Research Roundup: April 2020

GCB News

Research Roundup: April 2020

Here are summaries of a selection of the papers published by GCB faculty in April 2020:

development

Amy Goldberg and team created a model that provide a framework to quantitatively study assortative mating under flexible scenarios of admixture over time. Read more

Embryonic development is a complex process that is difficult to observe, but Xiling Shen and team found a way. They implanted a window to the mouse uterus to visualize the developing embryo from embryonic day 9.5 to birth. Read more

We do not have a strong understanding of the genetic basis for divergence in developmental gene expression among species. Greg Wray and team quantified transcription in hybrids of Heliocidaris tuberculata and Heliocidaris erythrogramma, two closely related sea urchins with highly divergent developmental gene expression and life histories. Their work provides insights into the genetic basis for the evolution of key life history traits. Read more 

The Echinodermata is characterized by a secondarily evolved pentameral body plan. While the evolutionary origin of this body plan has been the subject of debate, the molecular mechanisms underlying its development are poorly understood. Greg Wray collaborated with researchers in Sydney, Australiaassembled a de novo developmental transcriptome from the embryo through metamorphosis in the sea star Parvulastra exigua. Read more

cancer

Androgen deprivation therapy (ADT) is a common treatment for men with metastatic prostate cancer, but it can cause various metabolic disturbances. Ashley Chi and team assessed the metabolomic effects of ADT in the serum of 20 men who were receiving ADT for prostate cancer. Read more 

Platinum-based chemotherapies are a mainstay in managing solid tumors and inducing cell death, but they are highly toxic and half of cancer patients have tumors that are resistant or become resistant to this treatment. David Hsu was part of a team that worked to better define he roles of nucleotide excision repair and DNA damage in platinum chemotherapy resistance by profiling DNA damage and repair efficiency in seven oxaliplatinsensitive and three oxaliplatin-resistant colorectal cancer cell lines. Read more 

To help explain the principles underlying a RAS mutation tropism of urethane, David Macalpine collaborated with researchers in the Department of Pharmacology and Cancer Biology to adapt an error-corrected, high throughput sequencing approach to detect mutations in Ras genes in a mouse model at a high sensitivity. Read more

CRISPR

Charlie Gersbach and team used CRISPR-based gene activators to turn on the PAX7 gene. This gene controls the gene network that specifies muscle progenitor cells, which leads to activation of muscle genes and generation of cells that participate in muscle repair after transplantation into damaged tissue. Read more

Data reliability

Although DNA methylation data are used widely by researchers in many fields, the reliability of these data are surprisingly variable. Avshalom Caspi, Terrie Moffitt and team, including the Genomic Analysis and Bioinformatics core facility correlated repeat measurements of the same DNA samples using the Illumina HumanMethylation450K and the Infinium MethylationEPIC BeadChips in 350 blood DNA samples. Their findings remind us that research is only as robust as its foundations. They hope these finding will improve the integrity of DNA methylation studies and serve as a cautionary reminder for those generating and implementing big data of any type: reliability is a fundamental aspect of replicability. Read more 

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