Uneven distribution of cobamide biosynthesis and dependence in bacteria predicted by comparative genomics.

The vitamin B12 family of cofactors known as cobamides are essential for a variety of microbial metabolisms. We used comparative genomics of 11,000 bacterial species to analyze the extent and distribution of cobamide production and use across bacteria. We find that 86% of bacteria in this data set have at least one of 15 cobamide-dependent enzyme families, but only 37% are predicted to synthesize cobamides de novo. The distribution of cobamide biosynthesis and use vary at the phylum level. While 57% of Actinobacteria are predicted to biosynthesize cobamides, only 0.6% of Bacteroidetes have the complete pathway, yet 96% of species in this phylum have cobamide-dependent enzymes. The form of cobamide produced by the bacteria could be predicted for 58% of cobamide-producing species, based on the presence of signature lower ligand biosynthesis and attachment genes. Our predictions also revealed that 17% of bacteria have partial biosynthetic pathways, yet have the potential to salvage cobamide precursors. Bacteria with a partial cobamide biosynthesis pathway include those in a newly defined, experimentally verified category of bacteria lacking the first step in the biosynthesis pathway. These predictions highlight the importance of cobamide and cobamide precursor salvaging as examples of nutritional dependencies in bacteria

Making common ground with strangers at Furnace Park

In this article we seek to widen the debate about the sites and processes of encounter with strangers by examining the ways in which ‘strangeness’ necessarily fades within the familiarisation processes at play in any sustained and situated place-making. Our analysis draws upon our experiences of encountering strangers – and of our familiarisation with them – in the initial, year-long, site acquisition and preparation phase of a project to create Furnace Park, an experimental urban space in a run-down backwater of central Sheffield. We show the tensions between a project commitment to the formation of a loose, open place and the pressures (which arose from our encounters with the urban development system) to render both the project and the site certain, bounded and less-than-strange. Furthermore, at Furnace Park the site itself presented to us as a non-human stranger, which we were urged to render familiar but which kept eluding that capture. We therefore show how the geographies of strange encounters could productively be widened to embrace both recent scholarship on the material-affective strangeness of ground itself, and a greater attentiveness to the familiarisation effects born of the intersection of diverse communities of practices within place-making projects

Out of the Frying Pan into the Viva

Women today are making clear inroads into the academy and, at undergraduate level at least, are engaging in greater numbers than men. However, at postgraduate level the picture changes, especially at doctoral level, and fewer women than men undertake research degrees. However, little is known about women’s experiences of doctoral research, including the viva. The authors seek to address the lack of research about women’s experience of the PhD viva. The research carried out by the authors emphasises both the lack of power felt by women in the current examination process and the lack of consistency in practice across universities. The authors argue that if the viva is to be more than just a process which reinforces existing patterns of power, it cannot continue to be a ritual where only certain voices are allowed to be heard. They conclude by suggesting reforms that they believe would make the system fairer to all

Case Report: Color as a Therapeutic Intervention

Peer reviewedFinal Accepted Versio

Penalized Ordinal Regression Methods for Predicting Stage of Cancer in High-Dimensional Covariate Spaces

The pathological description of the stage of a tumor is an important clinical designation and is considered, like many other forms of biomedical data, an ordinal outcome. Currently, statistical methods for predicting an ordinal outcome using clinical, demographic, and high-dimensional correlated features are lacking. In this paper, we propose a method that fits an ordinal response model to predict an ordinal outcome for high-dimensional covariate spaces. Our method penalizes some covariates (high-throughput genomic features) without penalizing others (such as demographic and/or clinical covariates). We demonstrate the application of our method to predict the stage of breast cancer. In our model, breast cancer subtype is a nonpenalized predictor, and CpG site methylation values from the Illumina Human Methylation 450K assay are penalized predictors. The method has been made available in the ordinalgmifs package in the R programming environment

Using behavioural insights to improve the healthiness of children’s packed lunches.

Background Childhood obesity continues to rise in the UK from 9.3% in children aged 4-5 years to 19.8% by age 10-11. Only 1 in 100 school packed lunches meet national recommendations for school meals in England with 82% containing unhealthy snacks and 61% sugar sweetened drinks. Encouraging parents to identify healthier choices could reduce added sugar content and improve the healthiness of school lunches. Methods A cluster randomised controlled trial was implemented in 17 primary schools (8 intervention, 9 control) in England. The intervention comprised of 3 packs of materials delivered to parents who make children lunches (7-11 years). Materials were designed using behavioural-insights to raise awareness of added sugar and offer healthier options. The materials were delivered over a 4-week period in intervention schools. Photographs of the contents of the packed lunches were taken at 3 time points; 1719 pre-intervention, 1745 post-intervention & 1725 at 3 month follow-up. Visible items in each photograph were coded for nutritional content. A parental survey was conducted at post follow up to explore parental knowledge, attitudes and beliefs about healthier packed lunches. Results The coding and analysis is underway and findings will be presented in November. Presented data will describe group differences pre-intervention, post-intervention and follow up from the >5000 lunch boxes for 1) the number lunch boxes that contain surgery food; 2) the average number of sugary food items; 3) the average grams of sugar in lunch boxes; and 4) the proportion of lunch boxes that contain fruit or vegetables. Conclusions This study was funded by Public Health England to explore whether low cost, low intensive interventions can have a significant impact on changing health behaviours. There is a lack of evidence on improving the nutritional quality of packed lunches and if improvements are identified there are potential implications for child health, nutrition and obesity rates. Key messages: •The study aims to ascertain the effectiveness of a behavioural-insight informed intervention in changing the healthiness of packed lunches provided by parents of primary school aged children. •This low cost, low intensity intervention has the potential to improve the healthiness of primary school age children’s diets.Public Health Englan

STEAM on the Quad

STEAM on the Quad is a family-oriented educational program, initiated in 2016, involving K-12 youth. Participants are able to do hands-on activities that improve their knowledge and interest in the science, technology, engineering, arts and math fields. The event is a collaborative project between Ohio State – Lima and OSU Extension. The 4-H programs of Putnam, Hardin and Allen counties hosted activities that featured Bluetooth sports, circuitry, Lego zip lines, virtual reality, graphics tablets, solar panels, sculpture building, hovercrafts and sewing. Community partners included the Allen County Soil and Water Conservation District, ArtSpace/Lima, YWCA Child Care, the Neil Armstrong Museum, and the Lima YMCA Bean City Bots Robotics Team. Ohio State – Lima faculty from biology, education, engineering, geology, and theater engaged K-12 students and their families in a variety of hands-on projects, as did Ohio State law enforcement. Ohio State staff and students aided in these endeavors and in logistical support. Outcomes and Impacts: 1) Connect local families, faculty, educators, and businesses to promote STEAM education through innovation, learning, and creativity in collaboration with Ohio State. 2) Take Ohio State's current resources and equipment and create programming that reaches new audiences, while bringing local 4-H members to an Ohio State campus. 3) Create a program model that can be reproduced by Extension in Ohio and other states. Outcomes and impacts will consist of recording the attendance and partnerships created through the STEAM programming, categorized by age group, program area, and type of use. Each student will complete a retrospective pre- and post-survey to see if our key STEM metrics are met. Finally, program evaluations will illustrate usage by parents and will collect open-ended feedback about how the STEAM programming has benefited their child. Quarterly progress reports will be provided to the university.AUTHOR AFFILIATION: Kelly Coble, Educator, 4-H Youth Development, The Ohio State University Extension, Allen County, [email protected] (Corresponding Author); Jason Hedrick, Educator, 4-H Youth Development, The Ohio State University Extension, Putnam County; Mark Light, Educator, 4-H Youth Development, The Ohio State University Extension, Hardin County; Amanda Raines, Program Assistant, 4-H Youth Development, The Ohio State University Extension, Hardin County; Sarah Jackson, Program Assistant, 4-H Youth Development, The Ohio State University Extension, Allen County.STEAM on the Quad is a family-oriented educational program, initiated in 2016, involving K-12 youth. Participants did hands-on activities that improved their knowledge and interest in the science, technology, engineering, arts and math fields. The event is a collaborative project between Ohio State – Lima and OSU Extension. The 4-H programs of Putnam, Hardin and Allen counties hosted activities that featured Bluetooth sports, Lego zip lines, virtual reality, graphics tablets, solar panels, sculpture building, hovercrafts and sewing. Community partners included the Allen County Soil and Water Conservation District, ArtSpace/Lima, YWCA Child Care, the Neil Armstrong Museum, and the Lima YMCA Bean City Bots robotics team. Ohio State – Lima faculty from biology, education, engineering, and theater engaged K-12 students and their families in a variety of hands-on projects, as did Ohio State law enforcement. Ohio State staff and students aided in these actvities and logistical support

Fact Sheet: Oral presentations: preparation and delivery

Presentations can be positive experiences. There are a few things you can do to ease the strain to ensure that your presentation runs smoothly. This resource has been prepared to assist you with the planning and delivery of your next paper presentation

Behavioral alterations and Fos protein immunoreactivity in brain regions of bile duct-ligated cirrhotic rats

Hepatic encephalopathy (HE) encompasses a variety of neuropsychiatric symptoms, including anxiety and psychomotor dysfunction. Although HE is a frequent complication of liver cirrhosis, the neurobiological substrates responsible for its clinical manifestations are largely unclear. In the present study, male Wistar rats were bile duct-ligated (BDL), a procedure which induces liver cirrhosis, and on the 21st day after surgery tested in the elevated plus-maze (EPM) and in an open field for anxiety and locomotor activity measurements. Analysis of Fos protein immunoreactivity (Fos-ir) was used to better understand the neurobiological alterations present in BDL animals. Plasma levels of ammonia were quantified and histopathological analysis of the livers was performed. BDL rats showed a significant decrease in the percentage of entries and time spent in the open arms of the EPM, an anxiogenic effect. These animals also presented significant decreases in Fos-ir in the lateral septal nucleus and medial amygdalar nucleus. Their ammonia plasma levels were significantly higher when compared to the sham group and the diagnosis of cirrhosis was confirmed by histopathological analysis. These results indicate that the BDL model induces anxiogenic results, possibly related to changes in the activation of anxiety-mediating circuitries and to increases in ammonia plasma levels.A Encefalopatia hepática (HE) engloba uma variedade de sintomas neuropsiquiátricos, incluindo ansiedade e disfunção psicomotora. Embora seja uma complicação frequente da cirrose hepática, os substratos neurobiológicos responsáveis por suas manifestações clínicas são em grande parte desconhecidos. No presente estudo, ratos Wistar machos foram submetidos ao procedimento cirúrgico de ligação e secção do ducto biliar (BDL; bile-duct ligation), para indução da cirrose hepática e, no 21º dia após a cirurgia, submetidos aos testes comportamentais no labirinto em cruz elevado (LCE) e campo aberto para avaliação da ansiedade e atividade locomotora. A análise da imunorreatividade à proteína Fos (Fos-ir) foi utilizada para melhor compreender as alterações neurobiológicas presentes nos animais do grupo BDL. Foi realizada a quantificação da concentração de amônia plasmática e análise histopatológica dos fígados. Os ratos do grupo BDL mostraram diminuição significativa na porcentagem de entradas e tempo gasto nos braços abertos do LCE, caracterizando efeito ansiogênico. Estes animais também apresentaram redução significativa na Fos-ir no núcleo septal lateral e núcleo medial da amígdala. A concentração plasmática de amônia foi significativamente mais elevada que a do grupo sham e o diagnóstico de cirrose foi confirmado por análise histopatológica. Estes resultados indicam que o modelo de HE induzido por BDL induz efeito ansiogênico possivelmente relacionado à ativação de circuitos mediadores da ansiedade e à hiperamonemia.Universidade Federal de São Paulo (UNIFESP) Departamento de BiociênciasUniversidade de São Paulo Instituto de Ciências Biomédicas Departamento de AnatomiaUNIFESP, Depto. de BiociênciasSciEL