Research Roundup: December 2018

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Research Roundup: December 2018

Here are summaries of a selection of the papers published by GCB faculty in December 2018:

Disease and Mental Health

Charlie Gersbach was part of a team that used adeno-associated virus-mediated (AAV-mediated) CRISPR gene editing therapy on mouse models to treat Duchenne muscular dystrophy. The team discovered they need to increase the levels of guide RNA to improve the effectiveness of this gene editing approach. Read more

Inflammation often induces regeneration to repair the tissue damage. However, chronic inflammation can transform temporary organ or tissue inflammation into a fertile ground for tumor development. Xiling Shen and team show that the microRNA miR-34a acts as a safeguard to protect the stem cell niche and reparative regeneration during inflammation. Read more

Terrie Moffitt was part of a team that investigated correlations between air pollution and mental health problems in childhood and adolescence using participants from the Environmental Risk Longitudinal Twin Study in London. Read more

DNA Methylation

Jenny Tung, Sayan Mukherjee and team investigated the evolution of genome-wide DNA methylation levels in the baboon genus Papio. They found that most of the rate and distribution of DNA methylation changes mirror genetic structure, but at some CpG sites, DNA methylation levels themselves may have been a target of positive selection that helped develop fitness-related traits. Read more

Changes in DNA methylation are involved in development, disease, and the response to environmental conditions. Jenny Tung, Tim Reddy and team used mSTARR-seq to identify thousands of methylation-dependent regulatory elements in the human genome. Read more

Ecology

Tom Mitchell-Olds and team used 149 populations of sexual and apomictic lineages in the genus Boechera (rock cress) and characterized the reproductive mode, ploidy, and species identity or hybrid parentage of each individual, and then used a multipronged statistical approach to identify ecological differentiation between sexuals and asexuals; investigate the impacts polyploidy and hybridization on ecological differentiation; and determine the environmental variables underlying ecological differentiation. Read more

Gene Expression and Regulation

As part of the PsychENCODE Consotrium, Greg Crawford was part of a team that set out to discover gene-regulatory elements and chart their dynamic activity during prenatal human cortical development, focusing on enhancers, which carry most of the weight upon regulation of gene expression. Read more

Jenny Tung and team manipulated the social status in female rhesus macaques to investigate how status differences alter the gene expression and chromatin accessibility response to glucocorticoids, which are the hormones involved in regulating stress. Read more

Tim Reddy, Andrew Allen and team used high-throughput reporter assays to measure environmentally responsive regulatory element activity throughout the human genome. Read more

New methods, models, and more

John Rawls was part of a team that developed a method for high-resolution imaging and manipulation of organized granulomas called mycobacterial granuloma explant model (Myco-GEM). The Myco-GEM approach allows culture of granulomas ex vivo for at least seven days, enabling longer-term imaging of cellular and bacterial dynamics within fully organized granulomas by epifluorescent, confocal, and light sheet microscopy techniques. Read more

As part of the PsychENCODE Consortium, Greg Crawford was part of a team that developed a comprehensive online resource and integrative models for the functional genomics of the human brain, which have uncovered genomic elements and networks in the brain and provided insight into the molecular mechanisms underlying psychiatric disorders. Their deep-learning model improves disease risk prediction over traditional approaches and can be extended with additional data types. Read more

In a proof-of-principle study, Xiling Shen and team explored a strategy that combines in vitro-transcribed mRNA to recruit and reprogram immune effector cells in a mouse model that have the capacity to fulfill complex biological tasks in vivo. Read more

Lingchong You and team used a framework typical of microbial communities to test their ability to survive a disturbance and applied it to the bacterial response to antibiotic treatment. Read more

Reviews

In this review, Sandeep Dave and Jennifer Shingleton discuss research from Pilar Dominguez of Cornell University on the mechanistic link between TET2 mutation and germinal center B-cell transformation. Read more

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