The Sorghum bicolor reference genome: improved assembly, gene annotations, a transcriptome atlas, and signatures of genome organization.

Sorghum bicolor is a drought tolerant C4 grass used for the production of grain, forage, sugar, and lignocellulosic biomass and a genetic model for C4 grasses due to its relatively small genome (approximately 800 Mbp), diploid genetics, diverse germplasm, and colinearity with other C4 grass genomes. In this study, deep sequencing, genetic linkage analysis, and transcriptome data were used to produce and annotate a high-quality reference genome sequence. Reference genome sequence order was improved, 29.6 Mbp of additional sequence was incorporated, the number of genes annotated increased 24% to 34 211, average gene length and N50 increased, and error frequency was reduced 10-fold to 1 per 100 kbp. Subtelomeric repeats with characteristics of Tandem Repeats in Miniature (TRIM) elements were identified at the termini of most chromosomes. Nucleosome occupancy predictions identified nucleosomes positioned immediately downstream of transcription start sites and at different densities across chromosomes. Alignment of more than 50 resequenced genomes from diverse sorghum genotypes to the reference genome identified approximately 7.4 M single nucleotide polymorphisms (SNPs) and 1.9 M indels. Large-scale variant features in euchromatin were identified with periodicities of approximately 25 kbp. A transcriptome atlas of gene expression was constructed from 47 RNA-seq profiles of growing and developed tissues of the major plant organs (roots, leaves, stems, panicles, and seed) collected during the juvenile, vegetative and reproductive phases. Analysis of the transcriptome data indicated that tissue type and protein kinase expression had large influences on transcriptional profile clustering. The updated assembly, annotation, and transcriptome data represent a resource for C4 grass research and crop improvement

Peroxidase expression in a cereal cyst nematode (Heterodera avenae) resistant hexaploid wheat line.

The incompatible interaction between plant and pathogen is often determined by the hypersensitive reaction (HR). This response is associated with accumulation of reactive oxygen species (ROS), which results in adverse growth conditions for pathogens. Two major mechanisms involving either NADPH oxidases or peroxidases have been proposed for generation of ROS. Peroxidases (PER, EC 1.11.1.7), present in all land plants, are members of a large multigenic family with high number of isoforms involved in a broad range of physiological processes. PER genes, which are expressed in nematode feeding sites, have been identified in several plant species (Zacheo et al. 1997). A strong correlation between HR and PER activities at four and seven days post nematode infection, was detected in roots of wheat lines carrying Cre2, Cre5 (from Ae. ventricosa) or Cre7 (from Ae. triuncialis) Heterodera avenae resistance genes (Andrés et al. 2001; Montes et al. 2003, 2004). We have studied changes in root of peroxidase mRNAs levels after infection by H. avenae of a wheat/Ae. ven¬tricosa introgression line (H-93-8) carrying Cre2 (Delibes et al. 1993). We also report and classify the predicted protein sequences derived from complete peroxidase transcripts

Gendered geographies of environmental injustice

This is the accepted version of the following article: Buckingham, S. and Kulcur, R. (2009), Gendered Geographies of Environmental Injustice. Antipode, 41: 659–683. doi: 10.1111/j.1467-8330.2009.00693.x, which has been published in final form at http://onlinelibrary.wiley.com/doi/10.1111/j.1467-8330.2009.00693.x/abstract. Copyright @ 2009 The Authors.As environmental justice concerns become more widely embedded in environmental organizations and policy making, and increasingly the focus of academic study, the gender dimension dissolves into an exclusive focus on race/ethnicity and class/income. While grass roots campaigning activities were often dominated by women, in the more institutionalized activities of organizations dominated by salaried professionals, gender inequality is neglected as a vector of environmental injustice, and addressing this inequality is not considered a strategy for redress. This paper explores some of the reasons why this may be so, which include a lack of visibility of gendered environmental injustice; professional campaigning organizations which are themselves gender blind; institutions at a range of scales which are still structured by gender (as well as class and race) inequalities; and an intellectual academy which continues to marginalize the study of gender – and women’s – inequality. The authors draw on experience of environmental activism, participant observation, and other qualitative research into the gendering of environmental activity, to first explore the constructions of scale to see how this might limit a gender-fair approach to environmental justice. Following this, the practice of ‘gender mainstreaming’ in environmental organizations and institutions will be examined, demonstrating how this is limited in scope and fails to impact on the gendering of environmental injustice

Comprehensive Genome Analysis on the Novel Species Sphingomonas panacis DCY99(T) Reveals Insights into Iron Tolerance of Ginseng

Plant growth-promoting rhizobacteria play vital roles not only in plant growth, but also in reducing biotic/abiotic stress. Sphingomonas panacis DCY99(T) is isolated from soil and root of Panax ginseng with rusty root disease, characterized by raised reddish-brown root and this is seriously affects ginseng cultivation. To investigate the relationship between 159 sequenced Sphingomonas strains, pan-genome analysis was carried out, which suggested genomic diversity of the Sphingomonas genus. Comparative analysis of S. panacis DCY99(T) with Sphingomonas sp. LK11 revealed plant growth-promoting potential of S. panacis DCY99(T) through indole acetic acid production, phosphate solubilizing, and antifungal abilities. Detailed genomic analysis has shown that S. panacis DCY99(T) contain various heavy metals resistance genes in its genome and the plasmid. Functional analysis with Sphingomonas paucimobilis EPA505 predicted that S. panacis DCY99(T) possess genes for degradation of polyaromatic hydrocarbon and phenolic compounds in rusty-ginseng root. Interestingly, when primed ginseng with S. panacis DCY99(T) during high concentration of iron exposure, iron stress of ginseng was suppressed. In order to detect S. panacis DCY99(T) in soil, biomarker was designed using spt gene. This study brings new insights into the role of S. panacis DCY99(T) as a microbial inoculant to protect ginseng plants against rusty root disease

Seeing the way: visual sociology and the distance runner's perspective

Employing visual and autoethnographic data from a two‐year research project on distance runners, this article seeks to examine the activity of seeing in relation to the activity of distance running. One of its methodological aims is to develop the linkage between visual and autoethnographic data in combining an observation‐based narrative and sociological analysis with photographs. This combination aims to convey to the reader not only some of the specific subcultural knowledge and particular ways of seeing, but also something of the runner's embodied feelings and experience of momentum en route. Via the combination of narrative and photographs we seek a more effective way of communicating just how distance runners see and experience their training terrain. The importance of subjecting mundane everyday practices to detailed sociological analysis has been highlighted by many sociologists, including those of an ethnomethodological perspective. Indeed, without the competence of social actors in accomplishing these mundane, routine understandings and practices, it is argued, there would in fact be no social order

Television news and the symbolic criminalisation of young people

This is an Author's Accepted Manuscript of an article published in Journalism Studies, 9(1), 75 - 90, 2008, copyright Taylor & Francis, available online at: http://www.tandfonline.com/10.1080/14616700701768105.This essay combines quantitative and qualitative analysis of six UK television news programmes. It seeks to analyse the representation of young people within broadcast news provision at a time when media representations, political discourse and policy making generally appear to be invoking young people as something of a folk devil or a locus for moral panics. The quantitative analysis examines the frequency with which young people appear as main actors across a range of different subjects and analyses the role of young people as news sources. It finds a strong correlation between young people and violent crime. A qualitative analysis of four “special reports” or backgrounders on channel Five's Five News explores the representation of young people in more detail, paying attention to contradictions and tensions in the reports, the role of statistics in crime reporting, the role of victims of crime and the tensions between conflicting news frames.Arts and Humanities Research Counci

A Fungal Effector With Host Nuclear Localization and DNA-Binding Properties Is Required for Maize Anthracnose Development

Plant pathogens have the capacity to manipulate the host immune system through the secretion of effectors. We identified 27 putative effector proteins encoded in the genome of the maize anthracnose pathogen Colletotrichum graminicola that are likely to target the host’s nucleus, as they simultaneously contain sequence signatures for secretion and nuclear localization. We functionally characterized one protein, identified as CgEP1. This protein is synthesized during the early stages of disease development and is necessary for anthracnose development in maize leaves, stems, and roots. Genetic, molecular, and biochemical studies confirmed that this effector targets the host’s nucleus and defines a novel class of double-stranded DNA-binding protein. We show that CgEP1 arose from a gene duplication in an ancestor of a lineage of monocot-infecting Colletotrichum spp. and has undergone an intense evolution process, with evidence for episodes of positive selection. We detected CgEP1 homologs in several species of a grass-infecting lineage of Colletotrichum spp., suggesting that its function may be conserved across a large number of anthracnose pathogens. Our results demonstrate that effectors targeted to the host nucleus may be key elements for disease development and aid in the understanding of the genetic basis of anthracnose development in maize plants.Fil: Vargas, Walter Alberto. Universidad de Salamanca; España. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Sanz Martín, José M.. Universidad de Salamanca; EspañaFil: Rech, Gabriel E.. Universidad de Salamanca; EspañaFil: Armijos Jaramillo, Vinicio D.. Universidad de Salamanca; EspañaFil: Rivera Rodriguez, Lina Patricia. Universidad de Salamanca; EspañaFil: Echeverria, María de Las Mercedes. Universidad Nacional de Mar del Plata. Facultad de Ciencias Agrarias; ArgentinaFil: Díaz Mínguez, José M.. Universidad de Salamanca; EspañaFil: Thon, Michael R.. Universidad de Salamanca; EspañaFil: Sukno, Serenella A.. Universidad de Salamanca; Españ