bluuebunny/crossref_metadata_2025 huggingface dataset:
The Vesicle-inducing Protein 1 from Synechocystis sp. PCC 6803 Organizes into Diverse Higher-Ordered Ring Structures
Authors: Fuhrmann Eva , Bultema Jelle B. , Kahmann Uwe , Rupprecht Eva , Boekema Egbert J. , Schneider Dirk
Published: September 2009

The vesicle-inducing protein in plastids 1 (Vipp1) was found to be involved in thylakoid membrane formation in chloroplasts and cyanobacteria. In contrast to chloroplasts, it has been suggested that in cyanobacteria the protein is only tightly associated with the cytoplasmic membrane. In the present study we analyze and describe the subcellular localization and the oligomeric organization of Vipp1 from the cyanobacterium Synechocystis PCC 6803. Vipp1 forms stable dimers and higher-ordered oligomers in the cytoplasm as well as at both the cytoplasmic and thylakoid membrane. Vipp1 oligomers are organized in ring structures with a variable diameter of 25–33 nm and corresponding calculated molecular masses of ∼1.6–2.2 MDa. Six different types of rings were found with an unusual 12–17-fold symmetrical conformation. The simultaneous existence of multiple types of rings is very unusual and suggests a special function of Vipp1. Involvement of diverse ring structures in vesicle formation is suggested.
DNA from a 100-year-old holotype confirms the validity of a potentially extinct hummingbird species
Authors: Kirchman Jeremy J. , Witt Christopher C. , McGuire Jimmy A. , Graves Gary R.
Published: September 2009

We used mtDNA sequence data to confirm that the controversial 100-year-old holotype of the Bogotá sunangel (
Heliangelus zusii
) represents a valid species. We demonstrate that
H. zusii
is genetically well differentiated from taxa previously hypothesized to have given rise to the specimen via hybridization. Phylogenetic analyses place
H. zusii
as sister to a clade of mid- to high-elevation Andean species currently placed in the genera
Taphrolesbia
and
Aglaiocercus. Heliangelus zusii
, presumed extinct, has never been observed in nature by biologists. We infer that the species occupied a restricted distribution between the upper tropical and temperate zones of the northern Andes and that it was most probably driven to extinction by deforestation that accompanied human population growth during the nineteenth and early twentieth centuries. We demonstrate the feasibility of obtaining DNA from nearly microscopic tissue samples from old hummingbird specimens and suggest that these methods could be used to resolve the taxonomy of dozens of avian taxa known only from type specimens.
Meta-analysis in applied ecology
Authors: Stewart Gavin
Published: September 2009

This overview examines research synthesis in applied ecology and conservation. Vote counting and pooling unweighted averages are widespread despite the superiority of syntheses based on weighted combination of effects. Such analyses allow exploration of methodological uncertainty in addition to consistency of effects across species, space and time, but exploring heterogeneity remains controversial. Meta-analyses are required to generalize in ecology, and to inform evidence-based decision-making, but the more sophisticated statistical techniques and registers of research used in other disciplines must be employed in ecology to fully realize their benefits.
Environmental modulation of metabolic allometry in ornate rainbowfishRhadinocentrus ornatus
Authors: Vaca H. Fabian , White Craig R.
Published: September 2009

The nature of the relationship between the metabolic rate (MR) and body mass (M) of animals has been the source of controversy for over seven decades, with much of the focus on the value of the scaling exponentb, where MR is proportional toMb. While it is well known that MR does not generally scale isometrically (i.e.bis seldom equal to 1), the value ofbremains the subject of heated debate. In the present study, we examine the influence of an ecologically relevant abiotic variable, pH, on the metabolic allometry of an Australian freshwater fish,Rhadinocentrus ornatus. We show that the value ofbis lower for rainbowfish acclimated to acidic (pH 5.0) conditions compared to rainbowfish acclimated to alkaline conditions (pH 8.5), but that acute exposure to altered pH does not alter the value ofb. This significant effect of an abiotic variable on metabolic allometry supports a growing body of evidence that there is no universal value ofband demonstrates that experimental manipulations of metabolic allometry represent powerful, and as yet underused, tools to understand the factors that constrain and influence the allometry of metabolic rate.
A strain of the bacterial symbiont
Regiella insecticola
protects aphids against parasitoids
Authors: Vorburger Christoph , Gehrer Lukas , Rodriguez Paula
Published: September 2009

Aphids commonly harbour facultative bacterial endosymbionts and may benefit from their presence through increased resistance to parasitoids. This has been demonstrated for
Hamiltonella defensa
and
Serratia symbiotica
, while a third common endosymbiont,
Regiella insecticola
, did not provide such protection. However, this symbiont was recently detected in a highly resistant clone of the peach-potato aphid,
Myzus persicae
, from Australia. To test if resistance was indeed conferred by the endosymbiont, we eliminated it from this clone with antibiotics, and we transferred it to two other clones of the same and one clone of a different aphid species (
Aphis fabae
). Exposing these lines to the parasitoid
Aphidius colemani
showed clearly that unlike other strains of this bacterium, this specific isolate of
R. insecticola
provides strong protection against parasitic wasps, suggesting that the ability to protect their host against natural enemies may evolve readily in multiple species of endosymbiotic bacteria.
Changes in reflectin protein phosphorylation are associated with dynamic iridescence in squid
Authors: Izumi Michi , Sweeney Alison M. , DeMartini Daniel , Weaver James C. , Powers Meghan L. , Tao Andrea , Silvas Tania V. , Kramer Ryan M. , Crookes-Goodson Wendy J. , Mäthger Lydia M. , Naik Rajesh R. , Hanlon Roger T. , Morse Daniel E.
Published: September 2009

Many cephalopods exhibit remarkable dermal iridescence, a component of their complex, dynamic camouflage and communication. In the speciesEuprymnascolopes, the light-organ iridescence is static and is due to reflectin protein-based platelets assembled into lamellar thin-film reflectors called iridosomes, contained within iridescent cells called iridocytes. Squid in the family Loliginidae appear to be unique in which the dermis possesses a dynamic iridescent component with reflective, coloured structures that are assembled and disassembled under the control of the muscarinic cholinergic system and the associated neurotransmitter acetylcholine (ACh). Here we present the sequences and characterization of three new members of the reflectin family associated with the dynamically changeable iridescence inLoligoand not found in staticEuprymnairidophores. In addition, we show that application of genistein, a protein tyrosine kinase inhibitor, suppresses ACh- and calcium-induced iridescence inLoligo. We further demonstrate that two of these novel reflectins are extensively phosphorylated in concert with the activation of iridescence by exogenous ACh. This phosphorylation and the correlated iridescence can be blocked with genistein. Our results suggest that tyrosine phosphorylation of reflectin proteins is involved in the regulation of dynamic iridescence inLoligo.
Predicting the direction of ornament evolution in Trinidadian guppies (
Poecilia reticulata
)
Authors: Kemp Darrell J. , Reznick David N. , Grether Gregory F. , Endler John A.
Published: September 2009

Sexual selection is thought to be opposed by natural selection such that ornamental traits express a balance between these two antagonistic influences. Phenotypic variation among populations may indicate local shifts in this balance, or that different stable ‘solutions’ are possible, but testing these alternatives presents a major challenge. In the guppy (
Poecilia reticulata
), a small freshwater fish with male-limited ornamental coloration, these issues can be addressed by transplanting fish among sites of varying predation pressure, thus effectively manipulating the strength and nature of natural selection. Here, we contrast the evolutionary outcome of two such introductions conducted in the Trinidadian El Cedro and Aripo Rivers. We use sophisticated colour appraisal methods that account for full spectrum colour variation and which incorporate the very latest visual sensitivity data for guppies and their predators. Our data indicate that ornamentation evolved along different trajectories: whereas Aripo males evolved more numerous and/or larger orange, black and iridescent markings, El Cedro males only evolved more extensive and brighter iridescence. Examination of the El Cedro experiment also revealed little or no ornamental evolution at the control site over 29 years, which contrasts markedly with the rapid (approx. 2–3 years) changes reported for introduction populations. Finally, whole colour-pattern analysis suggested that the greatest visual difference between El Cedro introduction and control fish would be perceived by the two most salient viewers: guppies and the putatively dangerous predator
Crenicichla alta
. We discuss whether and how these evolutionary trajectories may result from founder effects, population-specific mate preferences and/or sensory drive.
Flexible task allocation and the organization of work in ants
Authors: Robinson Elva J. H. , Feinerman Ofer , Franks Nigel R.
Published: September 2009

Flexibility in task performance is essential for a robust system of division of labour. We investigated what factors determine which social insect workers respond to colony-level changes in task demand. We used radio-frequency identification technology to compare the roles of corpulence, age, spatial location and previous activity (intra-nest/extra-nest) in determining whether worker ants (
Temnothorax albipennis
) respond to an increase in demand for foraging or brood care. The less corpulent ants took on the extra foraging, irrespective of their age, previous activity or location in the nest, supporting a physiological threshold model. We found no relationship between ants that tended the extra brood and corpulence, age, spatial location or previous activity, but ants that transported the extra brood to the main brood pile were less corpulent and had high previous intra-nest activity. This supports spatial task-encounter and physiological threshold models for brood transport. Our data suggest a flexible task-allocation system allowing the colony to respond rapidly to changing needs, using a simple task-encounter system for generalized tasks, combined with physiologically based response thresholds for more specialized tasks. This could provide a social insect colony with a robust division of labour, flexibly allocating the workforce in response to current needs.
High stimulus specificity characterizes anti-predator habituation under natural conditions
Authors: Hemmi Jan M. , Merkle Tobias
Published: September 2009

Habituation is one of the most fundamental learning processes that allow animals to adapt to dynamic environments. It is ubiquitous and often thought of as a simple form of non-associative learning. Very little is known, though, about the rules that govern habituation and their significance under natural conditions. Questions about how animals incorporate habituation into their daily behaviour and how they can assure only to habituate to non-relevant stimuli are still unanswered. Animals under threat of predation should be particularly selective about which stimuli they habituate to, since ignoring a real threat could be fatal. In this study, we tested the response of fiddler crabs,
Uca vomeris
, to repeatedly approaching dummy predators to find out whether these animals habituate to potential predators and to test the selectivity of the habituation process. The crabs habituated to model predators, even though they were confronted with real predators during the same habituation process. They showed remarkable selectivity towards the stimulus: a simple change in the approach distance of the stimulus led to a recovery in their responses. The results strongly indicate that in the context of predator avoidance, habituation under natural conditions is highly selective and a stimulus is not defined just by its current sensory signature, but also its spatio-temporal history.
A Nomadic Subtelomeric Disease Resistance Gene Cluster in Common Bean
Authors: David Perrine , Chen Nicolas W.G. , Pedrosa-Harand Andrea , Thareau Vincent , Sévignac Mireille , Cannon Steven B. , Debouck Daniel , Langin Thierry , Geffroy Valérie
Published: September 2009

The B4 resistance (R) gene cluster is one of the largest clusters known in common bean (Phaseolus vulgaris [Pv]). It is located in a peculiar genomic environment in the subtelomeric region of the short arm of chromosome 4, adjacent to two heterochromatic blocks (knobs). We sequenced 650 kb spanning this locus and annotated 97 genes, 26 of which correspond to Coiled-Coil-Nucleotide-Binding-Site-Leucine-Rich-Repeat (CNL). Conserved microsynteny was observed between the Pv B4 locus and corresponding regions of Medicago truncatula and Lotus japonicus in chromosomes Mt6 and Lj2, respectively. The notable exception was the CNL sequences, which were completely absent in these regions. The origin of the Pv B4-CNL sequences was investigated through phylogenetic analysis, which reveals that, in the Pv genome, paralogous CNL genes are shared among nonhomologous chromosomes (4 and 11). Together, our results suggest that Pv B4-CNL was derived from CNL sequences from another cluster, the Co-2 cluster, through an ectopic recombination event. Integration of the soybean (Glycine max) genome data enables us to date more precisely this event and also to infer that a single CNL moved from the Co-2 to the B4 cluster. Moreover, we identified a new 528-bp satellite repeat, referred to as khipu, specific to the Phaseolus genus, present both between B4-CNL sequences and in the two knobs identified at the B4 R gene cluster. The khipu repeat is present on most chromosomal termini, indicating the existence of frequent ectopic recombination events in Pv subtelomeric regions. Our results highlight the importance of ectopic recombination in R gene evolution.
Multiple origins of symbioses between ascomycetes and bryophytes suggested by a five‐gene phylogeny
Authors: Stenroos Soili , Laukka Tomi , Huhtinen Seppo , Döbbeler Peter , Myllys Leena , Syrjänen Kimmo , Hyvönen Jaakko
Published: September 2009

Numerous species of microscopic fungi inhabit mosses and hepatics. They are severely overlooked and their identity and nutritional strategies are mostly unknown. Most of these bryosymbiotic fungi belong to the Ascomycota. Their fruit‐bodies are extremely small, often reduced and simply structured, which is why they cannot be reliably identified and classified by their morphological and anatomical characters. A phylogenetic hypothesis of bryosymbiotic ascomycetes is presented. New sequences of 78 samples, including 61 bryosymbionts, were produced, the total amount of terminals being 206. Of these, 202 are Ascomycetes. Sequences from the following five gene loci were used: rDNA SSU, rDNA LSU, RPB2, mitochondrial rDNA SSU, and rDNA 5.8S. The program TNT was used for tree search and support value estimation. We show that bryosymbiotic fungi occur in numerous lineages, one of which represents a newly discovered lineage among the Ascomycota and exhibits a tripartite association with cyanobacteria and sphagna. A new genus Trizodia is proposed for this basal clade. Our results demonstrate that even highly specialized life strategies can be adopted multiple times during evolution, and that in many cases bryosymbionts appear to have evolved from saprobic ancestors.

 © The Willi Hennig Society 2009.
Prevalence of hepatitis B virus DNA polymerase mutations in treatment‐naïve patients with chronic hepatitis B
Authors: NGUYEN M. H. , GARCIA R. T. , TRINH H. N. , NGUYEN H. A. , NGUYEN K. K. , NGUYEN L. H. , LEVITT B.
Published: September 2009

Background  One of the most important factors in treatment failure using nucleos(t)ide analogues in chronic hepatitis B is anti‐viral resistance. Primary drug resistance refers to amino acid changes in the hepatitis B virus polymerase/reverse transcriptase (rt) that result in reduced susceptibility to anti‐viral agents. Pre‐existing drug resistance mutations may occur in untreated patients and may affect their treatment outcomes.

Aim  To determine the prevalence of hepatitis B DNA polymerase mutations in treatment‐naïve patients.

Methods  We used a direct PCR sequencing test to detect DNA polymerase mutations in 472 consecutive treatment‐naïve patients at two community gastroenterology clinics in Northern California.

Results  A majority of patients were Asians (>95%), had either genotype B or C (95%) and had no evidence of cirrhosis or liver cancer (94%). Mean age was 45 ± 13 and mean hepatitis B virus DNA was 5.3 ± 1.8 log10 IU/mL. Most patients did not have any detectable mutations (82.4%). Some (16.7%) had mutations of unknown clinical significance (rtV207M/L/I) and only 4 patients had rtA181A/S, rtA194S or M250I.

Conclusions  No rtM204V/I or rtN236T mutations were observed in our study. Less than 1% of our patients had mutations that can be associated with primary resistance to existing anti‐viral therapies for hepatitis B virus.
Identification of a 3.7‐Mb region for a marbling QTL on bovine chromosome 4 by identical‐by‐descent and association analysis
Authors: Yokouchi K. , Mizoguchi Y. , Watanabe T. , Iwamoto E. , Sugimoto Y. , Takasuga A.
Published: September 2009

QTL mapping for growth and carcass traits was performed using a paternal half‐sib family composed of 325 Japanese Black cattle offspring. Nine QTL were detected at the 1% chromosome‐wise significance level at a false discovery rate of less than 0.1. These included two QTL for marbling on BTA 4 and 18, two QTL for carcass weight on BTA 14 and 24, two QTL for longissimus muscle area on BTA 1 and 4, two QTL for subcutaneous fat thickness on BTA 1 and 15 and one QTL for rib thickness on BTA 6. Although the marbling QTL on BTA 4 has been replicated with significant linkages in two Japanese Black cattle sires, the three Q (more marbling) haplotypes, each inherited maternally, were apparently different. To compare the three Q haplotypes in more detail, high‐density microsatellite markers for the overlapping regions were developed within the 95% CIs (65 markers in 44–78 cM). A detailed haplotype comparison indicated that a small region (<3.7 Mb) around 46 cM was shared between the Qs of the two sires, whose dams were related. An association of this region with marbling was shown by a regression analysis using the local population, in which the two sires were produced and this was confirmed by an association study using a population collected throughout Japan. These results strongly suggest that the marbling QTL on BTA 4 is located in the 3.7‐Mb region at around 46 cM.
Postnatal transcription profile and polymorphism of the ADIPOR1 gene in five pig breeds
Authors: Stachowiak M. , Flisikowski K. , Szydlowski M. , Fries R. , Switonski M.
Published: September 2009

As a result of its role in energy homeostasis regulation, the ADIPOR1 gene is a candidate for fat deposition, an important production trait, in the pig. The aim of the study was to conduct a comparative analysis of the ADIPOR1 postnatal transcript level, in order to establish its promoter and 5′UTR sequences and to search the gene for polymorphisms. The transcription level was examined in longissimus dorsi and semimembranosus muscles collected from 180 pigs at 60–210 days of age, representing five pig breeds: Duroc, Polish Large White, Polish Landrace, Pietrain and Pulawska. We calculated highly significant breed by age by muscle interaction (P < 0.0001) and breed by muscle interactions (P < 0.01). The 5′UTR and promoter region of the porcine ADIPOR1 gene were amplified for the first time and their sequences were deposited in the GenBank database. In total, 21 novel and two previously described polymorphisms were found in the ADIPOR1 promoter, coding, intronic, 5′ and 3′ untranslated regions. The only SNP detected in the coding region was a synonymous substitution. Two polymorphisms in 3′UTR (c.*129A>C and c.*536A>G) showed no significant effect on the transcript level. Our results showed a high polymorphism of the ADIPOR1 and a complexity in its transcription level in the studied muscles. This complexity indicates that conclusions based on such studies should be carefully gradated.
Across‐line SNP association study of innate and adaptive immune response in laying hens
Authors: Biscarini F. , Bovenhuis H. , Van Arendonk J. A. M. , Parmentier H. K. , Jungerius A. P. , Van Der Poel J. J.
Published: September 2009

The aim of the present study was to detect quantitative trait loci (QTL) for innate and adaptive immunity in laying hens. For this purpose, the associations between 1022 single nucleotide polymorphism (SNP) markers and immune traits were studied in 583 hens from nine different layer lines. Immune traits were natural antibodies for keyhole limpet haemocyanin (KLH) and lipopolysaccharide (LPS) at 20, 40 and 65 weeks, acquired antibodies to the vaccinal virus of Newcastle disease at 20 weeks, and complement activity measured on sheep and bovine red blood cells at 20, 40 and 65 weeks. We adopted a novel approach based on across‐line analysis and testing of the SNP‐by‐line interaction. Among lines, linkage disequilibrium is conserved at shorter distances than in individual lines; therefore, SNPs significantly associated with immune traits across lines are expected to be near the functional mutations. In the analysis, the SNPs that had a significant across‐line effect but did not show significant SNP‐by‐line interaction were identified to test whether the association was consistent in the individual lines. Ultimately, 59 significant associations between SNPs and immune traits were detected. Our results confirmed some previously identified QTL and identified new QTL potentially involved in the immune function. We found evidence for a role of IL17A (chromosome 3) in natural and acquired antibody titres and in the classical and alternative pathways of complement activation. The major histocompatibility genes on chromosome 16 showed significant association with natural and acquired antibody titres and classical complement activity. The IL12B gene on chromosome 13 was associated with natural antibody titres.
Dwelling at the oxycline: does increased stratification provide a predation refugium for the Lake Victoria sardine Rastrineobola argentea?
Authors: Wanink Jan H. , Kashindye Jeremiah J. , Goudswaard P.C. (kees) , Witte Frans
Published: September 2009

1. We tested the hypothesis that increased hypoxia in Lake Victoria provides a refugium for the cyprinid dagaa (Rastrineobola argentea) against hypoxia‐sensitive Nile perch (Lates niloticus).  2. Hypoxia in the main habitat of dagaa was rare during 1979–80, but lasted 3–5 months in 1987 and 1988, during which time adult dagaa spent the day just above the oxycline instead of near the bottom.  3. Dissolved oxygen concentrations in the layer just above the oxycline were not critical for Nile perch, but a mass kill of this species following a sudden upwelling of hypoxic water suggested that oxycline‐dwelling is risky.  4. Our data suggest no difference between dagaa and Nile perch in the level at which dissolved oxygen starts to limit their vertical distribution in the water column, but dagaa seems to be even more sensitive to extreme hypoxia (<1–2 mg O2 L−1) than Nile perch.  5. We argue that oxycline‐dwelling dagaa are not seeking a predation refugium but that they are limited by low oxygen levels in reaching their feeding areas near the bottom.
Variation in phytoplankton composition and limnological features in a water–water ecotone of the Lower Paraná Basin (Argentina)
Authors: Izaguirre Irina , O'Farrell Inés , Tell Guillermo
Published: September 2009

1. Structure and dynamics of phytoplankton were studied at six sites in a reach of the Lower Paraná River floodplain, from the main course to a marginal shallow lake, connected through a stream. This system is defined as a water–water ecotone and thus, the aim of this work is to analyse the spatial changes of phytoplankton along the transitional system.  2. Temporal fluctuations in number of species and phytoplankton density were more pronounced in the river than in the shallow lake. Even though most species were ubiquitous, there was a clear segregation of the most abundant populations across the ecotone. Aulacoseira granulata var. granulata and other centric diatoms decreased towards the lentic system.  3. Transparency varied according to river discharge, being higher in the lake during high water phases, while the opposite behaviour was observed during dry periods. These fluctuations were related to precipitation and resuspension processes.  4. Nitrate concentration diminished towards the lake while soluble reactive phosphorus remained fairly homogeneous across the ecotone.
Spatial and temporal variability of fires in relation to ecosystems, land tenure and rainfall in savannas of northern South America
Authors: ROMERO‐RUIZ M. , ETTER A. , SARMIENTO A. , TANSEY K.
Published: September 2009

Fire is a predominant factor forcing global terrestrial biomass dynamics, with more than 30% of the land surface showing frequent burning, particularly in the tropics, where it mostly affects savannas ecosystems annually. Savannas, which cover approximately 269 million ha in South America, play a major role in the global carbon cycle. They are affected by increasing human pressures and global climate change. Using satellite data, this study quantifies vegetation burning in the Colombian Llanos savannas for the period 2000–2008, and analyzes how fire spatial pattern, frequency and extent vary with ecosystem type, land tenure and rainfall. On average 2.75±0.5 million ha (24±4.2%) of the savannas burn each year. Burned area is highly variable, with 3.4 million ha burned in 2002–2003 and <1.9 million ha in 2005–2006. However, during the 2000–2008 period near of 3.7 million ha (33.5%) of the savannas never burned. Compared with the average 8–10 years of fire return time for the tropics and subtropics, these savannas burn twice as often. In addition, the average burn size figure for tropical and subtropical grassland savannas (with <5% trees) of 7000 ha (median 5000 ha), is about seven times the average burned patch size we found in our study. Fires predominate in the well‐drained high plain savannas, lowest figures occurring along the Andean foothills, in forested areas and in pasture and croplands. Annual proportion burned varies with land tenure, being highest in National Parks. This study is the first complete regional map of fire disturbance in a South American savanna. This detailed regional data provides a unique opportunity for increasing the accuracy of global carbon emission calculations.
Turnover of labile and recalcitrant soil carbon differ in response to nitrate and ammonium deposition in an ombrotrophic peatland
Authors: CURREY PAULINE M. , JOHNSON DAVID , SHEPPARD LUCY J. , LEITH IAN D. , TOBERMAN HANNAH , Van Der WAL RENÉ , DAWSON LORNA A. , ARTZ REBEKKA R. E.
Published: September 2009

The effects of 4 years of simulated nitrogen deposition, as nitrate (NO3−) and ammonium (NH4+), on microbial carbon turnover were studied in an ombrotrophic peatland. We investigated the mineralization of simple forms of carbon using MicroResp™ measurements (a multiple substrate induced respiration technique) and the activities of four soil enzymes involved in the decomposition of more complex forms of carbon or in nutrient acquisition: N‐acetyl‐glucosaminidase (NAG), cellobiohydrolase (CBH), acid phosphatase (AP), and phenol oxidase (PO). The potential mineralization of labile forms of carbon was significantly enhanced at the higher N additions, especially with NH4+ amendments, while potential enzyme activities involved in breakdown of more complex forms of carbon or nutrient acquisition decreased slightly (NAG and CBH) or remained unchanged (AP and PO) with N amendments. This study also showed the importance of distinguishing between NO3− and NH4+ amendments, as their impact often differed. It is possible that the limited response on potential extracellular enzyme activity is due to other factors, such as limited exposure to the added N in the deeper soil or continued suboptimal functioning of the enzymes due to the low pH, possibly via the inhibitory effect of low phenol oxidase activity.
Phylogeography of the ground squirrel subgenusXerospermophilusand assembly of the Mojave Desert biota
Authors: Bell Kayce C. , Hafner David J. , Leitner Philip , Matocq Marjorie D.
Published: September 2009

Aim The Mohave ground squirrel (Xerospermophilus mohavensis) is one of a few endemic species of the Mojave Desert of south‐western North America. We describe phylogeographic patterns within this species and its sister taxon (Xerospermophilus tereticaudus) and test hypotheses concerning their biogeographical history using genetic signatures of stable versus expanding populations. We compare these patterns with those of other Mojave species to evaluate the role of vicariance in producing phylogeographic structure during the assembly of the Mojave Desert biota.

Location The Mojave Desert and adjacent desert regions of south‐western North America.

Methods Complete cytochromebgene sequences ofX. mohavensis(46 individuals representing 11 localities) andX. tereticaudus(38 individuals representing 14 localities) were analysed using Bayesian methods to infer phylogenetic relationships. Genetic signals of stable or expanding populations were examined based on the distribution of recent mutations and pairwise differences, as well as with a coalescent‐based approach.

Results The two species are reciprocally monophyletic and may have diverged in response to the late Pliocene–early Pleistocene uplift of the Transverse Ranges and Mojave block. Little phylogeographic structure is evident withinX. mohavensis, but there is a signature of northern expansion from a presumably full‐pluvial refugium in the Mojave River basin. Four geographic subgroups are evident withinX. tereticaudus, and there is a signature of northern expansion from a presumably full‐pluvial refugium in the Sonoran coastal plains. Roughly congruent phylogeographic patterns are found within five arid‐adapted taxa, indicating a strong element of vicariance during the assembly of the generally transitional Mojave Desert biota.

Main conclusions We present a preliminary model for the historical assembly of the Mojave Desert biota that indicates a strong vicariant element producing autochthonous lineages (includingX. mohavensis) that diverged during the major geological and climatic events of the last 5 Myr. Phylogeographic partitioning within the Mojave Desert underscores the necessity of immediate conservation measures for this unique and fragile arid ecosystem that is locked between two large metropolitan population centres and is the target of continued adverse environmental impact.
Variation in arbuscular mycorrhizal fungi colonization modifies the expression of tolerance to above‐ground defoliation
Authors: Garrido Etzel , Bennett Alison E. , Fornoni Juan , Strauss Sharon Y.
Published: September 2009

1. Plant association with arbuscular mycorrhizal fungi (AMF) has been considered a factor increasing plant tolerance to herbivory. However, this positive effect could decrease with colonization density if the benefit : cost ratio of the AMF–plant association changes. We measured plant performance and tolerance to defoliation across a gradient of commercial AMF (Glomussp.) inoculum concentration.

2. Six genetic families ofDatura stramoniumwere grown under greenhouse conditions and subjected to five increasing levels of AMF inoculum concentration and to defoliation treatments, i.e. the presence/absence of 50% artificial damage, following a full‐factorial design.

3. AMF colonization increased linearly with inoculum concentration while foliar area, root mass, flowering phenology and seed production expressed nonlinear functions. Plant genetic variation in the benefit function of AMF colonization was also detected. We show a negative interaction between AMF concentration and plant tolerance to defoliation.

4. Synthesis. The negative correlation between plant tolerance and AMF concentration suggests that defoliation can reduce AMF benefits and that natural variations in AMF can limit the evolution of optimum levels of tolerance. Moreover, genetic variation in the shape of the reaction norms to AMF in the presence/absence of defoliation suggests that plants may evolve in response to variation in densities of AMF and herbivores.
Computer‐aided system for health economic evaluation
Authors: Lin Wen‐Chou , Yen Amy Ming‐Fang , Chang Chi‐Ming , Chao Chih‐Hsung , Chen Tony Hsiu‐Hsi
Published: September 2009

Background  Health policy makers are usually stranded by the complicated infrastructure and intensive computation related to economic evaluation.

Objectives  It is therefore valuable to develop a computer‐aided tool to help health personnel to perform economic evaluation with ease.

Method  The infrastructure for economic evaluation was first designed. Markov process with micro‐simulation was applied to model the disease natural history or lifetime sequale to project the effectiveness by comparing all possible decisions. All the essential elements of economic evaluation together with sensitivity analysis are encoded in this computer‐aided software written with SAS Screen Control Language in user‐defined menu style.

Illustration  Screening versus no screening for colorectal cancer was used as an example.

Conclusion  The computer‐aided model for economic evaluation was developed in this study. It is anticipated that the flexibility and user‐defined menu style facilitate the wide application of economic evaluation to health care intervention program.
A combined diabetes renal clinic improves risk factor management and progression of renal disease in a district general hospital
Authors: Patel Manish , Shilliday Ilona R. , McKay Gerard A.
Published: September 2009

Aims  Aggressive management of vascular risk factors reduces the rate of progression to end‐stage renal failure in patients with diabetic nephropathy. The aim of our audit was to clarify whether improvements in patient care could be demonstrated within a short time period after establishing a combined diabetes renal clinic in a district general hospital.

Methods  A retrospective analysis of weight, glycaemic control, blood pressure control, rate of decline in renal function and appropriate use of medications for vascular risk management for patients in a district general hospital was performed before and after attendance at a combined diabetes renal clinic.

Results  Data were complete for 45 patients. There was no significant change in weight from 14 months before attending the combined clinic, referral to the clinic and after 14 months of mean follow‐up. An improvement in mean systolic blood pressure was achieved at the combined diabetes renal clinic (from 147 to 134 mmHg with an average fall of 16.5 mmHg, P < 0.01). The mean glycated haemoglobin (HbA1c) improved from 8.6% to 8% (P = 0.002). The rate of decline in estimated glomerular filtration rate of 1.16 mL min−1 per month prior to referral improved to 0.21 mL min−1 per month on attending the combined clinic (P = 0.002).

Conclusions  Vascular risk factor management was improved and decline in renal function slowed in patients with diabetic nephropathy within a short period of establishing a combined diabetes renal clinic in a district general hospital.
Responsiveness of the EQ‐5D to HADS‐identified anxiety and depression
Authors: Whynes David K.
Published: September 2009

Rationale  The use of generic measures of health‐related quality of life enables cost effectiveness comparisons of different health care interventions to be made. Nevertheless, there exists a concern that generic instruments may be insufficiently sensitive to detect the differences or changes in outcome identified by condition‐specific instruments. This paper compares the psychometric properties of the EQ‐5D generic instrument with a widely used specific measure of distress, the Hospital Anxiety and Depression Scale (HADS).

Method  The analysis was based on data obtained from a large sample of women (n = 3119) with low‐grade cervical cytological abnormalities detected at routine screening. These women completed EQ‐5D and HADS questionnaires at recruitment and at 12 months thereafter. We examined the strength of association between HADS‐determined severity of distress and EQ‐5D scores at recruitment and between changes in severity and in scores over time.

Results  A higher likelihood of HADS‐identified anxiety and/or depression was associated with significantly lower EQ‐5D index and visual analogue scores. Over time, the EQ‐5D score rose significantly when the likelihood of an individual representing a HADS‐defined anxiety and/or depression case decreased.

Conclusion  We conclude that the EQ‐5D has shown itself to be responsive to differing degrees of HADS‐assessed distress, although generalization beyond the UK context requires further investigation.
The utility of the Illness Perception Questionnaire in the evaluation of mental health practitioners' perspectives on patients with schizophrenia
Authors: Fleming Mick P. , Martin Colin R. , Miles Jeremy , Atkinson John
Published: September 2009

Rationale, aims, objectives  The Illness Perception Questionnaire (IPQ) was designed as a measure of illness perception and has been used extensively for measuring the perceptions of people with physical illness. Latterly modified versions of the IPQ have been used to measure the illness perceptions of people with mental health problems and their carers. This study examined the utility of a modified version of the IPQ to measure changes in mental health practitioners' illness perceptions about schizophrenia after undertaking psychosocial intervention training.

Method  A total of 245 mental health practitioners who undertook psychosocial intervention training completed a modified version of the IPQ before and after training. The structure of the questionnaire was tested using confirmatory factor analysis. The internal consistency of sub‐scales embedded in the instrument was also examined.

Results  The hypothesized structure failed to account for the data. Model fit indices revealed a poor fit to the data across all models evaluated. Cronbach's alpha revealed a number of sub‐scales in the instrument to have mediocre internal consistency characteristics.

Conclusions  The modified version of the IPQ is not suitable for evaluating the impact of psychosocial intervention training on changes in illness perceptions of schizophrenia in mental health practitioners. However, the study has highlighted the need to develop a valid and reliable measure to assess the illness perceptions health professionals have of patients in their care.
Revitalizing primary health care and family medicine/primary care in India – disruptive innovation?
Authors: Biswas Rakesh , Joshi Ankur , Joshi Rajeev , Kaufman Terry , Peterson Chris , Sturmberg Joachim P. , Maitra Arjun , Martin Carmel M.
Published: September 2009

Context India has rudimentary and fragmented primary health care (PHC) and family medicine systems, yet it also has the policy expectation that PHC should meet the needs of extremely large populations with slums and difficult to reach groups, rapid social and epidemiological transition from developing to developed nation profiles. Historically, the system has lacked impetus to achieve PHC.

Objective To provide an overview of PHC approaches and the current state of PHC and family medicine in India in order to assess the opportunities for their revitalization.

Methods A narrative review of the published and grey literature on PHC, family medicine, Web2.0 and health informatics key papers and policy documents, pertinent to India.

Outcomes A conceptual framework and recommendations for policy makers and practitioner audiences.

Findings PHC is constructed through systems of local providers who address individual, family and local community basic health needs with strong community participation. Successful PHC is a pre‐eminent strategy for India to address the determinants of health and the almost chaotic of massive social transition in its institutions and health care sector. There is a lack of an articulated comprehensive framework for the publicly stated goals of improving health and implementing PHC. Also, there exists a very limited education and organization of a medical and PHC workforce who are trained and resourced to address individual, family and local community health and who have become increasingly specialized. However, emerging technology, Health2.0 and user generated health care informatics, which are largely conducted through mobile phones, are co‐evolving patient‐driven health systems, and potentially enhance PHC and family medicine workforce development.

Conclusions In order to improve health outcomes in an equitable manner in India, there is a pressing need for a framework for implementing PHC. The co‐emergence of information technologies accessible to the mass population and user‐driven health care provide a potential catalyst or innovation for this transition.
Part 1 – unravelling primary health care conceptual predicaments through the lenses of complexity and political economy: a position paper for progressive transformation
Authors: Félix‐Bortolotti Margot
Published: September 2009

Objective  To disentangle the concepts of primary health care and primary care as well as their conceptual and empirical ramifications for progressive transformation.

Methods  over 400 international and interdisciplinary abstracts and papers with 96 annotated bibliography abstracts of literature across multiple dimensions relating to the knowledge base around mechanisms in PHC development were reviewed. The text is confronted with the reality, as it exists in the field and makes the case for complexity perspectives to assess this phenomenon in its context.

Conclusion  PHC complexity is an important analytical tool to interrogate the ways in which this phenomenon is socially constructed as well as in the matrices in which it is embedded. It is also a potent analytical tool to assist in the deconstruction of prevalent linear thinking built around PHC as a whole.
Patients’ perceptions of discrimination during hospitalization
Authors: Hudelson Patricia , Kolly Véronique , Perneger Thomas
Published: September 2009

Objective  To identify sources of perceived discrimination during hospitalization and examine the relationship of perceived discrimination to patient and hospital stay characteristics, and to patient ratings of care.

Background  Patient experiences of discrimination within the health‐care system are associated with delays in care seeking, non‐adherence to medical advice and poorer health status. Most research to date has focused on race and ethnicity‐based discrimination, and few studies have included hospitalized patients.

Methods  Questions about patients’ experiences of discrimination were added to a regular patient opinion survey conducted at the Geneva University Hospitals. Participants were 1537 adult residents of Switzerland discharged from the hospital between 15 February and 15 March 2007.

Results  A total of 171 (11.1%) respondents reported at least one source of discrimination. Most (93, 54.4%) reported a single cause of discrimination. The most frequent causes of discrimination were language, age, nationality and having a disease that is viewed negatively by others. Fifteen percentage of non‐European respondents reported at least one of the following types of discrimination: language, nationality, religion and skin colour. Reporting discrimination from any cause was associated with higher Picker Patient Experience problem scores, and patients who reported discrimination were less likely to describe their care as very good or excellent and less likely to recommend the hospital to others.

Conclusions  Patient experiences of discrimination during hospitalization are relatively frequent and are associated with lower patient ratings of care. Collection of data on patient experiences of discrimination may contribute to the development of interventions aimed at ensuring respectful, quality care for all patients.
SURF1 missense mutations promote a mild Leigh phenotype
Authors: Piekutowska‐Abramczuk D , Magner M , Popowska E , Pronicki M , Karczmarewicz E , Sykut‐Cegielska J , Kmiec T , Jurkiewicz E , Szymanska‐Debinska T , Bielecka L , Krajewska‐Walasek M , Vesela K , Zeman J , Pronicka E
Published: September 2009

SURF1 gene mutations are the most common cause of Leigh syndrome (LS), a rare progressive neurodegenerative disorder of infancy, characterized by symmetric necrotizing lesions and hypervascularity in the brainstem and basal ganglia, leading to death before the age of 4 years. Most of the reported mutations create premature termination codons, whereas missense mutations are rare.

The aim of the study was to characterize the natural history of LS patients carrying at least one missense mutation in the SURF1 gene. Nineteen such patients (8 own cases and 11 reported in the literature) were compared with a reference group of 20 own c.845_846delCT homozygous patients, and with other LSSURF– cases described in the literature.

Disease onset in the studied group was delayed. Acute failure to thrive and hyperventilation episodes were rare, respiratory failure did not appear before the age of 4 years. Dystonia, motor regression and eye movement dissociation developed slowly. The number of patients who survived 7 years of life totaled 9 out of 15 (60%) in the ‘missense group’ and 1 out of 26 (4%) patients with mutations leading to truncated proteins.

In conclusion: (i) The presence of a missense mutation in the SURF1 gene may correlate with a milder course and longer survival of Leigh patients, (ii) normal magnetic resonance imaging (MRI) findings, normal blood lactate value, and only mild decrease of cytochrome c oxidase (COX) activity are not sufficient reasons to forego SURF1 mutation analysis in differential diagnosis.