bluuebunny/crossref_metadata_2025 huggingface dataset:
Genetic mixing from enhancement stocking in commercially exploited vendace populations
Authors: Mehner Thomas , Pohlmann Kirsten , Elkin Che , Monaghan Michael T. , Freyhof Jörg
Published: November 2009

1.  The annual release of hatchery‐bred larvae into naturally reproducing fish populations (enhancement stocking) is used commonly to increase native populations of fish where recruitment is presumably limited. Despite the widespread practice of enhancement stocking, its efficacy and sustainability are seldom monitored.

2.
 We used 1264 amplified fragment length polymorphism markers from 23 vendace Coregonus albula populations in northern Germany to determine whether stocking from external sources contributes to the catch in target populations and leads to hybridization between native and stocked fish. We examined the effects of historical factors as well as recent stocking effects by combined analysis of population‐based equilibrium between migration and drift (IBD) and individual‐based assessments of parentage and hybridization using Bayesian methods.

3.
 Stocking success and hybridization rates differed between north‐east and north‐west German lakes and corresponded negatively to geographical and genetic distances between source and target populations. When populations were compared with and without stocked individuals, we calculated that stocking reduced pairwise genetic distances by c. 11%.

4.  Lakes stocked with genetically similar fish exhibited direct recapture rates of 4% and increased levels of hybridization, leading to genetic homogenization. For lakes in which a genetically more distant source was stocked, recapture rates of stocked fish were 0% and hybridization was lower, with target populations remaining genetically distinct.

5.
 Synthesis and applications. Our results show that stocking from a genetically similar source can disrupt historical genetic differentiation and, possibly, local adaptation, whereas stocking from a genetically distant source only marginally contributed to the native populations and led to no detectable homogenization. The fitness disadvantage of fish stocked from distant sources therefore appears to form a natural impediment to genetic homogenization.
Occupancy estimation and the closure assumption
Authors: Rota Christopher T. , Fletcher Jr Robert J. , Dorazio Robert M. , Betts Matthew G.
Published: November 2009

1.  Recent advances in occupancy estimation that adjust for imperfect detection have provided substantial improvements over traditional approaches and are receiving considerable use in applied ecology. To estimate and adjust for detectability, occupancy modelling requires multiple surveys at a site and requires the assumption of ‘closure’ between surveys, i.e. no changes in occupancy between surveys. Violations of this assumption could bias parameter estimates; however, little work has assessed model sensitivity to violations of this assumption or how commonly such violations occur in nature.

2.  We apply a modelling procedure that can test for closure to two avian point‐count data sets in Montana and New Hampshire, USA, that exemplify time‐scales at which closure is often assumed. These data sets illustrate different sampling designs that allow testing for closure but are currently rarely employed in field investigations. Using a simulation study, we then evaluate the sensitivity of parameter estimates to changes in site occupancy and evaluate a power analysis developed for sampling designs that is aimed at limiting the likelihood of closure.

3.  Application of our approach to point‐count data indicates that habitats may frequently be open to changes in site occupancy at time‐scales typical of many occupancy investigations, with 71% and 100% of species investigated in Montana and New Hampshire respectively, showing violation of closure across time periods of 3 weeks and 8 days respectively.

4.  Simulations suggest that models assuming closure are sensitive to changes in occupancy. Power analyses further suggest that the modelling procedure we apply can effectively test for closure.

5.
 Synthesis and applications. Our demonstration that sites may be open to changes in site occupancy over time‐scales typical of many occupancy investigations, combined with the sensitivity of models to violations of the closure assumption, highlights the importance of properly addressing the closure assumption in both sampling designs and analysis. Furthermore, inappropriately applying closed models could have negative consequences when monitoring rare or declining species for conservation and management decisions, because violations of closure typically lead to overestimates of the probability of occurrence.
The maximum age of Hawaiian terrestrial lineages: geological constraints from Kōko Seamount
Authors: Clague David A. , Braga Juan C. , Bassi Davide , Fullagar Paul D. , Renema Willem , Webster Jody M.
Published: November 2009

Aim  To determine if Kōko Seamount submerged below sea level before Kure Island and Pearl and Hermes Reef formed, resulting in a period in which there were no extant islands. A period with no islands would eliminate prior terrestrial and shallow marine biotas that could migrate from island to island and require a restart of colonization from distant shores to populate the younger islands of the Hawaiian volcanic chain.

Location  Emperor Seamount Chain, north‐central Pacific Ocean.

Methods  We estimate subsidence rates for Kōko Seamount using ages determined from fossil large foraminifera and Sr‐isotopes, and maximum depths using palaeodepth estimates based on coralline algae. These data are combined with palaeolatitude changes as the Pacific Plate moved northwards, sea level variations, and sea surface temperature variations at the seamount through time to reconstruct the time and causes of submergence.

Results  Rounded carbonate clasts include three facies: zooxanthelate corals, bioclastic packstones to rudstones, and rhodolith floatstones. Two rudstones contain relatively deep‐water, coralline algal rhodoliths and large foraminifera indicative of Aquitanian (20.4–20 Ma) and Burdigalian (20–16 Ma) stages of the Early Miocene, consistent with Sr‐isotope ages of algae and one sample of large foraminifera. Corals grew on Kōko Seamount from c. 50 to 27.1 ± 0.4 Ma, the youngest Sr‐isotope age of a coral sample. These shallow, warm‐water coral reefs came under increasing stress as the volcano subsided at 0.012 ± 0.003 mm yr−1, and migrated northwards, and as global climate cooled. The summit submerged and shallow coral reef growth ceased before 29 Ma, probably around 33 Ma. The volcano continued its slow subsidence, and deep‐water carbonates accumulated until they too were unable to keep pace, dying out at c. 16 Ma.

Main conclusions  The final submergence of the summit of Kōko Seamount by about 33 Ma confirms that biota on older Hawaiian–Emperor Islands could not have migrated from island to island along the entire chain to eventually colonize the present Hawaiian Islands. There was a period between at least 33 and 29 Ma in which no islands existed, and distant colonization had to repopulate the younger portion of the Hawaiian chain, which began to emerge between about 29 and 23 Ma.
The relation between intrapersonal and interpersonal staff behaviour towards clients with ID and challenging behaviour: a validation study of the Staff–Client Interactive Behaviour Inventory
Authors: Willems A. P. A. M. , Embregts P. J. C. M. , Stams G. J. J. M. , Moonen X. M. H.
Published: November 2009

Background  Interpersonal staff behaviour is one of the instigating factors associated with challenging behaviour in clients with intellectual disabilities (ID). There are several studies focusing on the influence of intrapersonal staff characteristics – such as beliefs, attributions and emotional reactions – on staff behaviour. Little is known, however, about interpersonal staff behaviour itself. This study describes the development and validation of the Staff–Client Interactive Behaviour Inventory (SCIBI), measuring both intrapersonal and interpersonal staff behaviour in response to challenging behaviour in clients with ID.

Method  A total of 292 staff members, employed in residential and community services, completed the SCIBI for 34 clients with ID and challenging behaviour.

Results  Confirmatory factor analysis of a seven‐factor model – with assertive control, hostile, friendly and support‐seeking interpersonal behaviour; proactive thinking; self‐reflection; and critical expressed emotion as reliable factors – showed an exact fit to the data, indicating construct validity and reliability of the SCIBI. A series of multilevel regression analyses showed higher age of the client to be negatively associated with assertive control. Job experience, level of education, type and sex of staff predicted interpersonal behaviour. Also, intrapersonal staff behaviour, including critical expressed emotion, proactive thinking and self‐reflection, predicted interpersonal behaviour.

Conclusions  The SCIBI can be used to identify staff intrapersonal and interpersonal behaviour towards clients with ID and challenging behaviour. Results obtained with the SCIBI can provide new directions for individual client treatment plans and staff training programmes.
Testing the retention of attachments for implant overdentures – validation of an original force measurement system
Authors: FROMENTIN O. , LASSAUZAY C. , ABI NADER S. , FEINE J. , De ALBUQUERQUE JUNIOR R. F.
Published: November 2009

Summary  The aim of this study was to validate an original portable device to measure attachment retention of implant overdentures both in the lab and in clinical settings. The device was built with a digital force measurement gauge (Imada) secured to a vertical wheel stand associated with a customized support to hold and position the denture in adjustable angulations. Sixteen matrix and patrix cylindrical stud attachments (Locator®) were randomly assigned as in vitro test specimens. Attachment abutments were secured in an implant analogue hung to the digital force gauge or to the load cell of a traction machine used as the gold standard (Instron Universal Testing Machine). Matrices were secured in a denture duplicate attached to the customized support, permitting reproducibility of their position on both pulling devices. Attachment retention in the axial direction was evaluated by measuring maximum dislodging force or peak load during five consecutive linear dislodgments of each attachment on both devices. After a wear simulation, retention was measured again at several time periods. The peak load measurements with the customized Imada device were similar to those obtained with the gold standard Instron machine. These findings suggest that the proposed portable device can provide accurate information on the retentive properties of attachment systems for removable dental prostheses.
A strong genetic footprint of the re‐introduction history of Alpine ibex (Capra ibex ibex)
Authors: BIEBACH IRIS , KELLER LUKAS F.
Published: November 2009

A population’s neutral genetic variation is a composite of its size, degree of isolation and demographic history. Bottlenecks and founder events increase genetic drift, leading to the loss of genetic variation and increased genetic differentiation among populations. Gene flow has the opposite effects. Thus, gene flow can override the genetic patterns caused by founder events. Using 37 microsatellite loci, we investigated the effects of serial bottlenecks on genetic variation and differentiation among 42 Alpine ibex populations in Switzerland with known re‐introduction histories. We detected a strong footprint of re‐introduction events on contemporary genetic structure, with re‐introduction history explaining a substantial part of the genetic differentiation among populations. As a result of the translocation of a considerable number of individuals from the sole formerly surviving population in northern Italy, most of the genetic variation of the ancestral population is now present in the combined re‐introduced Swiss populations. However, re‐introductions split up the genetic variation among populations, such that each contemporary Swiss population showed lower genetic variation than the ancestral population. As expected, serial bottlenecks had different effects on the expected heterozygosity (He) and standardized number of alleles (sNa). While loss of sNa was higher in the first bottlenecks than in subsequent ones, He declined to a similar degree with each bottleneck. Thus, genetic drift was detected with each bottleneck, even when no loss of sNa was observed. Overall, more than a hundred years after the beginning of this successful re‐introduction programme, re‐introduction history was the main determinant of today’s genetic structure.
The noncosmopolitanism paradigm of freshwater zooplankton: insights from the global phylogeography of the predatory cladoceran Polyphemus pediculus (Linnaeus, 1761) (Crustacea, Onychopoda)
Authors: XU S. , HEBERT P. D. N. , KOTOV A. A. , CRISTESCU M. E.
Published: November 2009

A major question in our understanding of eukaryotic biodiversity is whether small bodied taxa have cosmopolitan distributions or consist of geographically localized cryptic taxa. Here, we explore the global phylogeography of the freshwater cladoceran Polyphemus pediculus (Linnaeus, 1761) (Crustacea, Onychopoda) using two mitochondrial genes, cytochrome c oxidase subunit I and 16s ribosomal RNA, and one nuclear marker, 18s ribosomal RNA. The results of neighbour‐joining and Bayesian phylogenetic analyses reveal an exceptionally pronounced genetic structure at both inter‐ and intra‐continental scales. The presence of well‐supported, deeply divergent phylogroups across the Holarctic suggests that P. pediculus represents an assemblage of at least nine, largely allopatric cryptic species. Interestingly, all phylogenetic analyses support the reciprocal paraphyly of Nearctic and Palaearctic clades. Bayesian inference of ancestral distributions suggests that P. pediculus originated in North America or East Asia and that European lineages of Polyphemus were established by subsequent intercontinental dispersal events from North America. Japan and the Russian Far East harbour exceptionally high levels of genetic diversity at both regional and local scales. In contrast, little genetic subdivision is apparent across the formerly glaciated regions of Europe and North America, areas that historical demographic analyses suggest that were recolonized just 5500–24 000 years ago.
Coalescent under the evolution of coadaptation
Authors: RYO TAKAHASI K.
Published: November 2009

Adaptation to novel environments arises either from new beneficial mutations or by utilizing pre‐existing genetic variation. When standing variation is used as the source of new adaptation, fitness effects of alleles may be altered through an environmental change. Alternatively, changes in epistatic genetic backgrounds may convert formerly neutral mutations into beneficial alleles in the new genetic background. By extending the coalescent theory to describe the genealogical histories of two interacting loci, I here investigated the hitchhiking effect of epistatic selection on the amount and pattern of sequence diversity at the linked neutral regions. Assuming a specific form of epistasis between two new mutations that are independently neutral, but together form a coadapted haplotype, I demonstrate that the footprints of epistatic selection differ markedly between the interacting loci depending on the order and relative timing of the two mutational events, even though both mutations are equally essential for the formation of an adaptive gene combination. Our results imply that even when neutrality tests could detect just a single instance of adaptive substitution, there may, in fact, be numerous other hidden mutations that are left undetected, but still play indispensable roles in the evolution of a new adaptation. We expect that the integration of the coalescent framework into the general theory of polygenic inheritance would clarify the connection between factors driving phenotypic evolution and their consequences on underlying DNA sequence changes, which should further illuminate the evolutionary foundation of coadapted systems.
High levels of population subdivision in a morphologically conserved Mediterranean toad (Alytes cisternasii) result from recent, multiple refugia: evidence from mtDNA, microsatellites and nuclear genealogies
Authors: GONÇALVES H. , MARTÍNEZ‐SOLANO I. , PEREIRA R. J. , CARVALHO B. , GARCÍA‐PARÍS M. , FERRAND N.
Published: November 2009

Pleistocene glaciations often resulted in differentiation of taxa in southern European peninsulas, producing the high levels of endemism characteristic of these regions (e.g. the Iberian Peninsula). Despite their small ranges, endemic species often exhibit high levels of intraspecific differentiation as a result of a complex evolutionary history dominated by successive cycles of fragmentation, expansion and subsequent admixture of populations. Most evidence so far has come from the study of species with an Atlantic distribution in northwestern Iberia, and taxa restricted to Mediterranean‐type habitats remain poorly studied. The Iberian Midwife toad (Alytes cisternasii) is a morphologically conserved species endemic to southwestern and central Iberia and a typical inhabitant of Mediterranean habitats. Applying highly variable genetic markers from both mitochondrial and nuclear genomes to samples collected across the species’ range, we found evidence of high population subdivision within A. cisternasii. Mitochondrial haplotypes and microsatellites show geographically concordant patterns of genetic diversity, suggesting population fragmentation into several refugia during Pleistocene glaciations followed by subsequent events of geographical and demographic expansions with secondary contact. In addition, the absence of variation at the nuclear β‐fibint7 and Ppp3caint4 gene fragments suggests that populations of A. cisternasii have been recurrently affected by episodes of extinction and recolonization, and that documented patterns of population subdivision are the outcome of recent and multiple refugia. We discuss the evolutionary history of the species with particular interest in the increasing relevance of Mediterranean refugia for the survival of genetically differentiated populations during the Pleistocene glaciations as revealed by studies in co‐distributed taxa.
Linking genotypes to phenotypes and fitness: how mechanistic biology can inform molecular ecology
Authors: DALZIEL ANNE C. , ROGERS SEAN M. , SCHULTE PATRICIA M.
Published: November 2009

The accessibility of new genomic resources, high‐throughput molecular technologies and analytical approaches such as genome scans have made finding genes contributing to fitness variation in natural populations an increasingly feasible task. Once candidate genes are identified, we argue that it is necessary to take a mechanistic approach and work up through the levels of biological organization to fully understand the impacts of genetic variation at these candidate genes. We demonstrate how this approach provides testable hypotheses about the causal links among levels of biological organization, and assists in designing relevant experiments to test the effects of genetic variation on phenotype, whole‐organism performance capabilities and fitness. We review some of the research programs that have incorporated mechanistic approaches when examining naturally occurring genetic and phenotypic variation and use these examples to highlight the value of developing a comprehensive understanding of the relationship between genotype and fitness. We give suggestions to guide future research aimed at uncovering and understanding the genetic basis of adaptation and argue that further integration of mechanistic approaches will help molecular ecologists better understand the evolution of natural populations.
The role of absC, a novel regulatory gene for secondary metabolism, in zinc‐dependent antibiotic production in Streptomyces coelicolor A3(2)
Authors: Hesketh Andy , Kock Holger , Mootien Saraspadee , Bibb Mervyn
Published: November 2009

The availability of zinc was shown to have a marked influence on the biosynthesis of actinorhodin in Streptomyces coelicolor A3(2). Production of actinorhodin and undecylprodigiosin was abolished when a novel pleiotropic regulatory gene, absC, was deleted, but only when zinc concentrations were low. AbsC was shown to control expression of the gene cluster encoding production of coelibactin, an uncharacterized non‐ribosomally synthesized peptide with predicted siderophore‐like activity, and the observed defect in antibiotic production was found to result from elevated expression of this gene cluster. Promoter regions in the coelibactin cluster contain predicted binding motifs for the zinc‐responsive regulator Zur, and dual regulation of coelibactin expression by zur and absC was demonstrated using strains engineered to contain deletions in either or both of these genes. An AbsC binding site was identified in a divergent promoter region within the coelibactin biosynthetic gene cluster, adjacent to a putative Zur binding site. Repression of the coelibactin gene cluster by both AbsC and Zur appears to be required to maintain appropriate intracellular levels of zinc in S. coelicolor.
The germinal centre kinase Don3 triggers the dynamic rearrangement of higher‐order septin structures during cytokinesis in Ustilago maydis
Authors: Böhmer Christian , Ripp Caroline , Bölker Michael
Published: November 2009

The dimorphic phytopathogenic fungus Ustilago maydis grows in its haploid phase by budding. Cytokinesis and separation of daughter cells are accomplished by the consecutive formation of two distinct septa. Here, we show that both septation events involve the dynamic rearrangement of septin assemblies from hourglass‐shaped collars into ring‐like structures. Using a chemical genetic approach we demonstrate that the germinal centre kinase Don3 triggers this septin reorganization during secondary septum formation. Although chemical inhibition of an analogue‐sensitive version of Don3 prevented septation, a stable septin collar was assembled at the presumptive septation site. Interestingly, the essential light chain of type II myosin, Cdc4, was already associated with this septin collar. Release of Don3 kinase inhibition triggered immediate dispersal of septin filaments and concomitant incorporation of Cdc4 into a contractile actomyosin ring, which also contained the F‐BAR domain protein Cdc15. Inhibition of actin polymerization or deletion of the cdc15 gene, did not affect assembly of the initial collar consisting of septin and myosin light chain. However, reassembly of septin filaments into a ring‐like structure was prevented in the absence of either F‐actin or Cdc15, indicating that septin ring formation in U. maydis depends on a functional contractile actomyosin ring.
Photooxidative stress‐induced and abundant small RNAs in Rhodobacter sphaeroides
Authors: Berghoff Bork A. , Glaeser Jens , Sharma Cynthia M. , Vogel Jörg , Klug Gabriele
Published: November 2009

Exposure to oxygen and light generates photooxidative stress by the bacteriochlorophyll a mediated formation of singlet oxygen (1O2) in Rhodobacter sphaeroides. Our study reports the genome‐wide search for small RNAs (sRNAs) involved in the regulatory response to 1O2. By using 454 pyrosequencing and Northern blot analysis, we identified 20 sRNAs from R. sphaeroides aerobic cultures or following treatment with 1O2 or superoxide (O–2). One sRNA was specifically induced by 1O2 and its expression depends on the extracytoplasmic function sigma factor RpoE. Two sRNAs induced by 1O2 and O–2 were cotranscribed with upstream genes preceded by promoters with target sequences for the alternative sigma factors RpoHI and RpoHII. The most abundant sRNA was processed in the presence of 1O2 but not by O–2. From this and a second sRNA a conserved 3′‐segment accumulated from a larger precursor. Absence of the RNA chaperone Hfq changed the half‐lives, abundance and processing of 1O2‐affected sRNAs. Orthologues of three sRNA genes are present in different alpha‐proteobacteria, but the majority was unique to R. sphaeroides or Rhodobacterales species. Our discovery that abundant sRNAs are affected by 1O2 exposure extends the knowledge on the role of sRNAs and Hfq in the regulatory response to oxidative stress.
Competitive activation of the Escherichia coli argO gene coding for an arginine exporter by the transcriptional regulators Lrp and ArgP
Authors: Peeters Eveline , Nguyen Le Minh Phu , Foulquié‐Moreno Maria , Charlier Daniel
Published: November 2009

In vivo and in vitro analyses indicate that transcription of the argO gene coding for an arginine exporter is regulated by the global transcriptional regulator Lrp, an effect that went by unnoticed in previous genome‐scale screenings of the Lrp regulatory network in Escherichia coli. Lrp activates the argO promoter fourfold; exogenous leucine antagonizes, but does not completely eliminate this effect. Activation by Lrp interferes with the previously demonstrated activation of the argO promoter by ArgP. This interference results from the mutual inhibitory binding of the two activators to overlapping targets. As a consequence, each regulator acts more potently in the absence of the other. Dimeric Lrp binds cooperatively to at least three regularly spaced semi‐palindromic binding sites. Leucine reduces complex formation approximately twofold but concomitantly enhances the cooperativity of the binding. Footprinting data suggest a severe Lrp‐induced deformation of the argO control region. Combined, the effector modulated activation of argO transcription by ArgP and Lrp must ensure an adapted and fine‐tuned synthesis of the transporter in response to environmental conditions. The repertoire of bacterial transcription regulation mechanisms is vast, but the competitive activation of a single promoter by two activator proteins as described here appears to be rare.
The BosR regulatory protein of Borrelia burgdorferi interfaces with the RpoS regulatory pathway and modulates both the oxidative stress response and pathogenic properties of the Lyme disease spirochete
Authors: Hyde Jenny A. , Shaw Dana K. , Smith III Roger , Trzeciakowski Jerome P. , Skare Jon T.
Published: November 2009

Borrelia burgdorferi, the Lyme disease spirochete, adapts as it moves between the arthropod and mammalian hosts that it infects. We hypothesize that BosR serves as a global regulator in B. burgdorferi to modulate the oxidative stress response and adapt to mammalian hosts. To test this hypothesis, a bosR mutant in a low‐passage B. burgdorferi isolate was constructed. The resulting bosR::kanR strain was altered when grown microaerobically or anaerobically suggesting that BosR is required for optimal replication under both growth conditions. The absence of BosR increased the sensitivity of B. burgdorferi to hydrogen peroxide and reduced the synthesis of Cdr and NapA, proteins important for cellular redox balance and the oxidative stress response, respectively, suggesting an important role for BosR in borrelial oxidative homeostasis. For the bosR mutant, the production of RpoS was abrogated and resulted in the loss of OspC and DbpA, suggesting that BosR interfaces with the Rrp2–RpoN–RpoS regulatory cascade. Consistent with the linkage to RpoS, cells lacking bosR were non‐infectious in the mouse model of infection. These results indicate that BosR is required for resistance to oxidative stressors and provides a regulatory response that is necessary for B. burgdorferi pathogenesis.
BslA, the S‐layer adhesin of B. anthracis, is a virulence factor for anthrax pathogenesis
Authors: Kern Justin , Schneewind Olaf
Published: November 2009

Microbial pathogens use adhesive surface proteins to bind to and interact with host tissues, events that are universal for the pathogenesis of infectious diseases. A surface adhesin of Bacillus anthracis, the causative agent of anthrax, required to mediate these steps has not been discovered. Previous work identified BslA, an S‐layer protein, to be necessary and sufficient for adhesion of the anthrax vaccine strain, Bacillus anthracis Sterne, to host cells. Here we asked whether encapsulated bacilli require BslA for anthrax pathogenesis in guinea pigs. Compared with the highly virulent parent strain B. anthracis Ames, bslA mutants displayed a dramatic increase in the lethal dose and in mean time‐to‐death. Whereas all tissues of animals infected with B. anthracis Ames contained high numbers of bacilli, only few vegetative forms could be recovered from internal organs of animals infected with the bslA mutant. Surface display of BslA occurred at the poles of encapsulated bacilli and enabled the binding of vegetative forms to host cells. Together these results suggest that BslA functions as the surface adhesin of the anthrax pathogen B. anthracis strain Ames.
Difference in the distribution and speciation of cellular nickel between nickel‐tolerant and non‐tolerant Nicotiana tabacum L. cv. BY‐2 cells
Authors: SAITO AKIHIRO , SAITO MISA , ICHIKAWA YUSUKE , YOSHIBA MASAAKI , TADANO TOSHIAKI , MIWA EITARO , HIGUCHI KYOKO
Published: November 2009

To evaluate Ni dynamics at the subcellular level, the distribution and speciation of Ni were determined in wild‐type (WT) and Ni‐tolerant (NIT) tobacco BY‐2 cell lines. When exposed to low but toxic levels of Ni, NIT cells were found to contain 2.5‐fold more Ni (14% of whole‐cell Ni values) in their cell walls than WT cells (6% of whole‐cell Ni values). In addition to higher levels of Ni in the apoplast, a higher proportion (94%) of symplastic Ni was localized in the vacuoles of NIT cells than in the vacuoles of WT cells (81%). The concentration of cytosolic Ni in the NIT cells was significantly lower (18 nmol g−1 FW) than that in the WT cells (85 nmol g−1 FW). In silico simulation showed that 95% of vacuolar Ni was in the form of Ni‐citrate complexes, and that free Ni2+ was virtually absent in the NIT cells. On the other hand, the amount of free metal ions was markedly increased in WT cells because free citrate was depleted by chelation of Ni. A protoplast viability assay using BCECF‐AM further demonstrated that the main mechanism that confers strong Ni tolerance was present in the symplast as opposed to the cell wall.
Genes mapping to boron tolerance QTL in barley identified by suppression subtractive hybridization
Authors: HASSAN MAHMOOD , OLDACH KLAUS , BAUMANN UTE , LANGRIDGE PETER , SUTTON TIM
Published: November 2009

Boron tolerance is a quantitative trait controlled by multiple genes. Suppression subtractive hybridization was carried out on root cDNA from bulked boron tolerant and intolerant doubled haploid barley lines grown under moderate boron stress to identify genes associated with boron tolerance. One hundred and eleven clones representing known proteins were found to be up‐regulated in the tolerant bulk upon boron stress. Nine clones were genetically mapped to previously reported boron tolerance QTL. These include a clone identical to the boron transporter gene Bot1 and a clone coding for a bromo‐adjacent homology domain‐containing protein, mapping to the 6H boron tolerance locus and co‐segregating with reduced boron intake in a Clipper × Sahara‐3771 mapping population. A third clone mapping to the 2H QTL region encoding an S‐adenosylmethionine decarboxylase precursor was found to provide tolerance to high boron by heterologous expression. Yeast cells expressing Sahara SAMDC were able to grow on 15 mm boron solid media and maintained cellular boron concentrations at 13% lower than control cells expressing empty vector. The data suggest that an antioxidative response mechanism involving polyamines and the ascorbate–glutathione pathway in Sahara barley may provide an advantage in tolerating high soil concentrations of boron.
Comparative analysis of the grain proteome fraction in barley genotypes with contrasting salinity tolerance during germination
Authors: WITZEL KATJA , WEIDNER ANNETTE , SURABHI GIRIDARA‐KUMAR , VARSHNEY RAJEEV K. , KUNZE GOTTHARD , BUCK‐SORLIN GERHARD H. , BÖRNER ANDREAS , MOCK HANS‐PETER
Published: November 2009

In the present paper, we based a search for candidates underlying different levels of salinity tolerance during germination in the Oregon Wolfe Barley mapping population (DOM × REC) by proteomic profiling of the mature grain of lines showing differing levels of salinity tolerance. By contrasting the parents DOM and REC, displaying divergent stress responses, and two tolerant and two sensitive segregants, six protein spots were identified that showed a differential abundance between the tolerant and the sensitive lines. The tolerant lines expressed a higher level of 6‐phosphogluconate dehydrogenase and glucose/ribitol dehydrogenase (Glc/RibDH). Both proteins were heterologously over‐expressed in an osmo‐sensitive yeast strain and over‐expression of Glc/RibDH resulted in an enhanced ability of yeast transformants to grow on salt containing media. A quantitative trait locus (QTL) analysis of the population germinating at different salt concentrations led to the identification of two chromosome regions on 5H and one on 7H associated with salt stress response. A dense barley transcript map was employed to map the genomic region of all identified proteins. Two of these, heat‐shock protein 70 and Glc/RibDH, co‐localized with the identified QTL on chromosome 5H. The putative functional role of the candidates is discussed.
Regulation of growth response to water stress in the soybean primary root. I. Proteomic analysis reveals region‐specific regulation of phenylpropanoid metabolism and control of free iron in the elongation zone
Authors: YAMAGUCHI MINEO , VALLIYODAN BABU , ZHANG JUAN , LENOBLE MARY E. , YU OLIVER , ROGERS ELIZABETH E. , NGUYEN HENRY T. , SHARP ROBERT E.
Published: November 2009

In water‐stressed soybean primary roots, elongation was maintained at well‐watered rates in the apical 4 mm (region 1), but was progressively inhibited in the 4–8 mm region (region 2), which exhibits maximum elongation in well‐watered roots. These responses are similar to previous results for the maize primary root. To understand these responses in soybean, spatial profiles of soluble protein composition were analysed. Among the changes, the results indicate that region‐specific regulation of phenylpropanoid metabolism may contribute to the distinct growth responses in the different regions. Several enzymes related to isoflavonoid biosynthesis increased in abundance in region 1, correlating with a substantial increase of isoflavonoid content in this region which could contribute to growth maintenance via various potential mechanisms. In contrast, caffeoyl‐CoA O‐methyltransferase, which is involved in lignin synthesis, was highly up‐regulated in region 2. This response was associated with enhanced accumulation of lignin, which may be related to the inhibition of growth in this region. Several proteins that increased in abundance in both regions of water‐stressed roots were related to protection from oxidative damage. In particular, an increase in the abundance of ferritin proteins effectively sequestered more iron and prevented excess free iron in the elongation zone under water stress.
Temporal heterogeneity of cold acclimation phenotypes in Arabidopsis leaves
Authors: GORSUCH PETER A. , PANDEY SUBEDAR , ATKIN OWEN K.
Published: November 2009

To predict the effects of temperature changes on plant growth and performance, it is crucial to understand the impact of thermal history on leaf morphology, anatomy and physiology. Here, we document a comprehensive range of leaf phenotypes in 25/20 °C‐grown Arabidopsis thaliana plants that were shifted to 5 °C for up to 2 months. When warm‐grown, pre‐existing (PE) leaves were exposed to cold, leaf thickness increased due to an increase in mesophyll cell size. Leaves that were entirely cold‐developed (CD) were twice as thick (eight cell layers) as their warm‐developed (WD) counterparts (six layers), and also had higher epidermal and stomatal cell densities. After 4 d of cold, PE leaves accumulated high levels of total non‐structural carbohydrates (TNC). However, glucose and starch levels declined thereafter, and after 45 d in the cold, PE leaves exhibited similar TNC to CD leaves. A similar phenomenon was observed in δ13C and a range of photosynthetic parameters. In cold‐treated PE leaves, an increase in respiration (Rdark) with cold exposure time was evident when measured at 25 °C but not 5 °C. Cold acclimation was associated with a large increase in the ratio of leaf Rdark to photosynthesis. The data highlight the importance of understanding developmental thermal history in determining individual phenotypic traits.
Molecular phylogenetic relationships between Albugo candida collections on the Brassicaceae in Australia
Authors: Petkowski J. E. , Cunnington J. H. , Minchinton E. J. , Cahill D. M.
Published: November 2009

Recent phylogenetic analyses of Albugo candida using the mitochondrial cytochrome c oxidase subunit II (cox2) gene, the nuclear ribosomal RNA large subunit (LSU) gene and the nuclear ribosomal RNA internal transcribed spacer (ITS) gene region have revealed significant genetic variation and led to the description of new species in the A. candida complex. This study examined the genetic diversity within Australian collections of A. candida from various Brassicaceae species in a range of geographic locations. Phylogenetic analysis of 31 Australian A. candida collections from 11 hosts using the rDNA ITS region, rDNA LSU region and cox2 mtDNA showed that the majority of Australian A. candida collections were the common form of A. candida. One collection from a common weed host, hairy bitter cress (Cardamine hirsuta), was found to belong to a previously reported but undescribed species, while three collections, also from C. hirsuta, were found to belong to a new undescribed species.
Molecular typing and spread of Clavibacter michiganensis subsp. michiganensis in greenhouses in Japan
Authors: Kawaguchi A. , Tanina K. , Inoue K.
Published: November 2009

Clavibacter michiganensis subsp. michiganensis (CMM) strains collected between 2005‐2008 from greenhouses in different locations in Okayama Prefecture, Japan, were fingerprinted by repetitive sequence‐based polymerase chain reaction (rep‐PCR) with ERIC and BOX primers. One hundred and eighty strains from eight different locations in Okayama were differentiated into four haplotypes (A to D) based on rep‐PCR. Regardless of the year of isolation, location or cultivar of tomato, the strains in each greenhouse and location belonged to the same haplotype, suggesting the strains originated from the previous greenhouse population. Based on Morisita’s index of dispersion (I), the distribution of diseased plants in the greenhouses, where disbudding and defoliation using either scissors or by hand were carried out in the same direction to promote the spread of CMM, occurred in an aggregated distribution in a quadrant along a row of plants, but the distribution of diseased plants indicated a random distribution in a quadrant along a furrow of plants (two adjoining rows of plants). These results showed that disbudding and defoliation contribute highly to the secondary spread of bacterial canker in commercial greenhouses.
The Effect of Microenvironmental CD40 Signals on TRAIL‐ and Drug‐induced Apoptosis in Follicular Lymphoma Cells
Authors: Nuutinen U. , Ropponen A. , Eeva J. , Eray M. , Pellinen R. , Wahlfors J. , Pelkonen J.
Published: November 2009

Follicular lymphoma (FL) cells are malignant counterparts of germinal centre (GC) B cells. Microenvironment of FL B cells has an important role in the progression of FL and might also have an impact on the treatment of FL. CD40 is an important mediator of microenvironmental survival signals in GCs. Here we studied responses of CD40 signalling on TRAIL‐, dexamethasone‐ and doxorubicin‐induced apoptosis in three human FL cell lines. In two of the FL cell lines, CD40 protected cells from apoptosis which was entirely dependent on the activation of NF‐κB. In one of the FL cell lines, CD40 induced apoptosis itself. However, inhibition of NF‐κB induced apoptosis in all three FL cell lines. Therefore, our results indicate that inhibitors of NF‐κB or critical downstream anti‐apoptotic targets of NF‐κB instead of blocking CD40 antibodies in combination with TRAIL or other cytotoxic agents should be considered in the treatment of FL in order to prevent the protective effect of the microenvironment.
Expansion ofPhragmites australisin the Liaohe Delta, north‐east China
Authors: JI Y H , ZHOU G S , LV G H , ZHAO X L , JIA Q Y
Published: November 2009

Based on satellite images and historical vegetation maps,Phragmites australis(common reed) in the Liaohe Delta, in north‐east China, has expanded from 78 078 ha in 1984 to 91 262 ha in 2006, averaging over 600 ha year−1. This study also attempted to elucidate the reason for this expansion, using both historical documents and field surveys. The results suggested that the expansion ofP. australiswas driven mainly by human activities. Freshwater irrigation reduced soil salinity; irrigation of land blocks divided by canals and ditches (square‐land irrigation) maintained optimal temperature, water and oxygen for the growth ofP. australis; deep freshwater irrigation and seawater irrigation eliminated some weeds; combined irrigation and burning eliminated an insect pest. These examples in the Liaohe Delta showed that water, salinity, oxygen, temperature and insect pests were important ecological factors that affected the growth ofP. australis. By harmonising these ecological factors, optimal conditions were created for the natural expansion ofP. australisand promoted the formation of monospecific stands ofP. australis.
The development and testing of a measure assessing clinician beliefs about patient self‐management
Authors: Hibbard Judith H. , Collins Peter Alf , Mahoney Eldon , Baker Laurence H.
Published: November 2009

Background  Clinicians have been slow to embrace support for patient self‐management.

Objective  To explore clinicians’ beliefs about patient self‐management and specifically assess which patient competencies clinicians believe are most important for their patients.

Methods  Using items adapted from the Patient Activation Measure (PAM) as a basis, a new measure that assesses clinicians’ beliefs about patient self‐management was created using Rasch analysis. The development and testing of the new measure Clinician Support for Patient Activation Measure (CS‐PAM) is described here. Primary care clinicians from the UK and the USA were recruited to participate in the survey (n = 175).

Findings  The CS‐PAM reliably measures clinician attitudes about the patient role in the care process. Clinicians strongly endorse that patients should follow medical advice but are less likely to endorse that patients should be able to make independent judgements or take independent actions. Endorsed to a lesser degree was the idea that patients should be able to function as a member of the care team. Least endorsed was the notion that patients should be independent information seekers.

Discussion  Clinicians’ views appear to be out of step with current policy directions and professional codes. Clinicians need support to transition to understand the need to support patients as independent actors.
Communicating the results of research: how do participants of a cardiac rehabilitation RCT prefer to be informed?
Authors: Dalal Hasnain , Wingham Jennifer , Pritchard Colin , Northey Sharon , Evans Philip , Taylor Rod S. , Campbell John
Published: November 2009

Objective  To determine the preferred means by which participants in a study of cardiac rehabilitation wish to be informed of the study’s results.

Design  Postal questionnaire survey of participants in a randomized controlled trial.

Setting  Cornwall, southwest England.

Participants  Patients recruited to the Cornwall Heart Attack Rehabilitation Management Study (CHARMS).

Method  Participants recruited to CHARMS who were alive 3 years and 9 months after the trial was completed were contacted by letter and invited to return a reply slip with four short questions indicating how they would prefer to be informed about the published results of the study.

Results  In March 2008, 191/230 participants originally recruited to CHARMS were still alive. General practitioners deemed 166/191 (88%) survivors medically appropriate to be contacted through a postal survey, and 154/166 (93%) participants responded to the invitation to participate in the follow‐up survey. 86% (143/166) of participants indicated that they wished to be informed about the results: 115 (80%) of these elected to receive information by letter and 25 (18%) of these preferred to attend a meeting. Men older than 65 years predominated in this latter group. Women respondents preferred to receive the study results by letter; none preferred communication by email or the web.

Conclusion  Survivors of acute myocardial infarction who participated in a RCT of cardiac rehabilitation wanted to receive a summary of the aggregate study results. Participants had preferences regarding how they would wish to be informed about the results of the study. Most participants preferred to be informed by letter or email, but some preferred the interaction of a group or a meeting.
An ethical justification for the Chronic Care Model (CCM)
Authors: Oprea Liviu , Braunack‐Mayer Annette , Rogers Wendy A. , Stocks Nigel
Published: November 2009

Background:  Chronic diseases are major causes of morbidity and mortality in developed countries. Their effects can be mitigated by high quality evidence‐based care, but this is not the norm in most systems. The Chronic Care Model (CCM) is an evidence‐based policy response to this practice gap, which uses multiple strategies to promote the quality of chronic care.

Objective:  To review CCM with an ethical lens.

Methods:  We reviewed the published empirical and non‐empirical articles of CCM to analyse the ethical underpinnings of this model.

Results and conclusions:  We argue that its principal ethical value lies in the institutional cooperation it builds between the stakeholders involved in health care services. First, we briefly describe CCM and argue that the pathways through which it aims to improve patients’ health outcomes are not made explicit. Second, we argue that the potential of CCM to be more beneficent, compared with traditional health care systems, depends on its capacity to promote mutual trust between health care providers and patients. There is no evidence to date that the implementation of CCM enhances mutual trust between health care professionals and patients. Third, we argue that CCM seeks to enhance human agency, allowing increased expression of individual autonomy and increased respect for individuals thereby expanding human freedom and avoiding social discrimination. However, we review the communication patterns that characterize the model of doctor–patient relationship promoted by this model and argue that these communication patterns raise ethical concerns that may prevent the model from reaching its expected outcomes.