Deep sequencing approaches for the analysis of prokaryotic transcriptional boundaries and dynamics

The identification of the protein-coding regions of a genome is straightforward due to the universality of start and stop codons. However, the boundaries of the transcribed regions, conditional operon structures, non-coding RNAs and the dynamics of transcription, such as pausing of elongation, are non-trivial to identify, even in the comparatively simple genomes of prokaryotes. Traditional methods for the study of these areas, such as tiling arrays, are noisy, labour-intensive and lack the resolution required for densely-packed bacterial genomes. Recently, deep sequencing has become increasingly popular for the study of the transcriptome due to its lower costs, higher accuracy and single nucleotide resolution. These methods have revolutionised our understanding of prokaryotic transcriptional dynamics. Here, we review the deep sequencing and data analysis techniques that are available for the study of transcription in prokaryotes, and discuss the bioinformatic considerations of these analyses

Investigating Performance and Usage of Input Methods for Soft Keyboard Hotkeys

Touch-based devices, despite their mainstream availability, do not support a unified and efficient command selection mechanism, available on every platform and application. We advocate that hotkeys, conventionally used as a shortcut mechanism on desktop computers, could be generalized as a command selection mechanism for touch-based devices, even for keyboard-less applications. In this paper, we investigate the performance and usage of soft keyboard shortcuts or hotkeys (abbreviated SoftCuts) through two studies comparing different input methods across sitting, standing and walking conditions. Our results suggest that SoftCuts not only are appreciated by participants but also support rapid command selection with different devices and hand configurations. We also did not find evidence that walking deters their performance when using the Once input method.Comment: 17+2 pages, published at Mobile HCI 202

Misincorporation by RNA polymerase is a major source of transcription pausingin vivo

The transcription error rate estimated from mistakes in end product RNAs is 10−3–10−5. We analyzed the fidelity of nascent RNAs from all actively transcribing elongation complexes (ECs) in Escherichia coli and Saccharomyces cerevisiae and found that 1–3% of all ECs in wild-type cells, and 5–7% of all ECs in cells lacking proofreading factors are, in fact, misincorporated complexes. With the exception of a number of sequence-dependent hotspots, most misincorporations are distributed relatively randomly. Misincorporation at hotspots does not appear to be stimulated by pausing. Since misincorporation leads to a strong pause of transcription due to backtracking, our findings indicate that misincorporation could be a major source of transcriptional pausing and lead to conflicts with other RNA polymerases and replication in bacteria and eukaryotes. This observation implies that physical resolution of misincorporated complexes may be the main function of the proofreading factors Gre and TFIIS. Although misincorporation mechanisms between bacteria and eukaryotes appear to be conserved, the results suggest the existence of a bacteria-specific mechanism(s) for reducing misincorporation in protein-coding regions. The links between transcription fidelity, human disease, and phenotypic variability in genetically-identical cells can be explained by the accumulation of misincorporated complexes, rather than mistakes in mature RNA

Variable Free Spectral Range Spherical Mirror Fabry-Perot Interferometer

A spherical Fabry-Perot interferometer with adjustable mirror spacing is used to produce interference fringes with frequency separation (c/2L)/N, N=2-15. The conditions for observation of these fringes are derived from the consideration of the eigenmodes of the cavity with high transverse indices.Comment: 11 pages, 7 figures, accepted to Siberian Journal of Physic

Evidence for a black hole in a radio-quiet quasar nucleus

We present the first milli-arcsecond resolution radio images of a radio-quiet quasar, detecting a high brightness temperature core with data from the VLBA. On maps made with lower-frequency data from MERLIN and the VLA jets appear to emanate from the core in opposite directions, which correspond to radio-emission on arcsecond scales seen with the VLA at higher frequencies. These provide strong evidence for a black-hole--based jet-producing central engine, rather than a starburst, being responsible for the compact radio emission in this radio-quiet quasar.Comment: 10 pages including 1 postscript figure; uses aaspp4.sty. Accepted for publication in Ap. J. Lett. Also available from http://www-astro.physics.ox.ac.uk/research/preprints

Effects of meal timing on anabolic hormone status and energy metabolism in neonatal dairy calves

Twelve neonatal Holstein bull calves (38.52 ± 5.87 kg) were fed milk replacer at a fixed or varied meal time to determine the effects on metabolic hormone secretion, average daily intake, growth, and energy metabolism. Body weights were measured every two weeks from birth to 8 weeks. Rumen fluid was collected every two weeks from week 2 through 8. Serial blood collections were conducted every two weeks from week 2 through 8. Blood was collected, beginning at 0530, at 0, 15, 30, 45, 60, 75, 90, 105, 120, 135, and 150 minutes. Plasma was analyzed for ghrelin, leptin, growth hormone (GH), and insulin-like growth factor-1 (IGF-1). Treatment did not affect body weight or average daily intake. Mean plasma ghrelin, leptin, GH, and IGF-1 concentrations were not affected by treatment. A treatment by week interaction was observed for plasma ghrelin concentrations. Plasma ghrelin concentrations were higher at weeks 2 and 4 in control calves. Plasma ghrelin concentrations decreased in all calves as they aged. A treatment by time interaction was observed for IGF-1, and a treatment by week by time interaction was observed for growth hormone and IGF-1. Growth hormone decreased as calves aged, while IGF-1 increased. There was no treatment effect or interactions of treatment and week on butyrate and propionate concentrations. However, both butyrate and propionate increased with age. Treatment and week effects were present for acetate, as well as a treatment by week interaction. Calves in the control group had a higher percentage of acetate. Acetate concentration increased in all calves as they aged. At weeks 4 and 8, intravenous glucose tolerance tests were performed to assess glucose clearance. A treatment effect was observed for glucose half life (T1/2), glucose clearance rate (k), and insulin. Glucose half- life was higher for calves in the control group, while the clearance rate was lower for the control group. Peak insulin concentrations were higher for calves in the treatment group. It is concluded that feeding time does not affect overall growth and feed intake, but does have an affect on the some of the regulatory mechanisms that control them

CAUSES OF MULTIFUNCTIONALITY: EXTERNALITIES OR POLITICAL PRESSURE

Resource /Energy Economics and Policy,

Agri-environmental Policy in the European Union: Who's in Charge?

The EU has argued that some agricultural subsidies are needed to provide the optimal amount of externalities (both positive and negative) produced by agriculture. The argument is that agriculture is "multifunctional" and externalities such as rural development and landscape would be underproduced, while some forms of pollution (such as nitrogen runoff) would be overproduced without government intervention. Meanwhile, the United States has raised the concern that multifunctionality is primarily an argument to transfer income to producers. One way to try and determine how much of these non-commodity payments are directed to externalities and how much is intended to distribute income to producers is to analyze the variation of the programs among the different member states of the EU. We estimate the degree to which environmental characteristics, agricultural characteristics and political economy variables determine the objective and amount of funding each member states uses to address environmental externalities (both positive and negative). Results indicate that little of the variance in agri-environmental expenditure can be explained by the difference in negative externalities, neither is there clear evidence that the payments are substituting for traditional agricultural subsidies. However, demand for environmental services and political variables seem to be the driving motivators behind a country's decision to spend money on agri-environmental programs.Environmental Economics and Policy,

Agri-environmental Policy in the European Union: Who's in Charge?

European Union (EU) agri-environmental programmes (AEPs) represent a significant step in the region's efforts to decouple agricultural output from production and export subsidies. While AEPs comprise only a small share of EU agricultural support, they have two possible external impacts: 1) the composition of the EU's imports and exports may change as their producers become more market responsive; and 2) the WTO's Green Box (subsides considered minimally trade distorting and hence not disciplined) may become increasingly contentious. Our concern is with the drivers of AEPs in the EU and their implications for Canada.Environmental Economics and Policy,

Diluting substantive equality: why the UK government doesn't know if its welfare reforms promote equality

The UK Coalition government introduced a raft of welfare reforms between 2010-2015. As part of its response to the financial crisis reforms were designed to cut public expenditure on social security and enhance work incentives. Policy makers are required by legislation to have due regard to the need to eliminate discrimination, advance equality of opportunity, and foster good relations between different people. This Public Sector Equality Duty is an evidence-based duty which requires public authorities to assess the likely effects of policy on vulnerable groups. This chapter explores the extent to which the Department for Work and Pensions adequately assessed the equality impacts of key welfare reforms when policy was being formulated. The chapter focuses on the assessment of the impact of reductions to welfare benefits on individuals with protected characteristics - age, disability, gender, gender reassignment, marriage and civil partnership, pregnancy and maternity, race, religion and belief, and sexual orientation - including individual and cumulative impacts. It also considers mitigating actions to offset negative impacts and how the collection of evidence on equality impacts was used when formulating policy. The chapter shows that the impacts of the reforms were only systematically assessed by age and gender, and, where data were available, by disability and ethnicity with no attempt to gauge cumulative impacts. There is also evidence of Equality Impact Assessments finding a disproportionate impact on individuals with protected characteristics where no mitigating action was taken