Large scale assessment of regulatory evolution and transcriptome complexity in mammals

AbstractIn addition to genetic changes affecting the function of gene products, changes in gene expression have been suggested to underlie many or even most of the phenotypic differences among mammals. However, detailed gene expression comparisons were, until recently, restricted to closely related species, owing to technological limitations. Thus, we took advantage of the latest technologies (RNA-Seq) to generate extensive qualitative and quantitative transcriptome data for a unique collection of somatic and germline tissues from representatives of all major mammalian lineages (placental mammals, marsupials and monotremes) and birds, the evolutionary outgroup.In the first major project of my thesis, we performed global comparative analyses of gene expression levels based on these data. Our analyses provided fundamental insights into the dynamics of transcriptome change during mammalian evolution (e.g., the rate of expression change across species, tissues and chromosomes) and allowed the exploration of the functional relevance and phenotypic implications of transcription changes at a genome-wide scale (e.g., we identified numerous potentially selectively driven expression switches).In a second project of my thesis, which was also based on the unique transcriptome data generated in the context of the first project we focused on the evolution of alternative splicing in mammals. Alternative splicing contributes to transcriptome complexity by generating several transcript isoforms from a single gene, which can, thus, perform various functions. To complete the global comparative analysis of gene expression changes, we explored patterns of alternative splicing evolution. This work uncovered several general and unexpected patterns of alternative splicing evolution (e.g., we found that alternative splicing evolves extremely rapidly) as well as a large number of conserved alternative isoforms that may be crucial for the functioning of mammalian organs.Finally, the third and final project of my PhD consisted in analyzing in detail the unique functional and evolutionary properties of the testis by exploring the extent of its transcriptome complexity. This organ was previously shown to evolve rapidly both at the phenotypic and molecular level, apparently because of the specific pressures that act on this organ and are associated with its reproductive function. Moreover, my analyses of the amniote tissue transcriptome data described above, revealed strikingly widespread transcriptional activity of both functional and nonfunctional genomic elements in the testis compared to the other organs. To elucidate the cellular source and mechanisms underlying this promiscuous transcription in the testis, we generated deep coverage RNA-Seq data for all major testis cell types as well as epigenetic data (DNA and histone methylation) using the mouse as model system. The integration of these complete dataset revealed that meiotic and especially post-meiotic germ cells are the major contributors to the widespread functional and nonfunctional transcriptome complexity of the testis, and that this "promiscuous" spermatogenic transcription is resulting, at least partially, from an overall transcriptionally permissive chromatin state. We hypothesize that this particular open state of the chromatin results from the extensive chromatin remodeling that occurs during spermatogenesis which ultimately leads to the replacement of histones by protamines in the mature spermatozoa. Our results have important functional and evolutionary implications (e.g., regarding new gene birth and testicular gene expression evolution).Generally, these three large-scale projects of my thesis provide complete and massive datasets that constitute valuables resources for further functional and evolutionary analyses of mammalian genomes.

Comparative Lessons on Corporate law and CSR: Hard Law as Solution? Do the French offer the way ahead?

This paper provides a comparative analysis of corporate law and CSR and asks whether there are lessons for Australia from corporate law and CSR developments in France. This presentation presents a summary of the provisions of the new French Act Number 2010-788 passed on 12 July 2010 – called “Grenelle 2” –. Firstly, article 225 of Law’s Grenelle 2 changes the Commercial Code to extend the reach of non-financial reporting and to ensure its pertinence. Secondly, article 227 Law’s Grenelle 2 amends certain provisions of the Commercial and Environmental Codes and incorporates into substantive law the liability of parent companies for their subsidiaries. In fine, article 224 of Law’s Grenelle 2 reinforces the pressure on the market to act in a responsible manner. It modifies article 214-12 of the Monetary and Financial Code in order to compel institutional investors (mutual funds and fund management companies) to take social, environmental and governance criteria into account in their investment policy.

Design and construction of a new Drosophila species, D.synthetica, by synthetic regulatory evolution

Here, I merge the principles of synthetic biology1,2 and regulatory evolution3-11 to create a new species12-15 with a minimal set of known elements. Using preexisting transgenes and recessive mutations of Drosophila melanogaster, a transgenic population arises with small eyes and a different venation pattern that fulfills the criteria of a new species according to Mayr's "Biological Species Concept"7,10. The genetic circuit entails the loss of a non-essential transcription factor and the introduction of cryptic enhancers. Subsequent activation of those enhancers causes hybrid lethality. The transition from "transgenic organisms" towards "synthetic species", such as Drosophila synthetica, constitutes a safety mechanism to avoid hybridization with wild type populations and preserve natural biodiversity16-18. Drosophila synthetica is the first transgenic organism that cannot hybridize with the original wild type population but remains fertile when crossed with other transgenic animals.

Regulatory evolution and the origin of the bilaterians

The adult body plan of bilaterians is achieved by imposing regional specifications on pluripotential cells. The establishment of spatial domains is governed in part by regulating expression of transcription factors. The key to understanding bilaterian evolution is contingent on our understanding of how the regulation of these transcription factors influenced bilaterian stem-group evolution.

Social insect genomes exhibit dramatic evolution in gene composition and regulation while preserving regulatory features linked to sociality.

Genomes of eusocial insects code for dramatic examples of phenotypic plasticity and social organization. We compared the genomes of seven ants, the honeybee, and various solitary insects to examine whether eusocial lineages share distinct features of genomic organization. Each ant lineage contains ∼4000 novel genes, but only 64 of these genes are conserved among all seven ants. Many gene families have been expanded in ants, notably those involved in chemical communication (e.g., desaturases and odorant receptors). Alignment of the ant genomes revealed reduced purifying selection compared with Drosophila without significantly reduced synteny. Correspondingly, ant genomes exhibit dramatic divergence of noncoding regulatory elements; however, extant conserved regions are enriched for novel noncoding RNAs and transcription factor-binding sites. Comparison of orthologous gene promoters between eusocial and solitary species revealed significant regulatory evolution in both cis (e.g., Creb) and trans (e.g., fork head) for nearly 2000 genes, many of which exhibit phenotypic plasticity. Our results emphasize that genomic changes can occur remarkably fast in ants, because two recently diverged leaf-cutter ant species exhibit faster accumulation of species-specific genes and greater divergence in regulatory elements compared with other ants or Drosophila. Thus, while the "socio-genomes" of ants and the honeybee are broadly characterized by a pervasive pattern of divergence in gene composition and regulation, they preserve lineage-specific regulatory features linked to eusociality. We propose that changes in gene regulation played a key role in the origins of insect eusociality, whereas changes in gene composition were more relevant for lineage-specific eusocial adaptations.

Multigene Family Evolution: Perspectives from Insect Chemoreceptors.

Understanding the birth and diversification of multigene families is a fundamental evolutionary problem. I argue for the insect chemoreceptor superfamily as an outstanding model. Although these receptors are currently the preserve of neuroscientists, putative homologous genes exist in diverse animal and plant genomes, implying an ancient origin. Moreover, functional studies suggest that they act as ligand-gated ion channels in both chemosensory and non-chemosensory processes. This family permits synergism of investigations into its structural and regulatory evolution with ecological studies of the selective pressures driving these changes. In addition, sequence divergence in these receptors can be exploited through co-evolutionary and comparative genomics analyses to help to elucidate their 3D structure and signaling mechanisms, and to reveal experimentally-accessible candidate loci to explore the genetic basis of adaptation.

The life history of retrocopies illuminates the evolution of new mammalian genes.

New genes contribute substantially to adaptive evolutionary innovation, but the functional evolution of new mammalian genes has been little explored at a broad scale. Previous work established mRNA-derived gene duplicates, known as retrocopies, as models for the study of new gene origination. Here we combine mammalian transcriptomic and epigenomic data to unveil the processes underlying the evolution of stripped-down retrocopies into complex new genes. We show that although some robustly expressed retrocopies are transcribed from preexisting promoters, most evolved new promoters from scratch or recruited proto-promoters in their genomic vicinity. In particular, many retrocopy promoters emerged from ancestral enhancers (or bivalent regulatory elements) or are located in CpG islands not associated with other genes. We detected 88-280 selectively preserved retrocopies per mammalian species, illustrating that these mechanisms facilitated the birth of many functional retrogenes during mammalian evolution. The regulatory evolution of originally monoexonic retrocopies was frequently accompanied by exon gain, which facilitated co-option of distant promoters and allowed expression of alternative isoforms. While young retrogenes are often initially expressed in the testis, increased regulatory and structural complexities allowed retrogenes to functionally diversify and evolve somatic organ functions, sometimes as complex as those of their parents. Thus, some retrogenes evolved the capacity to temporarily substitute for their parents during the process of male meiotic X inactivation, while others rendered parental functions superfluous, allowing for parental gene loss. Overall, our reconstruction of the "life history" of mammalian retrogenes highlights retroposition as a general model for understanding new gene birth and functional evolution.

Lamprey Dlx genes and early vertebrate evolution

Gnathostome vertebrates have multiple members of the Dlx family of transcription factors that are expressed during the development of several tissues considered to be vertebrate synapomorphies, including the forebrain, cranial neural crest, placodes, and pharyngeal arches. The Dlx gene family thus presents an ideal system in which to examine the relationship between gene duplication and morphological innovation during vertebrate evolution. Toward this end, we have cloned Dlx genes from the lamprey Petromyzon marinus, an agnathan vertebrate that occupies a critical phylogenetic position between cephalochordates and gnathostomes. We have identified four Dlx genes in P. marinus, whose orthology with gnathostome Dlx genes provides a model for how this gene family evolved in the vertebrate lineage. Differential expression of these lamprey Dlx genes in the forebrain, cranial neural crest, pharyngeal arches, and sensory placodes of lamprey embryos provides insight into the developmental evolution of these structures as well as a model of regulatory evolution after Dlx gene duplication events.

Avaliação das reformas recentes no setor elétrico brasileiro e sua relação com o desenvolvimento do mercado livre de energia

São muitos os desafios intrínsecos ao bom funcionamento de um setor tão complexo quanto o elétrico, em que os efeitos de determinada medida podem levar anos até a maturidade, e só então ser totalmente conhecidos os seus impactos sobre a estrutura setorial como um todo, dificilmente antecipados pelos formuladores das reformas implementadas. Tomando o setor elétrico como pano de fundo, o escopo desta dissertação é apresentar as bases para o que seria uma reforma ideal, denominada na literatura “reforma de livro texto” e, em seguida, discorrer sobre a evolução regulatória do setor elétrico brasileiro de 1930 até o início de 2014, detalhando, especialmente, as características das reformas ocorridas em 1995 e 2004. Com esse esforço de pesquisa, que adota a técnica bibliográfica e se estrutura em quatro capítulos, pretende-se analisar a situação atual do mercado livre de energia elétrica brasileiro e propor melhorias passíveis de implementação com o objetivo de desenvolver este mercado no Brasil.

Understanding China's climate change mitigation policy development: Structures, processes and outcomes

Climate change is one of the most important and urgent issues of our time. Since 2006, China has overtaken the United States as the world’s largest greenhouse gas (GHG) emitter. China’s role in an international climate change solution has gained increased attention. Although much literature has addressed the functioning, performance, and implications of existing climate change mitigation policies and actions in China, there is insufficient literature that illuminates how the national climate change mitigation policies have been formulated and shaped. This research utilizes the policy network approach to explore China’s climate change mitigation policy making by examining how a variety of government, business, and civil society actors have formed networks to address environmental contexts and influence the policy outcomes and changes. The study is qualitative in nature. Three cases are selected to illustrate structural and interactive features of the specific policy network settings in shaping different policy arrangements and influencing the outcomes in the Chinese context. The three cases include the regulatory evolution of China’s climate change policy making; the country’s involvement in the Clean Development Mechanism (CDM) activity, and China’s exploration of voluntary agreement through adopting the Top-1000 Industrial Energy Conservation Program. The historical analysis of the policy process uses both primary data from interviews and fieldwork, and secondary data from relevant literature. The study finds that the Chinese central government dominates domestic climate change policy making; however, expanded action networks that involve actors at all levels have emerged in correspondence to diverse climate mitigation policy arrangements. The improved openness and accessibility of climate change policy network have contributed to its proactive engagement in promoting mitigation outcomes. In conclusion, the research suggests that the policy network approach provides a useful tool for studying China’s climate change policy making process. The involvement of various types of state and non-state actors has shaped new relations and affected the policy outcomes and changes. In addition, through the cross-case analysis, the study challenges the “fragmented authoritarianism” model and argues that this once-influential model is not appropriate in explaining new development and changes of policy making processes in contemporary China.

La protección a las víctimas de trata de personas en Brasil

La trata de personas es una acción ilegal presente en todomundo, incluso en Brasil. El Protocolo de las Naciones Unidascontra la Trata de Personas fue ratificado por Brasil en 2004. Apesar de esto, aún la evolución normativa del país no ha sidosignificativa. Este artículo busca analizar la protección normativaexistente y futura a las víctimas, especialmente extranjeras, detrata de personas en Brasil. Así, inicialmente se presenta lo que secomprende como trata de personas, con base en el Protocolo delas Naciones Unidas para prevenir, reprimir y sancionar la trata depersonas, especialmente mujeres y niños, y son apuntadas algunasconsideraciones sobre la realidad de la trata de personas en elmundo y en Brasil. En la secuencia son presentadas las medidasde protección a las víctimas, y previstas en el Protocolo de lasNaciones Unidas. Por último, son enumeradas y analizadas lasacciones normativas existentes y los proyectos de ley que puedencambiar esta realidad. La conclusión del estudio indica que Brasilaún tiene una débil protección para las víctimas extranjeras detrata de personas, pero hay una perspectiva optimista de mejoríacon los proyectos de ley que tramitan en el Congreso Nacional.

L'identita visiva pubblica. Nuovi paradigmi di comunicazione

La ricerca proposta affronta il tema dell’identità visiva — uno dei più caratterizzanti e complessi del progetto di comunicazione — applicato alla dimensione pubblica, partendo dalla comprensione e dalla misurazione del profondo mutamento che ha portato alla sua trasformazione da stemma a marchio e poi a logo, da immagine coordinata a brand a progetto di service e experience. La ricognizione dell’evoluzione della comunicazione pubblica e l’analisi del contesto dell’eredità culturale della “grafica di pubblica utilità” forniscono il primo framework di indagine nel quale si prospetta una lettura della complessità della trasformazione del progetto di identità visiva come occasione per un suo ripensamento. Un secondo framework è individuato nel contesto della comunicazione pubblica italiana in cui l’organizzazione e la progettazione di un sistema “istituzione-design-cittadino” è ancora in transizione. L’analisi dell’evoluzione normativa, dei touchpoint, delle pratiche progettuali, degli strumenti e dei ruoli permette di inquadrare gli attuali spazi e paradigmi di interazione che vedono nel servizio digitale la forma prevalente di relazione tra cittadini e dimensione pubblica Attraverso l'esperienza diretta, l’analisi dei casi studio come strumento di indagine e la sistematizzazione di cinque cluster, la tesi propone una rinnovata definizione di identità visiva pubblica che, distaccandosi da una predominante connotazione marketing-oriented, sia funzionale alla costruzione di esperienze utili, e percezioni di queste, rafforzando e stimolando nuovi paradigmi di relazione tra cittadini e dimensione pubblica. Si propone inoltre una prospettiva progettuale che evolve dalla necessità di individuare nuovi percorsi e modalità di rapportarsi con il progetto di pubblica utilità e per la cittadinanza che rifuggono la manifestazione dell’equivoco - piuttosto comune nel contesto pubblico italiano - del confrontarsi con i cosiddetti «wicked problems» (Buchanan, 1992) ricercando, in termini di comunicazione pubblica soluzioni chiuse ed esclusivamente formali, ritenendo che queste possano avere una reale efficacia nel plasmare i rapporti tra cittadini e dimensione pubblica.

Complete Genome Viral Phylogenies Suggests the Concerted Evolution of Regulatory Cores and Accessory Satellites

We consider the concerted evolution of viral genomes in four families of DNA viruses. Given the high rate of horizontal gene transfer among viruses and their hosts, it is an open question as to how representative particular genes are of the evolutionary history of the complete genome. To address the concerted evolution of viral genes, we compared genomic evolution across four distinct, extant viral families. For all four viral families we constructed DNA-dependent DNA polymerase-based (DdDp) phylogenies and in addition, whole genome sequence, as quantitative descriptions of inter-genome relationships. We found that the history of the polymerase gene was highly predictive of the history of the genome as a whole, which we explain in terms of repeated, co-divergence events of the core DdDp gene accompanied by a number of satellite, accessory genetic loci. We also found that the rate of gene gain in baculovirus and poxviruses proceeds significantly more quickly than the rate of gene loss and that there is convergent acquisition of satellite functions promoting contextual adaptation when distinct viral families infect related hosts. The congruence of the genome and polymerase trees suggests that a large set of viral genes, including polymerase, derive from a phylogenetically conserved core of genes of host origin, secondarily reinforced by gene acquisition from common hosts or co-infecting viruses within the host. A single viral genome can be thought of as a mutualistic network, with the core genes acting as an effective host and the satellite genes as effective symbionts. Larger virus genomes show a greater departure from linkage equilibrium between core and satellites functions.

Evolution of the gene regulatory network controlling flower dorsoventral asymmetry

Tese de Doutoramento em Biologia de Plantas.