Can germination explain the distribution of tree species in a savanna wetland?

The relationship between seed germination and ecological niche is determined by matching germination characteristics with environmental features. In this study, we selected tree species occurring in the largest savanna wetland in South America – the Pantanal. Very few species are endemic or exclusively found in savanna wetlands, and the majority of tree species occurring in the Pantanal are also found in the neighbouring Brazilian Cerrado, a drier vegetation type that does not flood. We investigated the relationship between germination characteristics and occurrence of savanna trees in wetlands testing the hypothesis that such seeds are tolerant to flooding. We also addressed the question of whether seed tolerance to flood, assessed by survival analysis, explains tree distribution along a gradient of flooding intensity. In this flooding gradient, widely distributed species are those that occur in areas subjected to low as well as to high flooding intensity whereas restricted distributed species are those that occur only in areas subjected to a low level of flood. Seeds from tree species occurring in areas subjected to different flooding intensities were collected. Seed tolerance and germination during and after both one and two months of simulated flood were evaluated. Our results show that seeds of most of the studied savanna species tolerated submergence, which helps to explain their occurrence and wide distribution in wetlands. Nevertheless, germination behaviour checked by survival functions (i.e. how germination is distributed over time) partially explained tree species distribution along a flooding gradient. We conclude that seed tolerance to flooding is one of the components of the regeneration niche that determines tree occurrence and distribution at the regional scale, from savanna to wetland, but not at a local scale along a flooding gradient.     

Can respect be key to gender justice?

Equality and respect are, together with dignity, considered foundational values in international human rights discourse. While equality in particular has been established as a widely accepted goal in the women's rights movement, respect is, however, less commonly invoked. Based on long‐term ethnographic fieldwork conducted among the Arsi Oromo of Ethiopia, this article examines the notion of wayyuu, a tacit moral model of respect and sacredness that is central to institutions and norms that have secured women certain rights and power. These norms and institutions represent a challenge to the liberal feminist conceptualization of gender equality that dominates international women's rights discourse. Drawing on theories of respect and on feminist and anthropological discussions of equality, I argue that even though there are certain limitations inherent in wayyuu, the sacredness it entails and the implications this has had for women's status and power among the Arsi Oromo call for an exploration of respect not as an alternative to equality, but as a complementary notion which to a greater extent could be included in global discussions of gender justice.     

Trade-offs in the vertical distribution of zooplankton: ideal free distribution with costs?

Zooplankton vertical migratory patterns are a classic example of optimal habitat choice. We hypothesize that zooplankton distribute themselves vertically in the water column according to an ideal free distribution (IFD) with costs such as to optimize their fitness. In lakes with a deep-water chlorophyll maximum, zooplankton are faced with a trade-off, either experiencing high food (high reproductive potential) but low temperature (slow development) in the hypolimnion or high temperature and low food in the epilimnion. Thus, in the absence of fish predation (e.g. at night) they should allocate the time spent in the different habitats according to fitness gain dependent on the temperature gradient and distribution of food. We tested this hypothesis with a Daphnia hyalina x galeata clone in large indoor columns (Plön Plankton Towers) and with a dynamic energy budget model. In the tower experiments, we simulated a deep-water algal maximum below the thermocline with epilimnetic/hypolimnetic temperature differences of 2, 5 and 10 degrees C. Experimental data supported the model. We found a significantly larger proportion of daphniids in the hypolimnion when the temperature difference was smaller. Our results are consistent with the concept of IFD with costs originally developed for stream fishes. This concept can be applied to predict the vertical distribution of zooplankton in habitats where fish predation is of minor importance.     

Genetic determinants of mortality. Can findings from genome-wide association studies explain variation in human mortality?

Twin studies have estimated the heritability of longevity to be approximately 20–30 %. Genome-wide association studies (GWAS) have revealed a large number of determinants of morbidity, but so far, no new polymorphisms have been discovered to be associated with longevity per se in GWAS. We aim to determine whether the genetic architecture of mortality can be explained by single nucleotide polymorphisms (SNPs) associated with common traits and diseases related to mortality. By extensive quality control of published GWAS we created a genetic score from 707 common SNPs associated with 125 diseases or risk factors related with overall mortality. We prospectively studied the association of the genetic score with: (1) time-to-death; (2) incidence of the first of nine major diseases (coronary heart disease, stroke, heart failure, diabetes, dementia, lung, breast, colon and prostate cancers) in two population-based cohorts of Dutch and Swedish individuals (N = 15,039; age range 47–99 years). During a median follow-up of 6.3 years (max 22.2 years), we observed 4,318 deaths and 2,132 incident disease events. The genetic score was significantly associated with time-to-death [hazard ratio (HR) per added risk allele = 1.003, P value = 0.006; HR 4th vs. 1st quartile = 1.103]. The association between the genetic score and incidence of major diseases was stronger (HR per added risk allele = 1.004, P value = 0.002; HR 4th vs. 1st quartile = 1.160). Associations were stronger for individuals dying at older ages. Our findings are compatible with the view of mortality as a complex and highly polygenetic trait, not easily explainable by common genetic variants related to diseases and physiological traits.     

Can information sharing explain recruitment to food from communal roosts?

The debate over whether communal nests and roosts function primarilyas information centers (they facilitate the sharing of foraginginformation) remains unresolved. Here I use evolutionary gametheory to investigate the relative importance of this influentialhypothesis and an alternative: that roosts, in particular,function as recruitment centers (they facilitate aggregationat food patches). Basing my model on juvenile common raven (Corvus corax) behavior, I assume there is no net cost to beingat food patches in groups, and foragers roost communally. Moreover,one strategic outcome is the observed raven behavior: individualssearch independently and recruit from the roost once a patchis found (they play Search-and-Recruit, or SR). I investigatethe stability of this in two scenarios that differ in the magnitudeof the lost opportunity costs to mutants playing SR in populations of other strategies. When these costs only involve a chanceof not being in a group at a located carcass, SR is the onlyevolutionarily stable strategy under all conditions. However,when these costs also include missing opportunities to be sociallydominant, SR no longer enjoys exclusive dominance in the strategyset. Nevertheless, in both cases, there are conditions where group foraging benefits have no effect on the evolutionary stabilityof SR. Thus, contrary to assertions in the literature, theopportunity to share foraging information can be sufficientto drive the evolution and maintenance of recruitment to foodfrom communal roosts. However, I conclude that both informationand grouping benefits are likely to underlie communal roostingbehavior in my focal system.     

Can We Negotiate with a Tumor?

Recent progress in deciphering the molecular portraits of tumors promises an era of more personalized drug choices. However, current protocols still follow standard fixed-time schedules, which is not entirely coherent with the common observation that most tumors do not grow continuously. This unpredictability of the increases in tumor mass is not necessarily an obstacle to therapeutic efficiency, particularly if tumor dynamics could be exploited. We propose a model of tumor mass evolution as the integrated result of the dynamics of two linked complex systems, tumor cell population and tumor microenvironment, and show the practical relevance of this nonlinear approach.     

How quantitative is quantitative PCR with respect to cell counts?

Quantitative diagnostic PCR systems based upon rDNA targeted primer and probe combinations were developed for the detection of Escherichia coli, Pseudomonas aeruginosa, Pseudomonas fluorescens, Pseudomonas alcaligenes, enterococci, Staphylococcus aureus, and Staphylococcus epidermidis. Primers and probes were designed in silico using the ARB software package (TU Munich) in combination with Primer Design software of PE Applied Biosystems. Purified genomic DNA or bacterial cells of target and reference organisms were used for the evaluation of the PCR assays applying the TaqMan technique on an ABI PRISM TM 7700 Sequence Detection System (PE Applied Biosystems). Sensitive, reliable and reproducible quantification of target rDNA could be achieved applying primer-probe combinations that mediate in vitro amplification of DNA fragments smaller than 100 base pairs. Large amounts of non target DNA (1 mg per sample) remarkably affected the quantification potential of the approach resulting in an underestimation of the amounts of target DNA. One of the principal goals was to use quantitative PCR to study the correlation of gene and cell numbers depending on the growth behavior of target organisms and to explore the potential to estimate cell numbers from target DNA quantification. A clear correlation of rDNA quantification and bacterial growth was observed, however, cell numbers cannot directly be estimated from quantitative PCR data, given that the cellular genome content varies with the growth phase of the organisms. In the case of Escherichia coli the cell numbers which could be assigned to a certain number of rDNA targets varied reasonably depending upon the growth phase of batch cultures.     

To hatch or not to hatch? Egg hatch response to larval density and to larval contact in a treehole mosquito

Abstract.

• 1 We investigated the effect on egg hatch of exposure to: (1) varying larval density, and (2) larval contact in Aedes triseriatus Say (Diptera: Culicidae). For 2 days in the laboratory we submerged eggs into a treehole water medium containing 0 (control), 4, 12 or 24 larvae that could either contact the eggs directly or were separated from them by a screen. Following treatment, abundance of microorganisms on the egg surfaces, a food source for newly hatched larvae and a proposed hatching stimulus, was assessed by counts made from serial dilutions of samples.
• 2 We discovered a complex hatching response to larval contact and to larval density, and an interaction between these two factors in their effect on microbial growth. Hatching was inhibited in the 0-larva control, even though microorganisms grew abundantly on the eggs. Hatch rate, as well as microbial counts, were high for eggs in direct contact with 4 larvae. As density increased in the larval contact treatment, microorganisms disappeared from the egg surfaces and hatch rate declined.
• 3 When protected from larval grazing, eggs supported numerous microbial colonies irrespective of larval density. In contrast to the contact treatment group, egg hatch increased with increasing larval density. These observations suggest that the combination of microbial growth and a larval factor stimulates hatch. This hatching response may have evolved because both abundant microorganisms and numerous larvae reflect a habitat of good quality.

     

Barnacle larval supply to sheltered rocky shores: a limiting factor?

In northwest Europe, sheltered rocky shores are dominated by fucoid canopy algae and barnacles are rare, although the latter are extremely abundant on exposed shores. The supply of the intertidal barnacle Semibalanus balanoides (L.) to sheltered, fucoid dominated rocky shores was investigated to determine the importance of larval supply in limiting the abundance of adults in shelter. Larval supply was measured at two spatial scales, at the scale of shore (100s of metres), by comparing larval concentrations at exposed and sheltered sites, and at a smaller spatial scale (m), by examining the role of fucoid canopies in limiting supply to the substratum. Replicate plankton trawls were carried out above the intertidal zone at high water at two sheltered sites and nearby exposed headlands. The concentration of S. balanoides cyprid larvae was significantly higher at the sheltered sites on two out of three sampling occasions with up to 14 times greater larvae on one occasion than the nearby exposed site. The effect of the macroalgal canopy on supply to the substratum was assessed in two ways: directly, by pumping water from the substratum in areas with and without Ascophyllum nodosum (L.) Le Jolis, and indirectly by measuring cyprid settlement in a canopy-manipulation experiment. Pumped plankton samples from mid tide level showed that the A. nodosum canopy did not form a barrier to larval supply and may have had a positive effect on larval concentrations at the substratum. Cyprid settlement was assessed in the mid shore A. nodosum and low shore Fucus serratus L. zones to areas with canopy algae (but protected from the sweeping effects of macroalgal fronds) and without canopy. Settlement over three consecutive 24-h periods showed a consistent pattern; settlement was consistently lower beneath the F. serratus canopy than in cleared areas, suggesting that this algal species forms a barrier, limiting supply of cyprid larvae to the substratum.     

Does soil moisture availability explain liana seedling distribution across a tropical rainfall gradient?

Liana density tends to increase with decreasing rainfall and increasing seasonality. However, the pattern of liana distribution may be due to differences in soil water retention capacity, not rainfall and seasonality per se. We tested the effect of rainfall and soil substrate with respect to the distribution of liana seedlings in six sites across a rainfall gradient from the wet Atlantic to the dry Pacific in central Panama. Soils were either limestone, with low water‐holding capacity, or laterite, with higher water‐holding capacity. We sampled liana seedlings at each site using three 1 × 100 m transect. We found that relative liana seedling density was higher on limestone soils compared to laterite soils regardless of the amount of rainfall. Furthermore, liana community composition on limestone soils was more similar to dry forest sites than to adjacent wet and moist forest sites. Liana seedling species diversity relative to trees was significantly higher in a low‐fertility dry forest site compared to a high‐fertility forest, but did not differ from the other sites. Thus, liana seedling density and community structure may be driven more by soil type and thus by soil moisture availability than strictly by mean annual rainfall and the seasonality of rainfall.     

AffyMAPSDetector: a software tool to characterize Affymetrix GeneChip™ expression arrays with respect to SNPs

Background  

Affymetrix gene expression arrays incorporate paired perfect match (PM) and mismatch (MM) probes to distinguish true signals from those arising from cross-hybridization events. A MM signal often shows greater intensity than a PM signal; we propose that one underlying cause is the presence of allelic variants arising from single nucleotide polymorphisms (SNPs). To annotate and characterize SNP contributions to anomalous probe binding behavior we have developed a software tool called AffyMAPSDetector.     

Can species distribution models be used to describe plant abundance patterns?

In recent years, there has been increasing interest in modelling of species abundance data in addition to presence data. In this study, we assessed the similarities and differences between presence‐absence distributions and abundance distributions along similar environmental gradients, derived, respectively, from presence‐absence and abundance data. Moreover, we examined the possibility of using presence‐absence distribution models to derive abundance distributions. For this purpose, we used Braun‐Blanquet abundance scores for 243 vascular species at 10 996 French forest sites. Species distribution models were used to analyse the link between the patterns of occurrence, low abundance and high abundance for each species with regard to mean annual temperature, June water balance, and soil pH. For each species, differences in the modelled distributions were characterised by the ecological optimum and ecological amplitude. A comparison of the presence‐absence and abundance distributions for all species revealed similar optima and different amplitudes along the three ecological factors. An abundant‐centre distribution was observed in environmental space, with species abundance being greatest at the optimal conditions and lower at less favourable conditions of the species occurrence response. Geographical habitat mapping also shows centred, high‐abundance suitability within the presence habitat of each species. We conclude that species distribution models derived from presence‐absence data provide useful information about the ecological optima of abundance distributions but overestimate the range of habitats suitable for high species abundance. This study demonstrates the utility of presence‐absence data for ecologist and conservation biologist when they are interested in the optimal conditions of high species abundance.     

Can telomere shortening explain sigmoidal growth curves?

A general branching process model is proposed to describe the shortening of telomeres in eukaryotic chromosomes. The model is flexible and incorporates many special cases to be found in the literature. In particular, we show how telomere shortening can give rise to sigmoidal growth curves, an idea first expressed by Portugal et al. [A computational model for telomere-dependent cell-replicative aging, BioSystems 91 (2008), pp. 262-267]. We also demonstrate how other types of growth curves arise if telomere shortening is mitigated by other cellular processes. We compare our results with published data sets from the biological literature.     

Can mechanism help explain insect host choice?

Evolutionary theory predicts that herbivorous insects should lay eggs on plants in a way that reflects the suitability of each plant species for larval development. Empirical studies, however, often fail to find any relationship between an adult insect's choice of host-plant and offspring fitness, and in such cases, it is generally assumed that other 'missing' factors (e.g. predation, host-plant abundance, learning and adult feeding sites) must be contributing to overall host suitability. Here, I consider an alternative theory - that a fitness cost inherent in the olfactory mechanism could constrain the evolution of insect host selection. I begin by reviewing current knowledge of odour processing in the insect antennal lobe with the aid of a simple schematic: the aim being to explain the workings of this mechanism to scientists who do not have prior knowledge in this field. I then use the schematic to explore how an insect's perception of host and non-host odours is governed by a set of processing rules, or algorithm. Under the assumptions of this mechanistic view, the perception of every plant odour is interrelated, and seemingly bad host choices can still arise as part of an overall adaptive behavioural strategy. I discuss how an understanding of mechanism can improve the interpretation of theoretical and empirical studies in insect behaviour and evolution.     

Can root trait diversity explain complementarity effects in a grassland biodiversity experiment?

Aims The positive relationship between plant biodiversity and community productivity is well established. However, our knowledge about the mechanisms underlying these positive biodiversity effects is still limited. One of the main hypotheses is that complementarity in resource uptake is responsible for the positive biodiversity effects: plant species differ in resource uptake strategy, which results in a more complete exploitation of the available resources in space and time when plant species are growing together. Recent studies suggest that functional diversity of the community, i.e. the diversity in functional characteristics ('traits') among species, rather than species richness per se, is important for positive biodiversity effects. However, experimental evidence for specific trait combinations underlying resource complementarity is scarce. As the root system is responsible for the uptake of nutrients and water, we hypothesize that diversity in root traits may underlie complementary resource use and contribute to the biodiversity effects.Methods In a common garden experiment, 16 grassland species were grown in monoculture, 4-species mixtures differing in root trait diversity and 16-species mixtures. The 4-species mixtures were designed to cover a gradient in average rooting depth. Above-ground biomass was cut after one growing season and used as a proxy for plant productivity to calculate biodiversity effects.Important findings Overall, plant mixtures showed a significant increase in biomass and complementarity effects, but this varied greatly between communities. However, diversity in root traits (measured in a separate greenhouse experiment and based on literature) could not explain this variation in complementarity effects. Instead, complementarity effects were strongly affected by the presence and competitive interactions of two particular species. The large variation in complementarity effects and significant effect of two species emphasizes the importance of community composition for positive biodiversity effects. Future research should focus on identifying the traits associated with the key role of particular species for complementarity effects. This may increase our understanding of the links between functional trait composition and biodiversity effects as well as the relative importance of resource complementarity and other underlying mechanisms for the positive biodiversity effects.     

Can species‐specific prey responses to chemical cues explain prey susceptibility to predation?

The perception of danger represents an essential ability of prey for gaining an informational advantage over their natural enemies. Especially in complex environments or at night, animals strongly rely on chemoreception to avoid predators. The ability to recognize danger by chemical cues and subsequent adaptive responses to predation threats should generally increase prey survival. Recent findings suggest that European catfish (Silurus glanis) introduction induce changes in fish community and we tested whether the direction of change can be attributed to differences in chemical cue perception. We tested behavioral response to chemical cues using three species of freshwater fish common in European water: rudd (Scardinius erythrophthalmus), roach (Rutilus rutilus), and perch (Perca fluviatilis). Further, we conducted a prey selectivity experiment to evaluate the prey preferences of the European catfish. Roach exhibited the strongest reaction to chemical cues, rudd decreased use of refuge and perch did not alter any behavior in the experiment. These findings suggest that chemical cue perception might be behind community data change and we encourage collecting more community data of tested prey species before and after European catfish introduction to test the hypothesis. We conclude that used prey species can be used as a model species to verify whether chemical cue perception enhances prey survival.     

Can molecular cell biology explain chromosome motions?

Background

Mitotic chromosome motions have recently been correlated with electrostatic forces, but a lingering "molecular cell biology" paradigm persists, proposing binding and release proteins or molecular geometries for force generation.

Results

Pole-facing kinetochore plates manifest positive charges and interact with negatively charged microtubule ends providing the motive force for poleward chromosome motions by classical electrostatics. This conceptual scheme explains dynamic tracking/coupling of kinetochores to microtubules and the simultaneous depolymerization of kinetochore microtubules as poleward force is generated.

Conclusion

We question here why cells would prefer complex molecular mechanisms to move chromosomes when direct electrostatic interactions between known bound charge distributions can accomplish the same task much more simply.