Large-scale and significant expression from pseudogenes in Sodalis glossinidius – a facultative bacterial endosymbiont

The majority of bacterial genomes have high coding efficiencies, but there are some genomes of intracellular bacteria that have low gene density. The genome of the endosymbiont Sodalis glossinidius contains almost 50 % pseudogenes containing mutations that putatively silence them at the genomic level. We have applied multiple ‘omic’ strategies, combining Illumina and Pacific Biosciences Single-Molecule Real-Time DNA sequencing and annotation, stranded RNA sequencing and proteome analysis to better understand the transcriptional and translational landscape of Sodalis pseudogenes, and potential mechanisms for their control. Between 53 and 74 % of the Sodalis transcriptome remains active in cell-free culture. The mean sense transcription from coding domain sequences (CDSs) is four times greater than that from pseudogenes. Comparative genomic analysis of six Illumina-sequenced Sodalis isolates from different host Glossina species shows pseudogenes make up ~40 % of the 2729 genes in the core genome, suggesting that they are stable and/or that Sodalis is a recent introduction across the genus Glossina as a facultative symbiont. These data shed further light on the importance of transcriptional and translational control in deciphering host–microbe interactions. The combination of genomics, transcriptomics and proteomics gives a multidimensional perspective for studying prokaryotic genomes with a view to elucidating evolutionary adaptation to novel environmental niches

Suited for Success? : Suits, Status, and Hybrid Masculinity

This document is the Accepted Manuscript version. The final, definitive version of this paper has been published in Men and Masculinities, March 2017, doi: https://doi.org/10.1177/1097184X17696193, published by SAGE Publishing, All rights reserved.This article analyzes the sartorial biographies of four Canadian men to explore how the suit is understood and embodied in everyday life. Each of these men varied in their subject positions—body shape, ethnicity, age, and gender identity—which allowed us to look at the influence of men’s intersectional identities on their relationship with their suits. The men in our research all understood the suit according to its most common representation in popular culture: a symbol of hegemonic masculinity. While they wore the suit to embody hegemonic masculine configurations of practice—power, status, and rationality—most of these men were simultaneously marginalized by the gender hierarchy. We explain this disjuncture by using the concept of hybrid masculinity and illustrate that changes in the style of hegemonic masculinity leave its substance intact. Our findings expand thinking about hybrid masculinity by revealing the ways subordinated masculinities appropriate and reinforce hegemonic masculinity.Peer reviewe

Conserved noncoding sequences highlight shared components of regulatory networks in dicotyledonous plants

Conserved noncoding sequences (CNSs) in DNA are reliable pointers to regulatory elements controlling gene expression. Using a comparative genomics approach with four dicotyledonous plant species (Arabidopsis thaliana, papaya [Carica papaya], poplar [Populus trichocarpa], and grape [Vitis vinifera]), we detected hundreds of CNSs upstream of Arabidopsis genes. Distinct positioning, length, and enrichment for transcription factor binding sites suggest these CNSs play a functional role in transcriptional regulation. The enrichment of transcription factors within the set of genes associated with CNS is consistent with the hypothesis that together they form part of a conserved transcriptional network whose function is to regulate other transcription factors and control development. We identified a set of promoters where regulatory mechanisms are likely to be shared between the model organism Arabidopsis and other dicots, providing areas of focus for further research

A Systematic Review Examining the Experimental Methodology Behind In Vivo Testing of Hiatus Hernia and Diaphragmatic Hernia Mesh

INTRODUCTION: Mesh implants are regularly used to help repair both hiatus hernias (HH) and diaphragmatic hernias (DH). In vivo studies are used to test not only mesh safety, but increasingly comparative efficacy. Our work examines the field of in vivo mesh testing for HH and DH models to establish current practices and standards. METHOD: This systematic review was registered with PROSPERO. Medline and Embase databases were searched for relevant in vivo studies. Forty-four articles were identified and underwent abstract review, where 22 were excluded. Four further studies were excluded after full-text review-leaving 18 to undergo data extraction. RESULTS: Of 18 studies identified, 9 used an in vivo HH model and 9 a DH model. Five studies undertook mechanical testing on tissue samples-all uniaxial in nature. Testing strip widths ranged from 1-20 mm (median 3 mm). Testing speeds varied from 1.5-60 mm/minute. Upon histology, the most commonly assessed structural and cellular factors were neovascularisation and macrophages respectively (n = 9 each). Structural analysis was mostly qualitative, where cellular analysis was equally likely to be quantitative. Eleven studies assessed adhesion formation, of which 8 used one of four scoring systems. Eight studies measured mesh shrinkage. DISCUSSION: In vivo studies assessing mesh for HH and DH repair are uncommon. Within this relatively young field, we encourage surgical and materials testing institutions to discuss its standardisation

Protein processing characterized by a gel-free proteomics approach

We describe a method for the specific isolation of representative N-terminal peptides of proteins and their proteolytic fragments. Their isolation is based on a gel-free, peptidecentric proteomics approach using the principle of diagonal chromatography. We will indicate that the introduction of an altered chemical property to internal peptides holding a free α-N-terminus results in altered column retention of these peptides, thereby enabling the isolation and further characterization by mass spectrometry of N-terminal peptides. Besides pointing to changes in protein expression levels when performing such proteome surveys in a differential modus, protease specificity and substrate repertoires can be allocated since both are specified by neo-N-termini generated after a protease cleavage event. As such, our gel-free proteomics technology is widely applicable and amenable for a variety of proteome-driven protease degradomics research

'Lad culture' in higher education: agency in the sexualisation debates

This paper reports on research funded by the National Union of Students, which explored women students’ experiences of ‘lad culture’ through focus groups and interviews. We found that although laddism is only one of various potential masculinities, for our participants it dominated social and sexual spheres of university life in problematic ways. However, their objections to laddish behaviours did not support contemporary models of ‘sexual panic’, even while oppugning the more simplistic celebrations of young women’s empowerment which have been observed in debates about sexualisation. We argue that in their ability to reject ‘lad culture’, our respondents expressed a form of agency which is often invisibilised in sexualisation discussions and which could be harnessed to tackle some of the issues we uncovered

Direct characterization of the native structure and mechanics of cyanobacterial carboxysomes

Carboxysomes are proteinaceous organelles that play essential roles in enhancing carbon fixation in cyanobacteria and some proteobacteria. These self-assembling organelles encapsulate Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) and carbonic anhydrase using a protein shell structurally resembling an icosahedral viral capsid. The protein shell serves as a physical barrier to protect enzymes from the cytosol and a selectively permeable membrane to mediate transport of enzyme substrates and products. The structural and mechanical nature of native carboxysomes remain unclear. Here, we isolate functional β-carboxysomes from the cyanobacterium Synechococcus elongatus PCC7942 and perform the first characterization of the macromolecular architecture and inherent physical mechanics of single β-carboxysomes using electron microscopy, atomic force microscopy (AFM) and proteomics. Our results illustrate that the intact β-carboxysome comprises three structural domains, a single-layered icosahedral shell, an inner layer and paracrystalline arrays of interior Rubisco. We also observe the protein organization of the shell and partial β-carboxysomes that likely serve as the β-carboxysome assembly intermediates. Furthermore, the topography and intrinsic mechanics of functional β-carboxysomes are determined in native conditions using AFM and AFM-based nanoindentation, revealing the flexible organization and soft mechanical properties of β-carboxysomes compared to rigid viruses. Our study provides new insights into the natural characteristics of β-carboxysome organization and nanomechanics, which can be extended to diverse bacterial microcompartments and are important considerations for the design and engineering of functional carboxysomes in other organisms to supercharge photosynthesis. It offers an approach for inspecting the structural and mechanical features of synthetic metabolic organelles and protein scaffolds in bioengineering

From toothpick legs to dropping vaginas: Gender and sexuality in Joan Rivers' stand-up comedy performance

This is the author's accepted manuscript. The final published article is available from the link below. Copyright @ 2011 Intellect.This article employs sociocultural analysis to examine Joan Rivers’ stand-up comedy performances in order to reveal how she successfully operates in a sphere of artistic expression that has been, and continues to be, male-dominated. The analysis uncovers how Rivers’ stand-up comedy performance involves a complex combination of elements and how it fuses features that are regarded as ‘traditionally masculine’, such as aggression, with features frequently used by other female stand-up comedians, such as self-deprecating comedy and confessional comedy. Furthermore, the analysis exposes the complex ways in which constructions of gender and sexuality are negotiated and re-negotiated in Rivers’ stand-up comedy performance, and illustrates how dominant ideological identity constructions can be simultaneously reinforced and subverted within the same comic moment