DNA Methylation Analysis Validates Organoids as a Viable Model for Studying Human Intestinal Aging.

Background & aimsThe epithelia of the intestine and colon turn over rapidly and are maintained by adult stem cells at the base of crypts. Although the small intestine and colon have distinct, well-characterized physiological functions, it remains unclear if there are fundamental regional differences in stem cell behavior or region-dependent degenerative changes during aging. Mesenchyme-free organoids provide useful tools for investigating intestinal stem cell biology in vitro and have started to be used for investigating age-related changes in stem cell function. However, it is unknown whether organoids maintain hallmarks of age in the absence of an aging niche. We tested whether stem cell-enriched organoids preserved the DNA methylation-based aging profiles associated with the tissues and crypts from which they were derived.MethodsTo address this, we used standard human methylation arrays and the human epigenetic clock as a biomarker of age to analyze in vitro-derived, 3-dimensional, stem cell-enriched intestinal organoids.ResultsWe found that human stem cell-enriched organoids maintained segmental differences in methylation patterns and that age, as measured by the epigenetic clock, also was maintained in vitro. Surprisingly, we found that stem cell-enriched organoids derived from the small intestine showed striking epigenetic age reduction relative to organoids derived from colon.ConclusionsOur data validate the use of organoids as a model for studying human intestinal aging and introduce methods that can be used when modeling aging or age-onset diseases in vitro

Using Survey Data to (Help) Parameterize Human Terrain Models

2nd International Conference on Cross-cultural Decision Making, San Francisco, CA, July 2012

How are nature-based solutions contributing to priority societal challenges surrounding human well-being in the United Kingdom: a systematic map

Background: The concept of nature-based solutions (NBS) has evolved as an umbrella concept to describe approaches to learning from and using nature to create sustainable socio-ecological systems. Furthermore, NBS often address multiple societal challenges that humans are facing in the medium to long-term and as such can enhance human well-being (HWB). This study was commissioned to fulfil the need for a targeted systematic evidence map on the linkage between NBS and HWB to support focused research going forward that addresses the key knowledge needs of policy makers in the UK and beyond. Methods: A consultation with policy makers and government agency staff (n = 46), in the four component parts of the UK (England, Wales, Scotland, Northern Ireland) was conducted in spring 2019. This identified four key societal challenges of operational experience lacking a scientific evidence base. Three of these challenges related to management issues: NBS cost-efficacy, governance in planning, environmental justice. The fourth challenge related to the acoustic environment (soundscape). Using systematic methods, this study searched for and identified studies that assessed NBS on HWB with regard to these four selected societal challenges. Review findings: A total of 7287 articles were returned from the systematic search and screened for suitability at the level of title and abstract. A total of 610 articles passed screening criteria to warrant full text screening. Of these, 115 studies met the full text criteria for eligibility in the final systematic map database. Included studies were coded for twelve NBS interventions and ten HWB related outcome categories. Most of the evidence reviewed referred to natural, blue or green infrastructure in the urban environment and focused on economic, material and health aspects of HWB. Less than 2% of studies identified in the searches robustly reported the role of NBS actions or interventions on HWB compared with non-NBS actions or interventions. Conclusion: This systematic map found the evidence base is growing on NBS-HWB linkages, but significant biases persist in the existing literature. There was a bias in favour of the urban environment and restoration studies focused on conservation aspects, with only a few studies investigating the full suite of advantages to HWB that can be delivered from NBS actions and interventions. The soundscape was the least studied of the societal challenges identified as being of key importance by policy makers, with cost-efficiency the most reported. There was a lack of robust long-term studies to clearly test the potential of NBS regarding the HWB outcomes compared with non-NBS alternatives. This lack of robust primary knowledge, covering all four key societal challenges identified, confirms that the knowledge gaps identified by the policy makers persist, and highlights a clear research need for long-term, transdisciplinary studies that focus on comparisons between NBS and non-NBS alternatives

Easy on that trigger dad: a study of long term family photo retrieval

We examine the effects of new technologies for digital photography on people's longer term storage and access to collections of personal photos. We report an empirical study of parents' ability to retrieve photos related to salient family events from more than a year ago. Performance was relatively poor with people failing to find almost 40% of pictures. We analyze participants' organizational and access strategies to identify reasons for this poor performance. Possible reasons for retrieval failure include: storing too many pictures, rudimentary organization, use of multiple storage systems, failure to maintain collections and participants' false beliefs about their ability to access photos. We conclude by exploring the technical and theoretical implications of these findings

Combining Slaughterhouse Surveillance Data with Cattle Tracing Scheme and Environmental Data to Quantify Environmental Risk Factors for Liver Fluke in Cattle.

Liver fluke infection causes serious disease (fasciolosis) in cattle and sheep in many regions of the world, resulting in production losses and additional economic consequences due to condemnation of the liver at slaughter. Liver fluke depends on mud snails as an intermediate host and infect livestock when ingested through grazing. Therefore, environmental factors play important roles in infection risk and climate change is likely to modify this. Here, we demonstrate how slaughterhouse data can be integrated with other data, including animal movement and climate variables to identify environmental risk factors for liver fluke in cattle in Scotland. We fitted a generalized linear mixed model to the data, with exposure-weighted random and fixed effects, an approach which takes into account the amount of time cattle spent at different locations, exposed to different levels of risk. This enabled us to identify an increased risk of liver fluke with increased animal age, rainfall, and temperature and for farms located further to the West, in excess of the risk associated with a warmer, wetter climate. This model explained 45% of the variability in liver fluke between farms, suggesting that the unexplained 55% was due to factors not included in the model, such as differences in on-farm management and presence of wet habitats. This approach demonstrates the value of statistically integrating routinely recorded slaughterhouse data with other pre-existing data, creating a powerful approach to quantify disease risks in production animals. Furthermore, this approach can be used to better quantify the impact of projected climate change on liver fluke risk for future studies

TobEA: an atlas of tobacco gene expression from seed to senescence.

RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.BACKGROUND: Transcriptomics has resulted in the development of large data sets and tools for the progression of functional genomics and systems biology in many model organisms. Currently there is no commercially available microarray to allow such expression studies in Nicotiana tabacum (tobacco). RESULTS: A custom designed Affymetrix tobacco expression microarray was generated from a set of over 40k unigenes and used to measure gene expression in 19 different tobacco samples to produce the Tobacco Expression Atlas (TobEA). TobEA provides a snap shot of the transcriptional activity for thousands of tobacco genes in different tissues throughout the lifecycle of the plant and enables the identification of the biological processes occurring in these different tissues. 772 of 2513 transcription factors previously identified in tobacco were mapped to the array, with 87% of them being expressed in at least one tissue in the atlas. Putative transcriptional networks were identified based on the co-expression of these transcription factors. Several interactions in a floral identity transcription factor network were consistent with previous results from other plant species. To broaden access and maximise the benefit of TobEA a set of tools were developed to provide researchers with expression information on their genes of interest via the Solanaceae Genomics Network (SGN) web site. The array has also been made available for public use via the Nottingham Arabidopsis Stock Centre microarray service. CONCLUSIONS: The generation of a tobacco expression microarray is an important development for research in this model plant. The data provided by TobEA represents a valuable resource for plant functional genomics and systems biology research and can be used to identify gene targets for both fundamental and applied scientific applications in tobacco