How does the richness of wood-decaying fungi relate to wood microclimate?

Microclimatic conditions in dead wood influence fungal growth and hence also species composition, but it remains unclear how they influence species richness in nature. We analysed fungal species richness based on the occurrence of fruit bodies on 2 m long segments of both standing and lying trunks of Norway spruce (Picea abies). The number of non-red-listed species was related positively to moisture, and negatively to both temperature extremes and fluctuations. The numbers of both red-listed and non-red-listed species were further differently influenced by trunk diameter and by trunk properties related to the progression in wood decay. These results indicate that the richness of fungal communities in dead wood is shaped by an interaction of wood decay, moisture and temperature fluctuations.     

How does variation in total and relative abundance contribute to gradients of species diversity?

Patterns of biodiversity provide insights into the processes that shape biological communities around the world. Variation in species diversity along biogeographical or ecological gradients, such as latitude or precipitation, can be attributed to variation in different components of biodiversity: changes in the total abundance (i.e., more‐individual effects) and changes in the regional species abundance distribution (SAD). Rarefaction curves can provide a tool to partition these sources of variation on diversity, but first must be converted to a common unit of measurement. Here, we partition species diversity gradients into components of the SAD and abundance using the effective number of species (ENS) transformation of the individual‐based rarefaction curve. Because the ENS curve is unconstrained by sample size, it can act as a standardized unit of measurement when comparing effect sizes among different components of biodiversity change. We illustrate the utility of the approach using two data sets spanning latitudinal diversity gradients in trees and marine reef fish and find contrasting results. Whereas the diversity gradient of fish was mostly associated with variation in abundance (86%), the tree diversity gradient was mostly associated with variation in the SAD (59%). These results suggest that local fish diversity may be limited by energy through the more‐individuals effect, while species pool effects are the larger determinant of tree diversity. We suggest that the framework of the ENS‐curve has the potential to quantify the underlying factors influencing most aspects of diversity change.     

How does salinity influence habitat selection and growth in juvenile American eels Anguilla rostrata?

The influence of salinity on habitat selection and growth in juvenile American eels Anguilla rostrata captured in four rivers across eastern Canada was assessed in controlled experiments in 2011 and 2012. Glass eels were first categorized according to their salinity preferences towards fresh (FW), salt (SW) or brackish water (BW) and the growth rate of each group of elvers was subsequently monitored in controlled FW and BW environments for 7 months. Most glass eels (78–89%) did not make a choice, i.e. they remained in BW. Salinity preferences were not influenced by body condition, although a possible role of pigmentation could not be ruled out. Glass eels that did make a choice displayed a similar preference for FW (60–75%) regardless of their geographic origin but glass eels from the St Lawrence Estuary displayed a significantly higher locomotor activity than those from other regions. Neither the salinity preferences showed by glass eels in the first experiment nor the rearing salinities appeared to have much influence on growth during the experiments. Elvers from Nova Scotia, however, reached a significantly higher mass than those from the St Lawrence Estuary thus supporting the hypothesis of genetically (or epigenetically) based differences for growth between A. rostrata from different origins. These results provide important ecological knowledge for the sustained exploitation and conservation of this threatened species.     

The current excitement in bioinformatics-analysis of whole-genome expression data: how does it relate to protein structure and function?

Whole-genome expression profiles provide a rich new data-trove for bioinformatics. Initial analyses of the profiles have included clustering and cross-referencing to 'external' information on protein structure and function. Expression profile clusters do relate to protein function, but the correlation is not perfect, with the discrepancies partially resulting from the difficulty in consistently defining function. Other attributes of proteins can also be related to expression-in particular, structure and localization-and sometimes show a clearer relationship than function.     

How many functional transport pathways does Plasmodium falciparum induce in the membrane of its host erythrocyte?

Intraerythrocytic malaria parasites induce considerable change in the permeability of the membrane of their host cell. Using classical techniques of radiolabel uptake and iso-osmotic lysis, the permeability characteristics of the host-cell membrane have been determined. In a recent analysis of these results, we concluded that there are at least two types of channel that conform to the data: a low copy number (four channels per cell) type that mediates the transport of cations, anions and most other osmolytes that were tested, and a high copy number (300-400 channels per cell) type that is an anion channel that could also mediate the translocation of purine nucleosides. Patch-clamping experiments using cells infected with Plasmodium falciparum reveal 200-1000 anion channels of more than one type that are of host-cell endogenous provenance. Recent reports show that parasites can grow normally in erythrocytes that lack these endogenous agencies and in which the anion channels are not expressed, although their osmolyte permeability is present. We suggest that only the latter type of channel is important for normal development of the parasite.     

Responses of nitrification and denitrification to nitrogen and phosphorus fertilization: does the intrinsic soil fertility matter?

Plant and Soil - Nitrogen (N) is not only a major regulator of productivity in terrestrial systems but can also be a pollutant. While the effects of fertilizer addition to soil N cycling processes...     

How does stone-tool use emerge? Introduction of stones and nuts to naïve chimpanzees in captivity

Nut-cracking behavior has been reported in several communities in West Africa but not in East and Central Africa. Furthermore, even within nut-cracking communities, there are individuals who do not acquire the skill. The present study aimed to clarify the cognitive capability required for nut-cracking behavior and the process through which the the nut-cracking behavior emerges. To examine emergence, we provided three naïve adult chimpanzees with a single opportunity to observe human models. A human tester demonstrated nut-cracking behavior using a pair of stones and then supplied stones and nuts to the chimpanzee subjects. Two out of three chimpanzees proceeded to hit a nut on an anvil stone using a hammer stone, one of whom succeeded in cracking open the nuts during the first test session. The third chimpanzee failed to crack open nuts. We used four variables (object, location, body part used, and action) to describe stone/nut manipulation in order to analyze further the patterns of object manipulation exhibited by the subjects. The analysis revealed that there were three main difficulties associated with nut-cracking behavior. (1) The chimpanzee who failed at the task never showed hitting action. (2) The chimpanzee who failed at the task manipulated nuts but rarely stones. (3) The combination of three objects was not commonly observed in the three chimpanzees. We also discuss our results with reference to the effect of enculturation in captivity and the social context of learning in the wild.     

How does a mistletoe affect the water,nitrogen and carbon balance of two mangrove ecosystem species?

Abstract. The effect of a mistletoe, Phthirusa maritima , on the water, nitrogen and carbon balance of two mangrove host species, Conocarpus erectus and Coccoloba uvifera , was studied. Several daily cycles of water potential and its components (pressure-volume curves); leaf nitrogen content (Kjeldahl method); leaf conductance, transpiration rates and carbon assimilation (portable gas exchange system) were measured on mistletoe, infested and uninfested plants in the Caribbean coast of Venezuela. The mistletoe on both host species showed higher transpiration rates and lower CO₂ assimilation rates, and therefore lower water use efficiencies. With respect to infested and uninfested plants, C. erectus did not show large differences in the parameters measured with the exception of assimilation rates which were significantly lower in the infested plants. On the other hand, C. uvifera did show differences in all parameters and, therefore, was affected to a greater degree by the mistletoe. The behaviour of mistletoeinfested and uninfested plants, with respect to habitats with different degrees of water stress and with respect to the salinity gradient in which these mangroves grow, is discussed.     

Use of hunters in wildlife surveys: does hunter and forest grouse habitat selection coincide?

Wildlife monitoring performed by volunteer personnel may suffer from bias with regard to their habitat use. Such errors can lead to erroneous population estimates, evidently influencing both management programmes and research that are based on the monitoring. We used a dataset on hunters’ habitat use in forest while searching for black grouse (Tetrao tetrix) and capercaillie (Tetrao urogallus) to test whether hunters’ utilisation of the habitat was independent of that of grouse or if it corresponded to the grouse habitat preference. Twenty volunteer hunters with dogs registered their tracks and all observations of capercaillie and black grouse in Østfold County, Norway, during August 2003 and 2004. We performed an ecological niche factor analysis (ENFA) and a K-select analysis with respect to hunters’ selection for habitat, described with ecogeographical variables related to forest stand characteristics, as well as the habitat preference of the observed grouse, conditional on the habitat utilisation of the hunters. Individual ENFA on the hunter's tracks revealed large variation in the habitat preferences of the hunters. The K-select indicated few overall patterns in the habitat characteristics of grouse observations, conditional on the hunters selected habitat. Accordingly, the results indicate that hunters’ observation of grouse prior to the hunt may give indicators of changes in grouse density unbiased by habitat preference due to the large between-hunter variation in habitat preference, given that a sufficient number of hunters is used. This suggests that such monitoring programmes can provide information about fluctuations in grouse population sizes valuable for both the management and research of forest grouse species.     

How do salinity and water stress affect transport of water,assimilates and ions to tomato fruits?

The study was conducted in order to determine whether water stress affects the accumulation of dry matter in tomato fruits similarly to salinity, and whether the increase in fruit dry matter content is solely a result of the decrease in water content. Although the rate of water transport to tomato fruits decreased throughout the entire season in saline water irrigated plants, accumulation rates of dry matter increased significantly. Phloem water transport contributed 80–85% of the total water transport in the control and water-stressed plants, and over 90% under salinity. The concentration of organic compounds in the phloem sap was increased by 40% by salinity. The rate of ions transported via the xylem was also significantly increased by salinity, but their contribution to fruit osmotic adjustment was less. The rate of fruit transpiration was also markedly reduced by salinity. Water stress also decreased the rate of water transport to the tomato fruit and increased the rate of dry matter accumulation, but much less than salinity. The similar changes, 10–15%, indicate that the rise in dry matter accumulation was a result of the decrease in water transport. Other parameters such as fruit transpiration rates, phloem and xylem sap concentration, relative transport via phloem and xylem, solutes contributing to osmotic adjustment of fruits and leaves, were only slightly affected by water stress. The smaller response of these parameters to water stress as compared to salinity could not be attributed to milder stress intensity, as leaf water potential was found to be more negative. Measuring fruit growth of girdled trusses, in which phloem flow was inactive, and comparing it with ungirdled trusses validated the mechanistic model. The relative transport of girdled as compared to ungirdled fruits resembled the calculated values of xylem transport.     

How does variation in fetal loss affect the distribution of waiting times to conception?

Abstract

Unmeasured variation has long been a concern in analyses of the waiting time to conception. Recent work by Heckman and Walker (1991) and Trussell and Rodriguez (1990) has underscored the fact that statistical considerations alone cannot discriminate among likely models describing the distribution. Here, we specify a single theoretically important source of heterogeneity, namely variability in intrauterine mortality, and assess its effects on the waiting times to a conception which results in a live birth. We find that the effects of variation in fetal loss are confined to the tail of the distribution. Unless variation in fetal loss is extremely large or a substantial proportion of observed waiting times are initiated at late ages, variation in fetal loss does not appear to explain much variation in conception waits. We conclude that heterogeneity in fetal loss does not explain the variation in fecundability that has been observed for first birth intervals. This conclusion supports the hypothesis that at early ages (below age 35) variation in the waiting time to a fertile conception may largely reflect the proportion of nonsusceptible couples in the population. The analyses suggest that for the purposes of testing theoretically motivated models, future efforts should be directed toward examining reproductive experience after age 35 and toward incorporating information on characteristics of the fertile period as it becomes known.     

Sperm selection and genetic incompatibility: does relatedness of mates affect male success in sperm competition?

Sperm selection may be said to occur if females influence the relative success of ejaculates competing to fertilize their ova. Most evidence that female animals or their ova are capable of sperm selection relates to male genetic incompatibility, although relatively few studies focus on competition between conspecific males. Here I look for evidence of sperm selection with respect to relatedness of mates. Reduced fitness or inbreeding effects in offspring resulting from copulations between close relatives are well documented. If females are capable of sperm selection, they might therefore be expected to discriminate against the sperm of sibling males during sperm competition. I describe an experimental protocol designed to test for evidence of sperm selection while controlling for inbreeding effects. Using decorated field crickets (Gryllodes supplicans), I found that sibling males achieved lower fertilization success in competition with a male unrelated to the female than in competition with another sibling more frequently than expected by chance, although the mean paternity values did not differ significantly between treatments. The tendancy for sibling males to achieve relatively lower fertilization success in competition with males unrelated to the female could not be explained by the effects of increased ejaculate allocation, female control of sperm transfer or inbreeding. This study therefore provides some evidence in support of the idea that female insects (or their ova) may be capable of selection against sperm on the basis of genetic similarity of conspecific males.     

How does transferrin overcome the in vitro block to development of the mouse preimplantation embryo?

Transferrin promotes development of mouse embryos through the two-cell block in vitro. Uptake of transferrin into blastocysts was shown to occur by both receptor-mediated and nonspecific pathways, but neither pathway was used to a detectable extent by embryos before the eight-cell stage. Conversely, the dialysis of culture medium, non-permissive for development through the two-cell block, against a solution of transferrin rendered it capable of supporting development. It was therefore concluded that transferrin exerts its supportive effect on development in vitro via its chelating effects.     

How does a registry change in dynein's coiled-coil stalk drive binding of dynein to microtubules?

Dynein is a motor protein that transports cellular cargo along the microtubule (MT) by consuming ATP. Dynein's microtubule-binding domain (MTBD) is separated from the ATP-binding core by a ~15 nm stalk that consists of two α-helices forming an antiparallel coiled coil. It was previously suggested that the coiled-coil stalk creates a registry shift to modulate its binding affinity for MT. A crystal structure of the low-affinity form of MTBD was determined, but that of the high-affinity form with the registry shift is not yet available. In this study, we obtained an all-atom model structure for the high-affinity form of MTBD bound to MT by an anisotropic network model, protein-protein docking, and molecular dynamics simulations. We observe that the magnitude of the coiled-coil helix sliding is dramatically reduced near the two prolines that form the stalk-MTBD boundary and subsequently transformed to cyclic movements of MTBD helices, leading to formation of a new salt bridge with MT at the binding interface. The proposed mechanism explains the roles of highly conserved residues such as the two prolines at the stalk-MTBD boundary, the nonpolar tryptophan and proline residues near the binding interface, and the electropositive residues forming salt bridges with MT.     

How to analyze the anticoagulant and antithrombotic mechanisms of action in fucanome and galactanome?

Through the perspective of the current glycomics age, fucanomics and galactanomics denote the international projects concerned with the studies of the biomedically active marine sulfated fucose- or galactose-composed polysaccharides, named sulfated fucans (SFs), and sulfated galactans (SGs), respectively. SFs and SGs are isolated from algae or marine invertebrates. The range of therapeutic actions of SFs and SGs is impressively broad. When certain structural requirements are found, some SFs and SGs may exhibit beneficial properties in inflammation, nociception, hemostasis (coagulation and thrombosis), vascular biology (angiogenesis), oncology, oxidative-stress, and virus infections. Although many biomedical applications for SFs and SGs have been pointed out over the past two decades, only inflammation, hemostasis, cancer, and vascular biology have their mechanisms of action satisfactorily elucidated. In addition, advanced structure-function relationships have been achieved only for the anticoagulant and antithrombotic activities, in which glycans of well-defined structures have been assayed. Because of this, the activities of SFs and SGs in stopping the clot and thrombus formation represent the closest therapeutic areas of having these glycans truly explored for drug development. Here, through an analytical viewpoint, we present the common methods and protocols employed to achieve such advanced structure-function relationships of SFs and SGs in anticoagulation and antithrombosis.     

How does landscape context contribute to effects of habitat fragmentation on diversity and population density of butterflies?

Aim Studies on habitat fragmentation of insect communities mostly ignore the impact of the surrounding landscape matrix and treat all species equally. In our study, on habitat fragmentation and the importance of landscape context, we expected that habitat specialists are more affected by area and isolation, and habitat generalists more by landscape context. Location and methods The study was conducted in the vicinity of the city of Göttingen in Germany in the year 2000. We analysed butterfly communities by transect counts on thirty‐two calcareous grasslands differing in size (0.03–5.14 ha), isolation index (2100–86,000/edge‐to‐edge distance 55–1894 m), and landscape diversity (Shannon–Wiener: 0.09–1.56), which is correlated to percentage grassland in the landscape. Results A total of 15,185 butterfly specimens belonging to fifty‐four species are recorded. In multiple regression analysis, the number of habitat specialist (n = 20) and habitat generalist (n = 34) butterfly species increased with habitat area, but z‐values (slopes) of the species–area relationships for specialists (z = 0.399) were significantly steeper compared with generalists (z = 0.096). Generalists, but not specialists, showed a marginally significant increase with landscape diversity. Effects of landscape diversity were scale‐dependent and significant only at the smallest scale (landscape context within a 250 m radius around the habitat). Habitat isolation was not related to specialist and generalist species numbers. In multiple regression analysis the density of specialists increased significantly with habitat area, whereas generalist density increased only marginally. Habitat isolation and landscape diversity did not show any effects. Main conclusions Habitat area was the most important predictor of butterfly community structure and influenced habitat specialists more than habitat generalists. In contrast to our expectations, habitat isolation had no effect as most butterflies could cope with the degree of isolation in our study region. Landscape diversity appeared to be important for generalist butterflies only.     

How does onchocerciasis-related skin and eye disease in Africa depend on cumulative exposure to infection and mass treatment?

BackgroundOnchocerciasis (river-blindness) in Africa is targeted for elimination through mass drug administration (MDA) with ivermectin. Onchocerciasis may cause various types of skin and eye disease. Predicting the impact of MDA on onchocercal morbidity is useful for future policy development. Here, we introduce a new disease module within the established ONCHOSIM model to predict trends over time in prevalence of onchocercal morbidity.MethodsWe developed novel generic model concepts for development of symptoms due to cumulative exposure to dead microfilariae, accommodating both reversible (acute) and irreversible (chronic) symptoms. The model was calibrated to reproduce pre-control age patterns and associations between prevalences of infection, eye disease, and various types of skin disease as observed in a large set of population-based studies. We then used the new disease module to predict the impact of MDA on morbidity prevalence over a 30-year time frame for various scenarios.ResultsONCHOSIM reproduced observed age-patterns in disease and community-level associations between infection and disease reasonably well. For highly endemic settings with 30 years of annual MDA at 60% coverage, the model predicted a 70% to 89% reduction in prevalence of chronic morbidity. This relative decline was similar with higher MDA coverage and only somewhat higher for settings with lower pre-control endemicity. The decline in prevalence was lowest for mild depigmentation and visual impairment. The prevalence of acute clinical manifestations (severe itch, reactive skin disease) declined by 95% to 100% after 30 years of annual MDA, regardless of pre-control endemicity.ConclusionWe present generic model concepts for predicting trends in acute and chronic symptoms due to history of exposure to parasitic worm infections, and apply this to onchocerciasis. Our predictions suggest that onchocercal morbidity, in particular chronic manifestations, will remain a public health concern in many epidemiological settings in Africa, even after 30 years of MDA.     

How does timing,duration and severity of heat stress influence pollen-pistil interactions in angiosperms?

Reproductive development in sexual plants is substantially more sensitive to high temperature stress than vegetative development, resulting in negative implications for food and fiber production under the moderate temperature increases projected to result from global climate change. High temperature exposure either during early pollen development or during the progamic phase of pollen development will negatively impact pollen performance and reproductive output; both phases of pollen development are considered exceptionally sensitive to moderate heat stress. However, moderately elevated temperatures either before or during the progamic phase can limit fertilization by negatively impacting important pollen pistil interactions required for successful pollen tube growth toward the ovules. This mini-review identifies the impacts of heat stress on pollen-pistil interactions and sexual reproduction in angiosperms. A special emphasis is placed on the biochemical response of the pistil to moderately high temperature and the resultant influence on in vivo pollen performance and fertilization.Key words: pollen-pistil interaction, carbohydrates, heat stress, fertilization, pollen tube growth, climate changeSexual reproduction is substantially more sensitive to moderately high temperature stress than vegetative processes.¹ Consequently, the yield of crops with valuable reproductive structures used for food (i.e., grain crops and horticultural crops) and fiber (i.e., cotton) would be especially sensitive to moderately elevated temperatures projected to result from global climate change. Sexual reproduction in angiosperms occurs in essentially three stages: gametophyte development (from meiosis to pollination), the progamic phase (from pollination to zygote formation) and embryo development (from zygote to seed).² During the pro-gamic phase, a number of reproductive processes must occur in a highly concerted fashion for successful fertilization to occur. (1) Anther dehiscence allows mature pollen grains to be transferred to a receptive stigmatic surface; (2) pollen grains germinate and pollen tubes penetrate the stigmatic surface of the pistil; (3) pollen tubes grow through the transmitting tissue of the style and towards a sexually competent ovule; finally, (4) double fertilization produces a zygote and its associated endosperm. Inhibition of any one of the aforementioned processes during the progamic phase, will necessarily limit seed development.³Although the timing and precise coordination of events during the progamic phase are strongly determined by genotype and occur in a unique and well-defined manner for a given species,⁴ the environment encountered either before or during the pro-gamic phase also exerts considerable control over the fertilization process, and can strongly influence reproductive success.⁵ Consequently, high temperature has been shown to substantially limit fertilization in vivo.⁵ Depending upon the timing, duration and severity, heat stress can limit fertilization⁵ by (1) inhibiting male⁶ and female^5,7 gametophyte development, (2) inhibiting pollen germination,^6,8,9 (3) limiting pollen tube growth,^8–11 or (4) by altering the development of tissues required to carry out reproductive processes (i.e., anther and pistil tissues).¹ Although the existing literature concerning heat stress and reproductive development in sexual plants is exhaustive (reviewed in ref. ¹ and ²), the approaches used by various investigators to elucidate plant reproductive responses to high temperature vary substantially from study to study. Consequently, it is the aim of this review to characterize the impact of timing, duration and severity of heat stress on sexual processes occurring during the progamic phase. A special emphasis is placed on the biochemical response of the pistil to moderately high temperature and the resultant influence on in vivo pollen performance.     

How to assess the pathogenicity of mutations in Charcot-Marie-Tooth disease and other diseases?

Knowledge whether a certain DNA variant is a pathogenic mutation or a harmless polymorphism is a critical issue in medical genetics, in which results of a molecular analysis may serve as a basis for diagnosis and genetic counseling. Due to its genetic heterogeneity expressed at the levels of loci, genes and mutations, Charcot-Marie-Tooth (CMT) disease can serve as a model group of clinically homogenous diseases for studying the pathogenicity of mutations. Close to a 17p11.2-p12 duplication occurring in 70% of patients with the demyelinating form of CMT disease, numerous mutations have been identified in poorly characterized genes coding for proteins of an unknown function. Functional analyses, segregation analyses of large pedigrees, and inclusion of large control groups are required to assess the potential pathogenicity of CMT mutations. Hence, the pathogenicity of numerous CMT mutations remains unclear. Some variants detected in the CMT genes and originally described as pathogenic mutations have been shown to have a polymorphic character. In contrast, polymorphisms initially considered harmless were later reclassified as pathogenic mutations. However, the process of assessing the pathogenicity of mutations, as presented in this study for CMT disorders, is a more general issue concerning all disorders with a genetic background. Since the number of DNA variants is still growing, in the near future geneticists will increasingly have to cope with the problem of pathogenicity of identified genetic variants.     

How closely does genetic diversity in finite populations conform to predictions of neutral theory? Large deficits in regions of low recombination

Levels of genetic diversity in finite populations are crucial in conservation and evolutionary biology. Genetic diversity is required for populations to evolve and its loss is related to inbreeding in random mating populations, and thus to reduced population fitness and increased extinction risk. Neutral theory is widely used to predict levels of genetic diversity. I review levels of genetic diversity in finite populations in relation to predictions of neutral theory. Positive associations between genetic diversity and population size, as predicted by neutral theory, are observed for microsatellites, allozymes, quantitative genetic variation and usually for mitochondrial DNA (mtDNA). However, there are frequently significant deviations from neutral theory owing to indirect selection at linked loci caused by balancing selection, selective sweeps and background selection. Substantially lower genetic diversity than predicted under neutrality was found for chromosomes with low recombination rates and high linkage disequilibrium (compared with 'normally' recombining chromosomes within species and adjusted for different copy numbers and mutation rates), including W (median 100% lower) and Y (89% lower) chromosomes, dot fourth chromosomes in Drosophila (94% lower) and mtDNA (67% lower). Further, microsatellite genetic and allelic diversity were lost at 12 and 33% faster rates than expected in populations adapting to captivity, owing to widespread selective sweeps. Overall, neither neutral theory nor most versions of the genetic draft hypothesis are compatible with all empirical results.