bluuebunny/crossref_metadata_2025 huggingface dataset:
Sedation of ventilated patients in intensive care units: relatives’ experiences
Authors: Dreyer Anne , Nortvedt Per
Published: February 2008

Title.  Sedation of ventilated patients in intensive care units: relatives’ experiences

Aim.  This paper is a report of a study undertaken to explore the experiences of being relatives of ventilated and sedated patients in intensive care units.

Background.  In the last few years, issues about medically‐induced sleep as part of intensive care unit treatment have focused on the appropriate level of medication. There are no studies of the impact of relatives on assessment of sedation levels, but studies of family participation in intensive care units show that relatives see their role as more important for the patient than nurses do.

Method.  An explorative, descriptive design was adopted. In‐depth interviews were conducted with eight relatives of patients in 2003. The research question was: How do relatives experience having a close family member in a state of serious illness, being treated on a ventilator, and receiving medically induced sedation and pain relief? Kvale’s hermeneutical interpretation principles were used for data analysis.

Results.  Relatives interviewed seemed to go through various phases that were specifically connected to the actual situation in the intensive care unit. The main characteristic of these phases was a pattern in which participants gradually became active caregivers for the patient. Relatives wanted to be included in discussions about treatment.

Conclusion.  Relatives want to be included as caregivers when patients are under sedation in an intensive care unit. Relatives who know the patient can help evaluate the use of sedation and pain management to assist the nurses in giving the best care and the appropriate level of sedation for a patient.
Spatial match–mismatch in the Benguela upwelling zone: should we expect chlorophyll and sea‐surface temperature to predict marine predator distributions?
Authors: Grémillet David , Lewis Sue , Drapeau Laurent , Van Der Lingen Carl D. , Huggett Jenny A. , Coetzee Janet C. , Verheye Hans M. , Daunt Francis , Wanless Sarah , Ryan Peter G.
Published: February 2008

Remote‐sensing measurements of marine primary productivity are widely used to predict the distribution and movements of marine top predators, despite the fact that predators do not feed directly on phytoplankton but several trophic levels higher up the food chain.

To test for potential links between primary productivity and top‐predator feeding hotspots, we assessed spatial match–mismatch across four trophic levels of the Benguela upwelling zone (south‐east Atlantic). The food chain studied consisted of phytoplankton, zooplankton (copepods), pelagic fish (anchovies and sardines) and two top predators (Cape gannets Morus capensis and human fisheries).

Remote‐sensing data of sea‐surface temperature (SST) and chlorophyll_a concentration were used as indices of phytoplankton abundance throughout the study area. Copepod biomass and pelagic fish density were determined during at‐sea surveys in the South African section of the Benguela using net tows and hydro‐acoustics, respectively. Seabird (Cape gannet) home ranges and foraging zones were assessed from two Namibian breeding colonies (Mercury and Ichaboe) and two South African colonies (Lambert's Bay and Malgas) using global positioning system (GPS) tracking. Industrial fishing for anchovies and sardines was investigated using South African landing statistics and logbooks.

Our spatial analyses revealed a strong match of seabird at‐sea habitat and zones of high primary productivity throughout the southern Benguela. Conversely, there was a marked spatial mismatch between copepods and pelagic fish, as well as between pelagic fish, seabirds and human fisheries: copepods were present in the southern Benguela but pelagic fish usually feeding upon them were located further east (Indian Ocean), outside of the Benguela sensu stricto. Consequently, the majority of these pelagic fish were out of reach for seabirds and fisheries confined to the southern Benguela.

Synthesis and applications. Our study demonstrates the impact of an ecosystem shift across one of the world's most productive marine ecosystems and highlights the limitations of using remote‐sensed patterns of primary productivity to interpret the foraging behaviour of marine top predators. These findings underline the importance of a better knowledge of food web spatial dynamics to support ecosystem‐based fisheries management and the conservation of marine top predators.
InvasiveAcer platanoidesinhibits native sapling growth in forest understorey communities
Authors: Galbraith‐Kent Shannon L. , Handel Steven N.
Published: February 2008

Over three growing seasons, we tested how an invasive tree species (Acer platanoides) affected native plant growth in understorey communities of a suburban forest in central New Jersey, USA. We planted similar aged and sized saplings (≥ 0.25 m tall) into experimental plots identified with one of three treatments (0%, 25% and 50% of total stems are invasive species) and hypothesized native species would grow better in communities lacking invasive plants.

There was a plant survival rate of 90% for the duration of the experiment, but in treatments where natives competed withA. platanoides, growth of native species was significantly less than in the purely native stand. In 2006, the mean height ofA. rubrumwas 110 cm (±4 SE) in communities with the highest proportion ofA. platanoides, while it was 149 cm (±7 SE) in the 0% invasive communities. Conversely,A. platanoidesgrew similarly in treatments where it comprised two different proportions and beneath both canopy types (i.e. invasive and native).

Native saplings were 28% shorter beneath an invasive canopy (i.e.A. platanoides), compared with a native canopy. A striking interaction existed between community treatment and canopy type, as the invasive canopy had such a strong negative effect on native growth that the presence of invasive saplings was irrelevant. However, beneath a native canopy, the absence of invasive saplings significantly increased growth of native saplings. As the extent and rate of invasive proliferation often makes complete removal unrealistic, this study supports episodic removal (every 2–3 years) of this invasive sapling.

Synthesis. This experiment showed that native sapling growth was inhibited (i) when growing beneath an invasive canopy and (ii) when competing withA. platanoidesin forest understorey communities. It appears canopy type is more important, because the negative effects from an invasive canopy were strong enough that the co‐occurrence of invasive saplings had no impact on native growth. The capability ofA. platanoidesto inhibit native saplings through understorey competition and overstorey canopy effects, while not affecting conspecifics, may contribute to its success as an invader of North American forests.
100 years of vegetation decline and recovery in Lake Fure, Denmark
Authors: Sand‐Jensen Kaj , Pedersen Niels Lagergaard , Thorsgaard Inge , Moeslund Bjarne , Borum Jens , Brodersen Klaus Peter
Published: February 2008

We analysed the development of submerged macrophytes in Lake Fure, Denmark, experiencing a 30‐fold increase of phosphorus input from year 1900 to 1970 and a subsequent decline to twice the 1900 level in 2005. Nutrient enrichment stimulated phytoplankton growth and restricted macrophyte distribution by reducing water transparency from a summer mean of 5–6 m in the early 1900s to a minimum of 1.6 m at the peak of eutrophication, followed by recovery to a recent maximum of 4.1 m.

Macrophyte occurrence and abundance changed in accordance with altered environmental conditions and species’ life‐history traits. Small angiosperms, mosses and characeans disappeared in the 1970s to 1980s, along with all vegetation in deeper waters (5–8 m), and have only partly recovered recently. Tall angiosperms became dominant while small species vanished. All 10 characeans originally present disappeared at the peak of eutrophication, but four reappeared. Mesotrophic macroalgae were replaced by hypertrophic species whose dominance has persisted.

Species richness decreased from 37 to 13 species at the peak of eutrophication, before returning to 25 species during the recent recovery. Species richness increased with transparency because deeper growth generates more niches.

Reduction of species distribution and richness has been reversible following nutrient reduction of the long eutrophied lake, whereas species composition and abundance have not. The historical legacy of community composition is strong, as reflected by closer correlations to time than to measures of nitrogen and phosphorus availability and water transparency.

Synthesis. Although phosphorus input may decline further, reassembly of the original macrophyte community will face difficulties. Oligotrophic freshwater species have become rare throughout Denmark, reducing the probability of recolonization. Species reaching Lake Fure may fail to establish because sediments have become richer in nutrients and organic matter and less consolidated, while shading and competition have increased from emergent reeds, tall submerged angiosperms and fast‐growing macroalgae.
Plant functional composition influences rates of soil carbon and nitrogen accumulation
Authors: Fornara D. A. , Tilman D.
Published: February 2008

The mechanisms controlling soil carbon (C) and nitrogen (N) accumulation are crucial for explaining why soils are major terrestrial C sinks. Such mechanisms have been mainly addressed by imposing short‐term, step‐changes in CO2, temperature and N fertilization rates on either monocultures or low‐diversity plant assemblages. No studies have addressed the long‐term effects of plant functional diversity (i.e. plant functional composition) on rates of soil C accumulation in N‐limited grasslands where fixation is the main source of N for plants.

Here we measure net soil C and N accumulation to 1 m soil‐depth during a 12‐year‐long grassland biodiversity experiment established on agriculturally degraded soils at Cedar Creek, Minnesota, USA.

We show that high‐diversity mixtures of perennial grassland plant species stored 500% and 600% more soil C and N than, on average, did monoculture plots of the same species. Moreover, the presence of C4 grasses and legumes increased soil C accumulation by 193% and 522%, respectively. Higher soil C and N accrual resulted both from increased C and N inputs via (i) higher root biomass, and (ii) from greater root biomass accumulation to 60 cm soil depth resulting from the presence of highly complementary functional groups (i.e. C4 grasses and legumes).

Our results suggest that the joint presence of C4 grass and legume species is a key cause of greater soil C and N accumulation in both higher and lower diversity plant assemblages. This is because legumes have unique access to N, and C4 grasses take up and use N efficiently, increasing below‐ground biomass and thus soil C and N inputs.

Synthesis. We demonstrate that plant functional complementarity is a key reason why higher plant diversity leads to greater soil C and N accumulation on agriculturally degraded soils. We suggest the combination of key C4 grass–legume species may greatly increase ecosystem services such as soil C accumulation and biomass (biofuel) production in both high‐ and low‐diversity N‐limited grassland systems.
Consequences of non‐random species loss for decomposition dynamics: experimental evidence for additive and non‐additive effects
Authors: Ball Becky A. , Hunter Mark D. , Kominoski John S. , Swan Christopher M. , Bradford Mark A.
Published: February 2008

Although litter decomposition is a fundamental ecological process, most of our understanding comes from studies of single‐species decay. Recently, litter‐mixing studies have tested whether monoculture data can be applied to mixed‐litter systems. These studies have mainly attempted to detect non‐additive effects of litter mixing, which address potential consequences of random species loss – the focus is not on which species are lost, but the decline in diversityper se.

Under global change, species loss is likely to be non‐random, with some species more vulnerable to extinction than others. Under such scenarios, the effects of individual species (additivity) as well as of species interactions (non‐additivity) on decomposition rates are of interest.

To examine potential impacts of non‐random species loss on ecosystems, we studied additive and non‐additive effects of litter mixing on decomposition. A full‐factorial litterbag experiment was conducted using four deciduous leaf species, from which mass loss and nitrogen content were measured. Data were analysed using a statistical approach that first looks for additive identity effects based on the presence or absence of species and then significant species interactions occurring beyond those. It partitions non‐additive effects into those caused by richness and/or composition.

This approach addresses questions key to understanding the potential effects of species loss on ecosystem processes. If additive effects dominate, the consequences for decomposition dynamics will be predictable based on our knowledge of individual species, but not statistically predictable if non‐additive effects dominate.

We found additive (identity) effects on mass loss and non‐additive (composition) effects on litter nitrogen dynamics, suggesting that non‐random species loss could significantly affect this system. We were able to identify the species responsible for effects that would otherwise have been considered idiosyncratic or absent when analysed by the methods used in previous work.

Synthesis. We observed both additive and non‐additive effects of litter‐mixing on decomposition, indicating consequences of non‐random species loss. To predict the consequences of global change for ecosystem functioning, studies should examine the effects of both random and non‐random species loss, which will help identify the mechanisms that influence the response of ecosystems to environmental change.
Somatic mutation and the Antarctic ozone hole
Authors: Clarke Laurence J. , Ayre David J. , Robinson Sharon A.
Published: February 2008

Previous studies of Antarctic clonal moss populations using RAPD markers have reported extraordinarily high levels of genetic variation. This has been claimed to reflect somatic mutation, possibly resulting from elevated UV‐B radiation.

Our study used microsatellite markers to compare the genetic variation present within continental Antarctic, sub‐Antarctic and temperate populations of the moss Ceratodon purpureus.

In contrast to the RAPD studies, microsatellite data revealed that C. purpureus populations from continental Antarctica display less intra‐population genetic diversity than populations from a range of temperate and sub‐Antarctic sites.

Analysis of molecular variation (amova) revealed that populations within the Windmill Islands region of Antarctica were more genetically differentiated than populations spread among more widely separated temperate regions.

Synthesis. Our data provide no evidence of elevated mutation rates in the Antarctic, and imply climate change will present ongoing challenges for continental Antarctic moss populations that appear weakly interconnected and with less potential than temperate populations to adapt to environmental change.
Biological Flora of the British Isles: Mercurialis perennis L.
Authors: Jefferson Richard G.
Published: February 2008

This account reviews information on all aspects of the biology of Mercurialis perennis that are relevant to understanding its ecological characteristics and behaviour. The main topics are presented within the standard framework of the Biological Flora of the British Isles: distribution, habitat, communities, responses to biotic factors, responses to environment, structure and physiology, phenology, floral and seed characters, herbivores and disease, history and conservation.

Mercurialis perennis is a dioecious, clonal, perennial forb of woodland, hedgerows, limestone pavement, screes and tall‐herb communities. It is very tolerant of low light; it can also grow in unshaded conditions, although higher light flux densities result in lower shoot biomass. It is Eurocaucasic, occurring throughout temperate areas of Europe as far east as the Russian border.

Mercurialis perennis occurs on a wide variety of soil types over a pH range from 4.3 to 8.5, although it is most abundant on more base‐rich clay or loam soils with a low organic content. It seldom occurs on peat or very sandy soils. It can grow in soils with low availability of macronutrients but it responds positively to nutrient addition from atmospheric or agricultural sources. It is intolerant of waterlogging, mainly because of poor aerenchyma development; its limited capacity to oxygenate the root environment can lead to ferrous ion toxicity. The resulting superficial root development on heavy soils may confer drought susceptibility in summer.

Mercurialis perennis is predominantly wind‐pollinated. Ants are the main dispersal agents and the seed bears an elaiosome which offers them a lipid‐rich reward. Establishment from seed is uncommon and vegetative propagation is the main means of expansion, often leading to dense clonal stands of aerial shoots.

Mercurialis perennis has been described as a stress‐tolerant competitor. The persistence of its clones and slow dispersal have led to it being regarded an as indicator of ancient, semi‐natural woodland.
Effect of short‐term treatment with meloxicam and pimobendan on the renal function in healthy beagle dogs
Authors: FUSELLIER M. , DESFONTIS J.‐C. , LE ROUX A. , MADEC S. , GAUTIER F. , THULEAU A. , GOGNY M.
Published: February 2008

The aim of the study was to investigate the renal function in clinically normal dogs receiving meloxicam and pimobendan alone or in combination. Ten adult female beagle dogs were administered the treatment for 7 days in a randomized crossover trial (control/meloxicam/pimobendan/meloxicam and pimobendan). Renal function was assessed by blood urea, creatinine, sodium, potassium and chloride concentrations and by glomerular filtration rate, measured by means of renal scintigraphy [renal uptake of 99mTc‐diethylenetriaminepentacetic acid (DTPA)] and plasma clearance of 99mTc‐DTPA. As compared with the control group, renal uptake and plasma clearance of 99mTc‐DTPA were not significantly modified after a 7‐day period of treatment with meloxicam or pimobendan alone, or meloxicam and pimobendan in combination. Furthermore, urea, creatinine, sodium, potassium and chloride levels in the serum of the dogs during the 7‐day period treatment were not significantly modified in relation to the treatments. It was therefore concluded that meloxicam and pimobendan alone or in combination did not alter renal function in healthy dogs.
Landscape features affect gene flow of Scottish Highland red deer (Cervus elaphus)
Authors: PÉREZ‐ESPONA S. , PÉREZ‐BARBERÍA F. J. , MCLEOD J. E. , JIGGINS C. D. , GORDON I. J. , PEMBERTON J. M.
Published: February 2008

Landscape features have been shown to strongly influence dispersal and, consequently, the genetic population structure of organisms. Studies quantifying the effect of landscape features on gene flow of large mammals with high dispersal capabilities are rare and have mainly been focused at large geographical scales. In this study, we assessed the influence of several natural and human‐made landscape features on red deer gene flow in the Scottish Highlands by analysing 695 individuals for 21 microsatellite markers. Despite the relatively small scale of the study area (115 × 87 km), significant population structure was found usingF‐statistics (FST = 0.019) and the programstructure, with major differentiation found between populations sampled on either side of the main geographical barrier (the Great Glen). To assess the effect of landscape features on red deer population structure, the ArcMap GIS was used to create cost‐distance matrices for moving between populations, using a range of cost values for each of the landscape features under consideration. Landscape features were shown to significantly affect red deer gene flow as they explained a greater proportion of the genetic variation than the geographical distance between populations. Sea lochs were found to be the most important red deer gene flow barriers in our study area, followed by mountain slopes, roads and forests. Inland lochs and rivers were identified as landscape features that might facilitate gene flow of red deer. Additionally, we explored the effect of choosing arbitrary cell cost values to construct least cost‐distance matrices and described a method for improving the selection of cell cost values for a particular landscape feature.
°Molecular evidence for sequential colonization and taxon cycling in freshwater decapod shrimps on a Caribbean island
Authors: COOK BENJAMIN D. , PRINGLE CATHERINE M. , HUGHES JANE M.
Published: February 2008

Taxon cycling, i.e. sequential phases of expansions and contractions in species’ distributions associated with ecological or morphological shifts, are postulated to characterize dynamic biogeographic histories in various island faunas. The Caribbean freshwater shrimp assemblage is mostly widespread and sympatric throughout the region, although one species (Atyidae: Atya lanipes) is geographically restricted and ecologically and morphologically differentiated from other Atya species. Using patterns of nucleotide variation at the COI mtDNA gene in five species of freshwater shrimp (A. lanipes, A. scabra, A. innocuous; Xiphocarididae: Xiphocaris elongata; Palaemonidae: Macrobrachium faustinum) from Puerto Rico, we expected to detect a signature of sequential colonization in these shrimp, consistent with the concept of taxon cycling, and expected that A. lanipes would be at a different taxon stage (i.e. an early stage species) to all other species. We also examined patterns of genetic population structure in each species expected with poor, intermediate and well‐developed abilities for among‐river dispersal. Population expansions were detected in all species, although the relative timing of the expansions varied among them. Assuming that population expansions followed colonization of Puerto Rico by freshwater shrimp, results bear the hallmarks of sequential colonization and taxon cycling in this fauna. A. lanipes had a star phylogeny, low mean pairwise nucleotide differences and recent (Holocene) estimates for an in situ population expansion in Puerto Rico, and it was inferred as an early stage species in the taxon cycle undergoing a secondary phase of expansion. All other species were inferred as late stage species undergoing regional population expansions, as their mean pairwise nucleotide differences were relatively high and phylogenetic patterns were more complex than A. lanipes. High rates of gene flow without isolation by distance among rivers were detected in all species, although results should be treated cautiously as some populations are unlikely to be in mutation–drift equilibrium. Nested clade analysis produced inconsistent results among species that all have high rates of gene flow and expanding populations.
Divergence with gene flow between Ponto‐Caspian refugia in an anadromous cyprinid Rutilus frisii revealed by multiple gene phylogeography
Authors: KOTLÍK PETR , MARKOVÁ SILVIA , CHOLEVA LUKÁŠ , BOGUTSKAYA NINA G. , EKMEKÇI F. GULER , IVANOVA PETYA P.
Published: February 2008

The Black and Caspian Seas have experienced alternating periods of isolation and interconnection over many Milankovitch climate oscillations and most recently became separated when the meltwater overflow from the Caspian Sea ceased at the end of the last glaciation. Climate‐induced habitat changes have indisputably had profound impacts on distribution and demography of aquatic species, yet uncertainties remain about the relative roles of isolation and dispersal in the response of species shared between the Black and Caspian Sea basins. We examined these issues using phylogeographical analysis of an anadromous cyprinid fish Rutilus frisii. Bayesian coalescence analyses of sequence variation at two nuclear and one mitochondrial genes suggest that the Black and Caspian Seas supported separate populations of R. frisii during the last glaciation. Parameter estimates from the fitted isolation‐with‐migration model showed that their separation was not complete, however, and that the two populations continued to exchange genes in both directions. These analyses also suggested that majority of migrations occurred during the Pleistocene, showing that the variation shared between the Black and Caspian Seas is the result of ancient dispersal along the temporary natural connections between the basins, rather than of incomplete lineage sorting or recent human‐mediated dispersal. Gene flow between the refugial populations was therefore an important source of genetic variation, and we suggest that it facilitated the evolutionary response of the populations to changing climate.
Colonization history, ecological shifts and diversification in the evolution of endemic Galápagos weevils
Authors: SEQUEIRA A. S. , LANTERI A. A. , ALBELO L. ROQUE , BHATTACHARYA S. , SIJAPATI M.
Published: February 2008

Mitochondrial DNA sequence data were obtained for eight species of flightless Galapaganus endemic weevils and one winged close relative in order to study their colonization history and modes of diversification in the Galápagos Archipelago. Contrary to most other insular radiations, the phylogeny estimates we recovered for Galapaganus do not follow the progression rule of island biogeography. The penalized likelihood age estimates of colonization of the archipelago exceed the age of the emerged islands and underscore the potential role of now sunken seamounts for the early evolution of Galapaganus. The phylogeny proposes one intra‐island origin for Galapaganus endemics, but monophyly tests suggest a larger contribution of in‐situ speciation on older islands. Generalist habitat preferences were reconstructed as ancestral while shifts to highland habitats were reconstructed as having evolved independently on different islands. Magnitudes and patterns of diversification rate were found to differ between older and younger islands. Our analyses reveal that the colonization sequence of islands and timing of colonization of Galapaganus could be linked with the geological and volcanic history of the islands in a rather complex scenario. Even though most islands appear to have been colonized soon after their emergence, there are notable deviations from the pattern of sequential colonization expected under the progression rule when considering only the extant emerged islands. Patterns of diversification rate variation on older and younger islands correspond to the volcanic activity or remnants of such activity, while the pattern of independent evolution of restricted habitat preferences in different islands suggests that habitat shifts could also have contributed to species diversity in Galapaganus.
Reproductive isolation among two interfertileRhododendronspecies: low frequency of post‐F1hybrid genotypes in alpine hybrid zones
Authors: MILNE RICHARD I. , ABBOTT RICHARD J.
Published: February 2008

Hybrids between the acid‐loving speciesRhododendron ferrugineumand the basic soil speciesRhododendron hirsutumoccur on soils of intermediate pH in the European Alps. Material from two hybrid zones ~500 m apart, and also nearby populations of each parent species, was surveyed for presence/absence of 31 random amplified polymorphic DNA markers that distinguish parents. Based on morphological assessment, the material comprised 51 putative hybrids, 18 putativeR. ferrugineumindividuals and 26 putativeR. hirsutumplants. RAPD data were analysed using a Bayesian approach implemented by the programnewhybrids, and also by principal coordinates analysis. The identity of allR. ferrugineumplants examined was confirmed; however, of the putativeR. hirsutumindividuals examined, two were certainly and 11 possibly hybrid derivatives. Among all hybrid derivatives examined, about half were designated as F1s or a similar class, otherwise backcrosses toR. hirsutumappeared to be common whereas other hybrid classes were rare and backcrosses toR. ferrugineumpossibly absent. Despite this, artificially generated seed of F2class and backcrosses in each direction showed greater viability than one parent (R. hirsutum). Introgression fromR. ferrugineumwas also detected in a population that from morphology appeared to contain onlyR. hirsutum. Hence, the direction of backcrossing might be highly asymmetric within hybrid zones, causing unidirectional gene flow fromR. ferrugineumintoR. hirsutum. Conversely, the rarity of backcrosses toR. ferrugineum, F2s and later hybrid generations, which might be due to phenology effects and habitat‐mediated selection, could play a part in restricting gene flow towardsR. ferrugineum.
Mating for variety increases foraging activity in the harvester ant, Pogonomyrmex occidentalis
Authors: WIERNASZ DIANE C. , HINES JESSICA , PARKER DARA G. , COLE BLAINE J.
Published: February 2008

Multiple mating by females characterizes most insect species, but is relatively uncommon in social insects. Females may mate with multiple mates because they experience the direct benefits of increased survival or fecundity, to acquire high quality mates, or to lower the risk of reduced fecundity by mating with incompatible males. We used the extensive natural variation in mating frequency in the western harvester ant, Pogonomyrmex occidentalis, to test the hypothesis that increased mating by the queen leads to an increase in colony performance. Colonies with greater genetic diversity began to forage earlier in the day and foraged for longer time periods. The workers which initiated foraging were a nonrandom subset of the genotypes present in the colony. We used a statistical approach to correctly predict the direction and magnitude of the correlation between genetic diversity and colony foraging activity.
Cryptic speciation in the vermilion rockfish (Sebastes miniatus) and the role of bathymetry in the speciation process
Authors: HYDE J. R. , KIMBRELL C. A. , BUDRICK J. E. , LYNN E. A. , VETTER R. D.
Published: February 2008

A recent phylogenetic review of the genus Sebastes suggested the existence of a cryptic species of vermilion rockfish (Sebastes miniatus). To evaluate the geographical and bathymetric range of the Type 1 and Type 2 forms reported in that study, cytochrome b sequences were examined from 548 fish. Type 1 fish were found primarily south of Point Conception on reefs deeper than 100 m. Type 2 fish were common range‐wide at sites shallower than 100 m. Reproductive isolation between the two types was tested using nine microsatellite loci. Estimates of genetic divergence were made using the fixation index (FST) and correspondence between haplotype and genotype was tested by Bayesian population assignment and multivariate plotting of individual genotypes. Microsatellite analyses gave strong support for the presence of two distinct groups of genotypes. All fish with Type 1 haplotypes and fish with Type 2 haplotypes from < 100 m depth had genotypes unique to their haplotype group. However, most (68%) fish with Type 2 haplotypes from > 100 m depth assigned strongly to the Type 1 genotype group. Morphometric comparisons between the two genotypic groups revealed significant differences at three of the six examined measurements. Differences in both genetics, depth of occurrence, and morphology suggest these are separate species. This observation along with evidence of depth segregation in many recent species pairs led us to hypothesize a speciation model for Sebastes spp. by which the loss or truncation of a depth‐related ontogenetic migration can lead to the creation of reproductively isolated populations.
Novel ultrastructures of Treponema primitia and their implications for motility
Authors: Murphy Gavin E. , Matson Eric G. , Leadbetter Jared R. , Berg Howard C. , Jensen Grant J.
Published: February 2008

Members of the bacterial phylum Spirochaetes are generally helical cells propelled by periplasmic flagella. The spirochete Treponema primitia is interesting because of its mutualistic role in the termite gut, where it is believed to cooperate with protozoa that break down cellulose and produce H2 as a by‐product. Here we report the ultrastructure of T. primitia as obtained by electron cryotomography of intact, frozen‐hydrated cells. Several previously unrecognized external structures were revealed, including bowl‐like objects decorating the outer membrane, arcades of hook‐shaped proteins winding along the exterior and tufts of fibrils extending from the cell tips. Inside the periplasm, cone‐like structures were found at each pole. Instead of the single peptidoglycan layer typical of other Gram‐negative bacteria, two distinct periplasmic layers were observed. These layers formed a central open space that contained two flagella situated adjacent to each other. In some areas, the inner membrane formed flattened invaginations that protruded into the cytoplasm. High‐speed light microscopic images of swimming T. primitia cells showed that cell bodies remained rigid and moved in a helical rather than planar motion. Together, these findings support the ‘rolling cylinder’ model for T. primitia motility that posits rotation of the protoplasmic cylinder within the outer sheath.
Self‐tolerance of Human Natural Killer Cells Lacking Self‐HLA‐specific Inhibitory Receptors
Authors: Hasenkamp J. , Borgerding A. , Uhrberg M. , Falk C. , Chapuy B. , Wulf G. , Jung W. , Trümper L. , Glass B.
Published: February 2008

Natural killer (NK) cells identify cells with altered human leucocyte antigen (HLA) expression as targets through lacking engagement of self‐HLA‐specific inhibitory receptors (e.g. killer cell immunoglobulin‐like receptor, KIR). Thus, they eliminate cells with ‘missing self’ because of viral or malignant transformation. We performed analysis of HLA, KIR genotypes and KIR receptor expression patterns at single cell level in NK cells in 17 donors. The function of NK cell subsets is determined by degranulation assays using target cells expressing self, cognate, control or no HLA class I. Donors could be grouped into three groups: their NK cells possess potential for alloreactivity, autoreactivity based on the presence of NK cells expressing particular KIR only (mono‐KIR) in the absence of its ligand or lack alloreactivity. All donors possess NK cells lacking all detectable inhibitory receptors. Both potential autoreactive subpopulations did not respond to HLA class I‐positive target cells. They retain partial reactivity against HLA class I‐negative tumour target cells. Mono‐KIR NK cells without the corresponding ligands in the individuals and NK cells lacking all inhibitory receptors behave self‐tolerant. Our results suggest alternative mechanisms than HLA‐specific inhibitory receptors to control NK cell activity. But HLA seems to be involved in shaping effector function of the NK cell repertoire.
Effect of High Fat Diet on NKT Cell Function and NKT Cell‐mediated Regulation of Th1 Responses
Authors: Miyazaki Y. , Iwabuchi K. , Iwata D. , Miyazaki A. , Kon Y. , Niino M. , Kikuchi S. , Yanagawa Y. , Kaer L. Van , Sasaki H. , Onoé K.
Published: February 2008

Diet is one of the important factors that modulate immune responses. In the present study, we have examined the capacity of dietary lipids to modify immune responses in mice and we have investigated the contribution of glycolipid‐reactive natural killer T (NKT) cells in this process. Mice fed, high fat diet (HFD; 21.2% fat, 0.20% cholesterol) for 3 weeks, as compared with mice fed standard fat diet (SFD; 4.3% fat, 0.03% cholesterol), showed significantly reduced interferon‐γ production in sera at 6 or 12 h after intraperitoneal injection of an NKT cell ligand, α‐galactosylceramide. In contrast, production of interleukin‐13 was significantly higher at 2 and 6 h in HFD fed mice compared with mice on SFD. No difference was detected in the serum interleukin‐4 levels between these two groups of animals. The proportion of NKT cells in spleen and liver was reduced in mice fed HFD compared with those on SFD. In addition, activation of NKT cells assessed by up‐regulation of CD69 was suppressed specifically in liver from mice fed HFD. Recall responses of conventional T cells and delayed‐type hypersensitivity (Th1 type) against ovalbumin were significantly suppressed in mice fed HFD in comparison with those fed SFD. This suppression was not observed in CD1d−/− mice, suggesting that NKT cells in mice fed HFD played a role in suppressing Th1 responses. Taken together, our findings suggest a critical link between NKT cells, dietary lipid and adaptive immune responses.
An Optimized Immunomagnetic Bead‐based Negative Selection Protocol for CD4 T‐cell Isolation from Mouse Lymph Nodes and Spleen
Authors: Kamala T.
Published: February 2008

This study describes an immunomagnetic bead‐based methodology for optimal purification of mouse CD4+ T cells. It reproducibly yields highly pure CD4+ T cells from mouse lymph nodes (95–99%) and spleen (93–96%) with no residual antigen‐presenting cell (APC) function in the purified population. The recovery of the starting CD4+ T‐cell population is consistently high (>70%) and many samples can be simultaneously processed in a short period of time. The key factors responsible for improved purity are combinations of monoclonal antibodies that were found, through trial and error, to yield T cells of maximal purity achievable by non‐flow sort‐based negative selection. These cocktails efficiently target unwanted cell subsets with antibodies against multiple surface markers expressed by non‐CD4+ T cells. Because immunomagnetic bead‐based protocols do not require the expensive and cumbersome processes required by flow sort‐based purification, the methodology described here should find widespread use.
Synergistic Immune Responses Induced by Endogenous Retrovirus and Herpesvirus Antigens Result in Increased Production of Inflammatory Cytokines in Multiple Sclerosis Patients
Authors: Brudek T. , Christensen T. , Hansen H. J. , Petersen T. , Møller‐Larsen A.
Published: February 2008

Human endogenous retroviruses (HERV) and herpesviruses are increasingly associated with the pathogenesis of the neurological inflammatory disease multiple sclerosis (MS). Herpesviruses are capable of HERV activation and simultaneous presence of HERV and herpesvirus antigens have a synergistic effect on cell‐mediated immune responses, which tend to be higher in MS patients in comparison with healthy individuals. Here, we investigate whether these synergistic immune responses are reflected in changes in the production of proinflammatory cytokines. Using enzyme‐linked immunosorbent assays (ELISAs), we have performed a comparative study between MS patients and healthy controls to investigate the production of interferon (IFN)‐γ, interleukin (IL) 2, or IL‐10 as well as the balance between Th1 and Th2 responses in supernatants from peripheral blood mononuclear cells (PBMC) stimulated with HERV and herpes antigen combinations. We have found a significant disproportion in Th1/Th2 responses in PBMCs from MS patients caused by the joint presence of HERV and herpes antigens. The results also showed a significantly higher IFN‐γ production in cells from MS patients; additionally, this production correlated with the synergistic cell proliferations whereas we did not find such a correlation in healthy controls. Our findings suggest that the increased production of IFN‐γ and the induced imbalance in Th1/Th2 responses favouring the inflammatory reactions in MS patients may lead to progression of the disease.
Complement Activation by Neutrophil Granulocytes
Authors: Åsberg A. E. , Mollnes T. E. , Videm V.
Published: February 2008

Complement plays a vital role in the body’s defence systems. Cardiopulmonary bypass induces a detrimental inflammatory reaction in which the complement system is known to participate through direct effects as well as through activation of neutrophils, platelets and endothelial cells. On the other hand, it has been suggested that in the setting of cardiopulmonary bypass, complement may be activated by neutrophils, perhaps due to fragmentation caused by the heart–lung machine. We therefore investigated whether intact or fragmented neutrophils were able to activate the complement system, and whether neutrophil–platelet interaction could influence such complement activation. Lepirudin‐anticoagulated plasma was incubated at 37 °C with resting or activated intact neutrophils or neutrophils combined with platelets, or increasing amounts of fragmented neutrophils. Complement activation was evaluated by measurement of C1rs‐C1 inhibitor complexes, C4bc, C3bBbP, C3bc, C5a and sC5b‐9. We found significant activation of complement only by unphysiological doses of fragmented neutrophils or supernatant from fragmented neutrophils, consistent with a limited clinical significance related to neutrophil destruction during cardiopulmonary bypass. Unstimulated neutrophils induced C3bPBb formation but little formation of other activation products, indicating an increased C3 hydrolysis which was kept under control by regulatory mechanisms. Neutrophils and platelets combined increased classical activation and decreased alternative activation, similar to the findings with platelets alone. Our data confirm that in the setting of acute neutrophil fragmentation or activation, complement activation is much more important in the inflammatory network as an event upstream to neutrophil activation than vice versa.
HLA‐A*0201‐restricted Cytotoxic T‐cell Epitopes in Three PE/PPE Family Proteins of Mycobacterium tuberculosis
Authors: Chaitra M. G. , Shaila M. S. , Chandra N. R. , Nayak R.
Published: February 2008

CD8+ T cells are thought to play an important role in protective immunity against tuberculosis. We report the identification of three peptides derived from Rv1818c, Rv3812 and Rv3018c proteins of Mycobacterium tuberculosis that bound to HLA‐A*0201 molecules and their ability to induce in vitro T‐cell response in peripheral blood lymphocytes from HLA‐A*0201‐positive healthy individuals (PPD+) and patients with TB. The peptide‐specific cytotoxic T lymphocytes (CTL) generated were capable of recognizing peptide pulsed targets. Three 9‐mer peptides bound with high affinity to HLA‐A*0201 and displayed low dissociation rates of the bound peptide from HLA. Epitope‐specific recognition was demonstrated by the release of perforin and γ‐interferon. Overall, our results demonstrate the presence of HLA class I‐restricted CD8+ CTL against proteins from PE and PPE proteins of M. tuberculosis and identify epitopes that are strongly recognized by HLA‐A*0201‐restricted CD8+ T cells in humans. These epitopes thus represent potential subunit components for the design of vaccines against tuberculosis.
Allele and extended haplotype polymorphism of HLA‐A, ‐C, ‐B, ‐DRB1 and ‐DQB1 loci in Polish population and genetic affinities to other populations
Authors: Nowak J. , Mika‐Witkowska R. , Polak M. , Zajko M. , Rogatko‐Koroś M. , Graczyk‐Pol E. , Lange A.
Published: February 2008

Human leukocyte antigen (HLA)‐A, ‐C, ‐B, ‐DRB1 and ‐DQB1 alleles were typed in 200 Polish healthy volunteers recruited for stem cell donor registry, using sequence‐specific primer (SSP) and direct sequencing‐based methods. Enhanced Bayesian approach of expectation maximization algorithm provided by phase platform was used for extended HLA haplotype inferences. The numbers of identified alleles (four‐digit resolution) were 23, 23, 44, 27 and 18 alleles in HLA‐A, ‐C, ‐B, ‐DRB1 and ‐DQB1 loci, respectively, of both northern and southern European frequency characteristics. The most frequent extended haplotypes were Cw*0701‐B*0801‐DRB1*0301‐DQB1*0201 and Cw*0702‐B*0702‐DRB1*1501‐DQB1*0602, found in 25 and 23 copies, respectively, in 400 tested chromosomes. The extended haplotype found in the Polish population with higher frequency than in other European population was A*2501‐Cw*1203‐B*1801‐DRB1*1501‐DQB1*0602 (six copies) and especially its class I fragment (14 copies). The neighbour‐joining and correspondence analyses showed Central and northern European genetic affinities of Polish population. In most cases, the observed European allele and haplotype gradients display smooth topography around Polish population. Poles along with Western Slavs have their specific contribution in the demographic history of Europe. Our results will intensify the use of population data in stem cell donor search and can potentially improve current algorithms, facilitating selection of acceptable donors for patients in need of stem cell transplant.
Genetic analysis of autoimmune regulator haplotypes in alopecia areata
Authors: Wengraf D. A. , McDonagh A. J. G. , Lovewell T. R. J. , Vasilopoulos Y. , Macdonald‐Hull S. P. , Cork M. J. , Messenger A. G. , Tazi‐Ahnini R.
Published: February 2008

Alopecia areata is an immune‐mediated disorder, occurring with the highest observed frequency in the rare recessive autoimmune polyendocrinopathy–candidiasis–ectodermal dystrophy (APECED) syndrome caused by mutations of the autoimmune regulator (AIRE) gene on chromosome 21q22.3. We have previously detected association between alopecia areata and a single nucleotide polymorphism (SNP) in the AIRE gene in patients without APECED, and we now report the findings of an extended examination of the association of alopecia areata with haplotype analysis including six SNPs in the AIRE gene: C‐103T, C4144G, T5238C, G6528A, T7215C and T11787C. In Caucasian groups of 295 patients and 363 controls, we found strong association between the AIRE 7215C allele and AA [P = 3.8 × 10−8, OR (95% CI): 2.69 (1.8–4.0)]. The previously reported association between AA and the AIRE 4144G allele was no longer significant on correction for multiple testing. The AIRE haplotypes CCTGCT and CGTGCC showed a highly significant association with AA [P = 6.05 × 10−6, 9.47 (2.91–30.8) and P = 0.001, 3.51 (1.55–7.95), respectively]. To select the haplotypes most informative for analysis, we tagged the polymorphisms using SNPTag software. Employing AIRE C‐103T, G6528A, T7215C and T11787C as tag SNPs, two haplotypes were associated with AA; AIRE CGCT and AIRE CGCC [P = 3.84 × 10−7, 11.40 (3.53–36.9) and P = 3.94 × 10−4, 2.13 (1.39–3.24) respectively]. The AIRE risk haplotypes identified in this study potentially account for a major component of the genetic risk of developing alopecia areata.
An overview of the GAGE cancer/testis antigen family with the inclusion of newly identified members
Authors: Gjerstorff M. F. , Ditzel H. J.
Published: February 2008

GAGE cancer/testis antigens are frequently expressed in many different types of cancer, whereas their expression in normal tissues is limited to the germ cells of the immune‐privileged organs, testis and ovary. Thus, GAGE proteins may be attractive candidates for immunotherapy of cancer. This review describes the structure and phylogeny of the GAGE family members and presents a revised nomenclature, which will enable a more clear distinction of genes and gene products. The GAGE gene locus at chromosome X p11.23 consists of at least 16 genes, each of which is located in one of an equal number of highly conserved tandem repeats, and more genes remain to be identified. These genes are likely the creation of unequal replication under positive selection after the divergence of primates from other mammals. The encoded products are predicted to be highly similar small acidic proteins involved in germ cell biology. When expressed in tumor cells, GAGE proteins can elicit both cellular and humoral immune responses, indicating that they are appropriate targets for cancer immunotherapy. The potential use of GAGE proteins in cancer immunotherapy, including possible limitations, is also discussed.