A dominant negative mutant of the E. coli RNA helicase DbpA blocks assembly of the 50S ribosomal subunit

Escherichia coli DbpA is an ATP-dependent RNA helicase with specificity for hairpin 92 of 23S ribosomal RNA, an important part of the peptidyl transferase center. The R331A active site mutant of DbpA confers a dominant slow growth and cold sensitive phenotype when overexpressed in E. coli containing endogenous DbpA. Ribosome profiles from cells overexpressing DbpA R331A display increased levels of 50S and 30S subunits and decreased levels 70S ribosomes. Profiles run at low Mg2+ exhibit fewer 50S subunits and accumulate a 45S particle that contains incompletely processed and undermodified 23S rRNA in addition to reduced levels of several ribosomal proteins that bind late in the assembly pathway. Unlike mature 50S subunits, these 45S particles can stimulate the ATPase activity of DbpA, indicating that hairpin 92 has not yet been sequestered within the 50S subunit. Overexpression of the inactive DbpA R331A mutant appears to block assembly at a late stage when the peptidyl transferase center is formed, indicating a possible role for DbpA promoting this conformational change

Loss of a Conserved tRNA Anticodon Modification Perturbs Plant Immunity

[EN] tRNA is the most highly modified class of RNA species, and modifications are found in tRNAs from all organisms that have been examined. Despite their vastly different chemical structures and their presence in different tRNAs, occurring in different locations in tRNA, the biosynthetic pathways of the majority of tRNA modifications include a methylation step(s). Recent discoveries have revealed unprecedented complexity in the modification patterns of tRNA, their regulation and function, suggesting that each modified nucleoside in tRNA may have its own specific function. However, in plants, our knowledge on the role of individual tRNA modifications and how they are regulated is very limited. In a genetic screen designed to identify factors regulating disease resistance and activation of defenses in Arabidopsis, we identified SUPPRESSOR OF CSB3 9 (SCS9). Our results reveal SCS9 encodes a tRNA methyltransferase that mediates the 2'-O-ribose methylation of selected tRNA species in the anticodon loop. These SCS9-mediated tRNA modifications enhance during the course of infection with the bacterial pathogen Pseudomonas syringae DC3000, and lack of such tRNA modification, as observed in scs9 mutants, severely compromise plant immunity against the same pathogen without affecting the salicylic acid (SA) signaling pathway which regulates plant immune responses. Our results support a model that gives importance to the control of certain tRNA modifications for mounting an effective immune response in Arabidopsis, and therefore expands the repertoire of molecular components essential for an efficient disease resistance response.This work was supported by the National Science Foundation of China (grant 31100268 to PC) and the Spanish MINECO (BFU2012 to PV) and Generalitat Valenciana (Prometeo2014/020 to PV). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Ramirez Garcia, V.; González-García, B.; López Sánchez, A.; Castelló Llopis, MJ.; Gil, M.; Zheng, B.; Cheng, P.... (2015). Loss of a Conserved tRNA Anticodon Modification Perturbs Plant Immunity. PLoS Genetics. 11(10):1-27. https://doi.org/10.1371/journal.pgen.1005586S127111

Design components of lifestyles in sustainable urban systems : inter- and transdisciplinary studies

Three traditional strands of lifestyle research can be identified in more than a hundred years: consumer, health, and housing lifestyles. These traditional strands of lifestyle research were studied in different academic disciplines such as psychology, sociology, economics, medicine, urban studies, and environmental sciences. Lifestyles were, however, not explored in-depth from an interdisciplinary and transdisciplinary sustainability perspective on human- environment systems (HES). Fostering sustainable lifestyles in urban systems is of practical relevance, as the optimization of efficient technologies alone will not be enough to achieve a degree of environmental protection that maintains world’s capacities. Since a sustainable development depends on and influences the psychological and sociological matrix of HES, it is important to integrate the views of different stakeholder groups into urban planning. An understanding of the views of different stakeholder groups can aid urban planning to realize a sustainable transition of urban systems. The research question of this thesis is to create theoretical and empirical evidence in lifestyles in order to enable science and practice to plan a sustainable urban development that is successful in a market economy. Firstly, theoretical evidence is embedded into an interdisciplinary framework of HES. Secondly, empirical evidence is presented from two studies on the views of different stakeholder groups. This cumulative thesis consists of three related contributions: The first contribution provides a review of lifestyle research. It contributes to the critical question of how the buzzword “lifestyle” can be transformed into a scientific concept that can be used for science and practice on sustainable urban living. The second contribution provides a study of sustainability criteria that key financial stakeholders regard as important for the market success of sustainable real estate funds (S-REFs), and how they assess the market acceptance of such funds. The third contribution provides a scenario assessment of six urban planning scenarios by members of different stakeholder groups in the Canton of Basel-Stadt. It depicts different alternative futures with respect to the sustainability performance of “Erlenmatt”, a major urban redevelopment project in the Canton of Basel-Stadt. The case study area comprises 19.2 hectares composed of about eight hectares of parkways, public spaces, and a conservation area. Erlenmatt, a mixed-usage district with about 700 apartments for 1,800-2,000 inhabitants and 1,100-2,000 working places on 10 building plots, will be developed during the next 15-20 years. The empirical studies were conducted in the German-speaking parts of Switzerland. The views of housing suppliers, the non-profit & public sector, and housing target groups were studied (n = 182). Housing suppliers were investors, principals, real estate fund (REF) suppliers, project developers, responsible experts and architects. The non-profit & public sector consisted of planning administrators and representatives of sustainability non- governmental organizations (NGOs). Housing target groups were parents of young families and life science personnel with a modern orientation. The first contribution provided a lifestyle definition that is based on an interdisciplinary review of psychological and sociological lifestyle research. The lifestyle definition is based on the Lewinian field theory and HES. Lifestyles are patterns of thinking and behaviour with habitual and self-identificatory potential, through which individuals express social affiliation and distinction. The second contribution found that S-REFs serve as a responsible property investment that foster the expression of sustainable lifestyles. The contribution identified sustainability criteria and drivers for key financial stakeholders’ market acceptance of S-REFs. The third contribution found that more sustainable scenarios for the case study (Erlenmatt) are preferred with respect to desirability and utility, and that their probability is not estimated lower than other scenarios. The non-profit & public sector is most pessimistic about the probability of a sustainable district, whilst housing suppliers desire it less. The results suggest that stakeholder groups have to realize transitions for urban lifestyles and efficient technologies that perform well, create consent, and are successful in a market economy. Lifestyles provide incentives and barriers for regulating urban systems, and give in-depth information for their sustainable transition. Such a transition of urban systems requires the sustainable development of coupled HES. Real estate finance instruments and planning options, which foster a sustainable development, have to be assessed by different stakeholder groups using different assessment indicators. The aim is to choose an optimal strategy for implementation, which is thoroughly assessed as well as broadly accepted by different stakeholder groups. Drei Stränge der Lebensstilforschung können über den Verlauf von mehr als hundert Jahren identifiziert werden: Konsum-, Gesundheits- und Wohnlebensstile. Diese traditionellen Stränge der Lebensstilforschung wurden in verschiedenen wissenschaftlichen Disziplinen wie Psychologie, Soziologie, Wirtschaftswissenschaften, Medizin, Stadtforschung und Umweltwissenschaften untersucht. Lebensstile wurden jedoch nicht sehr eingehend von einer interdisziplinären und transdisziplinären Nachhaltigkeitsperspektive auf Mensch-Umwelt- Systeme (MUS) erforscht. Nachhaltige Lebensstile in Stadtsystemen zu fördern ist von praktischer Relevanz. Die Optimierung effizienter Technologien alleine wird nicht ausreichen, um einen Grad an Umweltschutz zu erreichen, der die Tragfähigkeit der Erde aufrecht erhält. Da eine nachhaltige Entwicklung von der psychologischen und soziologischen Matrix von MUS abhängt und diese beeinflusst, ist es von Bedeutung, die Ansichten verschiedener Interessengruppen in die Stadtplanung einzubinden. Ein Verständnis, welche Ansichten verschiedene Interessengruppen über Lebensstile haben, kann der Stadtplanung bei der nachhaltigen Umwandlung von Stadtsystemen helfen. Die Forschungsfrage dieser Arbeit ist theoretische und praktische Belege über Lebensstile zu finden um es Wissenschaft und Praxis zu ermöglichen eine nachhaltige Stadtentwicklung zu planen, die in einer Marktwirtschaft erfolgreich ist. Erstens wird das Lebensstil-Konzept theoretisch in einen interdisziplinären Rahmen von MUS eingebettet. Zweitens werden empirische Belege aus zwei Untersuchungen über die Ansichten verschiedener Interessengruppen präsentiert. Diese kumulative These besteht aus drei aufeinander bezogenen Beiträgen: Der erste Beitrag liefert eine Literaturübersicht zur Lebensstilforschung. Er trägt zur kritischen Frage bei, wie das Modewort „Lebensstil“ in ein wissenschaftliches Konzept umgeformt werden kann, das für die Wissenschaft und Praxis nachhaltigen Stadtlebens verwendet werden kann. Der zweite Beitrag liefert eine Studie über die Nachhaltigkeitskriterien, die Schlüsselfinanzakteure als wichtig für den Markterfolg von Nachhaltigen Immobilienfonds (NIFs) erachten, und wie sie die Marktakzeptanz solcher Fonds bewerten. Der dritte Beitrag liefert eine Szenariobewertung von sechs Stadtplanungsszenarien durch Mitglieder verschiedener Interessengruppen des Kantons Basel-Stadt. Er zeigt unterschiedliche alternative Zukünfte in Bezug auf die Nachhaltigkeitsleistung der „Erlenmatt“, einem größeren städtischen Umnutzungsprojekt im Kanton Basel-Stadt. Das Fallstudienareal umfasst 19,2 Hektar, davon etwa acht Hektar Parkanlagen, öffentliche Plätze und ein Naturschutzgebiet. Die Erlenmatt, ein gemischt genutztes Quartier mit etwa 700 Wohnungen für 1.800-2.000 Einwohner und 1.100-2.000 Arbeitsplätze auf 10 Baufeldern, wird im Verlauf der nächsten 15-20 Jahre entwickelt. Die empirischen Studien wurden in der deutschsprachigen Schweiz durchgeführt. Es wurden die Ansichten von Wohnanbietern, des gemeinnützigen & öffentlichen Sektors und von Bewohnerzielgruppen untersucht (n = 182). Wohnanbieter waren Investoren, Bauherren, Immobilienfondsanbieter, Projektentwickler, verantwortliche Fachpersonen und Architekten. Der gemeinnützige & öffentliche Sektor bestand aus Planungsbeauftragten und Vertretern von nachhaltigen Nichtregierungsorganisationen (NROs). Bewohnerzielgruppen waren Eltern von jungen Familien und Lebenswissenschaftspersonal mit einer modernen Grundorientierung. Der erste Beitrag lieferte eine Lebensstildefinition, die auf einem interdisziplinären Literaturüberblick der psychologischen und soziologischen Lebensstilforschung basiert. Die Lebensstildefinition basiert auf der Lewin’schen Feldtheorie und MUS. Lebensstile sind Denk- und Verhaltensmuster mit Gewohnheits- und Selbstidentifikationspotenzial, durch die Personen soziale Zugehörigkeit und Abgrenzung ausdrücken. Der zweite Beitrag fand, dass NIFs als verantwortliche Immobiliengeldanlage dienen, die den Ausdruck nachhaltiger Lebensstile fördern. Der Beitrag identifizierte Nachhaltigkeitskriterien und Treiber für die Marktakzeptanz von NIFs durch Schlüsselfinanzakteure. Der dritte Beitrag fand, dass nachhaltige Szenarien für die Fallstudie (Erlenmatt) in Bezug auf Erwünschtheit und Nutzen bevorzugt werden, und dass ihre Wahrscheinlichkeit nicht niedriger als die anderer Szenarien eingeschätzt wird. Der gemeinnützige & öffentliche Sektor ist über die Wahrscheinlichkeit eines nachhaltigen Quartiers am pessimistischsten, während Wohnanbieter es weniger wünschen. Die Ergebnisse deuten darauf hin, dass Interessengruppen die Umwandlung städtischer Lebensstile und effizienter Technologien verwirklichen müssen, die gut abschneiden, Konsens bilden und marktwirtschaftlich erfolgreich sind. Lebensstile schaffen Anreize und Barrieren für die Regulation von Stadtsystemen und geben eingehende Information für ihre nachhaltige Umwandlung. Eine solche Umwandlung von Stadtsystemen erfordert eine nachhaltige Entwicklung von gekoppelten MUS. Immobilienfinanzinstrumente und Planungsoptionen, die eine nachhaltige Entwicklung fördern, müssen von verschiedenen Interessengruppen unter Verwendung von verschiedenen Bewertungsindikatoren bewertet werden. Das Ziel ist eine optimale Implementierungsstrategie zu wählen, die von verschiedenen Interessengruppen sowohl gründlich bewertet als auch breit akzeptiert wird

A Practical Perspective on DNA Synthesis and Biological Security (12/4/2006 Draft)

This is the unabridged draft of the manuscript "DNA synthesis and biological security." An abridged form of this manuscript was later published as a peer review commentary in Nature Biotechnology (doi:10.1038/nbt0607-627)Few developments have leapfrogged over predecessor technology as quickly and extensively as synthetic biology. Based on cutting-edge DNA synthesis technology, synthetic biology has already fueled an expansion of opportunities in biological engineering, with advanced capabilities that surpass those provided by traditional recombinant DNA technology. Improvements in synthesis technology are accelerating the pace of innovation in everything from the development of renewable energy to the production of bulk and fine chemicals, from information processing to environmental monitoring, and from agricultural productivity to breakthroughs in human health and medicine. Synthetic biology promises vast improvements to our well-being and our understanding of the living world. Like any powerful technology, DNA synthesis has the potential to be misused. In the wrong hands, the new capabilities enabled by synthetic biology could give rise to both known and unforeseeable threats to our biological safety and security. Current government oversight of the DNA synthesis industry falls short of addressing this unfortunate reality. Here, we introduce and outline a practical plan for developing an effective governance framework for the DNA synthesis industry. A thoughtfully crafted and effectively implemented framework would protect our continued well-being in at least two ways. First, the framework would promote our biological safety and security. Second, the framework would encourage the further responsible development of synthetic biology technologies and their continued, overwhelmingly constructive application. The proposed plan represents the collective views of the International Consortium for Polynucleotide Synthesis, the U.S. Federal Bureau of Investigation, the Chief Executive Officers or Presidents of several of the principal synthetic biology companies, and representatives from academia. Our framework calls for the immediate and systematic implementation of a tiered DNA synthesis screening process. In order to establish accountability at the user level, individuals who place orders for DNA synthesis would be required to identify themselves, their home organization, and all relevant biosafety level information. Next, individual companies would use software tools to check synthesis orders against a set of select agents or sequences to help ensure regulatory compliance and flag synthesis orders for further review. Finally, DNA synthesis and synthetic biology companies would work together, and interface with appropriate government agencies, to rapidly and continually improve the underlying technologies used to screen orders and identify potentially dangerous sequences, as well as develop a clearly defined process to report behavior that falls outside of agreed-upon guidelines