The Impact of 18 Ancestral and Horizontally-Acquired Regulatory Proteins upon the Transcriptome and sRNA Landscape of Salmonella enterica serovar Typhimurium

Article Authors Metrics Comments Media Coverage Abstract Author Summary Introduction Results and Discussion Materials and Methods Supporting Information Acknowledgments Author Contributions References Reader Comments (0) Media Coverage (0) Figures Abstract We know a great deal about the genes used by the model pathogen Salmonella enterica serovar Typhimurium to cause disease, but less about global gene regulation. New tools for studying transcripts at the single nucleotide level now offer an unparalleled opportunity to understand the bacterial transcriptome, and expression of the small RNAs (sRNA) and coding genes responsible for the establishment of infection. Here, we define the transcriptomes of 18 mutants lacking virulence-related global regulatory systems that modulate the expression of the SPI1 and SPI2 Type 3 secretion systems of S. Typhimurium strain 4/74. Using infection-relevant growth conditions, we identified a total of 1257 coding genes that are controlled by one or more regulatory system, including a sub-class of genes that reflect a new level of cross-talk between SPI1 and SPI2. We directly compared the roles played by the major transcriptional regulators in the expression of sRNAs, and discovered that the RpoS (σ38) sigma factor modulates the expression of 23% of sRNAs, many more than other regulatory systems. The impact of the RNA chaperone Hfq upon the steady state levels of 280 sRNA transcripts is described, and we found 13 sRNAs that are co-regulated with SPI1 and SPI2 virulence genes. We report the first example of an sRNA, STnc1480, that is subject to silencing by H-NS and subsequent counter-silencing by PhoP and SlyA. The data for these 18 regulatory systems is now available to the bacterial research community in a user-friendly online resource, SalComRegulon

No measure for culture? Value in the new economy

This paper explores articulations of the value of investment in culture and the arts through a critical discourse analysis of policy documents, reports and academic commentary since 1997. It argues that in this period, discourses around the value of culture have moved from a focus on the direct economic contributions of the culture industries to their indirect economic benefits. These indirect benefits are discussed here under three main headings: creativity and innovation, employability, and social inclusion. These are in turn analysed in terms of three forms of capital: human, social and cultural. The paper concludes with an analysis of this discursive shift through the lens of autonomist Marxist concerns with the labour of social reproduction. It is our argument that, in contemporary policy discourses on culture and the arts, the government in the UK is increasingly concerned with the use of culture to form the social in the image of capital. As such, we must turn our attention beyond the walls of the factory in order to understand the contemporary capitalist production of value and resistance to it. </jats:p

A Precision Measurement of pp Elastic Scattering Cross Sections at Intermediate Energies

We have measured differential cross sections for \pp elastic scattering with internal fiber targets in the recirculating beam of the proton synchrotron COSY. Measurements were made continuously during acceleration for projectile kinetic energies between 0.23 and 2.59 GeV in the angular range $30 \leq \theta_{c.m.} \leq 90$ deg. Details of the apparatus and the data analysis are given and the resulting excitation functions and angular distributions presented. The precision of each data point is typically better than 4%, and a relative normalization uncertainty of only 2.5% within an excitation function has been reached. The impact on phase shift analysis as well as upper bounds on possible resonant contributions in lower partial waves are discussed.Comment: 23 pages 29 figure

(Im)possibilities of Autonomy:? Social Movements In and Beyond Capital, the State and Development

In this paper we interrogate the demand and practice of autonomy in social movements. We begin by identifying three main conceptions of autonomy: (1) autonomous practices vis-à-vis capital; (2) self-determination and independence from the state; and (3) alternatives to hegemonic discourses of development. We then point to limits associated with autonomy and discuss how demands for autonomy are tied up with contemporary re-organizations of: (1) the capitalist workplace, characterized by discourses of autonomy, creativity and self-management; (2) the state, which increasingly outsources public services to independent, autonomous providers, which often have a more radical, social movement history; and (3) regimes of development, which today often emphasize local practices, participation and self-determination. This capturing of autonomy reminds us that autonomy can never be fixed. Instead, social movements' demands for autonomy are embedded in specific social, economic, political and cultural contexts, giving rise to possibilities as well as impossibilities of autonomous practices

Occupy: 'struggles for the common or an 'anti-politics of dignity? Reflections on Hardt and Negri and John Holloway

This article provides a critical examination of Michael Hardt and Antonio Negri’s and John Holloway’s theory of revolutionary subjectivity, and does so by applying their theories to the Occupy movement of 2011. Its central argument is that one should avoid collapsing ‘autonomist’ and ‘open’ Marxism, for whilst both approaches share Tronti’s (1979) insistence on the constituent role of class struggle, and also share an emphasis on a prefigurative politics which engages a non-hierarchical and highly participatory politics, there nevertheless remain some significant differences between their approaches. Ultimately, when applied to Occupy Movement whilst their theory isn’t entirely unproblematic, I will argue that Hardt and Negri’s ‘autonomist’ approach offers the stronger interpretation, due mainly to their revised historical materialism

Antagonism, accommodation and agonism in critical management studies: alternative organizations as allies

Critical Management Studies has long been engaged in discussions about the purpose of critique and the possibilities of engagement. A recent expression calls for Critical Management Studies to moderate its ‘negative’ critique of management and instead use words like care, engagement and affirmation in order to enable ‘progressive’ engagement with managers. This ‘performative turn’ has been poorly received by some who see it as a dilution of radical intent. We argue for a middle ground between the antagonistic versions of Critical Management Studies that appear to want to oppose management, and ‘performative’ scholars who appear to accommodate with managerialism. We do this by planting the debate firmly within an empirical setting and a crisis that the first author experienced as a ‘critical scholar’ when conducting an ethnography at a sustainable financial services firm. In order to do this, we explore Chantal Mouffe’s concept of agonism to establish a particular mode of political engagement that acknowledges a space between being ‘for’ and being ‘against’. We conclude by suggesting that the exploration of alternative forms of organization and management, themselves already involved in struggle against a hegemonic present, should be the proper task of a discipline that wishes to engage with the present and remain ‘critical

A striking correspondence between the dynamics generated by the vector fields and by the scalar parabolic equations

The purpose of this paper is to enhance a correspondence between the dynamics of the differential equations $\dot y(t)=g(y(t))$ on $\mathbb{R}^d$ and those of the parabolic equations $\dot u=\Delta u +f(x,u,\nabla u)$ on a bounded domain $\Omega$. We give details on the similarities of these dynamics in the cases $d=1$, $d=2$ and $d\geq 3$ and in the corresponding cases $\Omega=(0,1)$, $\Omega=\mathbb{T}^1$ and dim($\Omega$)$\geq 2$ respectively. In addition to the beauty of such a correspondence, this could serve as a guideline for future research on the dynamics of parabolic equations

Fairness in Algorithmic Decision Making: An Excursion Through the Lens of Causality

As virtually all aspects of our lives are increasingly impacted by algorithmic decision making systems, it is incumbent upon us as a society to ensure such systems do not become instruments of unfair discrimination on the basis of gender, race, ethnicity, religion, etc. We consider the problem of determining whether the decisions made by such systems are discriminatory, through the lens of causal models. We introduce two definitions of group fairness grounded in causality: fair on average causal effect (FACE), and fair on average causal effect on the treated (FACT). We use the Rubin-Neyman potential outcomes framework for the analysis of cause-effect relationships to robustly estimate FACE and FACT. We demonstrate the effectiveness of our proposed approach on synthetic data. Our analyses of two real-world data sets, the Adult income data set from the UCI repository (with gender as the protected attribute), and the NYC Stop and Frisk data set (with race as the protected attribute), show that the evidence of discrimination obtained by FACE and FACT, or lack thereof, is often in agreement with the findings from other studies. We further show that FACT, being somewhat more nuanced compared to FACE, can yield findings of discrimination that differ from those obtained using FACE.Comment: 7 pages, 2 figures, 2 tables.To appear in Proceedings of the International Conference on World Wide Web (WWW), 201