Transparent soil for imaging the rhizosphere

Understanding of soil processes is essential for addressing the global issues of food security, disease transmission and climate change. However, techniques for observing soil biology are lacking. We present a heterogeneous, porous, transparent substrate for in situ 3D imaging of living plants and root-associated microorganisms using particles of the transparent polymer, Nafion, and a solution with matching optical properties. Minerals and fluorescent dyes were adsorbed onto the Nafion particles for nutrient supply and imaging of pore size and geometry. Plant growth in transparent soil was similar to that in soil. We imaged colonization of lettuce roots by the human bacterial pathogen Escherichia coli O157:H7 showing micro-colony development. Micro-colonies may contribute to bacterial survival in soil. Transparent soil has applications in root biology, crop genetics and soil microbiology

Transparent soil microcosms allow 3D spatial quantification of soil microbiological processes in vivo

The recently developed transparent soil consists of particles of Nafion, a polymer with a low refractive index (RI), which is prepared by milling and chemical treatment for use as a soil analogue. After the addition of a RI-matched solution, confocal imaging can be carried out in vivo and without destructive sampling. In a previous study, we showed that the new substrate provides a good approximation of plant growth conditions found in natural soils. In this paper, we present further development of the techniques for detailed quantitative analysis of images of root-microbe interactions in situ. Using this system it was possible for the first time to analyse bacterial distribution along the roots and in the bulk substrate in vivo. These findings indicate that the coupling of transparent soil with light microscopy is an important advance towards the discovery of the mechanisms of microbial colonisation of the rhizosphere

Methylomic trajectories across human fetal brain development

Open access articleEpigenetic processes play a key role in orchestrating transcriptional regulation during development. The importance of DNA methylation in fetal brain development is highlighted by the dynamic expression of de novo DNA methyltransferases during the perinatal period and neurodevelopmental deficits associated with mutations in the methyl-CpG binding protein 2 (MECP2) gene. However, our knowledge about the temporal changes to the epigenome during fetal brain development has, to date, been limited. We quantified genome-wide patterns of DNA methylation at ∼ 400,000 sites in 179 human fetal brain samples (100 male, 79 female) spanning 23 to 184 d post-conception. We identified highly significant changes in DNA methylation across fetal brain development at >7% of sites, with an enrichment of loci becoming hypomethylated with fetal age. Sites associated with developmental changes in DNA methylation during fetal brain development were significantly underrepresented in promoter regulatory regions but significantly overrepresented in regions flanking CpG islands (shores and shelves) and gene bodies. Highly significant differences in DNA methylation were observed between males and females at a number of autosomal sites, with a small number of regions showing sex-specific DNA methylation trajectories across brain development. Weighted gene comethylation network analysis (WGCNA) revealed discrete modules of comethylated loci associated with fetal age that are significantly enriched for genes involved in neurodevelopmental processes. This is, to our knowledge, the most extensive study of DNA methylation across human fetal brain development to date, confirming the prenatal period as a time of considerable epigenomic plasticity.MRCUniversity of Exeter Medical SchoolWellcome Trus

Epigenomic and transcriptomic signatures of a Klinefelter syndrome (47,XXY) karyotype in the brain

Klinefelter syndrome (KS) is the most common sex-chromosome aneuploidy in humans. Most affected individuals carry one extra X-chromosome (47,XXY karyotype) and the condition presents with a heterogeneous mix of reproductive, physical and psychiatric phenotypes. Although the mechanism(s) by which the supernumerary X-chromosome determines these features of KS are poorly understood, skewed X-chromosome inactivation (XCI), gene-dosage dysregulation, and the parental origin of the extra X-chromosome have all been implicated, suggesting an important role for epigenetic processes. We assessed genomic, methylomic and transcriptomic variation in matched prefrontal cortex and cerebellum samples identifying an individual with a 47,XXY karyotype who was comorbid for schizophrenia and had a notably reduced cerebellum mass compared with other individuals in the study (n = 49). We examined methylomic and transcriptomic differences in this individual relative to female and male samples with 46,XX or 46,XY karyotypes, respectively, and identified numerous locus-specific differences in DNA methylation and gene expression, with many differences being autosomal and tissue-specific. Furthermore, global DNA methylation, assessed via the interrogation of LINE-1 and Alu repetitive elements, was significantly altered in the 47,XXY patient in a tissue-specific manner with extreme hypomethylation detected in the prefrontal cortex and extreme hypermethylation in the cerebellum. This study provides the first detailed molecular characterization of the prefrontal cortex and cerebellum from an individual with a 47,XXY karyotype, identifying widespread tissue-specific epigenomic and transcriptomic alterations in the brain. © 2014 Landes Bioscience

Everyone counts? Design considerations in online citizen science

Effective classification of large datasets is a ubiquitous challenge across multiple knowledge domains. One solution gaining in popularity is to perform distributed data analysis via online citizen science platforms, such as the Zooniverse. The resulting growth in project numbers is increasing the need to improve understanding of the volunteer experience; as the sustainability of citizen science is dependent on our ability to design for engagement and usability. Here, we examine volunteer interaction with 63 projects, representing the most comprehensive collection of online citizen science project data gathered to date. Together, this analysis demonstrates how subtle project design changes can influence many facets of volunteer interaction, including when and how much volunteers interact, and, importantly, who participates. Our findings highlight the tension between designing for social good and broad community engagement, versus optimizing for scientific and analytical efficiency

A Survey of Crowdsourcing in Medical Image Analysis

Rapid advances in image processing capabilities have been seen across many domains, fostered by the application of machine learning algorithms to "big-data". However, within the realm of medical image analysis, advances have been curtailed, in part, due to the limited availability of large-scale, well-annotated datasets. One of the main reasons for this is the high cost often associated with producing large amounts of high-quality meta-data. Recently, there has been growing interest in the application of crowdsourcing for this purpose; a technique that a technique that is well established in a number of disciplines, including astronomy, ecology and meteorology for creating large-scale datasets across a range of disciplines, from computer vision to astrophysics. Despite the growing popularity of this approach, there has not yet been a comprehensive literature review to provide guidance to researchers considering using crowdsourcing methodologies in their own medical imaging analysis. In this survey, we review studies applying crowdsourcing to the analysis of medical images, published prior to July 2018. We identify common approaches and challenges and provide recommendations to researchers implementing crowdsourcing for medical imaging tasks. Finally, we discuss future opportunities for development within this emerging domain

Concert recording 2017-12-05a

[Track 1]. Lou Brouwer medley / Brouwer -- [Track 2]. One summer\u27s day / Daniel Asbun -- [Track 3]. What a friend we have in Jesus / Brad Paisley -- [Track 4]. Unity village / Pat Metheny -- [Track 5] Truth? / Asher Perkins -- [Track 6]. Invention no. 13 / J.S. Bach -- [Track 7]. Black Orpheus / Stan Getz arranged Luiz Bonfa -- [Track 8]. Five Hawaiian minutes / Shiro Mori -- [Track 9]. Birks works / Dizzy Gillespie -- [Track 10]. Perhaps / Charlie Parker -- [Track 11]. The river / King Gizzard and the Lizard Wizard -- [Track 12]. Minor swing / Django Reinhardt and Stephan Grappelli -- [Track 13]. Why break mine / Legally blind -- [Track 14]. Monochrome / Carlie Spiers -- [Track 15]. Stuck in voodoo / Dawson Scantling -- [Track 16]. I\u27m saved / Shelby Sprott -- [Track 17]. Newborn / Muse -- [Track 18]. Blueberry brain / Elephantom

A crowd of BashTheBug volunteers reproducibly and accurately measure the minimum inhibitory concentrations of 13 antitubercular drugs from photographs of 96-well broth microdilution plates

Tuberculosis is a respiratory disease that is treatable with antibiotics. An increasing prevalence of resistance means that to ensure a good treatment outcome it is desirable to test the susceptibility of each infection to different antibiotics. Conventionally, this is done by culturing a clinical sample and then exposing aliquots to a panel of antibiotics, each being present at a pre-determined concentration, thereby determining if the sample isresistant or susceptible to each sample. The minimum inhibitory concentration (MIC) of a drug is the lowestconcentration that inhibits growth and is a more useful quantity but requires each sample to be tested at a range ofconcentrations for each drug. Using 96-well broth micro dilution plates with each well containing a lyophilised pre-determined amount of an antibiotic is a convenient and cost-effective way to measure the MICs of several drugs at once for a clinical sample. Although accurate, this is still an expensive and slow process that requires highly-skilled and experienced laboratory scientists. Here we show that, through the BashTheBug project hosted on the Zooniverse citizen science platform, a crowd of volunteers can reproducibly and accurately determine the MICs for 13 drugs and that simply taking the median or mode of 11–17 independent classifications is sufficient. There is therefore a potential role for crowds to support (but not supplant) the role of experts in antibiotic susceptibility testing