Research Roundup: August 2019

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Research Roundup: August 2019

Here are summaries of a selection of the papers published by GCB faculty in August 2019:

New Models and Methods

Tim Reddy, Andrew Allen and team describe a Bayesian hierarchical model, called Bayesian Inference of Regulatory Differences, which produces more accurate predictions than existing methods when allele frequencies are low. This is of clear advantage in the search for disease-causing variants in DNA captured from patient cohorts. Read more

John Rawls and team modeled chronic intestinal damage in zebrafish larvae using the NSAID drug Glafenine. Read more


John Rawls was part of a team that show colonization of germ-free zebrafish and mice with microbiota leads to widespread transcriptional responses in olfactory organs as measured in bulk tissue transcriptomics and RT-qPCR. Read more

Doug Marchuk was part of a team that investigated the similarities and differences between transcriptomes of microdissected lesional neurovascular units from acute and chronic in vivo cerebral cavernous malformations in mice and cultured brain microvascular endothelial cells. Read more


In this review, Charlie Gersbach and Jennifer Kwon analyze two strategies that have been proposed in recent studies that reveal the potential to make the targeted insertion of DNA sequences into a genome much easier. Read more

Lingchong You and Helena Ma review two studies that have developed synthetic platforms that program spatial localization of genetic material or signaling molecules to enable asymmetric cell division in Escherichia coli. Read more

In a review by Amy Schmid and Rylee Hackley (UPGG), the team investigates the possibility of conserving the environmental stress response across he eukaryotic and archaeal domains of life. Read more

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Programmable Swarmbots Help Make Flexible Biological Tools

Lingchong You developed a new technology to create biologic drugs using specially engineering bacteria that burst and release useful proteins when they sense that their capsule is becoming too crowded.
The end goal of ECHO is to build a field-deployable device that can test small biological samples for evidence of epigenetic 'fingerprints' that reveal a detailed history of that individual’s exposure to dangerous materials or pathogens.

Identifying the Epigenetic Fingerprints of Weapons of Mass Destruction

Xiling Shen principal investigator in new DARPA project.
A cross-section of zebrafish gut showing the junctions between epithelial cells in green and a protein expressed on absorptive cells in pink.

Zebrafish Researchers Discover a Self-Defense Mechanism of the Gut

Banned painkiller had a unique effect on the model fish, so they shifted focus to figure out why