bluuebunny/crossref_metadata_2025 huggingface dataset:
Artemisia and Ambrosia hypersensitivity: co‐sensitization or co‐recognition?
Authors: Asero R. , Wopfner N. , Gruber P. , Gadermaier G. , Ferreira F.
Published: March 2006

Background
Ragweed and mugwort have nearly identical flowering periods. Clinical and serological studies showed that ragweed and mugwort sensitization are often associated and this poses relevant clinical problems in patients for whom specific immunotherapy is warranted.

Objective
To establish whether the concurrent ragweed and mugwort pollen hypersensitivity is the result of co‐sensitization or of co‐recognition by using purified recombinant allergens.

Methods
Sensitization to ragweed and mugwort pollen was assessed by skin prick test (SPT) in all patients reporting allergic symptoms in August and September. IgE reactivity of sera from 42 patients (26 Amb+/Art+, 14 Amb+/Art−, and two Amb−/Art+) to ragweed and mugwort pollen extract as well as to several recombinant ragweed (rAmb a 1, rAmb a 5, rAmb a 6, rAmb a 8, rAmb a 9, and Amb a 10) and mugwort (rArt v 1, rArt v 4, rArt v 5, rArt v 6, and three EF‐hand calcium‐binding protein) allergens was detected by dot‐blot and ELISA analyses.

Results
IgE reactivity of 372 weed pollen‐allergic patients was studied. Mugwort reactivity was strongly associated with ragweed hypersensitivity: only 10/147 (7%) mugwort‐hypersensitive patients were not sensitized to ragweed, whereas 225/362 (62%) ragweed‐hypersensitive patients were not sensitized to mugwort. In vitro, 90% of ragweed‐allergic patients reacted with rAmb a 1. Reactivity to other ragweed allergens ranged between 20% and 35%. Forty‐six percent of the mugwort‐sensitized patients recognized rArt v 1%, 25% reacted to Art v 4, Art v 5, and Art v 6, and 7% recognized the three‐EF hand calcium‐binding protein. Immunoblot inhibition experiments showed that pre‐incubation with ragweed pollen extract only weakly decreased IgE reactivity to mugwort allergens.

Conclusion
Patients showing both ragweed‐ and mugwort‐positive SPT and/or RAST are co‐sensitized. Future studies will establish whether IgE reactivity translates into clinical symptoms and, hence, if co‐sensitized patients should undergo specific immunotherapy with extracts of both mugwort and ragweed pollen.
Towards profiling the gene expression of fibroblasts from atopic dermatitis patients: human 8K complementary DNA microarray
Authors: Park Y.‐D. , Lyou Y.‐J. , Lee K.‐J. , Lee D.‐Y. , Yang J.‐M.
Published: March 2006

Background
High‐throughput technologies, including DNA‐chip array, have been used to search for the genes that are dysregulated in human diseases. The atopic dermatitis (AD)‐associated genes are gradually being reported; however, the differentially altered gene expression profiles of atopic fibroblasts have not been well elucidated.

Objective
We wanted to gain more insights into AD and to find candidate genes, especially in regards to the role of fibroblasts in the pathogenesis of AD.

Methods
cDNA microarray (8K) profiling of the primary cultured AD patients‐derived fibroblasts was conducted by a pooling method of the recruited 22 normal controls, the 10 extrinsic type (ADe) patients and the 10 intrinsic type (ADi) patients. SAM analysis of the microarray results (2‐fold cut‐off) was conducted to select the candidate genes. Quantification by real‐time PCRs confirmed the array data in the randomized paired samples (normal vs. ADe n=10; normal vs. ADi n=10).

Results
We listed the 22 up‐regulated and 95 down‐regulated genes in the AD fibroblasts. Real‐time PCR results showed that several genes such as hyaluronan synthase 2 (HAS2), TNF‐α‐induced protein 6 (TNFAIP6) and IL‐8 were matched with the array results with statistical significance.

Conclusion
These results suggest gene expression profiles that are associated with AD and this implied that fibroblasts may play important roles in the AD pathogenesis. We provided new insights into three candidate genes such as HAS2, TNFAIP6 and IL‐8 with respect to their involvement in AD disease.
Validation of a randomization procedure to assess animal habitat preferences: microhabitat use of tiger sharks in a seagrass ecosystem
Authors: HEITHAUS MICHAEL R. , HAMILTON IAN M. , WIRSING AARON J. , DILL LAWRENCE M.
Published: March 2006

Tiger sharks Galeocerdo cuvier are important predators in a variety of nearshore communities, including the seagrass ecosystem of Shark Bay, Western Australia. Because tiger sharks are known to influence spatial distributions of multiple prey species, it is important to understand how they use habitats at a variety of spatial scales. We used a combination of catch rates and acoustic tracking to determine tiger shark microhabitat use in Shark Bay.

Comparing habitat‐use data from tracking against the null hypothesis of no habitat preference is hindered in Shark Bay, as elsewhere, by the difficulty of defining expected habitat use given random movement. We used randomization procedures to generate expected habitat use in the absence of habitat preference and expected habitat use differences among groups (e.g. males and females). We tested the performance of these protocols using simulated data sets with known habitat preferences.

The technique correctly classified sets of simulated tracks as displaying a preference or not and was a conservative test for differences in habitat preferences between subgroups of tracks (e.g. males vs. females).

Sharks preferred shallow habitats over deep ones, and preferred shallow edge microhabitats over shallow interior ones. The use of shallow edges likely increases encounter rates with potential prey and may have profound consequences for the dynamics of Shark Bay's seagrass ecosystem through indirect effects transmitted by grazers that are common prey of tiger sharks.

Females showed a greater tendency to use shallow edge microhabitats than did males; this pattern was not detected by traditional analysis techniques.

The randomization procedures presented here are applicable to many field studies that use tracking by allowing researchers both to determine overall habitat preferences and to identify differences in habitat use between groups within their sample.
Effects of food availability on temporal activity patterns and growth of Atlantic salmon
Authors: ORPWOOD JAMES E. , GRIFFITHS SIÂN W. , ARMSTRONG JOHN D.
Published: March 2006

Patterns of sheltering and activity are of fundamental importance in the ecology of animals and in determining interactions among predators and prey. Balancing decreased mortality risk when sheltering with increased feeding rate when exposed is believed to be a key determinant of diel patterns of sheltering in many animals.

Despite lower foraging efficiency at night than during the day, Atlantic salmon Salmo salar parr are nocturnal during winter and at low summer temperatures. Nocturnal activity also occurs at warm water temperatures during summer, but little is known about the functional significance of this behaviour.

This study aimed to determine: (1) the preferred activity and shelter pattern of Atlantic salmon parr during warm summer months, and (2) their response to variations in food availability when balancing growth rate (G) and mortality risk (M), as expressed through time out of shelter. We differentiated among four potential responses to reduced food availability: (1) no response; (2) G decreases but M remains constant; (3) G remains constant but M increases; and (4) G decreases and M increases.

Time exposed from shelter was inversely related to food availability. Fish subject to high food availability were significantly less active during the day than those with restricted rations. However, food availability had no significant effect on the extent to which fish were active at night. There was no evidence of variation in growth rate with food availability.

Salmon were predominantly nocturnal at high ration levels, consistent with their previously reported behaviour during winter. Rather than switching to diurnal behaviour at high temperatures per se, as previously was supposed, it appears that the fish are diurnal only to the extent needed to sustain a growth rate, and this extent depends on food availability.

Atlantic salmon parr modulate the amount of time they are active rather than growth when responding to variations in food availability over an order of magnitude.
Modelling ecological niches with support vector machines
Authors: DRAKE JOHN M. , RANDIN CHRISTOPHE , GUISAN ANTOINE
Published: March 2006

The ecological niche is a fundamental biological concept. Modelling species’ niches is central to numerous ecological applications, including predicting species invasions, identifying reservoirs for disease, nature reserve design and forecasting the effects of anthropogenic and natural climate change on species’ ranges.

A computational analogue of Hutchinson's ecological niche concept (the multidimensional hyperspace of species’ environmental requirements) is the support of the distribution of environments in which the species persist. Recently developed machine‐learning algorithms can estimate the support of such high‐dimensional distributions. We show how support vector machines can be used to map ecological niches using only observations of species presence to train distribution models for 106 species of woody plants and trees in a montane environment using up to nine environmental covariates.

We compared the accuracy of three methods that differ in their approaches to reducing model complexity. We tested models with independent observations of both species presence and species absence. We found that the simplest procedure, which uses all available variables and no pre‐processing to reduce correlation, was best overall. Ecological niche models based on support vector machines are theoretically superior to models that rely on simulating pseudo‐absence data and are comparable in empirical tests.

Synthesis and applications. Accurate species distribution models are crucial for effective environmental planning, management and conservation, and for unravelling the role of the environment in human health and welfare. Models based on distribution estimation rather than classification overcome theoretical and practical obstacles that pervade species distribution modelling. In particular, ecological niche models based on machine‐learning algorithms for estimating the support of a statistical distribution provide a promising new approach to identifying species’ potential distributions and to project changes in these distributions as a result of climate change, land use and landscape alteration.
Spatial modelling of biodiversity at the community level
Authors: FERRIER SIMON , GUISAN ANTOINE
Published: March 2006

Statistical modelling is often used to relate sparse biological survey data to remotely derived environmental predictors, thereby providing a basis for predictively mapping biodiversity across an entire region of interest. The most popular strategy for such modelling has been to model distributions of individual species one at a time. Spatial modelling of biodiversity at the community level may, however, confer significant benefits for applications involving very large numbers of species, particularly if many of these species are recorded infrequently.

Community‐level modelling combines data from multiple species and produces information on spatial pattern in the distribution of biodiversity at a collective community level instead of, or in addition to, the level of individual species. Spatial outputs from community‐level modelling include predictive mapping of community types (groups of locations with similar species composition), species groups (groups of species with similar distributions), axes or gradients of compositional variation, levels of compositional dissimilarity between pairs of locations, and various macro‐ecological properties (e.g. species richness).

Three broad modelling strategies can be used to generate these outputs: (i) ‘assemble first, predict later’, in which biological survey data are first classified, ordinated or aggregated to produce community‐level entities or attributes that are then modelled in relation to environmental predictors; (ii) ‘predict first, assemble later’, in which individual species are modelled one at a time as a function of environmental variables, to produce a stack of species distribution maps that is then subjected to classification, ordination or aggregation; and (iii) ‘assemble and predict together’, in which all species are modelled simultaneously, within a single integrated modelling process. These strategies each have particular strengths and weaknesses, depending on the intended purpose of modelling and the type, quality and quantity of data involved.

Synthesis and applications. The potential benefits of modelling large multispecies data sets using community‐level, as opposed to species‐level, approaches include faster processing, increased power to detect shared patterns of environmental response across rarely recorded species, and enhanced capacity to synthesize complex data into a form more readily interpretable by scientists and decision‐makers. Community‐level modelling therefore deserves to be considered more often, and more widely, as a potential alternative or supplement to modelling individual species.
How do crop types influence breeding success in lesser kestrels through prey quality and availability? A modelling approach
Authors: RODRÍGUEZ CARLOS , JOHST KARIN , BUSTAMANTE JAVIER
Published: March 2006

In the middle of the 20th century the colonial lesser kestrel Falco naumanni experienced a marked decline in its western palaearctic breeding range. Although this decline has been attributed to changes in land use influencing breeding success through lowering the abundance and quality of prey, a quantification of these effects has not yet been undertaken.

To study how these two key factors influence breeding success, we developed an individual‐based model, which translates the hunting performance of each adult foraging trip into nestling growth and enables the effect of crop types on the breeding success of the lesser kestrel to be quantified. Both the authors’ own field data and published inferential and experimental studies were used to parameterize and validate the growth model.

Model results demonstrated that adult provisioning rates provide very little information on the relation between prey availability and breeding success.

On the other hand, the model indicated that small differences in prey abundance among crop types cause large differences in breeding success, highlighting the importance of crop composition in the vicinity of lesser kestrel colonies.

Mean prey biomass is an even more important influence on breeding success. Our results indicated a minimum mean prey size of 0·6 g, below which colonies become population sinks.

Synthesis and applications. We developed an individual‐based model that simulates the growth in body mass of a lesser kestrel brood as a function of prey abundance and prey size. These two key factors define a parameter space in which the conservation status of breeding colonies can be evaluated. We applied the model to six lesser kestrel breeding colonies with different mean prey size and different agricultural land use influencing prey abundance. Our model suggests that the habitat quality of two of these colonies is sufficient for population persistence, while management actions to increase habitat quality are required in the remaining four colonies. An increase in the availability of prey‐rich habitats such as field margins would achieve this goal without imposing too great a cost on the local farming community.
Assessing the viability of tiger subpopulations in a fragmented landscape
Authors: LINKIE MATTHEW , CHAPRON GUILLAUME , MARTYR DEBORAH J. , HOLDEN JEREMY , LEADER‐WILLIAMS NIGEL
Published: March 2006

Conservation managers require accurate and timely information on the occurrence, size and viability of populations, but this is often difficult for cryptic species living at low densities over large areas. This study aimed to provide such information for tigers in the 36 400‐km2 Kerinci Seblat (KS) region, Sumatra, by identifying and assessing subpopulation viability under different management strategies.

Tiger occurrence was mapped within a geographical information system (GIS) using repeat detection–non‐detection surveys to incorporate a function of detection probability into a logistic regression model. The landscape variables that influenced tiger occupancy were then used to construct a spatially explicit habitat model to identify core areas.

The number of tigers within each core area was estimated by calculating the area of different forest types and their respective tiger densities as determined through camera trapping. The viability of each subpopulation was then assessed under different management scenarios using a population viability analysis (PVA).

Tiger occurrence was negatively correlated with distance to public roads. Four core tiger areas were identified, all predominantly located within KS National Park, estimated to support subpopulations of 21, 105, 16 and three adult tigers, respectively. PVA showed that the three larger subpopulations could be demographically viable if well protected. However, if poaching removed ≥ 3 tigers per year, then only the largest subpopulation would not reach extinction within 50 years. Connectivity to this large subpopulation would ensure survival of the smaller subpopulations, through providing a source of tigers to offset poaching losses.

Synthesis and applications. Our key management recommendations for tigers in the Kerinci Seblat region of Sumatra stress the importance of maintaining connectivity between the smaller areas and the larger area, and minimizing poaching within these smaller areas. More widely, our research has shown the feasibility of using detection–non‐detection surveys combined with spatial modelling to provide timely information for conservation management.
Floodplain restoration by reinforcing hydrological connectivity: expected effects on aquatic mollusc communities
Authors: RECKENDORFER WALTER , BARANYI CHRISTIAN , FUNK ANDREA , SCHIEMER FRITZ
Published: March 2006

One of the main targets of river–floodplain restoration is the reconnection of former side channels. While there is information about the overall impact of such measures, far less is known about specific species’ response patterns to hydrological connectivity.

The present study examined the composition of aquatic mollusc communities based on the performance of individual species with respect to hydrological connectivity in the Donau‐Auen National Park, Austria. Species’ traits were used to make generalizations about community responses to hydrological changes.

We introduced a connectivity parameter (Cd, expressed in days year−1) that could easily be derived from the river hydrograph and altitude of the inflow areas. This parameter integrated several key features of floodplain waterbodies and reflected the cause–effect chain of restoration schemes, thus allowing the outcome of restoration measures to be quantitatively predicted. Endangered rheophilic mollusc species reached higher frequencies as connectivity increased; for most eurytopic molluscs, however, increased connectivity reduced abundance.

With respect to species’ traits, the proportion of large gastropods declined continuously with increasing Cd, whereas the percentage of gastropods with globolose shells and the relative number of strongly calcified (thick‐shelled) individuals both increased. Species dominating in isolated sites were characterized by a higher resistance to desiccation, a food preference for higher plants and a preference for less shaded habitats. They matured later and typically had more offspring than rheophilic species.

Species number peaked at connectivity (Cd) values of about 1 month year−1. Isolated and lotic habitats hosted significantly fewer mollusc species. Species turnover was highest when Cd was between 0 days and 2 months.

Synthesis and applications. Empirical models based on a connectivity parameter can be used to predict the consequences of restoration measures on the aquatic mollusc community in the Donau‐Auen National Park. The analysis of species’ traits also allows general prognoses for other river–floodplain systems. Furthermore, initial results based on other taxa indicate a broad applicability of the parameter. The methodology thus provides both an urgently needed and a practical tool for predicting the impact and success of restoration schemes.
Effects of density and floral morph on pollen flow and seed reproduction of an endangered heterostylous herb,Primula sieboldii
Authors: ISHIHAMA F. , UENO S. , TSUMURA Y. , WASHITANI I.
Published: March 2006

We assessed the effects of population density and the spatial arrangement of genetically compatible mates on the seed set and pollen flow of a heterostylous, bumblebee‐pollinated perennial,Primula sieboldiiE. Morren (Primulaceae), by using an experimental population under natural pollination conditions.

We also examined the intermorph differences in the pollen dispersal distance and the frequency of self‐ and intramorph fertilization.

Seed set was significantly correlated with the number of opposite‐morph flowers within 2 m in short‐styled genets, and within 3 m in long‐styled genets.

Mean pollen dispersal distance within the experimental population was 5.4 m, which was slightly shorter than that in a low‐density population measured in a previous study (7.2 m).

The proportions of seedlings sired by the same morph or selfed were 10.2% and 3.0%, respectively, in long‐styled mothers, compared with 1.9% and 0.0% among short‐styled mothers. However, these differences were not statistically significant and no marked differences in pollen dispersal distances were observed between the two morphs.

Our results suggest that the presence of opposite‐morph genets within several metres is essential for success of seed reproduction inP. sieboldii, irrespective of population density, and that stochastic deviation of the morph ratio in small populations is therefore likely to cause considerable reduction in seed set.
Ecological correlates of range structure in rare and scarce British plants
Authors: POCOCK MICHAEL J. O. , HARTLEY STEPHEN , TELFER MARK G. , PRESTON CHRISTOPHER D. , KUNIN WILLIAM E.
Published: March 2006

The distribution patterns of 391 rare and scarce British plants (species recorded in 100 or fewer 10 × 10 km squares) were characterized by their distributional area (area of occupancy at 1‐km scale: AOO1) and levels of aggregation (as reflected in fractal dimensions measured across two scales:D1−10andD10−100).

Eighteen plant traits were tested for relationships to AOO, and to fractal dimension while controlling for AOO. These included both directly heritable traits (e.g. life‐form) and emergent properties that are, at most, indirectly heritable (e.g. typical local density). The latter set included an index of net distributional change and an index of range dynamism.

Only two traits, habitat preference and local abundance, were significantly related to AOO1, but about half were associated with fractal dimension.

Relatively aggregated fine‐scale distributions (highD1−10) were related to high local abundance, lack of specialized, long‐distance dispersal mechanisms, habitat preference and an increasing range size with relatively few local extinctions (i.e. a positive index of change with low dynamism).

Relatively aggregated coarse‐scale distributions (highD10−100) were related to the use of insect pollinators, obligate outcrossing, habitat preference and relatively stable ranges (low dynamism).

Multivariate analyses of subsets of conceptually related variables showed that few variables interacted to affect distributional variables.

A highly significant negative relationship between dynamism and fractal dimension appears to be driven primarily by high rates of local extinction, leading to relatively scattered, diffuse range structures. Furthermore, it suggests that recent population trends may be inferred from snapshots of contemporary distribution patterns.

The role and interpretation of phylogenetically informed analyses in studies such as this are debatable. However, we found similar relationships in both phylogenetically informed and conventional analyses for all variables except pollination vector (a strongly conserved trait).

The spatial pattern of plant species distributions is associated with a range of ecological traits, particularly those describing past changes in distribution. The analysis of distribution patterns therefore has the potential to inform future conservation effort.
Biological flora of the British Isles: Cakile maritima Scop.
Authors: DAVY A. J. , SCOTT R. , CORDAZZO C. V.
Published: March 2006

This account reviews information on all aspects of the biology of Cakile maritima 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.

Cakile maritima (sea rocket) is a succulent, annual species that is confined to maritime strandlines on sand or shingle, and associated foredunes. British material is ssp. integrifolia (= ssp. maritima), found around the Atlantic and Mediterranean coasts of Europe. Cakile maritima shows considerable variation, within and between subspecies, especially in fruit morphology and leaf shape. A very closely related species, Cakile edentula, is native to the east coast of North America. Both species have been introduced to Pacific North America and Australia.

Populations of C. maritima tend be ephemeral and shifting, depending on dispersal by tides and wind. The fruits are 2‐segmented: the distal segments are readily detached and can float considerable distances in seawater; the proximal segments tend to shed their seed while attached to the maternal plant. Seeds require cold stratification and do not germinate at high salinity, or usually while retained in intact fruit segments. There is often a flush of germination in strandlines left by early season, equinoctial spring tides. Cakile maritima shows great phenotypic plasticity of form and reproductive output. Work on C. edentula suggests that abundance is regulated by a combination of density‐dependent and density‐independent processes. Landward dispersal of seeds from strandline populations may subsidise foredune populations, which themselves experience severe mortality from predators.

Cakile maritima is tolerant of salt spray and transient seawater inundation. Although beach and dune sand is a meagre source of macronutrients, C. maritima shows large growth responses to nitrogen addition and can exploit local nitrogen enrichment associated with mineralisation of organic detritus washed up on the strandline. Growth is stimulated by burial with blown sand and plants sometimes form the nuclei of early successional foredunes. The tissues are rich in glucosinolates; these may be responsible for the limited ranges of herbivores and fungal pathogens, and the absence of mycorrhiza.
Parallelism in gene transcription among sympatric lake whitefish (Coregonus clupeaformisMitchill) ecotypes
Authors: DEROME N. , DUCHESNE P. , BERNATCHEZ L.
Published: March 2006

We tested the hypothesis that phenotypic parallelism between dwarf and normal whitefish ecotypes (Coregonus clupeaformis,Salmonidae) is accompanied by parallelism in gene transcription. The most striking phenotypic differences between these forms implied energetic metabolism and swimming activity. Therefore, we predicted that genes showing parallel expression should mainly belong to functional groups associated with these phenotypes. Transcriptome profiles were obtained from white muscle by using a 3557 cDNA gene microarray developed for the Atlantic salmon (Salmo salar). A total of 1181 genes expressed in both lake populations hybridized on the array. Significant differential expression between ecotypes was detected for 134 (11.3%) and 195 (16.5%) gene clones in Cliff Lake and Indian Pond, respectively. Fifty‐one genes (4.3%) showed parallel differential expression between lakes, among which 35 were expressed in opposite directions. Sixteen genes (1.35%) showed true parallelism of transcription, which mainly belonged to energetic metabolism and regulation of muscle contraction functional groups. Variance in expression was significantly reduced for these genes compared to those not showing directionality in parallelism of expression. Candidate genes associated with parallelism in swimming activity and energetic metabolism based on their level and variance in expression were identified. These results add to the growing evidence that parallel phenotypic evolution also involves parallelism at both the genotypic and regulatory level, which may at least partly be associated with genetic constraints. It also provides further evidence for the determinant role of divergent natural selection in driving phenotypic divergence, and perhaps reproductive isolation, in the adaptive radiation of lake whitefish. This study adds to a nascent field employing microarrays as powerful tools for investigating the evolutionary processes of adaptive divergence among natural populations.
Population genetic structure and demographic history of the endemic Formosan lesser horseshoe bat (Rhinolophus monoceros)
Authors: CHEN SHIANG‐FAN , ROSSITER STEPHEN J. , FAULKES CHRISTOPHER G. , JONES GARETH
Published: March 2006

Intraspecific phylogenies can provide useful insights into how populations have been shaped by historical and contemporary processes. Taiwan formed around 5 million years ago from tectonic uplift, and has been connected to mainland Asia several times since its emergence. A central mountain range runs north to south, bisecting the island, and potentially impedes gene flow along an east–west axis. The Formosan lesser horseshoe bat (Rhinolophus monoceros) is endemic to Taiwan, where it is found mainly at low altitude. To determine the population structure and the demographic and colonization history of this species, we examined variation in the mitochondrial DNA control region in 203 bats sampled at 26 sites. We found very high haplotype and nucleotide diversity, which decreased from the centre to the south and north. Population differentiation followed a pattern of isolation by distance, though most regional genetic variance was attributable to differences between the relatively isolated southern population and those from other regions. A haplotype network was consistent with these findings and also suggested a southward colonization, followed by subsequent secondary contact between the south and other regions. Mismatch distributions were used to infer a past population expansion predating the last glacial maximum, and a neighbour‐joining tree showed thatR. monocerosformed a monophyletic grouping with respect to its sister taxa. Taken together, our results suggest that this taxon arose from a single period of colonization, and that demographic growth followed in the late Pleistocene. Current genetic structure reflects limited gene flow, probably coupled with stepwise colonization in the past. We consider explanations for the persistence of the species through multiple glacial maxima.
Mycobacterium tuberculosis malate synthase is a laminin‐binding adhesin
Authors: Kinhikar Arvind G. , Vargas Diana , Li Hualin , Mahaffey Spencer B. , Hinds Laura , Belisle John T. , Laal Suman
Published: March 2006

Mycobacterium tuberculosis (M. tb) uses the glyoxalate bypass for intracellular survival in vivo. These studies provide evidence that the M. tb malate synthase (MS) has adapted to function as an adhesin which binds to laminin and fibronectin. This binding is achieved via the unique C‐terminal region of the M. tb MS. The ability to function as an adhesin necessitates extracellular localization. We provide evidence that despite the absence of a Sec‐translocation signal sequence the M. tb MS is secreted/excreted, and is anchored on the cell wall by an undefined mechanism. The MS of Mycobacterium smegmatis is cytoplasmic but the M. tb MS expressed in M. smegmatis localizes to the cell wall and enhances the adherence of the bacteria to lung epithelial A549 cells. Antibodies to the C‐terminal laminin/fibronectin‐binding domain interfere with the binding of the M. tb MS to laminin and fibronectin and reduce the adherence of M. tb to A549 cells. Coupled to the earlier evidence of in vivo expression of M. tb MS during active but not latent infection in humans, these studies show that a housekeeping enzyme of M. tb contributes to its armamentarium of virulence promoting factors.
Dihydroxyacetone detoxification in Saccharomyces cerevisiae involves formaldehyde dissimilation
Authors: Molin Mikael , Blomberg Anders
Published: March 2006

To investigate Saccharomyces cerevisiae physiology during growth on the conditionally toxic triose dihydroxyacetone (DHA), protein expression was studied in strains overexpressing either of the two dihydroxyacetone kinase isogenes, DAK1 or DAK2, that grow well utilizing DHA as a carbon and energy source. DHA metabolism was found mostly similar to ethanol utilization, involving a strong component of glucose derepression, but also involved DHA‐specific regulatory changes. A specific and strong (10‐ to 30‐fold induction of formaldehyde dehydrogenase, Fdhlp, indicated activation of the formaldehyde dissimilation pathway in DHA medium. The importance of this pathway was further supported by impaired adaptation to DHA growth and DHA survival in a glutathione‐dependent formaldehyde dehydrogenase (SFA1) deletion mutant. Glutathione synthase (GSH1) deletion led to decreased DHA survival in agreement with the glutathione cofactor requirement for the SFA1‐encoded activity. DHA toxicity did, however, not solely appear related to formaldehyde accumulation, because SFA1 overexpression only enhanced formaldehyde but not DHA tolerance. In further agreement with a low DHA‐to‐formaldehyde flux, GSH supplements in the low µM range also fully suppressed the DHA sensitivity of a gsh1Δ strain. Under growth reduction on high (100 mM) DHA medium we report increased levels of advanced glycation end‐product (AGE) formation on total protein. Under these high‐DHA conditions expression of several stress‐related proteins, e.g. a heat‐shock protein (Hsp104p) and the oxidative stress indicator, alkyl hydroperoxide reductase (Ahp1p) was also found induced. However, hallmark determinants of oxidative stress tolerance (e.g. YAP1, SKN7, HYR1/GPX3 and SOD2) were redundant for DHA tolerance, thus indicating mechanisms of DHA toxicity largely independent of central oxidative stress defence mechanisms. We conclude that mechanisms for DHA growth and detoxification appear complex and that the evolutionary strive to minimize detrimental effects of this intracellular metabolite links to both formaldehyde and glutathione metabolism.
Analysis of FimX, a phosphodiesterase that governs twitching motility in Pseudomonas aeruginosa
Authors: Kazmierczak Barbara I. , Lebron Maria B. , Murray Thomas S.
Published: March 2006

Type IV pili (Tfp) are polar surface structures of Pseudomonas aeruginosa required for twitching motility, biofilm formation and adherence. One protein required for the assembly of tfp is FimX, which possesses both GGDEF and EAL domains characteristic of diguanylate cyclases and phosphodiesterases respectively. In this work we demonstrate that FimX has phosphodiesterase activity towards bis‐(3′‐5′)‐cyclic dimeric guanosine monophosphate (c‐di‐GMP), but does not show diguanylate cyclase activity. Instead, the imperfect GGDEF domain of FimX likely serves to activate phosphodiesterase activity when bound to GTP, as has recently been described for the Caulobacter crescentus composite GGDEF‐EAL protein, CC3396. Bacteria expressing FimX in which either the GGDEF or EAL domain is deleted or mutated have phenotypes indistinguishable from a ΔfimX strain, demonstrating the importance of both domains to function. Previous work has shown that FimX localizes to the bacterial pole. In this work we show that restriction of FimX to a single pole requires intact GGDEF and EAL domains. Deletion of the amino‐terminal REC domain of FimX, which contains a putative polar localization signal, results in a protein that still supports intermediate levels of pilus assembly and function. RFP–FimXΔREC, unlike RFP–FimX, is no longer localized to the bacterial pole, while transmission electron microscopy shows that surface pili can originate from non‐polar sites in this mutant. Although ΔfimX mutants show limited in vitro cytotoxicity, they are as virulent as the wild‐type strain in a murine model of acute pneumonia.
Response of sand ripples to change in oscillatory flow
Authors: DOUCETTE J. S. , O'DONOGHUE T.
Published: March 2006

Ripples take time to evolve to a new equilibrium state in response to a change in wave‐generated oscillatory flow. The paper presents results from flow tunnel experiments designed to examine oscillatory flow transient ripple processes under controlled, full‐scale laboratory conditions. The experiments include study of the growth of ripples from flat bed and the evolution of existing ripples to new equilibrium ripples in response to a step change in the flow. In general, ripples evolve through a combination of two main processes: (i) from a flat bed or from a bed consisting of ripples that are smaller than the equilibrium ripples through a combination of ‘slide’ and ‘merge’; (ii) from a bed consisting of ripples that are larger than the equilibrium ripples through a combination of ‘split’ and ‘merge’. The experimental results show that equilibrium ripple geometry is independent of initial bed morphology while the time to reach equilibrium is largely independent of the initial bed and the equilibrium ripple size. The time to reach equilibrium depends strongly on the mobility number, and a new empirical equation relating mobility number and the number of flow cycles to equilibrium is proposed. This equation is combined with a simple exponential function for ripple height growth or decay to produce a new empirical model for ripple height evolution, which gives a reasonably good overall agreement with the measurements. The model is based on experiments involving one sediment size only and further work is needed to develop the model for other sand sizes.
Sediment ingestion by worms and the production of bio‐clays: a study of macrobiologically enhanced weathering and early diagenetic processes
Authors: NEEDHAM S. J. , WORDEN R. H. , CUADROS J.
Published: March 2006

The experiments reported here show that a range of early diagenetic clay minerals can develop within ingested sand in the guts of creatures at a rate that is at least 2 or 3 orders of magnitude greater than in an abiotic environment. Early diagenesis in marine environments may be strongly influenced by the occurrence of sediment ingestion and excretion by animals. Using a set of artificial marine experiments and the common lugworm Arenicola marina, it is shown that sediment ingestion by macrobiota represents a new way in which to precipitate clay minerals or ‘bio‐clays’. Significant quantities of clay minerals can be the product of biological interaction within sediment. Tanks were constructed with artificially layered sediment and natural seawater. The experiments were conducted at room temperature for a total duration of 9 months. The silicate material fed to the worms was an unweathered, and thus clay mineral‐free, basalt from Iceland. Less than 2 μm fractions from original, control and faecal samples were periodically analysed using X‐ray diffraction (XRD) and Fourier transform infrared spectroscopy (FTIR). Faecal casts underwent mineral alteration as denoted by loss of primary minerals, especially plagioclase. New minerals in faecal casts from the lugworms included, kaolinite, illite, quartz and possibly chlorite. Inorganic weathering of similar parent basalt would probably produce an identical mineral assemblage but many more times slowly than with the macrobiotic mechanism demonstrated here.
Molecular phylogeny of the sawfly subfamily Nematinae (Hymenoptera: Tenthredinidae)
Authors: NYMAN TOMMI , ZINOVJEV ALEXEY G. , VIKBERG VELI , FARRELL BRIAN D.
Published: March 2006

Abstract Nematinae is one of the largest subfamilies in the sawfly family Tenthredinidae, but internal relationships are unknown in the absence of any formal phylogenetic analysis. To understand the internal phylogeny of Nematinae, we sequenced a portion of the mitochondrial cytochrome oxidase I gene and the nuclear elongation factor‐1α gene from thirteen outgroup taxa and sixty‐eight nematine species, the ingroup taxa of which represent all major genera and subgenera within the subfamily. Maximum parsimony and Bayesian phylogenetic analyses of the DNA sequence data show that: (1) Nematinae are monophyletic in a broad sense which includes Hoplocampa, Susana and the tribe Cladiini, which have been classified often into separate subfamilies; together with Craterocercus, these taxa form a paraphyletic basal grade with respect to the remaining Nematinae, but among‐group relationships within the grade remain weakly resolved; (2) the remainder of the ingroup, Nematinae s. str, is monophyletic in all combined‐data analyses; (3) within Nematinae s. str, the ‘Higher’ Nematinae is divided into three groups, Mesoneura and the large tribes Nematini and Pristiphorini; (4) although the traditional classifications at the tribal level are largely upheld, some of the largest tribes and genera are obviously para‐ or polyphyletic; (5) according to rate‐smoothed phylogenies dated with two fossil calibration points, Nematinae originated 50–120 million years ago. In addition, the results from all Bayesian analyses provide strong and consistent support for the monophyly of Tenthredinidae, which has been difficult to demonstrate in previous parsimony analyses of morphological and molecular data.
Does saltwater flushing reduce viability of diapausing eggs in ship ballast sediment?
Authors: Bailey Sarah A. , Nandakumar Kanavillil , MacIsaac Hugh J.
Published: March 2006

Flushing of ballast tanks with seawater has been proposed to reduce the risk of invasion associated with residual ballast in ‘no ballast on board’ ships. The efficacy of this procedure, however, has not been determined. Using diapausing eggs isolated from ballast sediments — as well as from Lake Erie sediment — this study investigated the impact of salinity (0, 8 and 35‰) and temperature (10, 20 and 30 °C) on the cumulative abundance and species richness of hatched zooplankton taxa. The rate and amount of hatching varied dramatically between sediments and across salinity–temperature regimes. Although exposure to saline water inhibited emergence of freshwater taxa during the exposure phase of all trials, mixed results were evident after diapausing eggs were returned to freshwater. The efficacy of salinity as a ballast treatment method was temperature dependent, although the direction of the effect was case‐specific. Exposure of eggs to saline water was less effective at 10 and 30 °C than at 20 °C. Although flushing ballast tanks with open ocean water is expected to significantly reduce the number of active invertebrates living in residual ballast water (a potentially larger source of invaders), our results indicate that the most effective treatment conditions for reduction of diapausing egg viability is 8‰ salinity at 20 °C.
Systemic stress increases serum leptin level
Authors: Konishi Noriaki , Otaka Michiro , Odashima Masaru , Jin Mario , Wada Isao , Komatsu Koga , Sato Toshihiro , Kato Sayuri , Matsuhashi Tamotsu , Watanabe Sumio
Published: March 2006

Background and Aim:  Leptin, the product of the obese (ob) gene, is a circulating peptide mainly synthesized by adipocytes. Leptin inhibits food intake and decreases body weight. A recent report has suggested that the gastric mucosa is also the source of leptin, and that the stomach leptin also contributes to the regulation of the serum leptin level. The aim of the present study was to investigate the effect of water‐immersion stress on serum, stomach and adipose tissue leptin levels to understand the relationship between stress and eating behavior.

Methods:  Male Sprague–Dawley rats were used in this experiment. The leptin level in the serum, gastric mucosa and adipose tissue was measured using ELISA system before and after the initiation of water‐immersion stress.

Results:  The serum leptin level was significantly increased by water‐immersion stress. The peak was observed 9 h after the initiation of the stress (P < 0.01). However, the gastric leptin level significantly decreased 6 and 9 h after the stress. The adipose tissue leptin level significantly increased 3 h after the stress.

Conclusions:  The results suggest that changes in serum leptin levels could be associated with stimulation of leptin secretion from the gastric mucosa and leptin production in the adipose tissue by systemic stress and that leptin might be regulated by stress‐related events.
Influence of methylated p15 INK4b and p16 INK4a genes on clinicopathological features in colorectal cancer
Authors: Ishiguro Atsushi , Takahata Takenori , Saito Masato , Yoshiya Gen , Tamura Yoshihiro , Sasaki Mutsuo , Munakata Akihiro
Published: March 2006

Background and Aim:  Genetic silencing by promoter methylation has attracted attention in the carcinogenesis of colorectal cancer. Methylation of the p16INK4a gene has been found in primary colorectal cancer. Although the p15INK4b gene displays high homology to the p16INK4a gene in the amino acid sequence, methylation of p15INK4b has not been fully studied. We investigated p15INK4b methylation status in patients with colorectal cancer to verify the association between the methylation of p15INK4b and clinicopathological features compared with p16INK4a.

Methods:  DNA samples from the tissues of primary colorectal cancer and corresponding adjacent normal colon mucosa were obtained from surgical resections of 88 patients (47 males and 41 females, aged 29–83 years). Methylation‐specific polymerase chain reaction was used to analyze p15INK4b and p16INK4a methylation status after bisulfite modification. Cumulative survival rates (mean follow‐up period: 53.2 months) were calculated by the Kaplan‐Meier analysis.

Results:  Methylations of p15INK4b and p16INK4a genes were detected in 23 (26.1%) and 20 (22.7%) colorectal cancers, respectively. Methylation of p15INK4b was not associated with any clinicopathological features. Compared with normal mucosa, the methylation of p15INK4b was more prominent in tumor tissue (P < 0.001). Reverse transcription‐polymerase chain reaction (RT‐PCR) revealed that p15INK4b methylaton decreased mRNA expression. Kaplan‐Meier analysis showed that patients with stage I‐II had a significant difference in survival rate between those with and without methylated p15INK4b (P = 0.018).

Conclusions:  Our results suggest that methylation of the p15INK4b gene contributes to the process of carcinogenesis in colorectal cancer as well as p16INK4a and is useful as a prognostic factor in the early stage.