bluuebunny/crossref_metadata_2025 huggingface dataset:
Toward a novel high‐resolution modeling approach for the study of chemical evolution of pollutant plumes during long‐range transport
Authors: Real E. , Pisso I. , Law K. S. , Legras B. , Bousserez N. , Schlager H. , Roiger A. , Attié J. L.
Published: June 2010

This paper presents results from a new method, ZooM‐CiTTy, that aims to accurately reproduce filamentation observed in profiles of chemically active species in the free troposphere. Lagrangian tracer reconstructions of aircraft measurements across pollutant plumes including a stochastic representation of mixing are coupled with photochemical trajectory simulations, initialized with global model fields. The results provide a high‐resolution simulation of trace gases along the flight track together with a detailed picture about the multiple air mass origins influencing chemical composition in the region where plume measurements were taken. This paper builds on results from Pisso et al. (2009) for the dynamic part of the model (the stochastic tracer reconstructions) and focuses on reconstruction of reactive species like O3. The model is evaluated for a case of long‐range transport of a forest fire plume from Alaska to Europe. Simulated trace species are compared with measurements made in the plume by the DLR Falcon aircraft flying over Europe, and the role of photochemistry in governing the chemical composition across the plume is evaluated. It is shown that the model reproduces well O3 and NOy concentrations and O3 production per CO in the plumes as well as gradients at plume edges. In particular, because ZooM‐CiTTy represents the contribution of several air masses to a measurement at a particular location, the model can reproduce so‐called mixing lines between air masses. Results show that photochemistry and mixing contributions vary in different parts of the plume and that resulting trace gas correlations are a combination of these different mixtures. One limitation of the method is the fact that mixing between air masses is only performed at the end of the trajectories. Errors on simulated O3 reconstruction from this formulation are evaluated. These errors seems to be negligible in this case (in the free troposphere, far from emission region) because strong gradients are maintained by large‐scale winds. Results from ZooM‐CiTTy are also used to evaluate errors due to nonlinearities in O3 photochemistry in coarse‐grid models. It is shown that in cases where strong gradients are maintained, errors in net O3 production can be as high as 50% at plumes edges. This new method is interesting to simulate relatively small layering structures observed in the free troposphere, but a more realistic treatment of mixing “en route” is needed if the model has to be used more extensively.
Hydrological influences on spatiotemporal variations of δ15N and δ18O of nitrate in a forested headwater catchment in central Japan: Denitrification plays a critical role in groundwater
Authors: Osaka Ken'ichi , Ohte Nobuhito , Koba Keisuke , Yoshimizu Chikage , Katsuyama Masanori , Tani Makoto , Tayasu Ichiro , Nagata Toshi
Published: June 2010

To elucidate the internal nitrogen cycle and nitrogen input and output, we measured δ15N‐NO3−, δ18O‐NO3−, and NO3− concentrations in rainfall, soil water from an unsaturated soil horizon, groundwater, and stream water at a small forested headwater catchment. In soil water, the mean NO3− concentration did not decrease concomitantly with soil depth, despite a drastic decrease of δ18O‐NO3− with soil depth, indicating immediate consumption of atmospheric NO3− and production of nitrified NO3−. The spatiotemporal distribution of δ15N‐NO3− and δ18O‐NO3− in soil water indicated that plant uptake contributed mainly to NO3− consumption and that denitrification was negligible. In contrast, denitrification played a critical role in groundwater in decreasing the NO3− concentration. Fluctuations of δ15N‐NO3−, δ18O‐NO3−, and NO3− concentration in groundwater, however, differed from expectations for occurrence resulting from denitrification only. A plausible explanation for the lack of a concurrent increase in δ15N and δ18O of NO3− is that nitrification and denitrification occur concurrently in groundwater and that denitrification is more important than nitrification. The amount of denitrification in the groundwater body was controlled primarily by groundwater residence time. The combination of hydrological flow path from groundwater to stream water and denitrification in the groundwater critically control the amount of leaching of NO3− and temporal distribution of NO3− concentration in stream water. The possibility exists that denitrification in groundwater strongly influences nitrogen leaching in forests because denitrification occurred even in this catchment, which consists of weathered granitic bedrock and predominantly typic udipsamment, with low organic matter content in the soil.
Marking the Fifth Anniversary of the Landing on Titan: Huygens Fifth Anniversary Meeting; Barcelona, Spain, 13–15 January 2010
Authors: Coustenis Athena , Lebreton Jean‐Pierre , Matson Dennis
Published: June 2010

On the occasion of the fifth anniversary of the European Space Agency's Huygens probe landing on Saturn's moon Titan (14 January 2005), approximately a hundred international scientists and engineers met at the CosmoCaixa Science Museum, in Spain, to assess what was discovered and what remains to be done by future spacecraft missions to Titan and the Saturnian system. The Huygens probe was deployed from NASA's Cassini spacecraft.

Speakers at the meeting pointed out that discoveries from the Cassini‐Huygens mission have shown that Titan is much more interesting than even their wildest expectations more than 20 years ago when the mission was conceived, in the 1980s, several years after the Voyager flybys. Perhaps most stunning are the many similarities between Titan and the Earth. Though there are important differences, when one views the lakes and seas, the fluvial terrain, the sand dunes, and other features through the hazy, nitrogen atmosphere, it calls to mind the geological processes that created analogous features on the Earth. On Titan it has been discovered that frozen water plays the geological role of rock, and liquid methane takes the role of terrestrial water. As Saturn proceeds along its orbit about the Sun, the seasons change on Titan. The seasonal effects on the transport of methane are starting to be seen. A large lake in the south polar region seems to be getting smaller as winter sets in.
The Mid‐Mediterranean Jet Artefact
Authors: Millot C. , Gerin R.
Published: June 2010

The Mid‐Mediterranean Jet has been considered to be, since the 1990s, a more or less continuous surface current meandering across most of the eastern basin of the Mediterranean Sea, generating a series of eddies. This relatively recent view of the current, which was not found in earlier circulation diagrams and does not have any theoretical support, emerges more or less from simple statistics applied to any kind of in situ data. Here we use a relatively large set of surface drifter trajectories, which provide reasonable sampling of the area of interest, to show how mesoscale anticyclonic eddies generated elsewhere with specific diameters, locations and displacements, can provide a misleading picture by suggesting the occurrence of a mid basin jet which is actually nothing more than a data analysis artefact.
High bicarbonate assimilation in the dark by Arctic bacteria
Authors: Alonso-Sáez Laura , Galand Pierre E , Casamayor Emilio O , Pedrós-Alió Carlos , Bertilsson Stefan
Published: June 2010

Although both autotrophic and heterotrophic microorganisms incorporate CO2 in the dark through different metabolic pathways, this process has usually been disregarded in oxic marine environments. We studied the significance and mediators of dark bicarbonate assimilation in dilution cultures inoculated with winter Arctic seawater. At stationary phase, bicarbonate incorporation rates were high (0.5–2.5 μg C L−1 d−1) and correlated with rates of bacterial heterotrophic production, suggesting that most of the incorporation was due to heterotrophs. Accordingly, very few typically chemoautotrophic bacteria were detected by 16S rRNA gene cloning. The genetic analysis of the biotin carboxylase gene accC putatively involved in archaeal CO2 fixation did not yield any archaeal sequence, but amplified a variety of bacterial carboxylases involved in fatty acids biosynthesis, anaplerotic pathways and leucine catabolism. Gammaproteobacteria dominated the seawater cultures (40–70% of cell counts), followed by Betaproteobacteria and Flavobacteria as shown by catalyzed reporter deposition fluorescence in situ hybridization (CARDFISH). Both Beta- and Gammaproteobacteria were active in leucine and bicarbonate uptake, while Flavobacteria did not take up bicarbonate, as measured by microautoradiography combined with CARDFISH. Within Gammaproteobacteria, Pseudoalteromonas-Colwellia and Oleispira were very active in bicarbonate uptake (ca. 30 and 70% of active cells, respectively), while the group Arctic96B-16 did not take up bicarbonate. Our results suggest that, potentially, the incorporation of CO2 can be relevant for the metabolism of specific Arctic heterotrophic phylotypes, promoting the maintenance of their cell activity and/or longer survival under resource depleted conditions.
Active methylotrophs in the sediments of Lonar Lake, a saline and alkaline ecosystem formed by meteor impact
Authors: Antony Chakkiath Paul , Kumaresan Deepak , Ferrando Lucia , Boden Rich , Moussard Hélène , Scavino Ana Fernández , Shouche Yogesh S , Murrell J Colin
Published: June 2010

Lonar Lake is a unique saline and alkaline ecosystem formed by meteor impact in the Deccan basalts in India around 52 000 years ago. To investigate the role of methylotrophy in the cycling of carbon in this unusual environment, stable-isotope probing (SIP) was carried out using the one-carbon compounds methane, methanol and methylamine. Denaturing gradient gel electrophoresis fingerprinting analyses performed with heavy 13C-labelled DNA retrieved from sediment microcosms confirmed the enrichment and labelling of active methylotrophic communities. Clone libraries were constructed using PCR primers targeting 16S rRNA genes and functional genes. Methylomicrobium, Methylophaga and Bacillus spp. were identified as the predominant active methylotrophs in methane, methanol and methylamine SIP microcosms, respectively. Absence of mauA gene amplification in the methylamine SIP heavy fraction also indicated that methylamine metabolism in Lonar Lake sediments may not be mediated by the methylamine dehydrogenase enzyme pathway. Many gene sequences retrieved in this study were not affiliated with extant methanotrophs or methylotrophs. These sequences may represent hitherto uncharacterized novel methylotrophs or heterotrophic organisms that may have been cross-feeding on methylotrophic metabolites or biomass. This study represents an essential first step towards understanding the relevance of methylotrophy in the soda lake sediments of an unusual impact crater structure.
Association of Obesity and Hypertension With Left Ventricular Geometry and Function in Children and Adolescents
Authors: Dhuper Sarita , Abdullah Rukhsana A. , Weichbrod Laya , Mahdi Eman , Cohen Hillel W.
Published: June 2010

Obesity, especially when complicated with hypertension, is associated with structural and functional cardiac changes. Recent studies have focused on the prognostic impact of the type of left ventricular (LV) geometric remodeling. This study looked at the prevalence and clinical correlates of LV geometric patterns and their relation to cardiac function in a sample of predominantly African‐American (AA) youth. Echocardiographic data was collected on 213 obese (BMI of 36.53 ± 0.53 kg/m2) and 130 normal‐weight subjects (BMI of 19.73 ± 0.21 kg/m2). The obese subjects had significantly higher LV mass index (LVMI; 49.6 ± 0.9 vs. 46.0 ± 1.0 g/m2.7, P = 0.01), relative wall thickness (RWT; 0.45 ± 0.00 vs. 0.40 ± 0.00, P < 0.001), left atrial (LA) index (33.2 ± 0.7 vs. 23.5 ± 0.6 ml/m, P < 0.001), more abnormal diastolic function by tissue Doppler E/Ea septal (7.5 ± 0.14 vs. 6.5 ± 0.12 ms, P < 0.001), E/Ea lateral (5.7 ± 0.12 vs. 4.8 ± 0.1 ms, P < 0.001), myocardial performance index (MPI; 0.43 ± 0.00 vs. 0.38 ± 0.00, P < 0.001), and Doppler mitral EA ratio (2.0 ± 0.04 vs. 2.4 ± 0.07, P < 0.001) but similar systolic function. Concentric remodeling (CR) was the most prevalent pattern noted in the obese group and concentric hypertrophy (CH) in the obese and hypertensive group. Obesity, hypertension, and CH were independent predictor of diastolic dysfunction. Systolic (SBP) and diastolic blood pressures (DBP) were the prime mediators for CH whereas obesity and diastolic blood pressure were predictors of CR. No significant association was observed between the geometric patterns and systolic function. Tracking LV hypertrophy (LVH) status and geometric adaptations in obesity may be prognostic tools for assessing cardiac risk and therapeutic end points with weight loss.
Comparing Trends in BMI and Waist Circumference
Authors: Walls Helen L. , Stevenson Christopher E. , Mannan Haider R. , Abdullah Asnawi , Reid Christopher M. , McNeil John J. , Peeters Anna
Published: June 2010

The nature of excess body weight may be changing over time to one of greater central adiposity. The aim of this study is to determine whether BMI and waist circumference (WC) are increasing proportionately among population subgroups and the range of bodyweight, and to examine the public health implications of the findings. Our data are from two cross‐sectional surveys (the US National Health and Nutrition Examination Studies (NHANES) in 1988–1994 (NHANES III) and 2005–2006), from which we have used samples of 15,349 and 4,176 participants aged ≥20 years. Between 1988–1994 and 2005–2006 BMI increased by an average of 1.8 kg/m2 and WC by 4.7 cm (adjusted for sex, age, race‐ethnicity, and education). The increase in WC was more than could be attributed simply to increases in BMI. This independent increase in WC (of on average, 0.9 cm) was consistent across the different BMI categories, sexes, education levels, and race‐ethnicity groups. It occurred in younger but not older age groups. Overall in each BMI category, the prevalence of low‐risk WC decreased and the prevalence of increased‐risk or substantially increased‐risk WC increased. These results suggest that the adverse health consequences associated with obesity may be increasingly underestimated by trends in BMI alone. Since WC is closely linked to adverse cardiovascular outcomes, it is important to know the prevailing trends in both of these parameters.
Annual and circadian activity patterns of badgers (Meles meles) in Białowieża Primeval Forest (eastern Poland) compared with other Palaearctic populations
Authors: Kowalczyk Rafał , Jȩdrzejewska Bogumiła , Zalewski Andrzej
Published: June 2010

Aim  The annual and circadian rhythms and duration of activity of Eurasian badger Meles meles (Linnaeus 1758) were studied in a low‐density population inhabiting the primeval woodland in the European temperate zone. Results were compared with available data from the literature on seasonal changes in body mass and winter inactivity of badgers from across the Palaearctic region.

Location  Field work was carried out in Białowieża Primeval Forest, eastern Poland. Biogeographical variation was reviewed based on twenty‐three localities in the Palaearctic region (from Western Europe to Central Siberia).

Methods  Thirteen badgers were radio‐collared in 1997–2001. Their circadian activity was sampled by 24‐h sessions of continuous radio‐tracking with location taken at 15‐min intervals. Annual activity was studied by radio‐tracking and inspections of setts. Earthworm (badgers’ main food) biomass was estimated in four types of habitats throughout the year.

Results  Badgers were nocturnal with one long bout of activity. Their rhythms of diel activity differed between spring and autumn, and between adult and subadult individuals. On average, badgers emerged from setts at 19:00 hours and returned to them at 03:42 hours. The highest level of activity was recorded between 20:00 and 03:00 hours. Duration of daily activity was, on average, 8.2 h day−1, but varied significantly between seasons. The seasonal changes were inversely related to the abundance of earthworms. Duration of activity also depended on daily temperature, especially in the cold season. In winter, badgers stayed inactive for an average of 96 days per year. In autumn, they built fat reserves and their body mass nearly doubled compared with the spring values.

The literature review on annual cycle of activity and body mass changes in Eurasian badgers showed that fat storage and duration of winter sleep strongly depended on climate (best approximated by January mean temperature). In regions with warm climates, badgers were active year round and their body mass changed only slightly, while in regions with severe winters badgers increased their body mass twofold from spring to autumn, and stayed inactive for as long as 6 months per year.

Main conclusion  We propose that, in the temperate and boreal zones of the Palaearctic region, the ultimate determinant of biogeographical variation in badgers’ annual activity is the winter shortage of earthworms, which are the main component of badger diet.
On the validity of Bergmann's rule
Authors: Meiri Shai , Dayan Tamar
Published: June 2010

AimWe reviewed the occurrence of Bergmann's rule in birds (ninety‐four species) and mammals (149 species), using only studies where statistical significance of the results was tested. We also tested whether studies using different characters as surrogates of body size have a different tendency to conform to Bergmann's rule, whether body size and nest type (in birds) have an influence on the tendency to conform to the rule, and whether sedentary birds conform to the rule more than migratory birds.

LocationWorldwide.

MethodsWe reviewed published data on geographic and temporal variation in body size, using only studies where the statistical significance of the results was tested. We asked how many species conform to the rule out of all species studied in each order and family.

ResultsOver 72% of the birds and 65% of the mammal species follow Bergmann's rule. An overall tendency to follow the rule occurs also within orders and families. Studies using body mass in mammals show the greatest tendency to adhere to Bergmann's rule (linear measurements and dental measurements show a weaker tendency); while in birds, studies using body mass and other surrogates (linear measurements and egg size) show a similar tendency. Birds of different body mass categories exhibit a similar tendency to follow Bergmann's rule, while in mammals the lower body size categories (4–50 and 50–500 g) show a significantly lower tendency to conform to the rule. Sedentary birds tend to conform to Bergmann's rule more than migratory species. Nest type does not affect the tendency to conform to Bergmann's rule.

Main conclusions Bergmann's rule is a valid ecological generalization for birds and mammals.
Large‐scale geographical trends in fruit traits of vertebrate‐dispersed temperate plants
Authors: Hampe Arndt
Published: June 2010

Aim  To assess large‐scale geographical trends in the character of fleshy, vertebrate‐dispersed fruits.

Location  Europe between central Sweden and southern Spain.

Methods  Analyses of fruit of sixty‐three plant species from twenty‐nine families were compiled from four regional data sets. Four structural and five chemical fruit traits were analysed intraspecifically to control rigorously for phylogenetic lineage effects. Trends were examined in relation to various biological features of the considered species.

Results  Contents of soluble carbohydrate and lipids decreased markedly northwards. Fruit diameter and fresh mass peaked at the wettest site, while the pulp water content remained more constant throughout the gradient than any other fruit trait. Ash content, seed number and seed mass did not change, while the nitrogen content showed conflicting trends. No relation was detected between observed variation in fruit traits and fruit type, fruit colour, ripening season, plant growth form, leaf longevity, or geographical distribution of the considered plant species.

Main conclusions  Considerable intraspecific variability exists in vertebrate‐dispersed fruits on large geographical scales. Climate presumably affects particularly those traits related to carbon and water gain and storage. Most research on fruit–frugivore interactions has been carried out on small spatial scales and failed to find matchings between frugivore communities and the character of fleshy fruits. I suggest that explicitly addressed large‐scale surveys on the geographical variability of fruits and their disperser assemblages are needed to elucidate their spatial patterns and to determine the extent to which fleshy fruit traits are shaped by animals and/or abiotic factors.
Modelling habitat‐suitability using museum collections: an example with three sympatric Apodemus species from the Alps
Authors: Reutter Brigitte A. , Helfer V. , Hirzel A. H. , Vogel P.
Published: June 2010

Aim, Location Although the alpine mouse Apodemus alpicola has been given species status since 1989, no distribution map has ever been constructed for this endemic alpine rodent in Switzerland. Based on redetermined museum material and using the Ecological‐Niche Factor Analysis (ENFA), habitat‐suitability maps were computed for A. alpicola, and also for the co‐occurring A. flavicollis and A. sylvaticus.

Methods In the particular case of habitat suitability models, classical approaches (GLMs, GAMs, discriminant analysis, etc.) generally require presence and absence data. The presence records provided by museums can clearly give useful information about species distribution and ecology and have already been used for knowledge‐based mapping. In this paper, we apply the ENFA which requires only presence data, to build a habitat‐suitability map of three species of Apodemus on the basis of museum skull collections.

Results Interspecific niche comparisons showed that A. alpicola is very specialized concerning habitat selection, meaning that its habitat differs unequivocally from the average conditions in Switzerland, while both A. flavicollis and A. sylvaticus could be considered as ‘generalists’ in the study area.

Main conclusions Although an adequate sampling design is the best way to collect ecological data for predictive modelling, this is a time and money consuming process and there are cases where time is simply not available, as for instance with endangered species conservation. On the other hand, museums, herbariums and other similar institutions are treasuring huge presence data sets. By applying the ENFA to such data it is possible to rapidly construct a habitat suitability model. The ENFA method not only provides two key measurements regarding the niche of a species (i.e. marginality and specialization), but also has ecological meaning, and allows the scientist to compare directly the niches of different species.
Templating efficiency of naked DNA
Authors: Kervio Eric , Hochgesand Annette , Steiner Ulrich E. , Richert Clemens
Published: June 2010

Template-directed synthesis of complementary strands is pivotal for life. Nature employs polymerases for this reaction, leaving the ability of DNA
itself
to direct the incorporation of individual nucleotides at the end of a growing primer difficult to assess. Using 64 sequences, we now find that any of the four nucleobases, in combination with any neighboring residue, support enzyme-free primer extension when primer and mononucleotide are sufficiently reactive, with ≥93% primer extension for all sequences. Between the 64 possible base triplets, the rate of extension for the poorest template, C
A
G, with
A
as templating base, and the most efficient template, T
C
T, with
C
as templating base, differs by less than two orders of magnitude. Further, primer extension with a balanced mixture of monomers shows ≥72% of the correct extension product in all cases, and ≥90% incorporation of the correct base for 46 out of 64 triplets in the presence of a downstream-binding strand. A mechanism is proposed with a binding equilibrium for the monomer, deprotonation of the primer, and two chemical steps, the first of which is most strongly modulated by the sequence. Overall, rates show a surprisingly smooth reactivity landscape, with similar incorporation on strongly and weakly templating sequences. These results help to clarify the substrate contribution to copying, as found in polymerase-catalyzed replication, and show an important feature of DNA as genetic material.
SOCIAL NETWORKS IN SLOVENIA
Authors: Hlebec Valentina , Filipovič Hrast Maša , Kogovšek Tina
Published: June 2010

The process generally referred to as ‘the transition’ implied a complex set of social changes in Central and Eastern European countries (CEE). On the one hand, there were institutional reforms which were launched to abolish the socialist economic and political systems. On the other hand, the provision of welfare was also affected by ‘transition’. The change could be observed at the institutional level (i.e., through the welfare state) as well as at the social and individual level – in the ways individuals associated, how they perceived new risks and with whom they engaged to confront them. In this article we focus on social support provision from informal sources, i.e., ego-centered social support networks, which are an important foundation for the quality of everyday life. We would like to find out whether changes in the socio-economic system are reflected in and accompanied by changes in social support providers. How have people responded to transition? Did the patterns of support and social support providers change in this period? Consequently, the research question addressed in this article is the following: do the current types of social networks differ from those in the 1980s? We try to answer it by analyzing and comparing the data on social support networks in 1987 and 2002. The data are interpreted in the context of the transition that was happening in Slovenia at the time.
Plakophilin 2 Couples Actomyosin Remodeling to Desmosomal Plaque Assembly via RhoA
Authors: Godsel Lisa M. , Dubash Adi D. , Bass-Zubek Amanda E. , Amargo Evangeline V. , Klessner Jodi L. , Hobbs Ryan P. , Chen Xinyu , Green Kathleen J.
Published: June 2010

Plakophilin 2 (PKP2), an armadillo family member closely related to p120 catenin (p120ctn), is a constituent of the intercellular adhesive junction, the desmosome. We previously showed that PKP2 loss prevents the incorporation of desmosome precursors enriched in the plaque protein desmoplakin (DP) into newly forming desmosomes, in part by disrupting PKC-dependent regulation of DP assembly competence. On the basis of the observation that DP incorporation into junctions is cytochalasin D–sensitive, here we ask whether PKP2 may also contribute to actin-dependent regulation of desmosome assembly. We demonstrate that PKP2 knockdown impairs cortical actin remodeling after cadherin ligation, without affecting p120ctn expression or localization. Our data suggest that these defects result from the failure of activated RhoA to localize at intercellular interfaces after cell–cell contact and an elevation of cellular RhoA, stress fibers, and other indicators of contractile signaling in squamous cell lines and atrial cardiomyocytes. Consistent with these observations, RhoA activation accelerated DP redistribution to desmosomes during the first hour of junction assembly, whereas sustained RhoA activity compromised desmosome plaque maturation. Together with our previous findings, these data suggest that PKP2 may functionally link RhoA- and PKC-dependent pathways to drive actin reorganization and regulate DP–IF interactions required for normal desmosome assembly.
A Poisson model for random multigraphs
Authors: Ranola John M. O. , Ahn Sangtae , Sehl Mary , Smith Desmond J. , Lange Kenneth
Published: June 2010

Motivation: Biological networks are often modeled by random graphs. A better modeling vehicle is a multigraph where each pair of nodes is connected by a Poisson number of edges. In the current model, the mean number of edges equals the product of two propensities, one for each node. In this context it is possible to construct a simple and effective algorithm for rapid maximum likelihood estimation of all propensities. Given estimated propensities, it is then possible to test statistically for functionally connected nodes that show an excess of observed edges over expected edges. The model extends readily to directed multigraphs. Here, propensities are replaced by outgoing and incoming propensities.

Results: The theory is applied to real data on neuronal connections, interacting genes in radiation hybrids, interacting proteins in a literature curated database, and letter and word pairs in seven Shaskespearean plays.

Availability: All data used are fully available online from their respective sites. Source code and software is available from http://code.google.com/p/poisson-multigraph/

Contact:  klange@ucla.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Homology of SMP domains to the TULIP superfamily of lipid-binding proteins provides a structural basis for lipid exchange between ER and mitochondria
Authors: Kopec Klaus O. , Alva Vikram , Lupas Andrei N.
Published: June 2010

Mitochondria must uptake some phospholipids from the endoplasmic reticulum (ER) for the biogenesis of their membranes. They convert one of these lipids, phosphatidylserine, to phosphatidylethanolamine, which can be re-exported via the ER to all other cellular membranes. The mechanisms underlying these exchanges between ER and mitochondria are poorly understood. Recently, a complex termed ER–mitochondria encounter structure (ERMES) was shown to be necessary for phospholipid exchange in budding yeast. However, it is unclear whether this complex is merely an inter-organelle tether or also the transporter. ERMES consists of four proteins: Mdm10, Mdm34 (Mmm2), Mdm12 and Mmm1, three of which contain the uncharacterized SMP domain common to a number of eukaryotic membrane-associated proteins. Here, we show that the SMP domain belongs to the TULIP superfamily of lipid/hydrophobic ligand-binding domains comprising members of known structure. This relationship suggests that the SMP domains of the ERMES complex mediate lipid exchange between ER and mitochondria.

Contact:  andrei.lupas@tuebingen.mpg.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
Importance of riparian remnants for frog species diversity in a highly fragmented rainforest
Authors: Rodríguez-Mendoza Clara , Pineda Eduardo
Published: June 2010

Tropical forests undergo continuous transformation to other land uses, resulting in landscapes typified by forest fragments surrounded by anthropogenic habitats. Small forest fragments, specifically strip-shaped remnants flanking streams (referred to as riparian remnants), can be particularly important for the maintenance and conservation of biodiversity within highly fragmented forests. We compared frog species diversity between riparian remnants, other forest fragments and cattle pastures in a tropical landscape in Los Tuxtlas, Mexico. We found similar species richness in the three habitats studied and a similar assemblage structure between riparian remnants and forest fragments, although species composition differed by 50 per cent. Frog abundance was halved in riparian remnants compared with forest fragments, but was twice that found in pastures. Our results suggest that riparian remnants play an important role in maintaining a portion of frog species diversity in a highly fragmented forest, particularly during environmentally stressful (hot and dry) periods. In this regard, however, the role of riparian remnants is complementary, rather than substitutive, with respect to the function of other forest fragments within the fragmented forest.
Carbonaceous preservation of Cambrian hexactinellid sponge spicules
Authors: Harvey Thomas H. P.
Published: June 2010

Early fossil sponges offer a direct window onto the evolutionary emergence of animals, but insights are limited by the paucity of characters preserved in the conventional fossil record. Here, a new preservational mode for sponge spicules is reported from the lower Cambrian Forteau Formation (Newfoundland, Canada), prompting a re-examination of proposed homologies and sponge inter-relationships. The spicules occur as wholly carbonaceous films, and are interpreted as the remains of robust organic spicule sheaths. Comparable sheaths are restricted among living taxa to calcarean sponges, although the symmetries of the fossil spicules are characteristic of hexactinellid sponges. A similar extinct character combination has been documented in the Burgess Shale fossil
Eiffelia
. Interpreting the shared characters as homologous implies complex patterns of spicule evolution, but an alternative interpretation as convergent autapomorphies is more parsimonious. In light of the mutually exclusive distributions of these same characters among the crown groups, this result suggests that sponges exhibited an early episode of disparity expansion followed by comparatively constrained evolution, a pattern shared with many other metazoans but obscured by the conventional fossil record of sponges.
Ancient fig wasps indicate at least 34 Myr of stasis in their mutualism with fig trees
Authors: Compton Stephen G. , Ball Alexander D. , Collinson Margaret E. , Hayes Peta , Rasnitsyn Alexandr P. , Ross Andrew J.
Published: June 2010

Fig wasps and fig trees are mutually dependent, with each of the 800 or so species of fig trees (Ficus, Moraceae) typically pollinated by a single species of fig wasp (Hymenoptera: Agaonidae). Molecular evidence suggests that the relationship existed over 65 Ma, during the Cretaceous. Here, we record the discovery of the oldest known fossil fig wasps, from England, dated at 34 Ma. They possess pollen pockets that contain fossilFicuspollen. The length of their ovipositors indicates that their host trees had a dioecious breeding system. Confocal microscopy and scanning electron microscopy reveal that the fossil female fig wasps, and more recent species from Miocene Dominican amber, display the same suite of anatomical characters associated with fig entry and pollen-carrying as modern species. The pollen is also typical of modernFicus. No innovations in the relationship are discernible for the last tens of millions of years.
Warm-water decapods and the trophic amplification of climate in the North Sea
Authors: Lindley J. A. , Beaugrand G. , Luczak C. , Dewarumez J.-M. , Kirby R. R.
Published: June 2010

A long-term time series of plankton and benthic records in the North Sea indicates an increase in decapods and a decline in their prey species that include bivalves and flatfish recruits. Here, we show that in the southern North Sea the proportion of decapods to bivalves doubled following a temperature-driven, abrupt ecosystem shift during the 1980s. Analysis of decapod larvae in the plankton reveals a greater presence and spatial extent of warm-water species where the increase in decapods is greatest. These changes paralleled the arrival of new species such as the warm-water swimming crab
Polybius henslowii
now found in the southern North Sea. We suggest that climate-induced changes among North Sea decapods have played an important role in the trophic amplification of a climate signal and in the development of the new North Sea dynamic regime.
Mechanism of variable structural colour in the neon tetra: quantitative evaluation of the Venetian blind model
Authors: Yoshioka S. , Matsuhana B. , Tanaka S. , Inouye Y. , Oshima N. , Kinoshita S.
Published: June 2010

The structural colour of the neon tetra is distinguishable from those of, e.g., butterfly wings and bird feathers, because it can change in response to the light intensity of the surrounding environment. This fact clearly indicates the variability of the colour-producing microstructures. It has been known that an iridophore of the neon tetra contains a few stacks of periodically arranged light-reflecting platelets, which can cause multilayer optical interference phenomena. As a mechanism of the colour variability, the Venetian blind model has been proposed, in which the light-reflecting platelets are assumed to be tilted during colour change, resulting in a variation in the spacing between the platelets. In order to quantitatively evaluate the validity of this model, we have performed a detailed optical study of a single stack of platelets inside an iridophore. In particular, we have prepared a new optical system that can simultaneously measure both the spectrum and direction of the reflected light, which are expected to be closely related to each other in the Venetian blind model. The experimental results and detailed analysis are found to quantitatively verify the model.
High-speed stream driven inferences of global wave distributions at geosynchronous orbit: relevance to radiation-belt dynamics
Authors: MacDonald Elizabeth A. , Blum Lauren W. , Gary S. Peter , Thomsen Michelle F. , Denton Michael H.
Published: June 2010

Three superposed epoch analyses of plasma data from geosynchronous orbit are compared to infer relative distributions of electromagnetic ion cyclotron (EMIC)- and whistler-mode wave instabilities. Both local-time and storm-time behaviours are studied with respect to dynamics of relativistic electrons. Using LANL-GEO particle data and a quasi-linear approximation for the wave growth allows us to estimate the instability of the two wave modes. This simple technique can allow powerful insights into wave–particle interactions at geosynchronous orbit. Whistler-wave activity peaks on the dayside during the early recovery phase and can continue to be above normal levels for several days. The main phase of all storms exhibits the most EMIC-wave activity, whereas in the recovery phase of the most radiation-belt-effective storms, a significantly suppressed level of EMIC activity is inferred. These key results indicate new dynamics relating to plasma delivery, source and response, but support generally accepted views of whistlers as a source process and EMIC-mode waves as a major loss contributor at geosynchronous orbit.
A Gibbs-potential-based formulation for obtaining the response functions for a class of viscoelastic materials
Authors: Rajagopal K. R. , Srinivasa A. R.
Published: June 2010

In this article, we demonstrate the use of a Gibbs-potential-based formulation as a means for developing a thermodynamically consistent model for a class of viscoelastic fluids of the rate type. Since one cannot always use a formulation based on a Helmholtz potential to model rate-type models, the formulation takes on added significance. The salient features of this approach are the following:

— this approach provides a thermodynamical rationalization of many commonly used models that are developed on purely phenomenological grounds; furthermore, the study provides a framework for generating other classes of models and allows for a relatively straightforward means for the inclusion of thermal effects,

— the approach provides a simple means for including anisotropic effects without the need for directors or other new internal variables, and

— the approach does not use any additional variables (such as conformation tensors or elastic strains measured from stress free configurations) other than the current (or Cauchy) stress, the current mass density and the velocity gradient.

We also show how the entire structure of the theory is obtained from just two scalar functions, the Gibbs potential and the rate of dissipation function.
Inbreeding depresses sperm competitiveness, but not fertilization or mating success in male
Tribolium castaneum
Authors: Michalczyk Łukasz , Martin Oliver Y. , Millard Anna L. , Emerson Brent C. , Gage Matthew J. G.
Published: June 2010

As populations decline to levels where reproduction among close genetic relatives becomes more probable, subsequent increases in homozygous recessive deleterious expression and/or loss of heterozygote advantage can lead to inbreeding depression. Here, we measure how inbreeding across replicate lines of the flour beetle
Tribolium castaneum
impacts on male reproductive fitness in the absence or presence of male–male competition. Effects on male evolution from mating pattern were removed by enforcing monogamous mating throughout. After inbreeding across eight generations, we found that male fertility in the absence of competition was unaffected. However, we found significant inbreeding depression of sperm competitiveness: non-inbred males won 57 per cent of fertilizations in competition, while inbred equivalents only sired 42 per cent. We also found that the P
2
‘offence’ role in sperm competition was significantly more depressed under inbreeding than sperm ‘defence’ (P
1
). Mating behaviour did not explain these differences, and there was no difference in the viability of offspring sired by inbred or non-inbred males. Sperm length variation was significantly greater in the ejaculates of inbred males. Our results show that male ability to achieve normal fertilization success was not depressed under strong inbreeding, but that inbreeding depression in these traits occurred when conditions of sperm competition were generated.
Corticosterone, testosterone and life-history strategies of birds
Authors: Hau Michaela , Ricklefs Robert E. , Wikelski Martin , Lee Kelly A. , Brawn Jeffrey D.
Published: June 2010

Steroid hormones have similar functions across vertebrates, but circulating concentrations can vary dramatically among species. We examined the hypothesis that variation in titres of corticosterone (Cort) and testosterone (T) is related to life-history traits of avian species. We predicted that Cort would reach higher levels under stress in species with higher annual adult survival rates since Cort is thought to promote physiological and behavioural responses that reduce risk to the individual. Conversely, we predicted that peak T during the breeding season would be higher in short-lived species with high mating effort as this hormone is known to promote male fecundity traits. We quantified circulating hormone concentrations and key life-history traits (annual adult survival rate, breeding season length, body mass) in males of free-living bird species during the breeding season at a temperate site (northern USA) and a tropical site (central Panama). We analysed our original data by themselves, and also combined with published data on passerine birds to enhance sample size. In both approaches, variation in baseline Cort (Cort0) among species was inversely related to breeding season length and body mass. Stress-induced corticosterone (MaxCort) also varied inversely with body mass and, as predicted, also varied positively with annual adult survival rates. Furthermore, species from drier and colder environments exhibited lower MaxCort than mesic and tropical species; T was lowest in species from tropical environments. These findings suggest that Cort0, MaxCort and T modulate key vertebrate life-history responses to the environment, with Cort0 supporting energetically demanding processes, MaxCort promoting survival and T being related to mating success.
Bird population trends are linearly affected by climate change along species thermal ranges
Authors: Jiguet Frédéric , Devictor Vincent , Ottvall Richard , Van Turnhout Chris , Van der Jeugd Henk , Lindström Åke
Published: June 2010

Beyond the effects of temperature increase on local population trends and on species distribution shifts, how populations of a given species are affected by climate change along a species range is still unclear. We tested whether and how species responses to climate change are related to the populations locations within the species thermal range. We compared the average 20 year growth rates of 62 terrestrial breeding birds in three European countries along the latitudinal gradient of the species ranges. After controlling for factors already reported to affect bird population trends (habitat specialization, migration distance and body mass), we found that populations breeding close to the species thermal maximum have lower growth rates than those in other parts of the thermal range, while those breeding close to the species thermal minimum have higher growth rates. These results were maintained even after having controlled for the effect of latitude
per se
. Therefore, the results cannot solely be explained by latitudinal clines linked to the geographical structure in local spring warming. Indeed, we found that populations are not just responding to changes in temperature at the hottest and coolest parts of the species range, but that they show a linear graded response across their European thermal range. We thus provide insights into how populations respond to climate changes. We suggest that projections of future species distributions, and also management options and conservation assessments, cannot be based on the assumption of a uniform response to climate change across a species range or at range edges only.
Influence of quaternary sea-level variations on a land bird endemic to Pacific atolls
Authors: Cibois Alice , Thibault Jean-Claude , Pasquet Eric
Published: June 2010

Little is known about the effect of quaternary climate variations on organisms that inhabited carbonate islands of the Pacific Ocean, although it has been suggested that one or several uplifted islands provided shelter for terrestrial birds when sea-level reached its highest. To test this hypothesis, we investigated the history of colonization of the Tuamotu reed-warbler (Acrocephalus atyphus) in southeastern Polynesia, and found high genetic structure between the populations of three elevated carbonate islands. Estimates of time since divergence support the hypothesis that these islands acted as refugia during the last interglacial maximum. These findings are particularly important for defining conservation priorities on atolls that endure the current trend of sea-level rise owing to global warming.
Potential role for vascular endothelial growth factor‐D as an autocrine factor for human gastric carcinoma cells
Authors: Tanaka Miwako , Kitadai Yasuhiko , Kodama Michiyo , Shinagawa Kei , Sumida Tomonori , Tanaka Shinji , Oue Naohide , Yasui Wataru , Chayama Kazuaki
Published: June 2010

Vascular endothelial growth factor (VEGF)‐D induces lymphangiogenesis by activating VEGF receptor (VEGFR)‐3, which is expressed mainly by lymphatic endothelial cells. VEGFR‐3 has also been detected in several types of malignant cells, but the significance of VEGFR‐3 expression by malignant cells remains unclear. We examined the expression and function of VEGF‐D/VEGFR‐3 in human gastric carcinoma cells. Expression of VEGF‐D and VEGFR‐3 was analyzed in three human gastric carcinoma cell lines and 29 surgical specimens. cDNA microarray analysis was used to examine the effect of VEGF‐D on the expression of genes associated with disease progression in VEGFR‐3‐expressing KKLS cells. VEGF‐D‐transfected cells and control cells were transplanted into the gastric wall of nude mice. In 10 of the 29 (34%) gastric carcinoma specimens and two of the three cell lines, cancer cells expressed both VEGF‐D and VEGFR‐3. In vitro treatment of KKLS cells with exogenous VEGF‐D increased expression of cyclin D1 and Bcl‐2 and stimulated cell proliferation. VEGF‐D transfection into KKLS cells resulted in stimulation of angiogenesis, lymphangiogenesis, and cell proliferation, and in inhibition of apoptosis. VEGF‐D may participate in the progression of human gastric carcinoma by acting via autocrine and paracrine mechanisms. (Cancer Sci 2010)