Mutations in cytochrome b that affect kinetics of the electron transfer reactions at center N in the yeast cytochrome bc1 complex

AbstractWe have examined the pre-steady-state kinetics and thermodynamic properties of the b hemes in variants of the yeast cytochrome bc1 complex that have mutations in the quinone reductase site (center N). Trp-30 is a highly conserved residue, forming a hydrogen bond with the propionate on the high potential b heme (bH heme). The substitution by a cysteine (W30C) lowers the redox potential of the heme and an apparent consequence is a lower rate of electron transfer between quinol and heme at center N. Leu-198 is also in close proximity to the bH heme and a L198F mutation alters the spectral properties of the heme but has only minor effects on its redox properties or the electron transfer kinetics at center N. Substitution of Met-221 by glutamine or glutamate results in the loss of a hydrophobic interaction that stabilizes the quinone ligands. Ser-20 and Gln-22 form a hydrogen-bonding network that includes His-202, one of the carbonyl groups of the ubiquinone ring, and an active-site water. A S20T mutation has long-range structural effects on center P and thermodynamic effects on both b hemes. The other mutations (M221E, M221Q, Q22E and Q22T) do not affect the ubiquinol oxidation kinetics at center P, but do modify the electron transfer reactions at center N to various extents. The pre-steady reduction kinetics suggest that these mutations alter the binding of quinone ligands at center N, possibly by widening the binding pocket and thus increasing the distance between the substrate and the bH heme. These results show that one can distinguish between the contribution of structural and thermodynamic factors to center N function

Nuclear Export of 60S Ribosomal Subunits Depends on Xpo1p and Requires a Nuclear Export Sequence-Containing Factor, Nmd3p, That Associates with the Large Subunit Protein Rpl10p

Nuclear export of ribosomes requires a subset of nucleoporins and the Ran system, but specific transport factors have not been identified. Using a large subunit reporter (Rpl25p-eGFP), we have isolated several temperature-sensitive ribosomal export (rix) mutants. One of these corresponds to the ribosomal protein Rpl10p, which interacts directly with Nmd3p, a conserved and essential protein associated with 60S subunits. We find that thermosensitive nmd3 mutants are impaired in large subunit export. Strikingly, Nmd3p shuttles between the nucleus and cytoplasm and is exported by the nuclear export receptor Xpo1p. Moreover, we show that export of 60S subunits is Xpo1p dependent. We conclude that nuclear export of 60S subunits requires the nuclear export sequence-containing nonribosomal protein Nmd3p, which directly binds to the large subunit protein Rpl10p

Fin du Monde, Fin du Mois, Même Combat: A Spatio-Temporal Analysis of Social and Environmental Inequalities in France

This study looks at issues of social and environmental justice in France. In particular, there are three case study cities: Toulouse, Marseille, and Lyon. These cities have suffered environmental degradation due to the industrial activities there that have been propagated by a capitalist regime and then perpetuated by media involvement. However, Lyon presents itself as a possible model moving forward. Citizens in this city have started to concern themselves over the state of their environment and protests and political actions are finally being taken. This study will analyze the demography of these three cities to find which neighborhoods and socioeconomic groups are suffering more than others from these events using census data from the L’Institut National de la Statistique et des Études Économiques. Air quality data from the European Environment Agency for Marseille and Lyon is also presented to analyze atmospheric pollution. This data is then used in ArcMap to create visuals that show the demographic makeup of neighborhoods as well as where they are in relation to highly polluted areas. Various literature is cited, analyzing the role of the media and how perspective on the temporality of events affects populations. I argue that reflections in the media pose these issues as mere “episodes” that can be ignored or saved for future generations, leading to the disenfranchisement of certain people.Bachelor of Art

Disulfide Bond Formation Involves a Quinhydrone-Type Charge–Transfer Complex

The chemistry of disulfide exchange in biological systems is well studied. However, the detailed mechanism of how oxidizing equivalents are derived to form disulfide bonds in proteins is not clear. In prokaryotic organisms, it is known that DsbB delivers oxidizing equivalents through DsbA to secreted proteins. DsbB becomes reoxidized by reducing quinones that are part of the membrane-bound electron-transfer chains. It is this quinone reductase activity that links disulfide bond formation to the electron transport system. We show here that purified DsbB contains the spectral signal of a quinhydrone, a charge-transfer complex consisting of a hydroquinone and a quinone in a stacked configuration. We conclude that disulfide bond formation involves a stacked hydroquinone-benzoquinone pair that can be trapped on DsbB as a quinhydrone charge-transfer complex. Quinhydrones are known to be redox-active and are commonly used as redox standards, but, to our knowledge, have never before been directly observed in biological systems. We also show kinetically that this quinhydrone-type charge-transfer complex undergoes redox reactions consistent with its being an intermediate in the reaction mechanism of DsbB. We propose a simple model for the action of DsbB where a quinhydrone-like complex plays a crucial role as a reaction intermediate

The potential contributions of concept maps for learning website to assessment for learning practices

The purpose of this paper is to examine the promising contributions of the Concept Maps for Learning (CMfL) website to assessment for learning practices. The CMfL website generates concept maps from relatedness degree of concepts pairs through the Pathfinder Scaling Algorithm. This website also confirms the established principles of effective assessment for learning, for it is capable of automatically assessing students’ higher order knowledge, simultaneously identifying strengths and weaknesses, immediately providing useful feedback and being user-friendly. According to the default assessment plan, students first create concept maps on a particular subject and then they are given individualized visual feedback followed by associated instructional material (e.g., videos, website links, examples, problems, etc.) based on a comparison of their concept map and a subject matter expert’s map. After studying the feedback and instructional material, teachers can monitor their students’ progress by having them create revised concept maps. Therefore, we claim that the CMfL website may reduce the workload of teachers as well as provide immediate and delayed feedback on the weaknesses of students in different forms such as graphical and multimedia. For the following study, we will examine whether these promising contributions to assessment for learning are valid in a variety of subjects

Exploring the Mobile Structural Assessment Tool: Concept Maps for Learning Website

In this paper, we describe how the pathfinder algorithm converts relatedness ratings of concept pairs to concept maps; we also present how this algorithm has been used to develop the Concept Maps for Learning website (www.conceptmapsforlearning.com) based on the principles of effective formative assessment. The pathfinder networks, one of the network representation tools, claim to help more students memorize and recall the relations between concepts than spatial representation tools (such as Multi- Dimensional Scaling). Therefore, the pathfinder networks have been used in various studies on knowledge structures, including identifying students’ misconceptions. To accomplish this, each student’s knowledge map and the expert knowledge map are compared via the pathfinder software, and the differences between these maps are highlighted. After misconceptions are identified, the pathfinder software fails to provide any feedback on these misconceptions. To overcome this weakness, we have been developing a mobile-based concept mapping tool providing visual, textual and remedial feedback (ex. videos, website links and applets) on the concept relations. This information is then placed on the expert concept map, but not on the student’s concept map. Additionally, students are asked to note what they understand from given feedback, and given the opportunity to revise their knowledge maps after receiving various types of feedback.En este artículo se describe cómo el algoritmo de búsqueda de ruta convierte puntajes de conceptos pareados en mapas conceptuales. También se presenta cómo este algoritmo ha sido utilizado para desarrollar estos mapas conceptuales para aprendizaje (www.conceptmapsforlearning.com) basados en los principios del aseguramiento formativo efectivo. Las redes de búsqueda de ruta, una de las herramientas de representación de redes, ayudan a memorizar a los estudiantes y enunciar las relaciones entre mapas más que las herramientas de expresión espacial (tales como el escalonamiento multidimensional). Por tanto, las redes de búsqueda de rutas han sido usadas en varios estudios de estructura del conocimiento incluyendo la identificación de malos conceptos usados por los estudiantes. Para lograr esto, cada mapa de conocimiento tanto del estudiante como del experto son comparados vía el software de búsqueda de ruta y se remarcan las diferencias entre éstos. Después que los malos conceptos son identificados, el software de búsqueda falla en entregar una retroalimentación en estos nodos conceptuales. Para superar esta debilidad, se desarrolla una herramienta de mapa conceptual móvil que manda retroalimentaciones visuales, textuales y remediales (e.g. vídeos, enlaces a páginas web y applets) en las relaciones de los conceptos. Adicionalmente, los estudiantes son preguntados acerca de qué entienden de la retroalimentación brindada y se les da la oportunidad de revisar sus mapas de conocimiento después de recibir varios tipos de retroalimentación

Making Interdisciplinary Collaboration Work: Key Ideas, a Case Study and Lessons Learned

This article discusses the ‘lessons learned’ from an attempt to establish an interdisciplinary education research group. The growth, development and dissolution of the group are treated as an instrumental case study. Current literature on interdisciplinary collaboration is synthesized in order to provide a frame for analysis. Data was collected over several years and included three rounds of written participant reflections and documentation of group activities and meetings. Five major themes arose from the research, covering issues such as disciplinary diversity, common ground, interpersonal relationships, career pressures, and the need for concrete problems and tangible progress. Based on these themes, a number of ‘lessons learned’ are discussed which will likely be of great interest to those considering similar interdisciplinary initiatives.Cet article discute des «leçons apprises» d’une tentative visant l’établissement d’un groupe de recherche sur l’enseignement interdisciplinaire. La croissance, le développement et la dissolution du groupe sont présentés comme une étude de cas déterminante. Les ouvrages actuels portant sur la collaboration interdisciplinaire sont synthétisés de sorte à produire un cadre pour l’analyse. La collecte des données s’est étendue sur plusieurs années et a impliqué trois cycles de réflexions écrites par les participants et de documentation des activités de groupe et des réunions. Cinq grands thèmes ont découlé de la recherche, portant sur des questions comme la diversité disciplinaire, le terrain d’entente, les relations interpersonnelles, les pressions professionnelles, et le besoin de problèmes concrets et de progrès tangibles. À partir de ces thèmes, on discute de plusieurs «leçons apprises» qui intéresseront sans doute ceux qui envisagent des initiatives interdisciplinaires similaires

Terminal Electron–Proton Transfer Dynamics in the Quinone Reduction of Respiratory Complex I

Complex I functions as a redox-driven proton pump in aerobic respiratory chains. By reducing quinone (Q), complex I employs the free energy released in the process to thermodynamically drive proton pumping across its membrane domain. The initial Q reduction step plays a central role in activating the proton pumping machinery. In order to probe the energetics, dynamics, and molecular mechanism for the proton-coupled electron transfer process linked to the Q reduction, we employ here multiscale quantum and classical molecular simulations. We identify that both ubiquinone (UQ) and menaquinone (MQ) can form stacking and hydrogen-bonded interactions with the conserved Q binding-site residue His-38 and that conformational changes between these binding modes modulate the Q redox potentials and the rate of electron transfer (eT) from the terminal N2 iron-sulfur center. We further observe that, while the transient formation of semiquinone is not proton-coupled, the second eT process couples semiconcerted proton uptake from conserved tyrosine (Tyr-87) and histidine (His-38) residues within the active site. Our calculations indicate that both UQ and MQ have low redox potentials around -260 and -230 mV, respectively, in the Q-binding site, respectively, suggesting that release of the Q toward the membrane is coupled to an energy transduction step that could thermodynamically drive proton pumping in complex I.Peer reviewe