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cell biology

Building a 3D Map of the Genome

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3D Genome Map

Credit: Chen et al., 2018

Researchers have learned a lot in recent years about how six-plus feet of human DNA gets carefully packed into a tiny cell nucleus that measures less than .00024 of an inch. Under those cramped conditions, we’ve been learning more and more about how DNA twists, turns, and spatially orients its thousands of genes within the nucleus and what this positioning might mean for health and disease.

Thanks to a new technique developed by an NIH-funded research team, there is now an even more refined view [1]. The image above features the nucleus (blue) of a human leukemia cell. The diffuse orange-red clouds highlight chemically labeled DNA found in close proximity to the tiny nuclear speckles (green). You’ll need to look real carefully to see the nuclear speckles, but these structural landmarks in the nucleus have long been thought to serve as storage sites for important cellular machinery.

A Tribute to Robert Goldman

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My lab has had a wonderfully productive collaboration with Robert Goldman at Northwestern University, Chicago. On September 25, 2018, Northwestern honored him at a celebratory symposium. Though I couldn’t attend the event, it was my pleasure to record this musical tribute to such a fantastic cell biologist. Credit: Wally Akinso

A Ray of Molecular Beauty from Cryo-EM

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Credit: Subramaniam Lab, National Cancer Institute, NIH

Walk into a dark room, and it takes a minute to make out the objects, from the wallet on the table to the sleeping dog on the floor. But after a few seconds, our eyes are able to adjust and see in the near-dark, thanks to a protein called rhodopsin found at the surface of certain specialized cells in the retina, the thin, vision-initiating tissue that lines the back of the eye.

This illustration shows light-activating rhodopsin (orange). The light photons cause the activated form of rhodopsin to bind to its protein partner, transducin, made up of three subunits (green, yellow, and purple). The binding amplifies the visual signal, which then streams onward through the optic nerve for further processing in the brain—and the ability to avoid tripping over the dog.

Watching Cancer Cells Play Ball

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Credit: Ning Wang, University of Illinois at Urbana-Champaign

As tumor cells divide and grow, they push, pull, and squeeze one another. While scientists have suspected those mechanical stresses may play important roles in cancer, it’s been tough to figure out how. That’s in large part because there hadn’t been a good way to measure those forces within a tissue. Now, there is.

As described in Nature Communications, an NIH-funded research team has developed a technique for measuring those subtle mechanical forces in cancer and also during development [1]. Their ingenious approach is called the elastic round microgel (ERMG) method. It relies on round elastic microspheres—similar to miniature basketballs, only filled with fluorescent nanoparticles in place of air. In the time-lapse video above, you see growing and dividing melanoma cancer cells as they squeeze and spin one of those cell-sized “balls” over the course of 24 hours.

An Architectural Guide to the Nuclear Pore Complex

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Credit: The Rockefeller University, New York

Sixty years ago, folk singer Pete Seeger recorded a song about helping those in need. The song starts like this: “Oh, had I a golden thread/And a needle so fine/I’d weave a magic strand/Of rainbow design.” In this brief animation, it seems like a golden thread and a needle are fast at work. But this rainbow design helps to answer a longstanding need for cell biologists: a comprehensive model of the thousands of pores embedded in the double-membrane barrier, or nuclear envelope, that divides the nucleus and its DNA from the rest of the cell.

These channels, called nuclear pore complexes (NPCs), are essential for life, tightly controlling which large macromolecules get in or out of the nucleus. Such activities include allowing vital proteins to enter the nucleus, blocking out harmful viruses, and shuttling messenger RNAs from the nucleus to the cytoplasm, where they are translated into proteins.

This computer simulation starts with an overhead view of the fully formed NPC structure. From this angle, the pore membrane (gray) appears to be at the base and is embroidered in four rings that are the channel’s main architectural support beams. There’s the cytoplasmic outer ring (yellow), the inner rings (purple, blue), the membrane ring (brown), and the nucleoplasmic outer ring (yellow). Each color represents different protein complexes, not rings per se, and the hole in the middle is the central channel through which molecules are transported. Filling the hole is a selective gating mechanism made of disordered protein (anchored to green) that helps to get the right molecules in and out.

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