Integrative Analysis of the Mitochondrial Proteome in Yeast

In this study yeast mitochondria were used as a model system to apply, evaluate, and integrate different genomic approaches to define the proteins of an organelle. Liquid chromatography mass spectrometry applied to purified mitochondria identified 546 proteins. By expression analysis and comparison to other proteome studies, we demonstrate that the proteomic approach identifies primarily highly abundant proteins. By expanding our evaluation to other types of genomic approaches, including systematic deletion phenotype screening, expression profiling, subcellular localization studies, protein interaction analyses, and computational predictions, we show that an integration of approaches moves beyond the limitations of any single approach. We report the success of each approach by benchmarking it against a reference set of known mitochondrial proteins, and predict approximately 700 proteins associated with the mitochondrial organelle from the integration of 22 datasets. We show that a combination of complementary approaches like deletion phenotype screening and mass spectrometry can identify over 75% of the known mitochondrial proteome. These findings have implications for choosing optimal genome-wide approaches for the study of other cellular systems, including organelles and pathways in various species. Furthermore, our systematic identification of genes involved in mitochondrial function and biogenesis in yeast expands the candidate genes available for mapping Mendelian and complex mitochondrial disorders in humans

Cross-Sample Validation Provides Enhanced Proteome Coverage in Rat Vocal Fold Mucosa

The vocal fold mucosa is a biomechanically unique tissue comprised of a densely cellular epithelium, superficial to an extracellular matrix (ECM)-rich lamina propria. Such ECM-rich tissues are challenging to analyze using proteomic assays, primarily due to extensive crosslinking and glycosylation of the majority of high Mr ECM proteins. In this study, we implemented an LC-MS/MS-based strategy to characterize the rat vocal fold mucosa proteome. Our sample preparation protocol successfully solubilized both proteins and certain high Mr glycoconjugates and resulted in the identification of hundreds of mucosal proteins. A straightforward approach to the treatment of protein identifications attributed to single peptide hits allowed the retention of potentially important low abundance identifications (validated by a cross-sample match and de novo interpretation of relevant spectra) while still eliminating potentially spurious identifications (global single peptide hits with no cross-sample match). The resulting vocal fold mucosa proteome was characterized by a wide range of cellular and extracellular proteins spanning 12 functional categories

Plasma-liquid interactions: a review and roadmap

Plasma-liquid interactions represent a growing interdisciplinary area of research involving plasma science, fluid dynamics, heat and mass transfer, photolysis, multiphase chemistry and aerosol science. This review provides an assessment of the state-of-the-art of this multidisciplinary area and identifies the key research challenges. The developments in diagnostics, modeling and further extensions of cross section and reaction rate databases that are necessary to address these challenges are discussed. The review focusses on non-equilibrium plasmas

Plasma–liquid interactions: a review and roadmap

Plasma–liquid interactions represent a growing interdisciplinary area of research involving plasma science, fluid dynamics, heat and mass transfer, photolysis, multiphase chemistry and aerosol science. This review provides an assessment of the state-of-the-art of this multidisciplinary area and identifies the key research challenges. The developments in diagnostics, modeling and further extensions of cross section and reaction rate databases that are necessary to address these challenges are discussed. The review focusses on non-equilibrium plasmas

The coherence(s) of institutional resource regimes: Typology and assessments from the case of water supply management

Coherence is pivotal to integrate governance and, presumably, to improve sustainability because of more coordination efficiency. The coherence of governance refers to the clarity and the compatibility of public policies and property rights. The institutional resource regimes framework put forward that integration also depends on the scope of uses regulated (extent). Coherence has been under-investigated in comparison to extent. Notably, there is no common avenue of appraising it. In this paper, we propose a typology of coherence and assess it through an operationalisation in the Swiss water supply sector. It offers methodological tools and theoretical developments contributing to the comparative analysis of these policy studies central aspects. The typology stands on the IRR definition of integration, and we introduce the relation of coherence to extent, which emphasises the impact of polycentricity and transaction costs. To put into practice the typology and assess the different types of coherence, we gathered data from 96 water utility managers in French-speaking Switzerland. Results indicate that extent-related coherence is troublesome while the discrete coherence of each public policy and property right reveal satisfying. Despite an increasing focus on horizontal issues (siloisation, intersectoral), we observe more coherence issues related to vertical aspects of the governance

Trois modèles comparés de gestion urbaine de l'eau en Europe: régulation des services, gestion des réseaux et participation à la decision

La gestion des services d'eau urbains en Europe dépend d'une règle commune, la Directive Cadre sur l'Eau. Promulguée en 2000, cette directive européenne vise à moderniser et accroitre la soutenabilité de la gestion de l'eau en instituant des principes communs. Dans le cas des services d'eau, elle s'accompagne de directives sur les marchés publiques, la concurrence et la délégation. Malgré ce cadre commun, une diversité de modes de gestion perdure en Europe. En particulier, trois modèles embrassent la diversité des situations: anglais, français et allemand (du plus libéral au moins libéral). Quatre grandes tendances, absentes lors du développement des services et des réseaux, marquent l'aujourd'hui et le futur des services d'eau : la prise en compte de l'environnement, la baisse des consommations, l'étalement urbain et la privatisation. Il s'agit dès lors de comprendre comment les services d'eau actuels peuvent transformer leur organisation afin de faire face à ces changements structurels. L'objectif de cette présentation est de proposer un exercice prospectif sur la vulnérabilité relative de chaque modèle face à ces tendances. Comment le modèle allemand intègre le mouvement de privatisation alors que le modèle anglais repose dessus ? Quels sont les avantages et inconvénients d'une gestion reposant sur le marché et les incitations (Angleterre) en comparaison à une gestion publique et locale (Allemagne) pour organiser la pérennité des réseaux ? Pour répondre à ce type de questions, nous abordons trois thèmes centraux à la gestion des services d'approvisionnement en eau potable: les modalités de régulation des services, la gestion des réseaux et la participation du public à la décision