420 research outputs found

    Phylogenetic and DNA methylation analysis reveal novel regions of variable methylation in the mouse IAP class of transposons

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    Abstract Background Select retrotransposons in the long terminal repeat (LTR) class exhibit interindividual variation in DNA methylation that is altered by developmental environmental exposures. Yet, neither the full extent of variability at these ā€œmetastable epialleles,ā€ nor the phylogenetic relationship underlying variable elements is well understood. The murine metastable epialleles, Avy and CabpIAP, result from independent insertions of an intracisternal A particle (IAP) mobile element, and exhibit remarkably similar sequence identity (98.5%). Results Utilizing the C57BL/6 genome we identified 10802 IAP LTRs overall and a subset of 1388 in a family that includes Avy and CabpIAP. Phylogenetic analysis revealed two duplication and divergence events subdividing this family into three clades. To characterize interindividual variation across clades, liver DNA from 17 isogenic mice was subjected to combined bisulfite and restriction analysis (CoBRA) for 21 separate LTR transposons (7 per clade). The lowest and highest mean methylation values were 59% and 88% respectively, while methylation levels at individual LTRs varied widely, ranging from 9% to 34%. The clade with the most conserved elements had significantly higher mean methylation across LTRs than either of the two diverged clades (pā€‰=ā€‰0.040 and pā€‰=ā€‰0.017). Within each mouse, average methylation across all LTRs was not significantly different (71%-74%, pā€‰>ā€‰0.99). Conclusions Combined phylogenetic and DNA methylation analysis allows for the identification of novel regions of variable methylation. This approach increases the number of known metastable epialleles in the mouse, which can serve as biomarkers for environmental modifications to the epigenome.http://deepblue.lib.umich.edu/bitstream/2027.42/112312/1/12864_2012_Article_4665.pd

    Using parent metaphors for learning about the neonatal care experience: an interpretive perspective

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    Ā© 2019 The Author(s). The final, definitive version of this paper has been published in Journal of Child Health Care by Sage Publications Ltd. All rights reserved. It is available at: https://doi.org/10.1177/1367493519875853.This study focuses on how metaphors are used by parents who have had a premature baby to describe their neonatal care experience and how these can contribute to empathic learning of health professionals. In health, metaphors are commonly used to communicate and explain difficult topics. When patients tell their story, metaphor can be a means of expression from which we can learn about their experience of illness or hospitalisation. Limited research exits on how metaphor can improve our understanding of parentā€™s emotional experience in neonatal care and subsequently inform education in this field. Employing narrative inquiry within an interpretive, constructivist paradigm, 20 narrative interviews with 23 parents of premature babies were analysed using a process of metaphor identification. Findings revealed common metaphors used to describe experience. Metaphor clusters used by parents in order of frequency were journeying, altered reality, darkness, breaking, connections, fighting, salvation and being on the edge. Parents widely used compelling and emotive metaphors to describe and express both difficult and challenging times as well as progression forward. Metaphors serve as a powerful way for health professionals to learn about the emotional experiences of parents and potentially enhance their empathic understanding.Peer reviewe

    Towards a method for rigorous development of generic requirements patterns

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    We present work in progress on a method for the engineering, validation and verification of generic requirements using domain engineering and formal methods. The need to develop a generic requirement set for subsequent system instantiation is complicated by the addition of the high levels of verification demanded by safety-critical domains such as avionics. Our chosen application domain is the failure detection and management function for engine control systems: here generic requirements drive a software product line of target systems. A pilot formal specification and design exercise is undertaken on a small (twosensor) system element. This exercise has a number of aims: to support the domain analysis, to gain a view of appropriate design abstractions, for a B novice to gain experience in the B method and tools, and to evaluate the usability and utility of that method.We also present a prototype method for the production and verification of a generic requirement set in our UML-based formal notation, UML-B, and tooling developed in support. The formal verification both of the structural generic requirement set, and of a particular application, is achieved via translation to the formal specification language, B, using our U2B and ProB tools

    The role of environmental exposures and the epigenome in health and disease

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    Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/152782/1/em22311_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/152782/2/em22311.pd

    BRANCHLESS TRICHOMES links cell shape and cell cycle control in Arabidopsis trichomes

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    Endoreplication, also called endoreduplication, is a modified cell cycle in which DNA is repeatedly replicated without subsequent cell division. Endoreplication is often associated with increased cell size and specialized cell shapes, but the mechanism coordinating DNA content with shape and size remains obscure. Here we identify the product of the BRANCHLESS TRICHOMES (BLT) gene, a protein of hitherto unknown function that has been conserved throughout angiosperm evolution, as a link in coordinating cell shape and nuclear DNA content in endoreplicated Arabidopsis trichomes. Loss-of-function mutations in BLT were found to enhance the multicellular trichome phenotype of mutants in the SIAMESE (SIM) gene, which encodes a repressor of endoreplication. Epistasis and overexpression experiments revealed that BLT encodes a key regulator of trichome branching. Additional experiments showed that BLT interacts both genetically and physically with STICHEL, another key regulator of trichome branching. Although blt mutants have normal trichome DNA content, overexpression of BLT results in an additional round of endoreplication, and blt mutants uncouple DNA content from morphogenesis in mutants with increased trichome branching, further emphasizing its role in linking cell shape and endoreplication. Ā© 2011. Published by The Company of Biologists Ltd

    Early life social and ecological determinants of global DNA methylation in wild spotted hyenas

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    Environmental factors early in life can have lasting influence on the development and phenotypes of animals, but the underlying molecular modifications remain poorly understood. We examined crossā€sectional associations among early life socioecological factors and global DNA methylation in 293 wild spotted hyenas (Crocuta crocuta) in the Masai Mara National Reserve, Kenya, grouped according to three age classes (cub, subadult and adult). Explanatory variables of interest included annual maternal rank based on outcomes of dyadic agonistic interactions, litter size, wild ungulate prey density and anthropogenic disturbance in the year each hyena was born based on counts of illegal livestock in the Reserve. The dependent variable of interest was global DNA methylation, assessed via the LUminometric Methylation Assay, which provides a percentage methylation value calculated at CCGG sites across the genome. Among cubs, we observed approximately 2.75% higher CCGG methylation in offspring born to highā€ than lowā€ranking mothers. Among cubs and subadults, higher anthropogenic disturbance corresponded with greater %CCGG methylation. In both cubs and adults, we found an inverse association between prey density measured before a hyena was 3Ā months old and %CCGG methylation. Our results suggest that maternal rank, anthropogenic disturbance and prey availability early in life are associated with later life global DNA methylation. Future studies are required to understand the extent to which these DNA methylation patterns relate to adult phenotypes and fitness outcomes.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/151897/1/mec15174_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/151897/2/mec15174.pd

    Functional conservation in the SIAMESE-RELATED family of cyclin-dependent kinase inhibitors in land plants

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    Ā© 2015 American Society of Plant Biologists. All rights reserved. The best-characterized members of the plant-specific SIAMESE-RELATED (SMR) family of cyclin-dependent kinase inhibitors regulate the transition from the mitotic cell cycle to endoreplication, also known as endoreduplication, an altered version of the cell cycle in which DNA is replicated without cell division. Some other family members are implicated in cell cycle responses to biotic and abiotic stresses. However, the functions of most SMRs remain unknown, and the specific cyclin- dependent kinase complexes inhibited by SMRs are unclear. Here, we demonstrate that a diverse group of SMRs, including an SMR from the bryophyte Physcomitrella patens, can complement an Arabidopsis thaliana siamese (sim) mutant and that both Arabidopsis SIM and P. patens SMR can inhibit CDK activity in vitro. Furthermore, we show that Arabidopsis SIM can bind to and inhibit both CDKA;1 and CDKB1;1. Finally, we show that SMR2 acts to restrict cell proliferation during leaf growth in Arabidopsis and that SIM, SMR1/LGO, and SMR2 play overlapping roles in controlling the transition from cell division to endoreplication during leaf development. These results indicate that differences in SMR function in plant growth and development are primarily due to differences in transcriptional and posttranscriptional regulation, rather than to differences in fundamental biochemical function
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