Unraveling the functional divergence of membrane-bound pyrophosphatases

Inorganic pyrophosphatases (PPases) are enzymes that hydrolyze pyrophosphate (PPi)which is produced as a byproduct in many important growth related processes e.g. in the biosynthesis of DNA, proteins and lipids. PPases can be either soluble or membranebound. Membrane-bound PPases (mPPases) are ion transporters that couple the energy released during PPi hydrolysis to Na+ or H+ transport. When I started the project, only three Na+-transporting mPPases were known to exist. In this study, I aimed to confirm if Na+-transport is a common function of mPPases. Furthermore, the amino acid residues responsible for determining the transporter specificity were unknown. I constructed a phylogenetic tree for mPPases and selected the representative bacterial and archaeal mPPases to be investigated. I expressed different prokaryotic mPPases in Escherichia coli, isolated these as inverted membrane vesicles and characterized their functions. In the first project I identified four new Na+-PPases, two K+-dependent H+-PPases and one K+-independent mPPase. The residues determining the transporter specificity were identified by site-directed mutagenesis. I showed that the conserved glutamate residues are important for specificity, though are not the only residues that influence it. This research clarified the ion transport specificities throughout the mPPase phylogenetic tree, and revealed that Na+ transport is a widespread function of mPPases. In addition, it became clear that the transporter specificity can be predicted from the amino acid sequence in combination with a phylogenetic analysis. In the second project, I identified a novel class of mPPases, which is capable of transporting both Na+ and H+ ions and is mainly found in bacteria of the human gastrointestinal tract. The physiological role of these novel enzymes may be to help the bacteria survive in the demanding conditions of the host. In the third project, I characterized the Chlorobium limicola Na+-PPase and found that this and related mPPases are able to transport H+ ions at subphysiological Na+ concentrations. In addition, the H+-transport activity was shown to be a common function of all studied Na+-PPases at low Na+ concentrations. I observed that mutating gate-lysine to asparagine eliminated the H+ but not the Na+ ion transport function, indicating the important role of the residue in the transport of H+. In the fourth project, I characterized the unknown and evolutionary divergent mPPase clade of the phylogenetic tree. The enzymes belonging to this clade are able to transport H+ ions and, based on their sequence, were expected to be K+- and Na+-independent. The sequences of membrane-bound PPase are usually highly conserved, but the enzymes belonging to this clade are more divergent and usually contain 100−150 extra amino acid residues compared to other known mPPases. Despite the vast sequence differences, these mPPases have the full set of important residues and, surprisingly, are regulated by Na+ and K+ ions. These enzymes are mainly of bacterial origin.

Macro- and Microevolution of Languages: Exploring Linguistic Divergence with Approaches from Evolutionary Biology

There are more than 7000 languages in the world, and many of these have emerged through linguistic divergence. While questions related to the drivers of linguistic diversity have been studied before, including studies with quantitative methods, there is no consensus as to which factors drive linguistic divergence, and how. In the thesis, I have studied linguistic divergence with a multidisciplinary approach, applying the framework and quantitative methods of evolutionary biology to language data. With quantitative methods, large datasets may be analyzed objectively, while approaches from evolutionary biology make it possible to revisit old questions (related to, for example, the shape of the phylogeny) with new methods, and adopt novel perspectives to pose novel questions. My chief focus was on the effects exerted on the speakers of a language by environmental and cultural factors. My approach was thus an ecological one, in the sense that I was interested in how the local environment affects humans and whether this human-environment connection plays a possible role in the divergence process. I studied this question in relation to the Uralic language family and to the dialects of Finnish, thus covering two different levels of divergence. However, as the Uralic languages have not previously been studied using quantitative phylogenetic methods, nor have population genetic methods been previously applied to any dialect data, I first evaluated the applicability of these biological methods to language data. I found the biological methodology to be applicable to language data, as my results were rather similar to traditional views as to both the shape of the Uralic phylogeny and the division of Finnish dialects. I also found environmental conditions, or changes in them, to be plausible inducers of linguistic divergence: whether in the first steps in the divergence process, i.e. dialect divergence, or on a large scale with the entire language family. My findings concerning Finnish dialects led me to conclude that the functional connection between linguistic divergence and environmental conditions may arise through human cultural adaptation to varying environmental conditions. This is also one possible explanation on the scale of the Uralic language family as a whole. The results of the thesis bring insights on several different issues in both a local and a global context. First, they shed light on the emergence of the Finnish dialects. If the approach used in the thesis is applied to the dialects of other languages, broader generalizations may be drawn as to the inducers of linguistic divergence. This again brings us closer to understanding the global patterns of linguistic diversity. Secondly, the quantitative phylogeny of the Uralic languages, with estimated times of language divergences, yields another hypothesis as to the shape and age of the language family tree. In addition, the Uralic languages can now be added to the growing list of language families studied with quantitative methods. This will allow broader inferences as to global patterns of language evolution, and more language families can be included in constructing the tree of the world’s languages. Studying history through language, however, is only one way to illuminate the human past. Therefore, thirdly, the findings of the thesis, when combined with studies of other language families, and those for example in genetics and archaeology, bring us again closer to an understanding of human history.

Avoiding Injury

Jim Baldassaro leaping over the opposing goalie in a 1981 game.

Genetic variation and evolutionary divergence within and among populations, species, and genera of the Cambarinae

Seven crayfish species from three genera of the subfamily Cambarinae were electrophoretically examined for genetic variation at a total of twenty-six loci. Polymorphism was detected primarily at three loci: Ao-2, Lap, and Pgi. The average heterozygosities over-all loci for each species were found to be very low when compared to most other invertebrate species that have been examined electrophoretically. With the exception of Cambarus bartoni, the interpopulation genetic identities are high within any given species. The average interspecific identities are somewhat lower and the average intergeneric identities are lower still. Populations, species and genera conform to the expected taxonomic progression. The two samples of ~ bartoni show high genetic similarity at only 50 percent of the loci compared. Locus by locus identity comparisons among species yield U-shaped distributions of genetic identities. Construction of a phylogenetic dendrogram using species mean genetic distances values shows that species grouping is in agreement with morphological taxonomy with the exception of the high similarity between Orconectespropinquus and Procambarus pictus. This high similarity suggests the possibility of a regulatory change between the two species. It appears that the low heterozygosities, high interpopulation genetic identities, and taxonomic mispositioning can all be explained on the basis of low mutation rates.

Explaining the Great Divergence: Medium and Message on the Eurasian Land Mass, 1700-1850

Between 1700 and 1850, per-capita income doubled in Europe while falling in the rest of Eurasia. Neither geography nor economic institutions can explain this sudden divergence. Here the consequences of differences in communications technology are examined. For the first time, there appeared in Europe a combination of a standardized medium (national vernaculars with a phonetic alphabet) and a non-standardized message (competing religious, political and scientific ideas). The result was an unprecedented fall in the cost of combining ideas and burst of productivity-raising innovation. Elsewhere, decreasing standardization of the medium and increasing standardization of the message blocked innovation.

Convergences ou divergence économique: le cas de la "Caricom".

Rapport de recherche

Le développement récent des trois "petites" télévisions francophones de Suisse, de Belgique et du Québec, convergence ou divergence?

Dans le cadre d’une sociologie des organisations portant sur les liens entre organisations télévisuelles et environnement, la présente thèse a pour objectif de cerner les modalités du développement récent de la télévision au Québec en le comparant à celui de la Belgique francophone et de la Suisse. Une telle comparaison repose sur un principe méthodologique simple: on cerne d’autant mieux la réalité que l’on étudie si on peut la comparer à une réalité équivalente d’autres sociétés. En s’appuyant sur des théories de développement organisationnel reliées au courant néo-fonctionnaliste et en adaptant des « histoires de cas » d’études organisationnelles à la réalité télévisuelle des années 90 et 2000, le chercheur a mis au point une grille de classification des données permettant d’étudier les composantes du développement de la télévision dans trois « petites » sociétés industrialisées. Dans un premier temps, il a pu constater une augmentation très importante du nombre de chaînes de télévision par rapport à ce qu’il était dans les années 50 à 70, le tout encadré par les autorités réglementaires en place. Par la suite, dans chacune de ces trois sociétés et sur une période de vingt-cinq ans, il a pu préciser les interactions et échanges entre organisations télévisuelles et environnement lesquels ont été, selon les cas, harmonieux, difficiles, voire même conflictuels. Après avoir comparé les modalités d’une telle augmentation entre les trois sociétés, le chercheur a pu constater une convergence de surface. On note bien quelques similitudes entre les trois sociétés, mais, surtout, chacune d’entre elles est restée sur son quant-à-soi. En Suisse, l’importance accordée au consensus social a favorisé un développement équilibré de l’augmentation des chaines. En Belgique, pays aux divisions profondes constamment réaffirmées, les oppositions ont permis, malgré tout, l’édification d’un ensemble audiovisuel relativement stable. Au Québec, avec une augmentation exponentielle du nombre de chaines, on a assisté à un véritable surdéveloppement de la télévision encouragé et planifié par les autorités gouvernementales canadiennes en réaction à un supposé envahissement culturel américain. Le CRTC, la régie des ondes canadiennes, a pesé de tout son poids pour favoriser l’augmentation du contenu canadien et de la production locale. Par ailleurs, cette augmentation s’est faite avec des ressources limitées. On en fait trop avec trop peu. C’est ce qui permettrait d’expliquer la baisse de qualité de la télévision québécoise contemporaine. Comme élément de solution aux problèmes que la télévision québécoise connait présentement, il faudrait considérer cette dernière pour ce qu’elle est véritablement: une petite télévision dans un univers industriellement hautement développé. Si une telle conception est très bien acceptée aussi bien en Belgique qu’en Suisse, elle ne l’est pas au Québec

Characterization of Histone H2A Derived Antimicrobial Peptides, Harriottins, from Sicklefin Chimaera Neoharriotta pinnata (Schnakenbeck, 1931) and Its Evolutionary Divergence with respect to CO1 and Histone H2A

Antimicrobial peptides (AMPs) are humoral innate immune components of fishes that provide protection against pathogenic infections. Histone derived antimicrobial peptides are reported to actively participate in the immune defenses of fishes. Present study deals with identification of putative antimicrobial sequences from the histone H2A of sicklefin chimaera, Neoharriotta pinnata. A 52 amino acid residue termed Harriottin-1, a 40 amino acid Harriottin-2, and a 21 mer Harriottin-3 were identified to possess antimicrobial sequence motif. Physicochemical properties andmolecular structure ofHarriottins are in agreement with the characteristic features of antimicrobial peptides, indicating its potential role in innate immunity of sicklefin chimaera. The histone H2A sequence of sicklefin chimera was found to differ from previously reported histone H2A sequences. Phylogenetic analysis based on histone H2A and cytochrome oxidase subunit-1 (CO1) gene revealed N. pinnata to occupy an intermediate position with respect to invertebrates and vertebrates

Characterizations of Bivariate Models Using Some Dynamic Conditional Information Divergence Measures

In this article, we study some relevant information divergence measures viz. Renyi divergence and Kerridge’s inaccuracy measures. These measures are extended to conditionally specifiedmodels and they are used to characterize some bivariate distributions using the concepts of weighted and proportional hazard rate models. Moreover, some bounds are obtained for these measures using the likelihood ratio order

Genetic divergence in lobsters (Crustacea: Palinuridae and Scyllaridae) from the Indian EEZ

The management of exploited species requires the identification of demographically isolated populations that can be considered as independent management units (MUs), failuring in which can lead to over -fishing and depletion of less productive stocks. By characterizing the distribution of genetic variation, population sub structuring can be detected and the degree of connectivity among populations can be estimated. The genetic variation can be observed using identified molecular markers of both nuclear and mitochondrial origin. Hence, the present work was undertaken to study the genetic diversity and population/stock structure in P. homarus homarus and T. unimaculatus from different landing centres along the Indian coast using nuclear (RAPD) and mitochondrial DNA marker tools which will help towards developing management strategies for management and conservation of these declining resources.To make consistent conservation and fisheries management decisions, accurate species identifications are needed. It is also suggested that it is not always desirable to rely on a single sequence for taxonomic identification. Thus, the feasibility of using partial sequences of additional mitochondrial genes like 16SrRNA, 12SrRNA and nuclear 18SrRNA has also been explored in our study. Phylogenies provide a sound foundation for establishing taxonomy. The present work also attempts to reconstruct the phylogeny of eleven species of commercially important lobsters from the Indian EEZ using molecular markers

Genomic architecture of adaptive color pattern divergence and convergence in Heliconius butterflies

Identifying the genetic changes driving adaptive variation in natural populations is key to understanding the origins of biodiversity. The mosaic of mimetic wing patterns in Heliconius butterflies makes an excellent system for exploring adaptive variation using next-generation sequencing. In this study, we use a combination of techniques to annotate the genomic interval modulating red color pattern variation, identify a narrow region responsible for adaptive divergence and convergence in Heliconius wing color patterns, and explore the evolutionary history of these adaptive alleles. We use whole genome resequencing from four hybrid zones between divergent color pattern races of Heliconius erato and two hybrid zones of the co-mimic Heliconius melpomene to examine genetic variation across 2.2 Mb of a partial reference sequence. In the intergenic region near optix, the gene previously shown to be responsible for the complex red pattern variation in Heliconius, population genetic analyses identify a shared 65-kb region of divergence that includes several sites perfectly associated with phenotype within each species. This region likely contains multiple cis-regulatory elements that control discrete expression domains of optix. The parallel signatures of genetic differentiation in H. erato and H. melpomene support a shared genetic architecture between the two distantly related co-mimics; however, phylogenetic analysis suggests mimetic patterns in each species evolved independently. Using a combination of next-generation sequencing analyses, we have refined our understanding of the genetic architecture of wing pattern variation in Heliconius and gained important insights into the evolution of novel adaptive phenotypes in natural populations.

Avoiding accidents. 'Evitar los accidentes'.

Se presenta una secuencia didáctica sobre normas básicas de Educación Vial contextualizadas en situaciones cotidianas donde el niño es sujeto activo. Se plantea un juego de mesa sencillo como hilo conductor de las actividades que inciden en el refuerzo de actitudes seguras.

Diversitat genètica de la truita comuna (Salmo trutta L.) a la Península Ibèrica: biogeografia i gestió

L'estudi de la diversitat i la diferenciació genètiques de les poblacions de truita comuna (Salmo trutta L.) a la Península Ibèrica ha confirmat l'elevada diferenciació observada en treballs previs i la divergència, ja descrita, entre les poblacions de la vessant atlàntica i la mediterrània. El resultats obtinguts, però, ens permeten observar patrons d'estructura poblacional tant en les poblacions atlàntiques com les mediterrànies. A l'Atlàntic s'observa un marcat patró hidrogràfic en la distribució de la diferenciació genètica, que contrasta fortament amb la distribució d'aquesta diferenciació en les poblacions mediterrànies, caracteritzades pels contactes secundaris entre llinatges durant les expansions pleniglacials i una forta divergència local conseqüència de la seva marginalitat i aïllament en els períodes interglacials. El manteniment d'aquesta diferenciació i individualitat descrites en les poblacions de truita de la Península, es veu seriosament compromès per les contínues repoblacions dels rius amb exemplars exògens d'origen nord europeu. La substitució dels genomes autòctons per la introducció de gens al.lòctons provoca una erosió dels patrimonis genètics natius i una homogeneïtzació de les poblacions, destruint els patrons de diferenciació existents. Al mateix temps, els nostres resultats indiquen que les conseqüències de les repoblacions no són sempre les mateixes. Concretament, es constata un fracàs de les repoblacions en rius intensament repoblats i sotmesos a pesca intensiva, que contrasta amb una enorme erosió de les poblacions quan les repoblacions s'efectuen sobre àrees protegides i sense cap mena de pressió pesquera. Això suggereix que múltiples factors com la gestió dels rius posterior a les repoblacions, l'estat de les poblacions o les condicions de l'hàbitat són determinants de la introducció efectiva dels exemplars alliberats; fet que dificulta la predicció sobre actuacions particulars. Malgrat aquesta introgressió de gens exògens que es detecta en moltes de les poblacions analitzades, els gens natius predominen en gairebé tots els rius de la Península. La conservació d'aquesta elevada riquesa genètica que encara resta en les poblacions de truita de la Península Ibèrica ha de ser l'objectiu final de qualsevol programa de gestió. Per això, defensem una gestió basada en el propi riu mitjançant una pesca sostinguda per la reproducció natural de les poblacions salvatges, acompanyada d'una millora i recuperació d'hàbitats adequats per la truita, i evitant, per sobre de tot, la introducció en els rius d'exemplars exògens, degut als efectes nocius i incontrolables que comporta aquest procés.