPase Ras1 activates the yeast‐to‐hypha transition in Candida albicans by activating cAMP synthesis. Here, we have characterized Ras2. Ras2 belongs to a group of atypical Ras proteins in some fungal species that share poor identity with other Ras GTPases with many variations in conserved motifs thought to be crucial for Ras‐associated activities. We find that recombinant Ras2 is enzymatically as active as Ras1. However, only RAS1 can rescue the lethality of the Saccharomyces cerevisiae ras1 ras2 mutant, suggesting functional divergence of the two genes. ras2Δ is normal in hyphal growth, but deleting RAS2 in the ras1Δ background greatly aggravates the hyphal defect, indicating that Ras2 also has a role in hyphal development. Strikingly, while RAS1 deletion causes a ∼20‐fold decrease in cellular cAMP, further deletion of RAS2 restores it to ∼30% of the wild‐type level. Consistently, while the ras1Δ mutant enters the stationary phase prematurely, the double mutant does so normally. Moreover, ras1Δ cells exhibit increased resistance to H2O2 and higher sensitivity to the heavy metal Co2+, whereas ras2Δ cells show the opposite phenotypes. Together, our data reveal a novel regulatory mechanism by which two antagonizing Ras GTPases balance each other in regulating multiple cellular processes in C. albicans.
In vitro detection and characterization of drug hypersensitivity using flow cytometry
Authors: Martin M. , Wurpts G. , Ott H. , Baron J. M. , Erdmann S. , Merk H. F. , Sachs B.
Published: October 2009

Background:  The lymphocyte transformation test (LTT) is the only in vitro test for detecting drug sensitization at the cellular level irrespective of the reaction’s phenotype. However, the LTT includes working with radioactive substances and is considered impracticable for routine laboratory investigation.

Objective:  The aim of this study was to assess drug‐specific cytokine production by means of flow cytometry as an alternative nonradioactive approach which may be more appropriate for routine testing and may provide in addition more information about the pathophysiology of the reaction than proliferation‐based assays, like the LTT.

Method:  Peripheral blood mononuclear cells of 19 patients were incubated with culprit drugs (n = 28) or irrelevant antigens (n = 10). Ten healthy persons served as controls for all different drugs (n = 15). Intracellular interleukin (IL)‐5, interferon (IFN)‐γ and IL‐10 production was investigated using flow cytometry. Accuracy of the flow cytometry test system was confirmed using different statistical tests, i.e. receiver operating characteristic curve and Mann–Whitney rank test. In addition, drug‐specific secretion of IL‐5, IL‐2 and IFN‐γ were analysed using enzyme‐linked immunosorbent assay (ELISA).

Results:  Drug‐specific cytokine production could be demonstrated in 75% of the patients using flow cytometry and in 79% using ELISA respectively. Combining ELISA and flow cytometry increased the sensitivity to 100%. Analysis of involved T‐cell subsets [e.g. CD4+ or CD8+; T helper (TH) 1 or TH 2] allowed characterization of the in vitro lymphocyte reactivity pattern.

Conclusions:  Analysis of drug‐specific cytokine production by means of flow cytometry proved a useful and reliable approach for the in vitro detection and characterization of drug hypersensitivities.
Functional analysis of CYP1B1 mutations and association of heterozygous hypomorphic alleles with primary open‐angle glaucoma
Authors: López‐Garrido M‐P , Blanco‐Marchite C , Sánchez‐Sánchez F , López‐Sánchez E , Chaqués‐Alepuz V , Campos‐Mollo E , Salinas‐Sánchez AS , Escribano J
Published: September 2009

López‐Garrido M‐P, Blanco‐Marchite C, Sánchez‐Sánchez F, López‐Sánchez E, Chaqués‐Alepuz V, Campos‐Mollo E, Salinas‐Sánchez AS, Escribano J. Functional analysis of CYP1B1 mutations and association of heterozygous hypomorphic alleles with primary open‐angle glaucoma.

Glaucoma is an inherited complex and heterogeneous disease, and one of the most prevalent causes of definitive blindness in the world. Recent reports have indicated that heterozygous mutations of the CYTOCHOROME P4501B1 (CYP1B1) gene are present in 4–10% of patients with primary open‐angle glaucoma (POAG). To further evaluate the role of CYP1B1 mutations in POAG we extended our previous association study and carried out a functional analysis of the mutations identified by polymerase chain reaction (PCR) DNA sequencing of the three exons of the gene in a total of 245 unrelated Spanish patients and 326 control subjects. Eight of nine different mutations identified in these patients were cloned and functionally assessed by measuring ethoxyresorufin O‐deethylation activity and CYP1B1 stability in transiently transfected HEK‐293T cells. All these mutants showed reduced catalytic activity, ranging from 20% to 60% of wild‐type and/or decreased protein stability and, therefore, they were classified as hypomorphic alleles. No null alleles were identified in these patients. We found heterozygous hypomorphic CYP1B1 mutations in 17 (6.7%) patients and in seven controls (2.1%) showing that these mutations are associated with an increased risk of POAG (p = 0.005; odds ratio = 3.2; 95% confidence interval = 1.30–9.19). Our data suggest that hypomorphic CYP1B1 mutations are, to date, the main known genetic risk factor in POAG.