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.

Literature and Mythology in Tennessee Williams's "Suddenly Last Summer": Fighting against Venus and Oedipus

The aim of this article is to analyze accurately the role played by two classical references, Venus and Oedipus, in Tennessee Williams Suddenly Last Summer, in accordance with the usual nature of studies on Classical Tradition a Greek and Roman- and focusing in this case on the relationship between literature and mythology. It is thanks to Venus and Oedipus that the playwright succeeds in showing the magnitude of mens and womens tragedy, which from his point of view is simply that they have failed to see either kindness in the face of God or to feel his loving and fatherly providence.

Competing linguae france: the place of english and spanish for chinese students

This research project focuses on the role of English and Spanish as linguae francae. More specifically, the research attempts to answer the following questions: (i) What is the place of English and Spanish as linguae francae in the world, in general, and in China, in particular? (ii) What kinds of foreign language teaching/learning attitudes and practices are characteristic of the Chinese educational system? (iii) What are the motivations, expectations and experience of Chinese students in study abroad programmes, in general, and in the programme of the University of Lleida, in particular? The study constitutes an attempt to answer each of these questions in two ways: a review of the literature and a pilot study with 26 Chinese students at UdL. The research reveals that even though English is a very dominant foreign language in China, Spanish is a language on the rise and mainly for economic reasons. The results of the study also point at the impact of the dominance of the grammar-translation method in the perspective of Chinese students about language learning. Finally, the study shows the relevance of taking part in a SA programme for Chinese students as well as their experience of them.

Host genetics and HIV-1: the final phase?

This is a crucial transition time for human genetics in general, and for HIV host genetics in particular. After years of equivocal results from candidate gene analyses, several genome-wide association studies have been published that looked at plasma viral load or disease progression. Results from other studies that used various large-scale approaches (siRNA screens, transcriptome or proteome analysis, comparative genomics) have also shed new light on retroviral pathogenesis. However, most of the inter-individual variability in response to HIV-1 infection remains to be explained: genome resequencing and systems biology approaches are now required to progress toward a better understanding of the complex interactions between HIV-1 and its human host.

Forensic intelligence framework-Part I: induction of a transversal model by comparing illicit drugs and false identity documents monitoring

Forensic intelligence is a distinct dimension of forensic science. Forensic intelligence processes have mostly been developed to address either a specific type of trace or a specific problem. Even though these empirical developments have led to successes, they are trace-specific in nature and contribute to the generation of silos which hamper the establishment of a more general and transversal model. Forensic intelligence has shown some important perspectives but more general developments are required to address persistent challenges. This will ensure the progress of the discipline as well as its widespread implementation in the future. This paper demonstrates that the description of forensic intelligence processes, their architectures, and the methods for building them can, at a certain level, be abstracted from the type of traces considered. A comparative analysis is made between two forensic intelligence approaches developed independently in Australia and in Europe regarding the monitoring of apparently very different kind of problems: illicit drugs and false identity documents. An inductive effort is pursued to identify similarities and to outline a general model. Besides breaking barriers between apparently separate fields of study in forensic science and intelligence, this transversal model would assist in defining forensic intelligence, its role and place in policing, and in identifying its contributions and limitations. The model will facilitate the paradigm shift from the current case-by-case reactive attitude towards a proactive approach by serving as a guideline for the use of forensic case data in an intelligence-led perspective. A follow-up article will specifically address issues related to comparison processes, decision points and organisational issues regarding forensic intelligence (part II).

Intercultural Competence of Masters of Science in Business Administration and in Technology

Tutkielman tavoitteena on selvittää minkälaista kulttuurienvälistä kompetenssia Lappeenrannan teknillisestä yliopistosta vastavalmistuneilla kauppatieteenmaistereilla sekä diplomi-insinööreillä tulisi olla työnantajien näkökulmasta. Tutkimuksen tarkoituksena on myös tarkastella, että voidaanko kaikkia Lappeenrannan teknillisestä yliopistosta valmistuvia kutsua Kansainvälisiksi Huippuosaajiksi sekä kuinka Lappeenrannan teknillinen yliopisto voisi parantaa vastavalmistuvien kulttuurienvälistä kompetenssia. Teoreettinen osa tarkastelee kulttuurienvälisen kommunikaation tärkeimpiä elementtejä, kulttuurienvälistä kompetenssia ja vastavalmistuneiden kauppatieteenmaistereiden sekä diplomi-insinöörien tarvitsemaa ammatillista osaamista. Empiria koostuu kymmenen työnantajien teemahaastattelun tuloksista. Lopuksi johtopäätöksissä empirian tuloksia verrataan teorian löydöksiin. Tulokset osoittavat että kulttuurienvälinen kompetenssi koostuu kolmesta dimensiosta: henkilökohtaisista ominaisuuksista, tiedosta ja kommunikointikyvystä. Henkilökohtaisiin ominaisuuksiin sisältyvät empaattisuus, epävarmuuden sietokyky sekä avoin ja utelias asenne. Tieto - ulottuvuus koostuu yleisestä ja erityisestä kulttuuritiedosta, kielitaidosta sekä ammatillisesta osaamisesta. Kommunikointikykyyn puolestaan sisältyvät hyvät vuorovaikutustaidot. Työnantajat olettavat nykyään vastavalmistuneilla olevan ammatillisen osaamisen ja kielitaidon lisäksi, kulttuuritietoutta sekä kansainvälistä kokemusta. Lappeenrannan teknillinen yliopisto voisi parantaa vastavalmistuneiden kulttuurienvälistä kompetenssia tarjoamalla kulttuurienvälisen kommunikaation opetusta.

Patients' Needs for Care in Public Mental Health: Unity and Diversity of Self-Assessed Needs for Care.

PURPOSE: Needs assessment is recognized to be a key element of mental health care. Patients tend to present heterogeneous profiles of needs. However, there is no consensus in previous research about how patients' needs are organized. This study investigates both general and specific dimensions of patients' needs for care. METHODS: Patients' needs were assessed with ELADEB, an 18-domain self-report scale. The use of a self-assessment scale represents a unique way of obtaining patients' perceptions. A patient-centered psychiatric practice facilitates empowerment as it is based on the patients' personal motivations, needs, and wants. Four seventy-one patients' profiles were analyzed through exploratory factor analysis. RESULTS: A four-factor bifactor model, including one general factor and three specific factors of needs, was most adequate. Specific factors were (a) "finances" and "administrative tasks"; (b) "transports," "public places," "self-care," "housework," and "food"; and (c) "family," "children," "intimate relationships," and "friendship." CONCLUSION: As revealed by the general factor, patients expressing urgent needs in some domains are also more susceptible to report urgent needs in several other domains. This general factor relates to high versus low utilizers of public mental healthcare. Patients also present specific needs in life domains, which are organized in three dimensions: management, functional disabilities, and familial and interpersonal relationships. These dimensions relate to the different types of existing social support described in the literature.

The use of future-oriented knowledge in regional innovation processes: Research on knowledge generation, transfer and conversion

The importance of the regional level in research has risen in the last few decades and a vast literature in the fields of, for instance, evolutionary and institutional economics, network theories, innovations and learning systems, as well as sociology, has focused on regional level questions. Recently the policy makers and regional actors have also began to pay increasing attention to the knowledge economy and its needs, in general, and the connectivity and support structures of regional clusters in particular. Nowadays knowledge is generally considered as the most important source of competitive advantage, but even the most specialised forms of knowledge are becoming a short-lived resource for example due to the accelerating pace of technological change. This emphasizes the need of foresight activities in national, regional and organizational levels and the integration of foresight and innovation activities. In regional setting this development sets great challenges especially in those regions having no university and thus usually very limited resources for research activities. Also the research problem of this dissertation is related to the need to better incorporate the information produced by foresight process to facilitate and to be used in regional practice-based innovation processes. This dissertation is a constructive case study the case being Lahti region and a network facilitating innovation policy adopted in that region. Dissertation consists of a summary and five articles and during the research process a construct or a conceptual model for solving this real life problem has been developed. It is also being implemented as part of the network facilitating innovation policy in the Lahti region.

Approaches to Supply Chain Risk Management: Identification, Analysis and Control

Supply chain risk management has emerged as an increasingly important issue in logistics as disruptions in the supply chain have become critical issues for many companies. The scientific literature on the subject is developing and in many respects the understanding of it is still in its infancy. Thus, there is a need for more information in order for scholars and practitioners to understand the causalities and interrelations that characterise the phenomenon. The aim of this dissertation is to narrow this gap by exploring key aspects of supply chain risk management through two maritime supply chains in the immediate region of the Gulf of Finland. The study contributes to the field in three different ways. Firstly, it facilitates the identification of risks on different levels of the supply chain through a systematic analysis of the processes and actors, and of the cognitive barriers that limit the actors’ visibility and their understanding of the operations and the risks involved. There is a clear need to increase collaboration and information exchange in order to improve visibility in the chain. Risk management should be a collaborative effort among the individual actors, aimed at obtaining a holistic picture. Secondly, the study contributes to the literature on risk analysis through the use of systemic frameworks that illustrate the causalities and linkages in the system, thereby making it easier to perceive the vulnerabilities. Thirdly, the study enhances current knowledge of risk control in identifying actor roles, risk visibility and risk controllability as being among the key factors determining risk-management effectiveness against supply-chain vulnerability. This dissertation is divided into two parts. The first part gives a general overview of the relevant literature, the research design and the conclusions of the study, and the second part comprises six research publications. Case-study methodology with systematic combining approach is used, where in-depth interviews, questionnaires and expert panel sessions are the main data collection methods. The study illustrates the current state of risk management in multimodal maritime supply chains, and develops frameworks for further analysis. The results imply that there are major differences between organizations in their ability to execute supply chain risk management. Further collaboration should be considered in order to facilitate the development of systematic and effective management processes.

The purpose of consumer co-operation: implications for the management and governance of co-operatives

Extant research on consumer co-operation has acknowledged that the corporate purpose of consumer co-operatives deviates significantly from the purpose of investor-owned firms (IOFs – the dominant form in market economies and in theory development in the field of business economics) and also suggested that the management of consumer co-operatives differs from the management of IOFs. Despite this, there is a scarcity of research focusing on the management of consumer co-operatives in general and the ways this different purpose manifests in their management in particular. In other words, research on consumer cooperatives has only started to discover the importance of identifying the premises of these organizations and generating management and organization theories that take them into account. The overall objective of this study is to map out some of the implications that the purpose of consumer co-operation has for the management and governance of consumer co-operatives. To put it more precisely, by combining interview data gathered from Finnish consumer cooperatives (S Group, OP Bank Group and POP Bank) and extant literature, this study aims to generate or elaborate on definitions and outlines of the features that co-operative purpose poses for the strategic management, governance and managerial competence needed for consumer co-operatives. The study consists of two parts. The first part introduces the research topic, methods and publications, as well as discusses the overall outcomes. The second part consists of four publications that address the research questions from different viewpoints. The analyses of this study indicate that due to the purpose of consumer co-operation, the roles of locality and regionality become emphasized in their management. While locality and regionality are potential sources of competitive advantage for consumer co-operatives, geographic boundness sets significant boundary conditions for the strategic management of these organizations. Further, the purpose of consumer co-operation may pose several challenges to governance and set specific competence demands for the managers of these organizations. Associating the observations from various streams of research on management and governance with the purpose of consumer co-operation and examining these issues further, the thesis contributes to elaboration of theory in the field. While the thesis is by no means comprehensive (but instead reflects a co-operative research project in its early stages), it does shed light on some key ideas of management and governance and offers leads to theory and, thereby, will prove useful to elaborators, disseminators and appliers of knowledge on co-operation.

Credibility and Signaling in Disinflation- a Cross Country Examination

This paper develops a model of money demand where the opportunity cost of holding money is subject to regime changes. The regimes are fully characterized by the mean and variance of inflation and are assumed to be the result of alternative government policies. Agents are unable to directly observe whether government actions are indeed consistent with the inflation rate targeted as part of a stabilization program but can construct probability inferences on the basis of available observations of inflation and money growth. Government announcements are assumed to provide agents with additional, possibly truthful information regarding the regime. This specification is estimated and tested using data from the Israeli and Argentine high inflation periods. Results indicate the successful stabilization program implemented in Israel in July 1985 was more credible than either the earlier Israeli attempt in November 1984 or the Argentine programs. Government’s signaling might substantially simplify the inference problem and increase the speed of learning on the part of the agents. However, under certain conditions, it might increase the volatility of inflation. After the introduction of an inflation stabilization plan, the welfare gains from a temporary increase in real balances might be high enough to induce agents to raise their real balances in the short-term, even if they are uncertain about the nature of government policy and the eventual outcome of the stabilization attempt. Statistically, the model restrictions cannot be rejected at the 1% significance level.

The Backing of Government Debt and the Price Level

This paper studies the interdependence between fiscal and monetary policies, and their joint role in the determination of the price level. The government is characterized by a long-run fiscal policy rule whereby a given fraction of the outstanding debt, say d, is backed by the present discounted value of current and future primary surpluses. The remaining debt is backed by seigniorage revenue. The parameter d characterizes the interdependence between fiscal and monetary authorities. It is shown that in a standard monetary economy, this policy rule implies that the price level depends not only on the money stock, but also on the proportion of debt that is backed with money. Empirical estimates of d are obtained for OECD countries using data on nominal consumption, monetary base, and debt. Results indicate that debt plays only a minor role in the determination of the price level in these economies. Estimates of d correlate well with institutional measures of central bank independence.

The Law and Economics of the Civil Law of Mandate

Présentation à la Annual Law & Economics Conference 2007, Université de Bologne.

A Teacher’s Formative Assessment Perceptions and Practices in Oral Intermediate English Courses at the Université de Montréal

Au cours des dernières années, les pratiques de l’évaluation comme aide à l’apprentissage (c’est-à-dire l’auto-évaluation, l’évaluation par les pairs, la rétroaction) dans la salle de classe ont été de plus en plus considérées comme des éléments essentiels (Black & Wiliam, 1998; Harlen & Winter, 2004; van de Watering & van der Rijt, 2006). Cependant, dans le domaine de l’apprentissage d’une langue seconde la recherche sur ce sujet est plutôt limitée. En nous fondant sur les études de Colby-Kelly et Turner (2007) et de Lyster et Ranta (1997), nous avons mené une recherche exploratoire visant à combler ce besoin. L’objectif général était de comprendre comment l’évaluation formative se réalise dans deux cours d’anglais intermédiaire à l’Université de Montréal, et de comparer comment ces pratiques sont perçues et vécues par la professeure et ses étudiants. Trois questions de recherche étaient posées: 1. Quelle est la nature de l’évaluation formative dans une salle de classe d’anglais langue seconde? 2. Est-ce que les pratiques de la professeure reflètent ce qu’elle pense de l’évaluation formative? 3. Quels sont les correspondances et différences entre les croyances de la professeure et les perceptions de ses étudiants quant aux bénéfices de l’évaluation formative pour l’apprentissage de l’anglais langue seconde? La collecte de données comprend des observations en classe, des entrevues auprès de la professeure et des questionnaires pour les étudiants. Pour répondre à notre première question de recherche, nous avons analysé la rétroaction donnée par la professeure pendant une production orale réalisée par ses étudiants à partir de la typologie de feedback et de uptake de l’étude de Lyster et Ranta (1997). En ce qui a trait à la deuxième question de recherche, nous avons fait des entrevues avec la professeure en vue d’expliciter ses perceptions relativement à l’évaluation formative. À la fin du trimestre, nous avons comparé ses réponses avec sa pratique à partir des enregistrements vidéo produits en classe. Finalement, pour répondre à notre dernière question de recherche nous avons comparé les réponses données par la professeure aux entrevues avec les réponses des étudiants à un questionnaire adapté à partir de celui de Colby-Kelly et Turner. Finalement, nous présentons et discutons les résultats les plus significatifs obtenus dans cette étude qualitative Nous concluons cette thèse en proposant de avenues pour des recherches futures.

Being a bereaved parent : early bereavement experiences and perspectives on paediatric palliative care and bereavement services

La mort d'un enfant est considérée comme l'une des expériences les plus difficiles à laquelle une personne puisse faire face. Les cliniciens, les hôpitaux et plusieurs organismes ont pour objectif d’aider les parents endeuillés, mais leurs efforts sont compliqués par un manque de recherche dans le domaine du deuil parental. Cette thèse est composée de trois articles, soit deux revues de littérature et une étude empirique, qui tentent de combler cette lacune et d’informer les services en soins palliatifs pédiatriques et les services de soutien au deuil en particulier. Le premier article porte sur les besoins des patients recevant des soins palliatifs pédiatriques et de leurs familles. Par le biais d’un méta-résumé de la recherche descriptive et qualitative récente, 10 domaines de besoins ont été identifiés qui correspondent aux lignes directrices actuelles en soins palliatifs pédiatriques et de fin de vie. Ces besoins sont présentés de manière à être facilement applicables à la pratique. Cependant, les résultats mettent aussi en évidence plusieurs aspects des soins identifiés comme déficitaires ou problématiques qui mériteraient une attention particulière dans le cadre de politiques futures. Dans le deuxième article, l'objectif était de résumer une vaste littérature d'une manière utile aux cliniciens. À cette fin, une synthèse narrative a permis d’intégrer la recherche quantitative et qualitative dans le domaine du deuil parental. Les résultats mettent en évidence les éléments susceptibles de favoriser l’adaptation des parents au deuil, éléments qui suggèrent par le fait même des avenues possibles de soutien et d'intervention. Cette synthèse a cependant cerné dans la littérature certaines failles méthodologiques qui rendent l'applicabilité clinique des résultats difficile. L'objectif du troisième article était d'informer les services de suivi et de soutien au deuil auprès des parents en se renseignant directement auprès de parents endeuillés. À cette fin, 21 parents (dont 8 couples) et 7 membres du personnel impliqués dans des activités de suivi de deuil de 2 hôpitaux pédiatriques ont été interrogés dans le cadre d’une description interprétative, et l'application clinique des résultats a été vérifiée par le biais de réunions avec des collaborateurs de recherche et les décideurs des centres hospitaliers. Les résultats décrivent comment les parents ont fait face à leur détresse dans la phase précoce de leur deuil, ainsi que leurs points de vue sur la façon dont les divers services de suivi de deuil ont été aidants. Les résultats suggèrent que les parents gèrent leurs sentiments intenses de douleur par une alternance de stratégies axées soit sur leur deuil ou sur leur quotidien et que dans plusieurs cas leurs relations avec autrui les ont aidé. Cette étude a également permis d'élucider la façon dont divers services de soutien aide les parents à aborder leur deuil. Les implications cliniques de ces résultats sont discutées ainsi que des recommandations à l’intention de ceux qui sont impliqués dans la provision des services en deuil.