Transcriptional profiling of colicin-induced cell death of Escherichia coli MG1655 identifies potential mechanisms by which bacteriocins promote bacterial diversity

We report the transcriptional response of Escherichia coli MG1655 to damage induced by colicins E3 and E9, bacteriocins that kill cells through inactivation of the ribosome and degradation of chromosomal DNA, respectively. Colicin E9 strongly induced the LexA-regulated SOS response, while colicin E3 elicited a broad response that included the induction of cold shock genes, symptomatic of translational arrest. Colicin E3 also increased the transcription of cryptic prophage genes and other laterally acquired mobile elements. The transcriptional responses to both these toxins suggest mechanisms that may promote genetic diversity in E. coli populations, pointing to a more general role for colicins in adaptive bacterial physiology than has hitherto been realized

The Roles of Extrinsic and Intrinsic Factors in the Freshwater Life-History Dynamics of a Migratory Salmonid

Key life-cycle transitions, such as metamorphosis or migration, can be altered by a variety of external factors, such as climate variation, strong species interactions, and management intervention, or modulated by density dependence. Given that these life-history transitions can influence population dynamics, understanding the simultaneous effects of intrinsic and extrinsic controls on life-history expression is particularly relevant for species of management or conservation importance. Here, we examined how life histories of steelhead (Oncorhynchus mykiss) are affected by weather, pink salmon abundance (Oncorhynchus gorbuscha), experimental nutrient addition, and density-dependent processes. We tested for impacts on the size of steelhead smolts (juveniles migrating to the sea), as well as their age and abundance across four decades in the Keogh River, British Columbia, Canada. Larger steelhead smolts were associated with warmer years and artificial nutrient addition. In addition, higher pink salmon abundance and artificial nutrient addition correlated with juvenile steelhead migrating at younger ages. While density dependence appeared to be the primary factor regulating the abundance of steelhead smolts, nutrient addition and temperature were positively and negatively associated with smolt production, respectively, prior to 1991, and pink salmon spawning abundance was positively associated with smolt production after 1990. Thus, this study provides evidence that the temporal dynamics of one species of salmon is linked to the juvenile life history of co-occurring steelhead. A complex interplay of species interactions, nutrient subsidies, density dependence, and climatic variation can control the life-history expression of species with complex life cycles

Publishing and sharing multi-dimensional image data with OMERO

Imaging data are used in the life and biomedical sciences to measure the molecular and structural composition and dynamics of cells, tissues, and organisms. Datasets range in size from megabytes to terabytes and usually contain a combination of binary pixel data and metadata that describe the acquisition process and any derived results. The OMERO image data management platform allows users to securely share image datasets according to specific permissions levels: data can be held privately, shared with a set of colleagues, or made available via a public URL. Users control access by assigning data to specific Groups with defined membership and access rights. OMERO’s Permission system supports simple data sharing in a lab, collaborative data analysis, and even teaching environments. OMERO software is open source and released by the OME Consortium at www.openmicroscopy.org

High frequency online data collection in an annual household panel study: some evidence on bias prevention and bias adjustment.

Understanding Society is the UK’s largest household panel survey. From April 2020, Understanding Society participants were invited to partake in a series of web surveys (the Understanding Society COVID-19 Study) designed to capture higher frequency information during the pandemic. To prevent bias, the COVID-19 Study invites the full range of Understanding Society participants – both those who regularly use the internet and those who do not – to take part and, furthermore, periodically invites a subset of non-respondents to a telephone follow-up. To adjust for bias, a weighting strategy is implemented that takes advantage of the rich background information available from past annual interviews. We examine the efficacy of these bias reduction and bias adjustment measures. We find that both the telephone follow-ups and weighting help to reduce bias, but that inviting those who do not regularly use the internet to the web survey appears to be of little benefit

Erratum: Author Correction: Identification of genes required for eye development by high-throughput screening of mouse knockouts.

[This corrects the article DOI: 10.1038/s42003-018-0226-0.]

Density profiles of dark matter haloes: diversity and dependence on environment

(Abridged) We study the outer density profiles of dark matter haloes predicted by a generalized secondary infall model and observed in a N-body cosmological simulation of a \Lambda CDM model. We find substantial systematic variations in shapes and concentrations of the halo profiles as well as a strong correlation of the profiles with the environment. In the N-body simulation, the average outer slope of the density profiles, \beta (\rho\propto r^{-\beta}), of isolated haloes is \approx 2.9; 68% of these haloes have values of \beta between 2.5 and 3.8. Haloes in dense environments of clusters are more concentrated and exhibit a broad distribution of \beta with values larger than for isolated haloes . Contrary to what one may expect, the haloes contained within groups and galaxy systems are less concentrated and have flatter outer density profiles than the isolated haloes. The concentration decreases with M_h, but its scatter for a given mass is substantial. The mass and circular velocity of the haloes are strongly correlated: M_h \propto V_m^{\alpha} with \alpha ~ 3.3 (isolated) and ~3.5 (haloes in clusters). For M_h=10^12M_sun the rms deviations from these relations are \Delta logM_h=0.12 and 0.18, respectively. Approximately 30% of the haloes are contained within larger haloes or have massive companions (larger than ~0.3 the mass of the current halo) within 3 virial radii. The remaining 70% of the haloes are isolated objects. The distribution of \beta as well as the concentration-mass and M_h-V_m relations for the isolated haloes agree very well with the predictions of our seminumerical approach which is based on a generalization of the secondary infall model and on the extended Press-Schechter formalism.Comment: 14 pages, 11 figures included, uses mn.sty, accepted by MNRAS. Minor modifications, new and updated reference

Forgotten Plotlanders: Learning from the survival of lost informal housing in the UK.

Colin Ward’s discourses on the arcadian landscape of ‘plotlander’ housing are unique documentations of the anarchistic birth, life, and death of the last informal housing communities in the UK. Today the forgotten history of ‘plotlander’ housing documented by Ward can be re-read in the context of both the apparently never-ending ‘housing crisis’ in the UK, and the increasing awareness of the potential value of learning from comparable informal housing from the Global South. This papers observations of a previously unknown and forgotten plotlander site offers a chance to begin a new conversation regarding the positive potential of informal and alternative housing models in the UK and wider Westernised world

Improving understanding of service-user involvement and identity : collaborative research traversing disability, activism and the academy

This article focuses on collaborative research traversing disability, activism and the academy to improve understanding of service-user involvement and identity. The project was undertaken by an organisation of disabled people, some of whom are, and some of whom are not, employed by academic institutions. It is an example of research fusion between disabled people’s activism and their work within the academy. The project aimed to identify meaningful ways of promoting involvement in the development of public services. Power relationships which shape the reality of disabled people’s participation in decision-making processes within services are critiqued. We explore ways in which disabled service users and our representative organisations can drive a form of political activism within services and through the academy to improve the lives of disabled people according to the priorities of disabled people themselves. This is not simply an academic project; we identify strategies for activism and change