Transcription factor target prediction using multiple short expression time series from Arabidopsis thaliana

BACKGROUND: The central role of transcription factors (TFs) in higher eukaryotes has led to much interest in deciphering transcriptional regulatory interactions. Even in the best case, experimental identification of TF target genes is error prone, and has been shown to be improved by considering additional forms of evidence such as expression data. Previous expression based methods have not explicitly tried to associate TFs with their targets and therefore largely ignored the treatment specific and time dependent nature of transcription regulation. RESULTS: In this study we introduce CERMT, Covariance based Extraction of Regulatory targets using Multiple Time series. Using simulated and real data we show that using multiple expression time series, selecting treatments in which the TF responds, allowing time shifts between TFs and their targets and using covariance to identify highly responding genes appear to be a good strategy. We applied our method to published TF - target gene relationships determined using expression profiling on TF mutants and show that in most cases we obtain significant target gene enrichment and in half of the cases this is sufficient to deliver a usable list of high-confidence target genes. CONCLUSION: CERMT could be immediately useful in refining possible target genes of candidate TFs using publicly available data, particularly for organisms lacking comprehensive TF binding data. In the future, we believe its incorporation with other forms of evidence may improve integrative genome-wide predictions of transcriptional networks

Changes in bacterial and fungal communities across compost recipes, preparation methods, and composting times. PLoS One

Abstract Compost production is a critical component of organic waste handling, and compost applications to soil are increasingly important to crop production. However, we know surprisingly little about the microbial communities involved in the composting process and the factors shaping compost microbial dynamics. Here, we used high-throughput sequencing approaches to assess the diversity and composition of both bacterial and fungal communities in compost produced at a commercial-scale. Bacterial and fungal communities responded to both compost recipe and composting method. Specifically, bacterial communities in manure and hay recipes contained greater relative abundances of Firmicutes than hardwood recipes with hay recipes containing relatively more Actinobacteria and Gemmatimonadetes. In contrast, hardwood recipes contained a large relative abundance of Acidobacteria and Chloroflexi. Fungal communities of compost from a mixture of dairy manure and silage-based bedding were distinguished by a greater relative abundance of Pezizomycetes and Microascales. Hay recipes uniquely contained abundant Epicoccum, Thermomyces, Eurotium, Arthrobotrys, and Myriococcum. Hardwood recipes contained relatively abundant Sordariomycetes. Holding recipe constant, there were significantly different bacterial and fungal communities when the composting process was managed by windrow, aerated static pile, or vermicompost. Temporal dynamics of the composting process followed known patterns of degradative succession in herbivore manure. The initial community was dominated by Phycomycetes, followed by Ascomycota and finally Basidiomycota. Zygomycota were associated more with manure-silage and hay than hardwood composts. Most commercial composters focus on the thermophilic phase as an economic means to insure sanitation of compost from pathogens. However, the community succeeding the thermophilic phase begs further investigation to determine how the microbial dynamics observed here can be best managed to generate compost with the desired properties

PaVESy: Pathway visualization and editing system

A data managing system for editing and visualization of biological pathways is presented. The main component of PaVESy (Pathway Visualization and Editing System) is a relational SQL database system. The database design allows storage of biological objects, such as metabolites, proteins, genes and respective relations, which are required to assemble metabolic and regulatory biological interactions. The database model accommodates highly flexible annotation of biological objects by user-defined attributes. In addition, specific roles of objects are derived from these attributes in the context of user-defined interactions, e.g. in the course of pathway generation or during editing of the database content. Furthermore, the user may organize and arrange the database content within a folder structure and is free to group and annotate database objects of interest within customizable subsets. Thus, we allow an individualized view on the database content and facilitate user customization. A JAVA-based class library was developed, which serves as the database programming interface to PaVESy. This API provides classes, which implement the concepts of object persistence in SQL databases, such as entries, interactions, annotations, folders and subsets. We created editing and visualization tools for navigation in and visualization of the database content. User approved pathway assemblies are stored and may be retrieved for continued modification, annotation and export. Data export is interfaced with a range of network visualization programs, such as Pajek or other software allowing import of SBML or GML data format

Abstract PaVESy: Combining profiling data with pathway knowledge

Since a couple of years high-throughput profiling methods are entering life sciences. For instance, a gene expression profile contains information about the transcriptional response of a complete genome to different experimental conditions. For scientists this abundance of data is often difficult to interpret. Several statistical methods are developed, and progress in data processing and management makes it more and more feasible to connect the results of a concrete experiment to the confirmed but seemly unmanageable knowledge already known. The pathway database software PaVES

Organic Farm Bedded Pack System Microbiomes: A Case Study with Comparisons to Similar and Different Bedded Packs

Animal housing and bedding materials influence cow and farm worker exposure to microbial pathogens, biocontrol agents, and/or allergens. This case study represents an effort to characterize the bacterial and fungal community of bedding systems using an amplicon sequencing approach supplemented with the ecological assessment of cultured Trichocomaceae isolates (focusing on Penicillium and Aspergillus species) and yeasts (Saccharomycetales). Bedding from five certified organic dairy farms in northern Vermont USA were sampled monthly between October 2015 and May 2016. Additional herd level samples from bulk tank milk and two bedding types were collected from two farms to collect fungal isolates for culturing and ecology. Most of the microorganisms in cattle bedding were microbial decomposers (saprophytes) or coprophiles, on account of the bedding being composed of dead plant matter, cattle feces, and urine. Composition of bacterial and fungal communities exhibited distinct patterns of ecological succession measured through time and by bedding depth. Community composition patterns were related to management practices and choice of bedding material. Aspergillus and Penicillium species exhibited niche differentiation expressed as differential substrate requirements; however, they generally exhibited traits of early colonizers of bedding substrates, typically rich in carbon and low in nitrogen. Pichia kudriavzevii was the most prevalent species cultured from milk and bedding. P. kudriavzevii produced protease and its abundance directly related to temperature. The choice of bedding and its management represent a potential opportunity to curate the microbial community of the housing environment

Assembling activity/setting participation with disabled young people

Rehabilitation research investigating activity participation has been largely conducted in a realist tradition that under-theorises the relationship between persons, technologies, and socio-material places. In this Canadian study we used a post-critical approach to explore activity/setting participation with 19 young people aged 14 to 23 years with complex communication and/or mobility impairments. Methods included integrated photo-elicitation, interviews, and participant observations of community-based activities. We present our results using the conceptual lens of assemblages to surface how different combinations of bodies, social meanings, and technologies enabled or constrained particular activities. Assemblages were analysed in terms of how they organised what was possible and practical for participants and their families in different contexts. The results illuminate how young people negotiated activity needs and desires in particular ‘spacings’ each with its own material, temporal, and social constraints and affordances. The focus on assemblages provides a dynamic analysis of how dis/abilities are enacted in and across geotemporal spaces, and avoids a reductive focus on evaluating the accessibility of static environmental features. In doing so the study reveals possible ‘lines of flight’ for healthcare, rehabilitation, and social care practices

Материалы к познанию Ostracoda Чёрного моря

Increased geographical mobility, improved medical treatment, and prolonged life expectancy have changed the way of life for older persons and their next of kin. This chapter discusses intergenerational care, mainly from the next of kin’s point of view, when an older family member and the next of kin live far from each other. The study is based on my—the author’s—autoethnographic account of the experience after my father suffered a stroke a few years ago. Inspired by Ellis et al. (2011, p. 392), who stated that autoethnography may ‘analyse personal experience in order to understand cultural experience’, I use my father’s and my own experiences to analyse how geographical distance and serious illness impact intergenerational care and kinship. While I argue that intergenerational care across geographical distance creates certain vulnerabilities, this specific situation also enables and enacts kinship relations. The study focused on practical support, emotional relations, and communication technologies, and their limitations when illness hits and life changes. It also adds to our understanding of aging, illness, and care across vast geographical distances. I claim that the autoethnographic approach accommodates the subjectivity, emotions and first-hand experiences between the older person and the next of kin. This geography of intergenerational care provides new knowledge about an experience, influencing the later years, for an increasing number of individuals and service-providing municipalities, especially in regions marked by outmigration and high youth mobility