Insights into the bilayer-mediated toppling mechanism of a folate-specific ECF transporter by cryo-EM

Energy-coupling factor (ECF)–type transporters are small, asymmetric membrane protein complexes (∼115 kDa) that consist of a membrane-embedded, substrate-binding protein (S component) and a tripartite ATP-hydrolyzing module (ECF module). They import micronutrients into bacterial cells and have been proposed to use a highly unusual transport mechanism, in which the substrate is dragged across the membrane by a toppling motion of the S component. However, it remains unclear how the lipid bilayer could accommodate such a movement. Here, we used cryogenic electron microscopy at 200 kV to determine structures of a folate-specific ECF transporter in lipid nanodiscs and detergent micelles at 2.7- and 3.4-Å resolution, respectively. The structures reveal an irregularly shaped bilayer environment around the membrane-embedded complex and suggest that toppling of the S component is facilitated by protein-induced membrane deformations. In this way, structural remodeling of the lipid bilayer environment is exploited to guide the transport process

Bohmian trajectories and Klein's paradox

We compute the Bohmian trajectories of the incoming scattering plane waves for Klein's potential step in explicit form. For finite norm incoming scattering solutions we derive their asymptotic space-time localization and we compute some Bohmian trajectories numerically. The paradox, which appears in the traditional treatments of the problem based on the outgoing scattering asymptotics, is absent.Comment: 14 pages, 3 figures; minor format change

Scraping the Social? Issues in live social research

What makes scraping methodologically interesting for social and cultural research? This paper seeks to contribute to debates about digital social research by exploring how a ‘medium-specific’ technique for online data capture may be rendered analytically productive for social research. As a device that is currently being imported into social research, scraping has the capacity to re-structure social research, and this in at least two ways. Firstly, as a technique that is not native to social research, scraping risks to introduce ‘alien’ methodological assumptions into social research (such as an pre-occupation with freshness). Secondly, to scrape is to risk importing into our inquiry categories that are prevalent in the social practices enabled by the media: scraping makes available already formatted data for social research. Scraped data, and online social data more generally, tend to come with ‘external’ analytics already built-in. This circumstance is often approached as a ‘problem’ with online data capture, but we propose it may be turned into virtue, insofar as data formats that have currency in the areas under scrutiny may serve as a source of social data themselves. Scraping, we propose, makes it possible to render traffic between the object and process of social research analytically productive. It enables a form of ‘real-time’ social research, in which the formats and life cycles of online data may lend structure to the analytic objects and findings of social research. By way of a conclusion, we demonstrate this point in an exercise of online issue profiling, and more particularly, by relying on Twitter to profile the issue of ‘austerity’. Here we distinguish between two forms of real-time research, those dedicated to monitoring live content (which terms are current?) and those concerned with analysing the liveliness of issues (which topics are happening?)

Playing dice with mice: building experimental futures in Singapore

This is a postprint of an article published in New Genetics and Society, 2011, Vol. 30, Issue 4 pp. 433 – 441 © 2011 copyright Taylor & Francis. New Genetics and Society is available online at: http://www.tandfonline.com/loi/cngs20#.UqsI0tJdU24This short paper adds to debates on the unfolding spaces and logics of biotechnological development bought together in the 2009 special issue of New Genetics and Society on ‘Biopolitics in Asia’. Though an unlikely comparison between the development of the genomic sciences and the building of gambling casinos in the city state of Singapore, it reflects on the nature of political and technological investments in this South-East Asian city. It argues that Western expectations of a link between scientific practices, and civic epistemologies linked to democratic decision-making, are replaced by a rather different future orientation to scientific experimentation, economic investment and social development in Singapore

Mobilizing Experimental Life: Spaces of Becoming with Mutant Mice

Copyright © 2013 SAGE Publications. Author's draft version; post-print. Final version published by Sage available on Sage Journals Online http://online.sagepub.com/This paper uses the figure of the inbred laboratory mouse to reflect upon the management and mobilization of biological difference in the contemporary biosciences. Working through the concept of shifting experimental systems, the paper seeks to connect practices concerned with standardization and control in contemporary research with the emergent and stochastic qualities of biological life. Specifically, it reviews the importance of historical narratives of standardization in experimental systems based around model organisms, before identifying a tension in contemporary accounts of the reproduction and differentiation of inbred mouse strains within them. Firstly, narratives of new strain development, foregrounding personal biography and chance discovery, attest to the contingency and situatedness of apparently universal biotechnological production. Secondly, discoveries of unexpected animal litters challenge efforts to standardize mouse phenotypes and control the reproduction of murine strains over space. The co-existence of these two narratives draws attention to the importance of and interplay between both chance and control, determination and emergence, and the making and moving of experimental life in biomedical research. The reception or denial of such biological excess reflects the distribution of agencies and the emerging spatialities of the global infrastructures of biotechnological development, with implications for future relations between animal lives and human becomings in experimental practice

Exploring sociodemographic correlates of suicide stigma in Australia: Baseline cross-sectional survey findings from the life-span suicide prevention trial studies

The risk of suicidal behaviour in Australia varies by age, sex, sexual preference and Indigenous status. Suicide stigma is known to affect suicide rates and help-seeking for suicidal crises. The aim of this study was to investigate the sociodemographic correlates of suicide stigma to assist in prevention efforts. We surveyed community members and individuals who had attended specific emergency departments for suicidal crisis. The respondents were part of a large-scale suicide prevention trial in New South Wales, Australia. The data collected included demographic characteristics, measures of help-seeking and suicide stigma. The linear regression analyses conducted sought to identify the factors associated with suicide stigma. The 5426 participants were predominantly female (71.4 %) with a mean (SD) age of 41.7 (14.8) years, and 3.9 % were Indigenous. Around one-third of participants reported a previous suicide attempt (n = 1690, 31.5 %) with two-thirds (n = 3545, 65.3 %) seeking help for suicidal crisis in the past year. Higher stigma scores were associated with Indigenous status (β 0.123, 95 % CI 0.074 – 0.172), male sex (β 0.527, 95 % CI 0.375 – 0.626) and regional residence (β 0.079, 95 % CI 0.015 – 0.143). Lower stigma scores were associated with younger age (β − 0.002, 95 % CI − 0.004 – − 0.001), mental illness (β − 0.095, 95 % CI − 0.139 to − 0.050), male bisexuality (β − 0.202, 95 % CI − 0.351 to − 0.052) and males who glorified suicide (β − 0.075, 95 % CI − 0.119 to − 0.031). These results suggested that suicide stigma differed across the community, varying significantly by sex, sexual orientation and Indigenous status. Targeted educational programs to address suicide stigma could assist in suicide prevention efforts

Grounding knowledge and normative valuation in agent-based action and scientific commitment

Philosophical investigation in synthetic biology has focused on the knowledge-seeking questions pursued, the kind of engineering techniques used, and on the ethical impact of the products produced. However, little work has been done to investigate the processes by which these epistemological, metaphysical, and ethical forms of inquiry arise in the course of synthetic biology research. An attempt at this work relying on a particular area of synthetic biology will be the aim of this chapter. I focus on the reengineering of metabolic pathways through the manipulation and construction of small DNA-based devices and systems synthetic biology. Rather than focusing on the engineered products or ethical principles that result, I will investigate the processes by which these arise. As such, the attention will be directed to the activities of practitioners, their manipulation of tools, and the use they make of techniques to construct new metabolic devices. Using a science-in-practice approach, I investigate problems at the intersection of science, philosophy of science, and sociology of science. I consider how practitioners within this area of synthetic biology reconfigure biological understanding and ethical categories through active modelling and manipulation of known functional parts, biological pathways for use in the design of microbial machines to solve problems in medicine, technology, and the environment. We might describe this kind of problem-solving as relying on what Helen Longino referred to as “social cognition” or the type of scientific work done within what Hasok Chang calls “systems of practice”. My aim in this chapter will be to investigate the relationship that holds between systems of practice within metabolic engineering research and social cognition. I will attempt to show how knowledge and normative valuation are generated from this particular network of practitioners. In doing so, I suggest that the social nature of scientific inquiry is ineliminable to both knowledge acquisition and ethical evaluations

Developing a Relational View of the Organizing Role of Objects: A study of the innovation process in computer games

Innovation processes create distinctive challenges for coordination. Objects are seen as supporting coordination in such settings by enabling the emergent action needed to deal with a dynamic and uncertain process. Thus, previous work has highlighted the role of different types of objects in coordinating the collaborative tasks undertaken by expert groups, either by motivating the creation of new knowledge or through the translation of understanding. Through an empirical study of innovation processes in the computer games sector, our paper adds to this previous work by finding that the relations between objects, and not the objects alone, help to orchestrate multiple collaborative tasks towards a final outcome within temporal and resource constraints. The relational view which emerges from this study shows how such a ‘system of objects’ is able to stabilize coordination of the process while preserving the emergence and autonomy of games developer practices needed to achieve innovation