Ep. 91: “3D Cell Library” Featuring Dr. Rick Horwitz and Dr. Graham Johnson

May 9, 2017

Dr. Graham Johnson, computational biologist and medical illustrator building multi-scale cell visualizations. Dr. Rick Horwitz, cell migration and architecture expert leading the Allen Institute. They explore the Allen Cell Explorer 3-D cell library, why iPS cells and cardiomyocytes were chosen, technical hurdles like imaging and segmentation, and using deep learning to predict whole-cell organization.

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INSIGHT

Modeling Whole Cells With Live Imaging

The Allen Institute seeks to model whole cells by quantifying positions and relationships of components using live-cell imaging and statistics.
Rick Horwitz explains they aim to map how many of everything exists and where, producing predictive, mechanistic models from structural organization.

INSIGHT

Structure Complements Genomics To Explain Function

Gene expression catalogs players but not organization; structure determines function at mesoscale and must be measured directly.
Rick Horwitz contrasts genomics with structural maps and says cell activities arise from nanoscale to mesoscale rearrangements.

ADVICE

Analyze Thousands Of Cells Not Dozens

Scale matters: analyze thousands of cells to convert variation into statistical, interpretable patterns rather than relying on a few examples.
Graham Johnson and Rick Horwitz say large datasets let you separate normal distributions from rare phenotypes.

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Guest:

In this episode, we bring you Drs. Rick Horwitz and Graham Johnson from the Allen Institute for Cell Sciences. They discuss the Allen Cell Explorer, a 3-D cell library created using induced pluripotent stem cells.

Featured Resource: STEMdiff™ Trilineage Differentiation Kit

Resources and Links

A March for Science Happened – Scientists had to engage and take their demands to political leaders and policymakers, so they stood for hours on a sodden National Mall and then marched through puddles to Capitol Hill.

HPV Vaccine as a Cancer Prevention Needs to be Emphasized – In the United States, HPV vaccination rates lag for girls and boys mainly because the message that the vaccine prevents cancer isn’t getting out there.

All Crossed Up-Neuron Miswiring Can Lead to Depression – Researchers have pinpointed a gene called Pcdhαc2 that keeps important brain cells in mice from crossing their wires, providing a possible link between brain wiring and mood disorders like depression.

Zika Virus Hangs Out in Your Body – Weeks after the virus disappears from the bloodstream, it still lingers in the lymph nodes and the central nervous system of rhesus monkeys.

CIRM is on Its Last Leg – Major investment in regenerative medicine enters its last stage — and the money might run out before treatments are ready.

CRISPR Editing to Fight Arthritis – Scientists have rewired stem cells’ genetic circuits known as SMART cells (Stem cells Modified for Autonomous Regenerative Therapy) to produce an anti-inflammatory arthritis drug when the cells encounter inflammation.

CRISPR and Stem Cells Identify Novel Chlamydia Drug Targets – Researchers at the Wellcome Trust Sanger Institute and their colleagues at the University of British Columbia have developed a novel method for studying how the bacterium Chlamydia trachomatis interacts with the human immune system.

Activating Stem Cells for Quicker Healing – Recent research, led by assistant professor of stem cell biology and regenerative medicine at the University of South Carolina Joseph T. Rodgers, has found a way to increase the body’s ability to heal after injury.

Photo Reference: Courtesy of Dr. Rick Horwitz and Dr. Graham Johnson

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