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We study the problem of visualizing phylogenetic networks, which are extensions of the Tree of Life in biology. We use a space filling visualization method, called DAGmaps, in order to obtain clear visualizations using limited space. In this paper, we first show that the general problem of drawing galled networks as DAGmaps is NP-complete. Next, we restrict our attention to galled trees and planar galled networks and present linear time algorithms for visualizing them as DAGmaps. Finally, we explore whether these graphs can be visualized using One-Dimensional DAGmaps. [ABSTRACT FROM AUTHOR]

Abstract The living organism is considered as an open system, to which Prigogine’s approach to the thermodynamics of such systems is applied. The approach allows one to formulate a law of individual growth and development (ontogenesis) of the living organism, whereas it has taken into account that the development and functioning of the system are occurring under the special internal program. The thermodynamic equation of growth provides a method of estimation of the specific entropy of organism. The theory is compared with experimental data, whereas estimates of the specific entropy of some species are obtained, showing a reduction of specific entropy in the evolutionary sequence: yeast–insects–reptiles–birds. Highlights • Prigogine’s approach is used to formulate the law of growth of living organisms. • The method of estimation of specific entropy of organisms is developed. • The specific entropy reduces in the sequence: yeast–insects–reptiles–birds. [ABSTRACT FROM AUTHOR]

In this study, following a systematic approach, we used aquatic species (bacteria Vibrio fischeri and microalgae Raphidocelis subcapitata ) and different human cell lines (Caco-2, HepG2, SV-80 and HaCaT) representing different tissues and exposure pathways, to investigate how two organic stabilizers (PVA and DMSO) used for NMs dispersion influence their physicochemical properties, the persistence of metals in suspension and the toxicity/ecotoxicity of two metallic NMs (nano-Ag and nano-Cu). Although the stabilizers are expected to contribute to improve the dispersion and stability of NMs, the results obtained clearly showed that no similar changes in toxicity and morphological properties of the nano-Ag can be expected after its stabilization with PVA. Thus, regarding human cell lines, the reduction in the average size of the PVA-nano-Ag was followed by a reduction or maintenance of its toxicity, but the opposite was observed for the aquatic species tested since an increase in the average size enhanced its toxicity. As far as nano-Cu is considered DMSO contributed for a better dispersion of this nanomaterial, however this was not translated in a similar toxicity/ecotoxicity modification. In summary, even for nano-Cu, for which few or no data exists regarding its toxicity after stabilization with organic compounds, it was confirmed with consistent data, that the toxicity of metallic NMs is a complex combination of average size, chemical composition, solubilization or persistence in suspension of the metallic forms, interaction with test medium components and sensitivity of test species and cell lines. The combination of all of these factors makes the toxicity of metallic NMs unpredictable and points for the need of an extensive evaluation of each new formulation. [ABSTRACT FROM AUTHOR]

Automatic identification of organism evolution still remains a challenging task, which is especially exiting, when the evolution of human is considered. The main aim of this work is to present a new idea to allow organism evolution analysis using neural networks. Here we show that it is possible to identify evolution of any organisms in a fully automatic way using the designed EvolutionXXI program, which contains implemented neural network. The neural network has been taught using cytochrome b sequences of selected organisms. Then, analyses have been carried out for the various exemplary organisms in order to demonstrate capabilities of the EvolutionXXI program. It is shown that the presented idea allows supporting existing hypotheses, concerning evolutionary relationships between selected organisms, among others, Sirenia and elephants, hippopotami and whales, scorpions and spiders, dolphins and whales. Moreover, primate (including human), tree shrew and yeast evolution has been reconstructed. [ABSTRACT FROM AUTHOR]

We related the vertical distribution and abundance of nearshore meroplankton at hourly time scales with internal tidal wave events. We proposed that significant changes in plankter abundance would occur across internal tidal fronts, and that surface and bottom strata would respond in opposite fashions. First-mode internal tidal bores propagating in the alongshore direction were detected in water-column currents and baroclinic temperature changes. Surface and bottom currents always flowed in opposite directions, and abrupt flow reversals coincided with large temperature changes during arrival of bores. Crab zoeae and barnacle cyprids were more abundant in the bottom strata, whereas barnacle nauplii showed the opposite pattern. Significant changes in vertical distribution and abundance of target meroplankters occurred across internal tidal fronts, especially for crabs at depth, with surface and bottom organisms responding in opposite fashions. Changes in plankter abundance were significantly correlated with current flows in the strata where they were most abundant. The manner in which plankters were affected (increasing or decreasing abundance) appeared to be modulated by their vertical position within the water column. The significant differences found at the high frequencies of this study, maintained across sampling days, suggest that nearshore meroplankton populations may have greater and more consistent temporal and vertical variability than previously considered. [ABSTRACT FROM AUTHOR]

Ras converting enzyme 1 (Rce1) is an endoprotease that catalyzes processing of the C-terminus of Ras protein by removing -aaX from the CaaX motif. The activity of Rce1 is crucial for proper localization of Ras to the plasma membrane where it functions. Ras is responsible for transmitting signals related to cell proliferation, cell cycle progression, and apoptosis. The disregulation of these pathways due to constitutively active oncogenic Ras can ultimately lead to cancer. Ras, its effectors and regulators, and the enzymes that are involved in its maturation process are all targets for anti-cancer therapeutics. Key enzymes required for Ras maturation and localization are the farnesyltransferase (FTase), Rce1, and isoprenylcysteine carboxyl methyltransferase (ICMT). Among these proteins, the physiological role of Rce1 in regulating Ras and other CaaX proteins has not been fully explored. Small-molecule inhibitors of Rce1 could be useful as chemical biology tools to understand further the downstream impact of Rce1 on Ras function and serve as potential leads for cancer therapeutics. Structure–activity relationship (SAR) analysis of a previously reported Rce1 inhibitor, NSC1011, has been performed to generate a new library of Rce1 inhibitors. The new inhibitors caused a reduction in Rce1 in vitro activity, exhibited low cell toxicity, and induced mislocalization of EGFP-Ras from the plasma membrane in human colon carcinoma cells giving rise to a phenotype similar to that observed with siRNA knockdowns of Rce1 expression. Several of the new inhibitors were more effective at mislocalizing K-Ras compared to a potent farnesyltransferase inhibitor (FTI), which is significant because of the preponderance of K-Ras mutations in cancer. [ABSTRACT FROM AUTHOR]

For some years now, interactions between societies and the biosphere have been the subject of socio-ecological studies (SESs), which analyse socio-ecological regimes, trajectories and transitions. This article follows the approach, and seeks to contribute to the analysis of socio-ecological urban trajectories since the Industrial Revolution. It draws on some key notions which are tested and applied to Paris. The urban socio-ecological regime of the industrial era has three major characteristics: i) the near-total externalisation of a more intensive urban metabolism, associated with the breakup of supply areas and the deepening, urban footprint on the environment; ii) the importance of infrastructure to this metabolism, which fits into a process of generalised networking led by engineers and leads to urban technical inter-dependencies; and iii) the urbanisation of landscapes associated with the proliferation of extra-territorial urban influences, despite the loss of certain skills available to the French capital. [ABSTRACT FROM AUTHOR]

The primary ecological risk of dimethyldithiocarbamate (DMDC), a dithiocarbamate fungicide (DTC) metabolite, was evaluated based on their probabilistic environmental concentration distributions (ECDs) in the coastal environment, Hiroshima Bay, Japan. And their behavior and temporal trends was further considered. This is the first report of the identification of DMDC from environmental seawater and sediment samples. DMDC concentrations in bottom seawater were substantially higher than those in surface seawater, which are associated with the leachability from sediments in bottom seawaters, and with photodegradation in surface seawaters. Furthermore, seasonal risks are dominated by higher concentrations from April to June, indicating temporal variation in the risk to exposed species. Hierarchical Bayesian analysis offered DMDC ECD medians and range (5th to 95th percentiles) of 0.85 ng L −1 (0.029, 22), 12 ng L −1 (3.2, 48) and 110 ng kg dry −1 (9.5, 1200) in surface seawater, bottom seawater and sediment, respectively. Considering that DMDC and DTCs have similar toxicological potential to aquatic organisms, the occurrence of the compound in water is likely to be of biological relevance. In summary, this work provides the first demonstration that the ecological risk of DMDC and its derived DTCs in Hiroshima Bay is relatively high, and that DTCs should be a high priority for future research on marine contamination, especially in bottom seawaters. [ABSTRACT FROM AUTHOR]

Fossilization of mammalian young is extremely rare, mainly due to the fragility of bones (smaller and less mineralized) and unfused sutures, which are difficult to preserve during fossil diagenesis. Here, we describe an unprecedented and very complete juvenile of a pampathere, an extinct lineage of Cingulata (Xenarthra). The fossil comprises parts of the skull, mandible, and osteoderms from most regions of the armor, which were exhumed in association at the Gruta do Urso cave, Brazilian Amazon region. Taxonomic analysis of osteoderms and craniofacial features allowed the identification of this specimen as Holmesina. This individual of Holmesina has most of its cranial sutures unfused or in a very initial stage of fusion, and the osteoderms are under mineralized and poorly developed, suggesting a juvenile ontogenetic stage, probably a lactating individual. Although Holmesina is a common South American megafauna representative, little is known about its biology and even less about its initial life. Based on the taphonomic aspects of the fossil, it was buried at the same place of death; but before, its carcass was partially consumed. This study brings valuable information on the earlier stages of anatomy and paleobiology of native extinct South American megafauna. • The first newborn pampathere reported is represent by associated fossil elements of skull, mandible and several osteoderms. • The pampathere carcass studied here was partially consumed before it was buried at the same place of its death. • New information on the biology of the initial life of pampatheres, an enigmatic lineage of South American megafaunal mammals. [ABSTRACT FROM AUTHOR]

The centennial of “On Growth and Form” is a good opportunity to reflect on the progress of the quantitative study of living systems and where we would like to see it heading. The era of the physical sciences being a mere vehicle for tool building for biological investigations is over. The approaches taken nowadays are analogous to those that physical scientists have taken within their respective fields for centuries, only that now they ask them about biological phenomena and function. Here I give a brief reflection on where we are and where we should direct our focus next, both from the perspective of the research endeavor as a whole, but also with respect to teaching the next generation of scientists joining the field. [ABSTRACT FROM AUTHOR]

Over millions of years, biological systems have evolved wide varieties of nanoparticles. Naturally occurring nanoparticles show great diversity: they may be intracellular or extracellular, formed of organic or inorganic materials and have wide-ranging biological roles. Despite this diversity, nanoparticles found in nature possess several characteristics that make them attractive for biomedical purposes. This review presents an overview of the most common biological nanoparticles and outlines the potential applications of natural and modified biological nanoparticles. [ABSTRACT FROM AUTHOR]

Highlights: [•] Intestinal PepT1 was significantly higher expressed in triploids than diploids and tetraploids. [•] High and low protein levels diets promote PepT1 expression in intestine. [•] Fish meal showed a significant increase of PepT1 expression than soybean meal in intestines. [•] Sodium butyrate additives could induce PepT1 which mediates by CDX2 and CREB. [Copyright &y& Elsevier]

Abstract: Energy allocation is an important component of life-history variation since it determines the tradeoff between growth and reproduction. In this study we investigated the state-dependent and sex-specific energy allocation pattern and the reproductive investment of a protogynous hermaphrodite fish with parental care. Individuals of Labrus bergylta, a temperate wrasse displaying two main different colour patterns (plain and spotted), were obtained from the fish markets in NW Spain between 2009 and 2012. Total energy of the gonad, liver, mesenteric fat and muscle (obtained by calorimetric analysis) and gut weight (as a proxy of feeding intensity) were modelled in relation to the reproductive phase of the individuals. A decrease in the energy stored as mesenteric fat from prespawning to spawning paralleled the increase in the gonad total energy in the same period. The predicted reduction in stored total energy over the reproductive cycle was higher than the energy required to develop the ovaries for the full range of female sizes analysed, suggesting a capital breeding strategy. Males stored less energy over a season and invested fewer resources in gamete production than females. Reproductive investment (both fecundity and energy required to produce the gonads) was higher in plain than in spotted females, which is in agreement with the different growth patterns described for the species. [Copyright &y& Elsevier]

This article explains the key role of model organisms within contemporary research, while at the same time acknowledging their limitations as biological models. We analyse the epistemic and social characteristics of model organism biology as a form of “big science”, which includes the development of large, centralised infrastructures, a shared ethos and a specific long-term vision about the “right way” to do research. In order to make wise use of existing resources, researchers now find themselves committed to carrying out this vision with its accompanying assumptions. By clarifying the specific characteristics of model organism work, we aim to provide a framework to assess how much funding should be allocated to such research. On the one hand, it is imperative to exploit the resources and knowledge accumulated using these models to study more diverse groups of organisms. On the other hand, this type of research may be inappropriate for research programmes where the processes of interest are much more delimited, can be usefully studied in isolation and/or are simply not captured by model organism biology. [ABSTRACT FROM AUTHOR]

Objective: To determine whether cognitive behavior therapy (CBT), which we had shown in a previous study to restore ovarian function in women with functional hypothalamic amenorrhea (EHA), could also ameliorate hypereortisolemia and improve other neuroendocrine and metabolic concomitants of in FHA. Design: Randomized controlled trial. Setting: Clinical research center at an academic medical university. Patient(s): Seventeen women with FHA were randomized either to CBT or observation. Intervention(s): CBT versus observation. Main Outcome Measure(s): Circulatory concentrations of cortisol, leptin, thyroid-stimulating hormone (TSH), total and free thyronine (T3), and total and free thyroxine (T4) before and immediately after completion of CBT or observation. [Each woman served as her own control.) Result(s): Cognitive behavior therapy but not observation reduced cortisol levels in women with FHA. There were no changes in cortisol, leptin, TSH, T3, or T4 levels in women randomized to observation. Women treated with CBT showed increased levels of leptin and TSH, but their levels of T3 and T4 remained unchanged. Conclusion(s): In women with FHA, CBT ameliorated hypexcortisolism and improved the neuroendocrine and metabolic concomitants of FHA while observation did not. We conclude that a cognitive, nonpharmacologic approach aimed at alleviating problematic attitudes not only can restore ovarian activity but also improve neuroendoctine and metabolic function in women with FHA. Clinical Trial Registration Number: NCT01674426. [ABSTRACT FROM AUTHOR]

Abstract: Throughout the last decades there has been a world-wide, general warming trend. In this study, we use the example of the Baltic Sea to resolve the overall estimated temperature trend into smaller, meso-scale spatial units. Afterwards, we investigate the spatially resolved potential impact of the temperature trend on larval survival for two important fish species, cod and sprat. We used two different sets of hydrographic data: (i) long-term temporally and depth-resolved data measured in situ originating from one geographic position and (ii) long-term horizontally resolved data, originating from a circulation model. In contrast to basin-wide integrated results, our modelling approach revealed different results related to smaller spatial scales. In shallow and coastal areas non-significant long-term temperature trends were observed. In some cases even decreasing temperature trends were found. Average distribution maps (1973–2010) of cod and sprat eggs and larvae confirmed the higher importance of central, deep basins as nursery grounds. Applying the temperature trends when calculating cod larval window of opportunity values, resulted in decreased durations of 1–3days (~3–13%) in most areas. Sprat larval window of opportunity values mainly increased up to 4days (~45%), indicating a potential reproduction advantage of sprat over cod under anticipated future temperature increase. [Copyright &y& Elsevier]

Clin Microbiol Infect 2012; 18 (Suppl. 4): 27-31 Abstract Most of the bacterial species that form part of the biosphere have never been cultivated. In this situation, a comprehensive study of bacterial communities requires the utilization of non-culture-based methods, which have been named metagenomics. In this paper we review the use of different metagenomic techniques for understanding the effect of antibiotics on microbial communities, to synthesize new antimicrobial compounds and to analyse the distribution of antibiotic resistance genes in different ecosystems. These techniques include functional metagenomics, which serves to find new antibiotics or new antibiotic resistance genes, and descriptive metagenomics, which serves to analyse changes in the composition of the microbiota and to track the presence and abundance of already known antibiotic resistance genes in different ecosystems. [ABSTRACT FROM AUTHOR]

Abstract: Differentiation of living fingers, fake fingers and fingers from dead bodies was investigated using spectral analysis. For this purpose, reflection and transmission spectra in the wavelength region from 400 to 1650nm were recorded from living volunteers and corpses. In an additional small test series (one living volunteer, three cadavers), time-resolved spectral images were prepared using reflectance (derived from pulse oximetry). The dynamic differences in the curves (including the absorption changes caused by the blanching effect and the pulse) provide initial approaches for the realisation of systems for liveness detection. Significant differences that would be useful for the integration into fingerprint recording systems of methods to defend against forgeries are discussed. [Copyright &y& Elsevier]

Essential genes are absolutely required for cell survival. Determination of the universal minimal set of genes needed to sustain life is, therefore, expected to contribute greatly to our understanding of life at its simplest level, with applications in medicine and synthetic biology. The search for the minimal genome has led to the identification of often variable gene sets. We argue here that, based on the outcome of these analyses, it is becoming increasingly evident that some genes, and the functions encoded by them, are absolutely necessary for the survival of any living entity, whereas others can be omitted. We also examine ways of determining the minimal genome and discuss possible practical applications of a minimal cell. [ABSTRACT FROM AUTHOR]

Abstract: The objective was to estimate the genuine microbial content of ice samples from refrozen water (accretion ice) from the subglacial Lake Vostok (Antarctica) buried beneath the 4-km thick East Antarctic ice sheet. The samples were extracted by heavy deep ice drilling from 3659m below the surface. High pressure, a low carbon and chemical content, isolation, complete darkness and the probable excess of oxygen in water for millions of years characterize this extreme environment. A decontamination protocol was first applied to samples selected for the absence of cracks to remove the outer part contaminated by handling and drilling fluid. Preliminary indications showed the accretion ice samples to be almost gas free with a low impurity content. Flow cytometry showed the very low unevenly distributed biomass while repeated microscopic observations were unsuccessful. We used strategies of Ancient DNA research that include establishing contaminant databases and criteria to validate the amplification results. To date, positive results that passed the artifacts and contaminant databases have been obtained for a pair of bacterial phylotypes only in accretion ice samples featured by some bedrock sediments. The phylotypes included the chemolithoautotrophic thermophile Hydrogenophilus thermoluteolus and one unclassified phylotype. Combined with geochemical and geophysical considerations, our results suggest the presence of a deep biosphere, possibly thriving within some active faults of the bedrock encircling the subglacial lake, where the temperature is as high as 50°C and in situ hydrogen is probably present. Our approach indicates that the search for life in the subglacial Lake Vostok is constrained by a high probability of forward-contamination. Our strategy includes strict decontamination procedures, thorough tracking of contaminants at each step of the analysis and validation of the results along with geophysical and ecological considerations for the lake setting. This may serve to establish a guideline protocol for studying extraterrestrial ice samples. [Copyright &y& Elsevier]

Abstract: In addition to its scientific interest, research on the last universal common ancestor (LUCA) and the lower part of the tree of life raises important and difficult issues in biology, but also in the philosophy of science as well as in philosophy in general. The way inquiries are formulated has to be scrutinized to avoid unanswerable questions. Preconceived ideas, poorly defined notions and abuse of metaphors are obstacles which can induce bias in studies and in the interpretation of their results. In the background, the question of life has recently re-emerged. [ABSTRACT FROM AUTHOR]

Abstract: In this manuscript, we report the discovery of the substituted 2-trifluoromethyl-2H-benzopyran-3-carboxylic acids as a novel series of potent and selective cyclooxygenase-2 (COX-2) inhibitors. We provide the structure–activity relationships, optimization of design, testing criteria, and human half-life data. The challenge of a surprisingly long half-life (t 1/2 =360h) of the first clinical candidate 1 and human t 1/2 had been difficult to predict based on allometric scaling for this class of highly ppb compounds. We used a microdose strategy which led to the discovery of clinical agents 18c-(S), 29b-(S), and 34b-(S) with human half-life of 57, 13, and 11h. [Copyright &y& Elsevier]

Abstract: In this Letter, we provide the structure–activity relationships, optimization of design, testing criteria, and human half-life data for a series of selective COX-2 inhibitors. During the course of our structure-based drug design efforts, we discovered two distinct binding modes within the COX-2 active site for differently substituted members of this class. The challenge of a undesirably long human half-life for the first clinical candidate 1 t 1/2 =360h was addressed by multiple strategies, leading to the discovery of 29b-( S ) (SC-75416) with t 1/2 =34h. [Copyright &y& Elsevier]

Abstract: What are mind, consciousness and happiness, in the fundamental context of life? We propose a convergent perspective (coupling evolutionary biology, genomics, neurobiology and clinical medicine) that could help us better understand what life, mind, consciousness and happiness are, as well as provides empirically testable practical implications. [Copyright &y& Elsevier]

Abstract: Evolutionary explanations of low fertility in modern affluent societies commonly state that low fertility is the outcome of high parental investments in the quality of their children. Although the empirical evidence that modern parents do face a quantity–quality trade-off is strong, two issues that are relevant from an evolutionary perspective have not received much attention. First, sex differences in the proximate aspects of quality have been largely ignored. Second, the relationship between the quantity of children and their reproductive success in contemporary low-fertility societies remains unclear. In this article, we study the quantity–quality trade-off as a trade-off between the number of children and the mate value and reproductive success of those children. We examine the trade-off in two steps. First, a lower number of children is expected to increase the mate value of these children. Second, greater mate value is expected to lead to greater reproductive success. Using sex-specific indicators of mate value, we test these hypotheses in a representative sample of the Dutch population aged 55–85 in 1992 (n=3229). This sample contains information on three successive generations in which the middle generation has completed fertility. We find support for the first hypothesis, but only partial support for the second hypothesis. A higher number of children is traded off against the mate value of the children, but not against their reproductive success. We conclude that the conditions under which the quantity of children is traded off against their reproductive success depend on the social environment. [Copyright &y& Elsevier]

If one was asked to produce a set of ‘Trump Cards™’ based upon ‘Forces of Nature Defining Life on Earth’ then which card would be ‘Top Trump’? I was recently chastised on the Darwin Today website for suggesting Darwin and ‘natural selection’ rather than, for example, Newton and ‘gravity’. Although there is no denying the significance of gravity, my argument in favour of natural selection is simply that gravity is just one factor that contributes towards an outcome which ultimately is defined by natural selection. Both the beauty and the brilliance of natural selection are reflected in its omnipotence to explain the myriad observations of life and, as I will affirm herein, its explanation of the biological essentiality of aluminium and silicon is no exception. [Copyright &y& Elsevier]

Abstract: Certain organisms found across a range of taxa, including bacteria, yeasts, plants and many invertebrates such as nematodes and tardigrades are able to survive almost complete loss of body water. The dry organisms may remain in this state, which is known as anhydrobiosis, for decades without apparent damage. When water again becomes available, they rapidly rehydrate and resume active life. Research in anhydrobiosis has focused mainly on sugar metabolism and stress proteins. Despite the discovery of various molecules which are involved in desiccation and water stress, knowledge of the regulatory network governing the stability of the cellular architecture and the metabolic machinery during dehydration is still fragmentary and not well understood. A combination of transcriptional, proteomic and metabolic approaches with bioinformatics tools can provide a better understanding of gene regulation that underlie the biological functions and physiology related to anhydrobiosis. The development of this concept will raise exciting possibilities and techniques for the preservation and stabilization of biological materials in the dry state. [Copyright &y& Elsevier]

Copyright of Basic & Applied Ecology is the property of Urban & Fischer Verlag and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Abstract: We report on the variation in energy reserves of individual C5 copepodites of Calanus finmarchicus from the Newfoundland continental shelf and the Labrador Sea collected from surface and overwintering (or bottom) depths prior to, during and after the expected timing of the onset of diapause. Overall, the trend was for a decreasing average prosome length as the year progressed for all locations although the decline was smallest in the Labrador Sea and greatest in the deep waters of the continental shelf. The size of the oil sac was closely linked to the weight of the copepodite but the form of this relationship showed substantial variations with depth and season. We show a clear increase in the relative oil sac volume for C. finmarchicus between late spring and late summer, by which time some animals had descended to diapause depths. The progressive decrease in oil sac volume of animals sampled at depth in the Labrador Sea between September and December suggests a significant loss of energy reserves during diapause. From the distribution of volumes and body sizes in December we estimate that 23–53% of individuals would not be able to meet the energetic cost of moulting and early gonad development. Overall, some of our observations appear to invalidate earlier hypotheses concerning the governing role of lipids in the life history of C. finmarchicus. However, assessment of the factors that influence entry into dormancy should be based on the relative probabilities of alternative strategies for successful reproduction (e.g. entering dormancy vs. continuing into a second generation). [Copyright &y& Elsevier]

Abstract: A large number of ultraviolet (UV)-absorbing compounds, usually present in personal-care products, textiles exposed to UV radiation and plastics materials, elicit hormonal activity in vitro and in vivo. Induction of vitellogenin, alterations in gonads, decrease in fertility and reproduction, and feminization in sex characteristics of male fish have been associated with frequently-used UV filters, including benzophenones and camphor-related substances. The lowest effect concentrations determined (3μg/L for 3-benzylidene camphor) are generally higher than those measured so far in the environment (ng/L to lower μg/L in water). However, the propensity for rapid accumulation and the potential for mixture effects warrant further research to evaluate the fate and the disposition of UV filters in the aquatic ecosystem. Moreover, the amounts of UV filters added to products are increasing, to date usually 10% (w/w), as a consequence of the higher protection factors demanded, and that requires formulations with higher percentages of UV filters or multi-component mixtures with more UV-absorbing substances. In addition, long-term exposure to UV-absorbing compounds may have negative effects at concentrations much lower than those considered at present. This article provides an overview of the most outstanding findings reported on toxic effects of UV filters in the aquatic environment. We also include environmental levels detected and analytical methodologies applied. [Copyright &y& Elsevier]

The technologies of metagenomics and metabolomics are broadening our knowledge of the roles the human gut microbiota play in health and disease. For many years now, probiotics and prebiotics have been included in foods for their health benefits; however, we have only recently begun to understand their modes of action. This review highlights recent advances in deciphering the mechanisms of probiosis and prebiosis, and describes how this knowledge could be transferred to select for enhancing functional foods targeting different populations. A special focus will be given to the addition of prebiotics and probiotics in functional foods for infants and seniors. [Copyright &y& Elsevier]

Copyright of Psychologie Française is the property of Elsevier B.V. and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Psychologie Française is the property of Elsevier B.V. and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Psychologie Française is the property of Elsevier B.V. and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Psychologie Française is the property of Elsevier B.V. and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Living organisms, from virus to human, rely on the transcription machinery to express specific parts of their genomes to execute critical biological functions during their life cycle by responding to environmental or developmental signals. Thus, transcription constitutes a critical step in regulating biological processes, and transcription factors have been considered as master switches for cell fate determination. Stem cell biology has benefited from rapid advances in recent years, largely because of the characterization of several transcription factors as master regulators of stem cell pluripotency. The same factors, viz. Oct4, Sox2, Nanog, Klf4, and Myc, have been shown to possess the magic power to reprogram somatic cells into pluripotent ones, a remarkable achievement with both practical and theoretical implications. This minireview summarizes recent advances in pluripotency and reprogramming by focusing on key transcription factors and the likely mechanisms. [ABSTRACT FROM AUTHOR]

Abstract: Disturbances play a major role in structuring the community composition in a variety of ecosystems. The potential impact of disturbances on sexual reproduction and genetic diversity of plants has so far received little attention. We examined the effects of disturbance by human trampling on the performance, sexual reproduction and clonal diversity in the woodland herb Anemone nemorosa in six sites disturbed by intensive recreational activities and in six undisturbed sites in suburban forests in Switzerland. Disturbance by human trampling decreased shoot height of A. nemorosa and altered the size-dependent flowering probability function. Furthermore, in disturbed sites an increased percentage of aborted seeds was found, resulting in a reduced sexual reproductive potential of A. nemorosa populations. Both clonal and genetic diversity of A. nemorosa were reduced in disturbed sites. Our study shows for the first time that disturbance by human trampling can decrease the genetic diversity in a clonal woodland plant. This suggests that genetic aspects of woodland plants should be considered in restoring degenerated forest sites. [Copyright &y& Elsevier]

Abstract: Gentiana pannonica scop. (Gentianaceae) is a long-lived perennial mountain species. It is a typical east−Alpine element. The centre of its distribution is situated in the eastern Alps, where the species occurs in alpine and subalpine areas. Besides the Alps, G. pannonica occurs also in the Bohemian Forest, Czech Republic. The reproduction strategy and genetic variation of this species endangered in the Czech Republic were studied. Genetic variation within and among six populations of G. pannonica in the Bohemian Forest and two populations in the Alps was studied using random amplified polymorphic DNAs (RAPD) markers. The variation found between populations from primary habitats and populations situated in the secondary mountain meadows accounted for 5% of the total genetic variation, whereas no significant genetic diversity was found between two different regions (Bohemian Forest, the Alps). Most of the variation is distributed among individuals within populations in the primary habitats, specifically 77% in the Bohemian Forest and 79% in the Alps. The pattern of among-population variation was substantially different between primary and secondary habitats. While among-population variation in primary habitats was low in both of the regions (21–23%), the proportion of RAPD variation among populations in secondary habitats was distinctly higher (65%). Within-population genetic variation was higher in primary habitats than in the secondary ones. This may be a consequence of processes such as genetic drift or bottleneck, and founder effects caused by changes in their distribution during the Holocene period. The differences of vegetation composition, seedlings recruitment and seed set were investigated in the field. Vegetation composition differed between primary and secondary habitats of G. pannonica and seedlings recruitment was recorded only in primary habitats. The reproduction output of the species under study is probably influenced by the availability of pollinators. [Copyright &y& Elsevier]

Abstract: The effect of wave exposure on the population and reproductive phenology of the common red alga, Gelidium pusillum (Stackhouse) Le Jolis, was investigated between July 2003 and June 2004, at Suan Song Tha Le, Songkla Province, Thailand. Lengths of thalli, percentage cover, percentage of reproductive fronds and the number of reproductive structures were examined monthly in relation to different degrees of wave exposure (sheltered vs. exposed), temperature, rainfall, day length and tidal cycles. Frond length and percentage cover of G. pusillum were different among sites and seasons. Shorter fronds were found on the exposed shore which had a greater percentage cover. Fronds bleached and died off during the summer months (April and May), which resulted in shorter fronds and reduced percentage cover in June. The thalli reproduced throughout the year, with a predominance of tetrasporophytes. The highest percentage of tetrasporic fronds was 33% in February 2004 and 13% of cystocarpic fronds in April 2004, but male gametophytic fronds were never observed. Rainfall showed a strongly negative influence on reproduction since no reproductive fronds were observed during the rainy season (R 2 =0.49, P =0.01). The dominance of G. pusillum at this study site and throughout elsewhere in turf habitats might be a function of persistent vegetative growth, densely clumped, and the ability to reproduce almost throughout the entire year. [Copyright &y& Elsevier]

Abstract: At evolutionary equilibrium, ecological factors will determine the optimal combination of life-history trait values of an organism. This optimum can be assessed by assuming that the species maximizes some criterion of fitness such as the Malthusian coefficient or lifetime reproductive success depending on the degree of density-dependence. We investigated the impact of the amount of resources and habitat stability on a plant''s age at maturity and life span by using an evolutionary optimization model in combination with empirical data. We conducted this study on sea beet, Beta vulgaris subsp. maritima, because of its large variation in life span and age at first reproduction along a latitudinal gradient including considerable ecological variation. We also compared the consequence in our evolutionary model of maximizing either the Malthusian coefficient or the lifetime reproductive success. Both the data analysis and the results of evolutionary modeling pointed to habitat disturbance and resources like length of the growing season as factors negatively related to life span and age at maturity in sea beet. Resource availability had a negative theoretical influence with the Malthusian coefficient as the chosen optimality criterion, while there was no influence in the case of lifetime reproductive success. As suggested by previous theoretical work the final conclusion on what criterion is more adequate depends on the assumptions of how in reality density-dependence restrains population growth. In our case of sea beet data R 0 seems to be less appropriate than λ. [Copyright &y& Elsevier]

Abstract: We studied the effects of long-term exposure (nine years) of birch (Betula papyrifera) trees to elevated CO2 and/or O3 on reproduction and seedling development at the Aspen FACE (Free-Air Carbon Dioxide Enrichment) site in Rhinelander, WI. We found that elevated CO2 increased both the number of trees that flowered and the quantity of flowers (260% increase in male flower production), increased seed weight, germination rate, and seedling vigor. Elevated O3 also increased flowering but decreased seed weight and germination rate. In the combination treatment (elevated CO2 +O3) seed weight is decreased (20% reduction) while germination rate was unaffected. The evidence from this study indicates that elevated CO2 may have a largely positive impact on forest tree reproduction and regeneration while elevated O3 will likely have a negative impact. [Copyright &y& Elsevier]

Abstract: We have compared the contributions of unit source fluxes over a clearcut area in a forest and over the contiguous forested area to the eddy-covariance (EC) flux of CO2 measured at a tall tower standing in the center of the clearcut under daytime convective conditions. Based on the comparison, the clearcut influence on EC flux measurements is evaluated from the footprint (or source area) perspective. The large-eddy simulation (LES) technique is used to simulate the bottom-up dispersion of two conservative and passive tracers that are released from the clearcut and from the forested area, respectively. Time series of LES-generated vertical velocity and mixing ratios of both tracers at all the levels are recorded every model time step at the tower location during the last hour of each LES run; this somewhat mimics real EC flux measurements at the tower. The contribution of the unit surface flux over the clearcut relative to that over the forested area decreases with increasing measurement height, decreasing convective boundary layer depth, increasing atmospheric stability, and decreasing size of the clearcut. These results are fitted to an empirical relation and used to evaluate flux measurements at the 447-m tall tower in Wisconsin, USA. The contribution of the unit flux over the clearcut to the EC flux measured at the 30-m level of the tower is larger than 50% of that over the forested area under most unstable conditions, while smaller than 2.5% at the 396-m level. Existing analytical footprint models underestimate the clearcut influence because effects of clearcut-induced heterogeneity of the turbulent flow are not taken into account. [Copyright &y& Elsevier]

Abstract: This study evaluated the potential effect of ionising radiation on population growth using simple population models and parameter values derived from chronic exposure experiments in two invertebrate species with contrasting life-history strategies. In the earthworm Eisenia fetida, models predicted increasing delay in population growth with increasing gamma dose rate (up to 0.6 generation times at 11mGyh−1). Population extinction was predicted at 43mGyh−1. In the microcrustacean Daphnia magna, models predicted increasing delay in population growth with increasing alpha dose rate (up to 0.8 generation times at 15.0mGyh−1), only after two successive generations were exposed. The study examined population effects of changes in different individual endpoints (including survival, number of offspring produced and time to first reproduction). Models showed that the two species did not respond equally to equivalent levels of change, the fast growing daphnids being more susceptible to reduction in fecundity or delay in reproduction than the slow growing earthworms. This suggested that susceptibility of a population to ionising radiation cannot be considered independent of the species'' life history. [Copyright &y& Elsevier]

Abstract: The ERICA Integrated Approach requires that a risk assessment screening dose rate is defined for the risk characterisation within Tiers 1 and 2. At Tier 3, no numerical screening dose rate is used, and the risk characterisation is driven by methods that can evaluate the possible effects of ionising radiation on reproduction, mortality and morbidity. Species sensitivity distribution has been used to derive the ERICA risk assessment predicted no-effect dose rate (PNEDR). The method used was based on the mathematical processing of data from FRED (FASSET radiation effects database merged with the EPIC database to form FREDERICA) and resulted in a PNEDR of 10μGy/h. This rate was assumed to ascribe sufficient protection of all ecosystems from detrimental effects on structure and function under chronic exposure. The value was weighed against a number of points of comparison: (i) PNEDR values obtained by application of the safety factor method, (ii) background levels, (iii) dose rates triggering effects on radioactively contaminated sites and (iv) former guidelines from literature reviews. In Tier 3, the effects analysis must be driven by the problem formulation and is thus highly case specific. Instead of specific recommendations on numeric values, guidance on the sorts of methods that may be applied for refined effect analysis is provided and illustrated. [Copyright &y& Elsevier]

Abstract: ICE1, an Arabidopsis thaliana transcription factor gene, was cloned by RT-PCR and successfully transformed into rice variety Kenjiandao 10 by the Agrobacterium-mediated transformation method. PCR amplification and Southern blot analysis indicated that ICE1 had been integrated into rice genome. Compared with the non-transgenic plants, the transgenic plants exhibited high resistance to hygromycin B and were consistent with the Mendelian inheritance of a single copy of the transgenic ICE1. Under the low temperature stress, the transgenic plants showed the lower mortality rate and the increased proline content. These results suggest that the Arabidopsis ICE1 is functional in rice and the over-expression of ICE1 improves the tolerance to cold stress in rice. [Copyright &y& Elsevier]

Abstract: Convexity, as a fundamental property of sets and functions defined on convex sets, plays an important role in many mathematical and applied disciplines, including extremal and optimal-control problems. We prove the set of all feasible projection matrices in a general class of matrix models for stage-structured population dynamics to be convex and the dominant eigenvalue (λ 1) of any projection 2×2 matrix to be either a convex, or a concave function on a simplex of the matrix first-row entries (i.e., stage-specific reproduction rates). The latter is also conjectured for the general n × n case. Though looking far from practical needs of matrix population models, this mathematical result has appeared to be quite useful in solving a practical problem to calibrate the projection matrix, i.e., to estimate all the stage-specific vital rates, from empirical data. The data from monitoring of individual life histories of marked plants on permanent sample plots during successive years enable direct calculation of the stage-specific survival and ontogenetic transition rates, but the rates of reproduction do remain uncertain as far as the parent plants can hardly be determined for the (not yet marked!) recruitment. To overcome this insurmountable uncertainty in data and to conclude the model calibration, we use a general principle that was proposed by Yuri M. Svirezhev in late 70s of the 20th century and applied by his students and followers in a number of applications, namely, to substitute an adaptation conjecture (“empirical generalization”) for the lack of data/information. We assume the unobservable stage-specific reproduction rates to be such that they furnish the maximum value to λ 1 under certain constraints which ensue from available data and knowledge. The calibration problem hereafter reduces to constraint maximization of λ 1 over a bounded convex set of unknown variables (stage-specific reproduction rates), the problem having a unique solution. This solution appears to differ from those proposed by a software package for ecological modelling (RAMAS® EcoLab), which were based on artificial assumptions of uniformity or singularity in the distribution of the reproduction rates among the stages. Expert knowledge, on the contrary, suggests a certain hierarchy among the rates, and whether the hierarchy admits the population growth can be tested vs. data by means of the former results concerning the potential-growth indicator function. [Copyright &y& Elsevier]

Abstract: The “biosphere–climate” system is subjected to different influences (influx of anthropogenic CO2 and pollutants, deforestation, harmful land management, biological species depopulation, etc.). Therefore, the vital question arises: “Can these influences lead to irreversible negative changes in the climate–biosphere system or a global ecological catastrophe?” The possibility of irreversible changes may be not very high, but one cannot ignore it. So the main aim of our investigation is to evaluate possible consequences of human impact on the biosphere focusing on irreversible changes of it. Traditional mathematical complicated models describe the biosphere in great detail, but the large number of equations and parameters leads to accumulation of uncertainties in the forecast due to inevitable uncertainties of experimental estimations of model parameters. An approach based on the principle of the worst scenario was proposed. Minimization of mathematical model with respect to this principle is conducted to study limiting (but possible) versions of models in which the contribution of the possible compensatory and smoothing mechanisms is minimal. Namely the most unfavorable scenarios (corresponding to the values of parameters at the boundaries of confidence interval) have to be considered in estimating consequences of anthropogenic impact. One of the fastest CO2 releasing mechanisms, based on the positive feedback effect, was considered in the context of the worst scenario principle. The family of simple mathematical models was created for biosphere dynamics representation on different timescales. The main result of the investigation consists in confirmation of the possibility of negative and irreversible changes in the “biosphere–climate” system, caused by amplification of the positive feedback: “anthropogenic emission of CO2 – temperature increase – additional CO2 emission due to decomposition of soil organics”. Crucial parameters of models, responsible for avalanche-like biosphere changes, are determined. A realizability of hypotheses on anthropogenic causes of Little Ice Age was estimated by corresponding minimal model. Model were used to show the feasibility of the mechanism describing the changing of agricultural field species into indigenous forests in Europe during the Plague, which led to CO2 decrease and temperature fall. [Copyright &y& Elsevier]

Abstract: The growth patterns of macroalgae in three-dimensional space can provide important information regarding the environments in which they live, and insights into changes that may occur when those environments change due to anthropogenic and/or natural causes. To decipher these patterns and their attendant mechanisms and influencing factors, a spatially explicit model has been developed. The model SPREAD (SPatially-explicit Reef Algae Dynamics), which incorporates the key morphogenetic characteristics of clonality and morphological plasticity, is used to investigate the influences of light, temperature, nutrients and disturbance on the growth and spatial occupancy of dominant macroalgae in the Florida Reef Tract. The model species, Halimeda and Dictyota spp., are modular organisms, with an “individual” being made up of repeating structures. These species can also propagate asexually through clonal fragmentation. These traits lead to potentially indefinite growth and plastic morphology that can respond to environmental conditions in various ways. The growth of an individual is modeled as the iteration of discrete macroalgal modules whose dynamics are affected by the light, temperature, and nutrient regimes. Fragmentation is included as a source of asexual reproduction and/or mortality. Model outputs are the same metrics that are obtained in the field, thus allowing for easy comparison. The performance of SPREAD was tested through sensitivity analysis and comparison with independent field data from four study sites in the Florida Reef Tract. Halimeda tuna was selected for initial model comparisons because the relatively untangled growth form permits detailed characterization in the field. Differences in the growth patterns of H. tuna were observed among these reefs. SPREAD was able to closely reproduce these variations, and indicate the potential importance of light and nutrient variations in producing these patterns. [Copyright &y& Elsevier]

Abstract: The red sea urchin Strongylocentrotus franciscanus is a long-lived species and may live in excess of 100 years based on tagging studies in the field and corroboration from radiocarbon analyses as reported in the literature. Size-specific survival estimates reported here show no change in annual survival probability across the 6 largest 0.5cm size classes from 14.6 to 18.1cm. In addition to no change in survival probability there is no reduction in reproductive capacity with size. Red sea urchins show no evidence of senescence and so do not fit well within the context of the disposable soma theory of the evolution of longevity. [Copyright &y& Elsevier]

Abstract: Strategies to combat desiccation are critical for organisms living in arid and semi-arid areas. Larvae of the Australian chironomid Paraborniella tonnoiri resist desiccation by reducing water loss. In contrast, larvae of the African species Polypedilum vanderplanki can withstand almost complete dehydration, referred to as anhydrobiosis. For successful anhydrobiosis, the dehydration rate of P. vanderplanki larvae has to be controlled. Here, we desiccated larvae by exposing them to different drying regimes, each progressing from high to low relative humidity, and examined survival after rehydration. In larvae of P. vanderplanki, reactions following desiccation can be categorized as follows: (I) no recovery at all (direct death), (II) dying by unrepairable damages after rehydration (delayed death), and (III) full recovery (successful anhydrobiosis). Initial conditions of desiccation severely affected survival following rehydration, i.e. P. vanderplanki preferred 100% relative humidity where body water content decreased slightly. In subsequent conditions, unfavorable dehydration rate, such as more than 0.7mg water lost per day, resulted in markedly decreased survival rate of rehydrated larvae. Slow dehydration may be required for the synthesis and distribution of essential molecules for anhydrobiosis. Larvae desiccated at or above maximum tolerable rates sometimes showed temporary recovery but died soon after. [Copyright &y& Elsevier]