Gene expression changes in the coccolithophore Emiliania huxleyi after 500 generations of selection to ocean acidification

Coccolithophores are unicellular marine algae that produce biogenic calcite scales and substantially contribute to marine primary production and carbon export to the deep ocean. Ongoing ocean acidification particularly impairs calcifying organisms, mostly resulting in decreased growth and calcification. Recent studies revealed that the immediate physiological response in the coccolithophore Emiliania huxleyi to ocean acidification may be partially compensated by evolutionary adaptation, yet the underlying molecular mechanisms are currently unknown. Here, we report on the expression levels of 10 candidate genes putatively relevant to pH regulation, carbon transport, calcification and photosynthesis in E. huxleyi populations short-term exposed to ocean acidification conditions after acclimation (physiological response) and after 500 generations of high CO2 adaptation (adaptive response). The physiological response revealed downregulation of candidate genes, well reflecting the concomitant decrease of growth and calcification. In the adaptive response, putative pH regulation and carbon transport genes were up-regulated, matching partial restoration of growth and calcification in high CO2-adapted populations. Adaptation to ocean acidification in E. huxleyi likely involved improved cellular pH regulation, presumably indirectly affecting calcification. Adaptive evolution may thus have the potential to partially restore cellular pH regulatory capacity and thereby mitigate adverse effects of ocean acidification.

Fault Tolerance Analysis and Self-Healing Strategy of Autonomous, Evolvable Hardware Systems

This paper presents an analysis of the fault tolerance achieved by an autonomous, fully embedded evolvable hardware system, which uses a combination of partial dynamic reconfiguration and an evolutionary algorithm (EA). It demonstrates that the system may self-recover from both transient and cumulative permanent faults. This self-adaptive system, based on a 2D array of 16 (4×4) Processing Elements (PEs), is tested with an image filtering application. Results show that it may properly recover from faults in up to 3 PEs, that is, more than 18% cumulative permanent faults. Two fault models are used for testing purposes, at PE and CLB levels. Two self-healing strategies are also introduced, depending on whether fault diagnosis is available or not. They are based on scrubbing, fitness evaluation, dynamic partial reconfiguration and in-system evolutionary adaptation. Since most of these adaptability features are already available on the system for its normal operation, resource cost for self-healing is very low (only some code additions in the internal microprocessor core)

Fighting fit: thermal plasticity of metabolic function and fighting success in the crayfish Cherax destructor

1. We examined the effect of thermal acclimation on fighting success and underlying performance traits in the crayfish Cherax destructor. We tested the hypothesis that animals will be more successful when fighting at their acclimation temperature than at a colder or warmer temperature, and that changes in metabolic capacity underlie differences in behavioural performance. 2. Thermal acclimation (to 20 degrees C and to 30 degrees C) had a significant effect on behavioural contests, and the likelihood of winning was significantly greater when individuals fought at their acclimation temperature against an individual from an alternate acclimation temperature. 3. The ratio of ADP stimulated respiration to proton leak (respiratory control ratio) of isolated mitochondria increased significantly in chelae muscle of the cold-acclimated group, and differences in respiratory control ratio between winners and losers were significantly correlated with the outcome of agonistic encounters. However, acclimation did not affect tall muscle mitochondria or the activity of pyruvate kinase in either chelae or tail muscle. 4. The force produced by closing chelae was thermally insensitive within acclimation groups, and there were no significant differences between acclimation treatments. None the less, differences in chelae width between contestants were significantly correlated with the outcome of agonistic encounters, but this perceived resource holding power did not reflect the actual power of force production. 5. Thermal acclimation in C destructor has beneficial consequences for dominance and competitive ability, and the success of cold acclimated animals at the cold temperatures can be at least partly explained by concomitant up-regulation of oxidative ATP production capacity.

Unexpected Activity of a Novel Kunitz-Type Inhibtior: Inhibition of Cysteine Proteases but not Serine Proteases

Kunitz-type (KT) protease inhibitors are low molecular weight proteins classically defined as serine protease inhibitors. We identified a novel secreted KT inhibitor associated with the gut and parenchymal tissues of the infective juvenile stage of Fasciola hepatica, a helminth parasite of medical and veterinary importance. Unexpectedly, recombinant KT inhibitor (rFhKT1) exhibited no inhibitory activity towards serine proteases but was a potent inhibitor of the major secreted cathepsin L cysteine proteases of F. hepatica, FhCL1 and FhCL2, and of human cathepsins L and K (Ki = 0.4 nM - 27 nM). FhKT1 prevented the auto-catalytic activation of FhCL1 and FhCL2 and formed stable complexes with the mature enzymes. Pull-down experiments from adult parasite culture medium showed that rFhKT1 interacts specifically with native secreted FhCL1, FhCL2 and FhCL5. Substitution of the unusual P1 Leu15 within the exposed reactive loop of FhKT1 for the more commonly found Arg (FhKT1Leu15/Arg15) had modest adverse effects on the cysteine protease inhibition but conferred potent activity against the serine protease trypsin (Ki = 1.5 nM). Computational docking and sequence analysis provided hypotheses for the exclusive binding of FhKT1 to cysteine proteases, the importance of the Leu15 in anchoring the inhibitor into the S2 active site pocket, and the inhibitor's selectivity towards FhCL1, FhCL2 and human cathepsins L and K. FhKT1 represents a novel evolutionary adaptation of KT protease inhibitors by F. hepatica, with its prime purpose likely in the regulation of the major parasite-secreted proteases and/or cathepsin L-like proteases of its host.

Influence de l’hypoxie dans la régulation du pH et les conséquences dans la progression tumorale et la résistance à la chimiothérapie

Résumé : La formation de métastases s’inscrit comme la finalité d’un processus darwinien dans lequel les cellules tumorales subissent des altérations génétiques et épigénétiques dans l’unique but de préserver un avantage prolifératif. L’environnement hypoxique, caractéristique des tumeurs solides, se révèle comme une pression de sélection et un facteur déterminant dans la progression tumorale. Face à l’hypoxie, une des adaptations majeures des cellules tumorales est le déséquilibre du pH cellulaire qui mène à la formation de métastases et à la résistance à la chimiothérapie. Cette thèse met en lumière de nouveaux liens moléculaires entre l’hypoxie et la régulation du pH dans des contextes d’invasion cellulaire et de chimiorésistance. Les échangeurs d’ions NHE1 et NHE6 sont au cœur de ces études où de nouveaux rôles dans la progression du cancer leur ont été attribués. Premièrement, nous avons observé l’influence de l’hypoxie sur la régulation de NHE1 par p90RSK et les conséquences fonctionnelles de cette interaction dans l’invasion cellulaire par les invadopodes. En conditions hypoxiques, NHE1 est activé par p90RSK résultant en une acidification extracellulaire. En modifiant le pH, NHE1 stimule la formation des invadopodes et la dégradation de la matrice extracellulaire. Ainsi, la phosphorylation de NHE1 par p90RSK en hypoxie apparaît comme un biomarqueur potentiel des cancers métastatiques. Peu étudié, le pH endosomal peut intervenir dans la chimiorésistance mais les mécanismes sont inconnus. Nous avons développé une méthode pour mesurer précisément le pH endosomal par microscopie. Ceci a permis d’illuminer un nouveau mécanisme de résistance induit par l’hypoxie et mettant en vedette l’échangeur NHE6. L’hypoxie favorise l’interaction de NHE6 avec RACK1 à la membrane plasmique empêchant la localisation endosomale de l’échangeur. Cette interaction mène à la séquestration de la doxorubicine dans des endosomes sur-acidifiés. Ces travaux mettent en évidence pour la première fois le rôle du pH endosomal et l’échangeur NHE6 comme des éléments centraux de la chimiorésistance induite par l’hypoxie. Cette thèse renforce donc l’idée voulant que les interactions entre les cellules tumorales et le microenvironnement hypoxique sont le « talon d’Achille » du cancer et la régulation du pH cellulaire est primordiale dans l’adaptation des cellules à l’hypoxie et l’instauration du phénotype malin du cancer. La découverte de nouveaux rôles pro-tumoraux pour NHE1 et NHE6 les placent à l’avant-plan pour le développement de stratégies thérapeutiques orientées contre la formation de métastases et la chimiorésistance.

Plant rhizosphere specificity and variability in the insect and plant adhesins, Madl and Mad2, within the genus Metarhizium suggest plant adaptation as an evolutionary force

Metarhizium is a soil-inhabiting fungus currently used as a biological control agent against various insect species, and research efforts are typically focused on its ability to kill insects. In section 1, we tested the hypothesis that species of Metarhizium are not randomly distributed in soils but show plant rhizosphere-specific associations. Results indicated an association of three Metarhizium species (Metarhizium robertsii, M. brunneum and M. guizhouense) with the rhizosphere of certain types of plant species. M. robertsii was the only species that was found associated with grass roots, suggesting a possible exclusion of M. brunneum and M. guizhouense, which was supported by in vitro experiments with grass root exudate. M. guizhouense and M. brunneum only associated with wildflower rhizosphere when co-occurring with M. robertsii. With the exception of these co-occurrences, M. guizhouense was found to associate exclusively with the rhizosphere of tree species, while M. brunneum was found to associate exclusively with the rhizosphere of shrubs and trees. These associations demonstrate that different species of Metarhizium associate with specific plant types. In section 2, we explored the variation in the insect adhesin, Madl, and the plant adhesin, Mad2, in fourteen isolates of Metarhizium representing seven different species. Analysis of the transcriptional elements within the Mad2 promoter region revealed variable STRE, PDS, degenerative TATA box, and TATA box-like regions. Phylogenetic analysis of 5' EF-Ia, which is used for species identification, as well as Madl and Mad2 sequences demonstrated that the Mad2 phylogeny is more congruent with 5' EF-1a than Madl. This suggests Mad2 has diverged among Metarhizium lineages, contributing to clade- and species-specific variation. While other abiotic and biotic factors cannot be excluded in contributing to divergence, it appears that plant associations have been the driving factor causing divergence among Metarhizium species.

Variability in the Insect and Plant Adhesins, Mad1 and Mad2, within the Fungal Genus Metarhizium Suggest Plant Adaptation as an Evolutionary Force

Several species of the insect pathogenic fungus Metarhizium are associated with certain plant types and genome analyses suggested a bifunctional lifestyle; as an insect pathogen and as a plant symbiont. Here we wanted to explore whether there was more variation in genes devoted to plant association (Mad2) or to insect association (Mad1) overall in the genus Metarhizium. Greater divergence within the genus Metarhizium in one of these genes may provide evidence for whether host insect or plant is a driving force in adaptation and evolution in the genus Metarhizium. We compared differences in variation in the insect adhesin gene, Mad1, which enables attachment to insect cuticle, and the plant adhesin gene, Mad2, which enables attachment to plants. Overall variation for the Mad1 promoter region (7.1%), Mad1 open reading frame (6.7%), and Mad2 open reading frame (7.4%) were similar, while it was higher in the Mad2 promoter region (9.9%). Analysis of the transcriptional elements within the Mad2 promoter region revealed variable STRE, PDS, degenerative TATA box, and TATA box-like regions, while this level of variation was not found for Mad1. Sequences were also phylogenetically compared to EF-1a, which is used for species identification, in 14 isolates representing 7 different species in the genus Metarhizium. Phylogenetic analysis demonstrated that the Mad2 phylogeny is more congruent with 59 EF-1a than Mad1. This would suggest that Mad2 has diverged among Metarhizium lineages, contributing to clade- and species-specific variation, while it appears that Mad1 has been largely conserved. While other abiotic and biotic factors cannot be excluded in contributing to divergence, these results suggest that plant relationships, rather than insect host, have been a major driving factor in the divergence of the genus Metarhizium.

Variability in the Insect and Plant Adhesins, Mad1 and Mad2, within the Fungal Genus Metarhizium Suggest Plant Adaptation as an Evolutionary Force

Several species of the insect pathogenic fungus Metarhizium are associated with certain plant types and genome analyses suggested a bifunctional lifestyle; as an insect pathogen and as a plant symbiont. Here we wanted to explore whether there was more variation in genes devoted to plant association (Mad2) or to insect association (Mad1) overall in the genus Metarhizium. Greater divergence within the genus Metarhizium in one of these genes may provide evidence for whether host insect or plant is a driving force in adaptation and evolution in the genus Metarhizium. We compared differences in variation in the insect adhesin gene, Mad1, which enables attachment to insect cuticle, and the plant adhesin gene, Mad2, which enables attachment to plants. Overall variation for the Mad1 promoter region (7.1%), Mad1 open reading frame (6.7%), and Mad2 open reading frame (7.4%) were similar, while it was higher in the Mad2 promoter region (9.9%). Analysis of the transcriptional elements within the Mad2 promoter region revealed variable STRE, PDS, degenerative TATA box, and TATA box-like regions, while this level of variation was not found for Mad1. Sequences were also phylogenetically compared to EF-1a, which is used for species identification, in 14 isolates representing 7 different species in the genus Metarhizium. Phylogenetic analysis demonstrated that the Mad2 phylogeny is more congruent with 59 EF-1a than Mad1. This would suggest that Mad2 has diverged among Metarhizium lineages, contributing to clade- and species-specific variation, while it appears that Mad1 has been largely conserved. While other abiotic and biotic factors cannot be excluded in contributing to divergence, these results suggest that plant relationships, rather than insect host, have been a major driving factor in the divergence of the genus Metarhizium.

Extending Alexander’s ecological dominance-social competition model : information behavior adaptation

Alexander’s Ecological Dominance and Social Competition (EDSC) model currently provides the most comprehensive overview of human traits in the development of a theory of human evolution and sociality (Alexander, 1990; Finn, Geary & Ward, 2005; Irons, 2005). His model provides a basis for explaining the evolution of human socio-cognitive abilities. Our paper examines the extension of Alexander’s model to incorporate the human trait of information behavior in synergy with ecological dominance and social competition as a human socio-cognitive competence. This paper discusses the various interdisciplinary perspectives exploring how evolution has shaped information behavior and why information behavior is emerging as an important human socio-cognitive competence. This paper outlines these issues, including the extension of Spink and Currier’s (2006a,b) evolution of information behavior model towards a more integrated understanding of how information behaviors have evolved (Spink & Cole, 2006).

FPGA implementation of an evolutionary algorithm for autonomous unmanned aerial vehicle on-board path planning

In this paper, a hardware-based path planning architecture for unmanned aerial vehicle (UAV) adaptation is proposed. The architecture aims to provide UAVs with higher autonomy using an application specific evolutionary algorithm (EA) implemented entirely on a field programmable gate array (FPGA) chip. The physical attributes of an FPGA chip, being compact in size and low in power consumption, compliments it to be an ideal platform for UAV applications. The design, which is implemented entirely in hardware, consists of EA modules, population storage resources, and three-dimensional terrain information necessary to the path planning process, subject to constraints accounted for separately via UAV, environment and mission profiles. The architecture has been successfully synthesised for a target Xilinx Virtex-4 FPGA platform with 32% logic slices utilisation. Results obtained from case studies for a small UAV helicopter with environment derived from LIDAR (Light Detection and Ranging) data verify the effectiveness of the proposed FPGA-based path planner, and demonstrate convergence at rates above the typical 10 Hz update frequency of an autopilot system.

Variations on a routine : how selection-adaptation-retention dynamics create variety in organisational routines

The question "what causes variety in organisational routines" is of considerable interest to organisational scholars, and one to which this thesis seeks to answer. To this end an evolutionary theory of change is advanced which holds that the dynamics of selection, adaptation and retention explain the creation of variety in organisational routines. A longitudinal, multi-level, multi-case analysis is undertaken in this thesis, using multiple data collection strategies. In each case, different types of variety were identified, according to a typology, together with how selection, adaptation and retention contribute to variety in a positive or negative sense. Methodologically, the thesis makes a contribution to our understanding of variety, as certain types of variety only become evident when examined by specific types of research design. The research also makes a theoretical contribution by explaining how selection, adaptation and retention individually and collectively contribute to variety in organisational routines. Moreover, showing that routines could be stable, diverse, adaptive and dynamic at the same time; is a significant, and novel, theoretical contribution.

Physical and linkage maps for Drosophila serrata, a model species for studies of clinal adaptation and sexual selection

Drosophila serrata is a member of the montium group, which contains more than 98 species and until recently was considered a subgroup within the melanogaster group. This Drosophila species is an emerging model system for evolutionary quantitative genetics and has been used in studies of species borders, clinal variation and sexual selection. Despite the importance of D. serrata as a model for evolutionary research, our poor understanding of its genome remains a significant limitation. Here, we provide a first-generation gene-based linkage map and a physical map for this species. Consistent with previous studies of other drosophilids we observed strong conservation of genes within chromosome arms homologous with D. melanogaster but major differences in within-arm synteny. These resources will be a useful complement to ongoing genome sequencing efforts and QTL mapping studies in this species

An expressed sequence tag (EST) library for Drosophila serrata, a model system for sexual selection and climatic adaptation studies

The native Australian fly Drosophila serrata belongs to the highly speciose montium subgroup of the melanogaster species group. It has recently emerged as an excellent model system with which to address a number of important questions, including the evolution of traits under sexual selection and traits involved in climatic adaptation along latitudinal gradients. Understanding the molecular genetic basis of such traits has been limited by a lack of genomic resources for this species. Here, we present the first expressed sequence tag (EST) collection for D. serrata that will enable the identification of genes underlying sexually-selected phenotypes and physiological responses to environmental change and may help resolve controversial phylogenetic relationships within the montium subgroup.

Gene duplication is an evolutionary mechanism for expanding spectral diversity in the long-wavelength photopigments of butterflies

Butterfly long-wavelength (L) photopigments are interesting for comparative studies of adaptive evolution because of the tremendous phenotypic variation that exists in their wavelength of peak absorbance (lambda(max) value). Here we present a comprehensive survey of L photopigment variation by measuring lambda(max) in 12 nymphalid and 1 riodinid species using epi-microspectrophotometry. Together with previous data, we find that L photopigment lambda(max) varies from 510-565 nm in 22 nymphalids, with an even broader 505- to 600-nm range in riodinids. We then surveyed the L opsin genes for which lambda(max) values are available as well as from related taxa and found 2 instances of L opsin gene duplication within nymphalids, in Hermeuptychia hermes and Amathusia phidippus, and 1 instance within riodinids, in the metalmark butterfly Apodemia mormo. Using maximum parsimony and maximum likelihood ancestral state reconstructions to map the evolution of spectral shifts within the L photopigments of nymphalids, we estimate the ancestral pigment had a lambda(max) = 540 nm +/- 10 nm standard error and that blueshifts in wavelength have occurred at least 4 times within the family. We used ancestral state reconstructions to investigate the importance of several amino acid substitutions (Ile17Met, Ala64Ser, Asn70Ser, and Ser137Ala) previously shown to have evolved under positive selection that are correlated with blue spectral shifts. These reconstructions suggest that the Ala64Ser substitution has indeed occurred along the newly identified blueshifted L photopigment lineages. Substitutions at the other 3 sites may also be involved in the functional diversification of L photopigments. Our data strongly suggest that there are limits to the evolution of L photopigment spectral shifts among species with only one L opsin gene and that opsin gene duplication broadens the potential range of lambda(max) values.