Combined transcriptomic and proteomic studies reveal non-canonical signaling functions in the jasmonate pathway

Abstract Lipid derived signals mediate many stress and defense responses in multicellular eukaryotes. Among these are the jasmonates, potently active signaling compounds in plants. Jasmonic acid (JA) and 12-oxo-phytodienoic acid (OPDA) are the two best known members of the large jasmonate family. This thesis further investigates their roles as signals using genomic and proteomic approaches. The study is based on a simple genetic model involving two key genes. The first is ALLENE OXIDE SYNTHASE (AOS), encoding the most important enzyme in generating jasmonates. The second is CORONATINE INSENSITIVE 1 (COI1), a gene involved in all currently documented canonical signaling responses. We asked the simple question: do null mutations in AOS and COI1 have analogous effects on the transcriptome ? We found that they do not. If most COI1-dependent genes were also AOS-dependent, the expression of a zinc-finger protein was AOS-dependent but was unaffected by the coi1-1 mutation. We thus supposed that a jasmonate member, most probably OPDA, can alter gene expression partially independently of COI1. Conversely, the expression of at least three genes, one of these is a protein kinase, was shown to be COI1-dependent but did not require a functional AOS protein. We conclude that a non-jasmonate signal might alter gene expression through COIL Proteomic comparison of coi1-1 and aos plants confirmed these observations and highlighted probable protein degradation processes controlled by jasmonates and COI1 in the wounded leaf. This thesis revealed new functions for COI1 and for AOS-generated oxylipins in the jasmonate signaling pathway. Résumé Les signaux dérivés d'acides gras sont des médiateurs de réponses aux stress et de la défense des eucaryotes multicellulaires. Parmi eux, les jasmonates sont de puissants composés de sig¬nalisation chez les plantes. L'acide jasmonique (JA) et l'acide 12-oxo-phytodienoïc (OPDA) sont les deux membres les mieux caractérisés de la grande famille des jasmonates. Cette thèse étudie plus profondément leurs rôles de signalisation en utilisant des approches génomique et protéomique. Cette étude est basée sur un modèle génétique simple n'impliquant que deux gènes. Le premier est PALLENE OXYDE SYNTHASE (AOS) qui encode l'enzyme la plus importante pour la fabrication des jasmonates. Le deuxième est CORONATINE INSENSITIVE 1 (COI1) qui est impliqué dans la totalité des réponses aux jasmonates connues à ce jour. Nous avons posé la question suivante : est-ce que les mutations nulles dans les gènes AOS et COI1 ont des effets analogues sur le transcriptome ? Nous avons trouvé que ce n'était pas le cas. Si la majorité des gènes dépendants de COI1 sont également dépendants d'AOS, l'expression d'un gène codant pour une protéine formée de doigts de zinc n'est pas affectée par la mutation de COI1 tout en étant dépendante d'AOS. Nous avons donc supposé qu'un membre de la famille des jasmonates, probablement OPDA, pouvait modifier l'expression de certains gènes indépendamment de COI1. Inversement, nous avons montré que, tout en étant dépendante de COI1, l'expression d'au moins trois gènes, dont un codant pour une protéine kinase, n'était pas affectée par l'absence d'une protéine AOS fonctionnelle. Nous en avons conclu qu'un signal autre qu'un jasmonate devait modifier l'expression de certains gènes à travers COI1. La comparaison par protéomique de plantes aos et coi1-1 a confirmé ces observations et a mis en évidence un probable processus de dégradation de protéines contrôlé par les jasmonates et COU_ Cette thèse a mis en avant de nouvelles fonctions pour COI1 et pour des oxylipines générées par AOS dans le cadre de la signalisation par les jasmonates.

Three essays in dynamic corporate finance

The three essays constituting this thesis focus on financing and cash management policy. The first essay aims to shed light on why firms issue debt so conservatively. In particular, it examines the effects of shareholder and creditor protection on capital structure choices. It starts by building a contingent claims model where financing policy results from a trade-off between tax benefits, contracting costs and agency costs. In this setup, controlling shareholders can divert part of the firms' cash ows as private benefits at the expense of minority share- holders. In addition, shareholders as a class can behave strategically at the time of default leading to deviations from the absolute priority rule. The analysis demonstrates that investor protection is a first order determinant of firms' financing choices and that conflicts of interests between firm claimholders may help explain the level and cross-sectional variation of observed leverage ratios. The second essay focuses on the practical relevance of agency conflicts. De- spite the theoretical development of the literature on agency conflicts and firm policy choices, the magnitude of manager-shareholder conflicts is still an open question. This essay proposes a methodology for quantifying these agency conflicts. To do so, it examines the impact of managerial entrenchment on corporate financing decisions. It builds a dynamic contingent claims model in which managers do not act in the best interest of shareholders, but rather pursue private benefits at the expense of shareholders. Managers have discretion over financing and dividend policies. However, shareholders can remove the manager at a cost. The analysis demonstrates that entrenched managers restructure less frequently and issue less debt than optimal for shareholders. I take the model to the data and use observed financing choices to provide firm-specific estimates of the degree of managerial entrenchment. Using structural econometrics, I find costs of control challenges of 2-7% on average (.8-5% at median). The estimates of the agency costs vary with variables that one expects to determine managerial incentives. In addition, these costs are sufficient to resolve the low- and zero-leverage puzzles and explain the time series of observed leverage ratios. Finally, the analysis shows that governance mechanisms significantly affect the value of control and firms' financing decisions. The third essay is concerned with the documented time trend in corporate cash holdings by Bates, Kahle and Stulz (BKS,2003). BKS find that firms' cash holdings double from 10% to 20% over the 1980 to 2005 period. This essay provides an explanation of this phenomenon by examining the effects of product market competition on firms' cash holdings in the presence of financial constraints. It develops a real options model in which cash holdings may be used to cover unexpected operating losses and avoid inefficient closure. The model generates new predictions relating cash holdings to firm and industry characteristics such as the intensity of competition, cash flow volatility, or financing constraints. The empirical examination of the model shows strong support of model's predictions. In addition, it shows that the time trend in cash holdings documented by BKS can be at least partly attributed to a competition effect.

Compliance with preoperative oral nutritional supplements in patients at nutritional risk─only a question of will?

BACKGROUND/OBJECTIVES: Preoperative nutrition has been shown to reduce morbidity after major gastrointestinal (GI) surgery in selected patients at risk. In a randomized trial performed recently (NCT00512213), almost half of the patients, however, did not consume the recommended dose of nutritional intervention. The present study aimed to identify the risk factors for noncompliance. SUBJECTS/METHODS: Demographic (n=5) and nutritional (n=21) parameters for this retrospective analysis were obtained from a prospectively maintained database. The outcome of interest was compliance with the allocated intervention (ingestion of ⩾11/15 preoperative oral nutritional supplement units). Uni- and multivariate analyses of potential risk factors for noncompliance were performed. RESULTS: The final analysis included 141 patients with complete data sets for the purpose of the study. Fifty-nine patients (42%) were considered noncompliant. Univariate analysis identified low C-reactive protein levels (P=0.015), decreased recent food intake (P=0.032) and, as a trend, low hemoglobin (P=0.065) and low pre-albumin (P=0.056) levels as risk factors for decreased compliance. However, none of them was retained as an independent risk factor after multivariate analysis. Interestingly, 17 potential explanatory parameters, such as upper GI cancer, weight loss, reduced appetite or co-morbidities, did not show any significant correlation with reduced intake of nutritional supplements. CONCLUSIONS: Reduced compliance with preoperative nutritional interventions remains a major issue because the expected benefit depends on the actual intake. Seemingly, obvious reasons could not be retained as valid explanations. Compliance seems thus to be primarily a question of will and information; the importance of nutritional supplementation needs to be emphasized by specific patients' education.

Acute schistosomiasis: a risk underestimated by travelers and a diagnosis frequently missed by general practitioners-a cluster analysis of 42 travelers.

BACKGROUND: In 2011, a patient was admitted to our hospital with acute schistosomiasis after having returned from Madagascar and having bathed at the Lily waterfalls. On the basis of this patient's indication, infection was suspected in 41 other subjects. This study investigated (1) the knowledge of the travelers about the risks of schistosomiasis and their related behavior to evaluate the appropriateness of prevention messages and (2) the diagnostic workup of symptomatic travelers by general practitioners to evaluate medical care of travelers with a history of freshwater exposure in tropical areas. METHODS: A questionnaire was sent to the 42 travelers with potential exposure to schistosomiasis. It focused on pre-travel knowledge of the disease, bathing conditions, clinical presentation, first suspected diagnosis, and treatment. RESULTS: Of the 42 questionnaires, 40 (95%) were returned, among which 37 travelers (92%) reported an exposure to freshwater, and 18 (45%) were aware of the risk of schistosomiasis. Among these latter subjects, 16 (89%) still reported an exposure to freshwater. Serology was positive in 28 (78%) of 36 exposed subjects at least 3 months after exposure. Of the 28 infected travelers, 23 (82%) exhibited symptoms and 16 (70%) consulted their general practitioner before the information about the outbreak had spread, but none of these patients had a serology for schistosomiasis done during the first consultation. CONCLUSIONS: The usual prevention message of avoiding freshwater contact when traveling in tropical regions had no impact on the behavior of these travelers, who still went swimming at the Lily waterfalls. This prevention message should, therefore, be either modified or abandoned. The clinical presentation of acute schistosomiasis is often misleading. General practitioners should at least request an eosinophil count, when confronted with a returning traveler with fever. If eosinophilia is detected, it should prompt the search for a parasitic disease.

Authorship in scientific publications: analysis and recommendations.

In 2008, a Swiss Academies of Arts and Sciences working group chaired by Professor Emilio Bossi issued a "Memorandum on scientific integrity and the handling of misconduct in the scientific context", together with a paper setting out principles and procedures concerning integrity in scientific research. In the Memorandum, unjustified claims of authorship in scientific publications are referred to as a form of scientific misconduct - a view widely shared in other countries. In the Principles and Procedures, the main criteria for legitimate authorship are specified, as well as the associated responsibilities. It is in fact not uncommon for disputes about authorship to arise with regard to publications in fields where research is generally conducted by teams rather than individuals. Such disputes may concern not only the question who is or is not to be listed as an author but also, frequently, the precise sequence of names, if the list is to reflect the various authors' roles and contributions. Subjective assessments of the contributions made by the individual members of a research group may differ substantially. As scientific collaboration - often across national boundaries - is now increasingly common, ensuring appropriate recognition of all parties is a complex matter and, where disagreements arise, it may not be easy to reach a consensus. In addition, customs have changed over the past few decades; for example, the practice of granting "honorary" authorship to an eminent researcher - formerly not unusual - is no longer considered acceptable. It should be borne in mind that the publications list has become by far the most important indicator of a researcher's scientific performance; for this reason, appropriate authorship credit has become a decisive factor in the careers of young researchers, and it needs to be managed and protected accordingly. At the international and national level, certain practices have therefore developed concerning the listing of authors and the obligations of authorship. The Scientific Integrity Committee of the Swiss Academies of Arts and Sciences has collated the relevant principles and regulations and formulated recommendations for authorship in scientific publications. These should help to prevent authorship disputes and offer guidance in the event of conflicts.