Posted on by Dr. Francis Collins
Technological advances with potential for improving human health sometimes come from the most unexpected places. An intriguing example is an electricity-conducting biological nanowire that holds promise for powering miniaturized pacemakers and other implantable electronic devices.
The nanowires come from a bacterium called Geobacter sulfurreducens, shown in the electron micrograph above. This rod-shaped microbe (white) was discovered two decades ago in soil collected from an unlikely place: a ditch outside of Norman, Oklahoma. The bug can conduct electricity along its arm-like appendages, and, in the hydrocarbon-contaminated, oxygen-depleted soil in which it lives, such electrical inputs and outputs are essentially the equivalent of breathing.
Scientists fascinated with G. sulfurreducens thought that its electricity had to be flowing through well-studied microbial appendages called pili. But, as the atomic structure of these nanowires (multi-colors, foreground) now reveals, these nanowires aren’t pili at all! Instead, the bacteria have manufactured unique submicroscopic arm-like structures. These arms consist of long, repetitive chains of a unique protein, each surrounding a core of iron-containing molecules.
The surprising discovery, published in the journal Cell, was made by an NIH-funded team involving Edward Egelman, University of Virginia Health System, Charlottesville. Egelman’s lab has had a long interest in what’s called a type 4 pili. These strong, adhering appendages help certain infectious bacteria enter tissues and make people sick. In fact, they enable bugs like Neisseria meningitidis to cross the blood-brain barrier and cause potentially deadly bacterial meningitis. While other researchers had proposed that those same type 4 pili allowed G. sulfurreducens to conduct electricity, Egelman wasn’t so sure.
So, he took advantage of recent advances in cryo-electron microscopy, which involves flash-freezing molecules at extremely low temperatures before bombarding them with electrons to capture their images with a special camera. The cryo-EM images allowed his team to nail down the atomic structure of the nanowires, now called OmcS filaments.
Using those images and sophisticated bioinformatics, Egelman and team determined that OmcS proteins uniquely fit into the nanowires’ long repetitive chains, spacing their iron-bearing cores at regular intervals to transfer electrons and convey electricity. In fact, bacteria unable to produce OmcS proteins make filaments that conduct electricity 100 times less efficiently.
With these cryo-EM structures in hand, Egelman says his team will continue to explore their conductive properties. Such knowledge might someday be used to build biologically-inspired nanowires, measuring 1/100,000th the width of a human hair, to connect miniature electronic devices directly to living tissues. This is one more example of how nature’s ability to invent is pretty breathtaking—surely one wouldn’t have predicted the discovery of nanowires in a bacterium that lives in contaminated ditches.
 Structure of Microbial Nanowires Reveals Stacked Hemes that Transport Electrons over Micrometers. Wang F, Gu Y, O’Brien JP, Yi SM, Yalcin SE, Srikanth V, Shen C, Vu D, Ing NL, Hochbaum AI, Egelman EH, Malvankar NS. Cell. 2019 Apr 4;177(2):361-369.
Electroactive microorganisms in bioelectrochemical systems. Logan BE, Rossi R, Ragab A, Saikaly PE. Nat Rev Microbiol. 2019 May;17(5):307-319.
High Resolution Electron Microscopy (National Cancer Institute/NIH)
Egelman Lab (University of Virginia, Charlottesville)
NIH Support: National Institute of General Medical Sciences; National Institute of Allergy and Infectious Diseases; Common Fund
Posted on by Dr. Francis Collins
Using a screwdriver on the tiny microcircuits arrayed inside a computer hard drive can be a real eye strain. Even more challenging is building the microcircuits or other electronic components at the nanoscale, one-billionth of a meter or less.
That’s why researchers are always on the lookout for new tools to help them work on such a minute scale. But some of these incredibly tiny tools and scaffolds can derive from very unexpected sources.
As published in the journal Science, an NIH-funded team has developed a technique called implosion fabrication to build impressively small and intricate components on the nanoscale . Its secret ingredient: water-swollen gels that you’d find in a baby’s disposable diaper.
A baby’s disposable diaper? If that sounds familiar, my blog highlighted a related technique called expansion microscopy a few years ago that uses water-swollen gels that are generated from a compound used in diapers called sodium polyacrylate.
The previously-reported microscopy technique, from the lab of Edward Boyden, Massachusetts Institute of Technology, Cambridge, embeds biological samples in a fine web of sodium polyacrylate. When water is added, the gel expands, blowing up the specimen to 100 times its original size. This groundbreaking technique, called expansion microscopy, has enabled labs around the world to use conventional microscopes for high-resolution, nanoscale imaging.
In the latest work, Boyden’s team, including co-first authors Daniel Oran and Samuel Rodriques, asked a simple question: What would happen if they applied the sample preparation technique used for expansion microscopy—only in reverse?
To find out, Boyden’s team created millimeter-sized blocks of the super-absorbent sodium polyacrylate diaper compound. After using a nifty trick for attaching molecular anchors in a 3D pattern, they dehydrated the gel and voila! The structures imploded and shrank down to one-thousandth their original size, while holding their 3D shape.
During the process, they can add to the anchors a range of functional molecules or elements. These include DNA, nanoparticles, semiconductors, or almost anything that’s needed.
While more work is needed to perfect the new technique, the researchers have already shown it can create objects one cubic millimeter in size, engineered to include intricate details down to about 50 nanometers. For comparison, a virus is about 30 to 50 nanometers.
These latest findings come as a reminder that advances in biomedicine often lead in wonderful and unexpected new directions. Out of the NIH-funded efforts related to The Brain Research through Advancing Innovative Neurotechnologies® (BRAIN) Initiative, members of the Boyden Lab wanted to see the brain better using basic microscopes. Now, we have a widely-applicable promising new approach to nanofabrication.
 3D nanofabrication by volumetric deposition and controlled shrinkage of patterned scaffolds. Oran D, Rodriques SG, Gao R, Asano S, Skylar-Scott MA, Chen F, Tillberg PW, Marblestone AH, Boyden ES. Science. 2018 Dec 14;362(6420):1281-1285.
Size of the Nanoscale (Nano.gov)
Synthetic Neurobiology Group, Ed Boyden (MIT, Cambridge, MA)
NIH Support: Common Fund; National Institute of Mental Health; National Institute of Biomedical Imaging and Bioengineering; National Human Genome Research Institute; National Institute on Drug Abuse; National Institute of Neurological Disorders and Stroke
Posted on by Dr. Francis Collins
Check out the world’s smallest board game, a nanoscale match of tic-tac-toe being played out in a test tube with X’s and O’s made of DNA. But the innovative approach you see demonstrated in this video is much more than fun and games. Ultimately, researchers hope to use this technology to build tiny DNA machines for a wide variety of biomedical applications.
Here’s how it works. By combining two relatively recent technologies, an NIH-funded team led by Lulu Qian, California Institute of Technology, Pasadena, CA, created a “swapping mechanism” that programs dynamic interactions between complex DNA nanostructures . The approach takes advantage of DNA’s modular structure, along with its tendency to self-assemble, based on the ability of the four letters of DNA’s chemical alphabet to pair up in an orderly fashion, A to T and C to G.
To make each of the X or O tiles in this game (displayed here in an animated cartoon version), researchers started with a single, long strand of DNA and many much shorter strands, called staples. When the sequence of DNA letters in each of those components is arranged just right, the longer strand will fold up into the desired 2D or 3D shape. This technique is called DNA origami because of its similarity to the ancient art of Japanese paper folding.
In the early days of DNA origami, researchers showed the technique could be used to produce miniature 2D images, such as a smiley face . Last year, the Caltech group got more sophisticated—using DNA origami to produce the world’s smallest reproduction of the Mona Lisa .
In the latest work, published in Nature Communications, Qian, Philip Petersen and Grigory Tikhomirov first mixed up a solution of nine blank DNA origami tiles in a test tube. Those DNA tiles assembled themselves into a tic-tac-toe grid. Next, two players took turns adding one of nine X or O DNA tiles into the solution. Each of the game pieces was programmed precisely to swap out only one of the tile positions on the original, blank grid, based on the DNA sequences positioned along its edges.
When the first match was over, player X had won! More importantly for future biomedical applications, the original, blank grid had been fully reconfigured into a new structure, built of all-new, DNA-constructed components. That achievement shows not only can researchers use DNA to build miniature objects, they can also use DNA to repair or reconfigure such objects.
Of course, the ultimate aim of this research isn’t to build games or reproduce famous works of art. Qian wants to see her DNA techniques used to produce tiny automated machines, capable of performing basic tasks on a molecular scale. In fact, her team already has used a similar approach to build nano-sized DNA robots, programmed to sort molecules in much the same way that a person might sort laundry . Such robots may prove useful in miniaturized approaches to drug discovery, development, manufacture, and/or delivery.
Another goal of the Caltech team is to demonstrate to the scientific community what’s possible with this leading-edge technology, in hopes that other researchers will pick up their innovative tools for their own applications. That would be a win-win for us all.
 Information-based autonomous reconfiguration in systems of DNA nanostructures. Petersen P, Tikhomirov G, Qian L. Nat Commun. 2018 Dec 18;9(1):5362
 Folding DNA to create nanoscale shapes and patterns. Rothemund PW. Nature. 2006 Mar 16;440(7082):297-302.
 Fractal assembly of micrometre-scale DNA origami arrays with arbitrary patterns. Tikhomirov G, Petersen P, Qian L. Nature. 2017 Dec 6;552(7683):67-71.
 A cargo-sorting DNA robot. Thubagere AJ, Li W, Johnson RF, Chen Z, Doroudi S, Lee YL, Izatt G, Wittman S, Srinivas N, Woods D, Winfree E, Qian L. Science. 2017 Sep 15;357(6356).
Paul Rothemund—DNA Origami: Folded DNA as a Building Material for Molecular Devices (Cal Tech, Pasadena)
The World’s Smallest Mona Lisa (Caltech)
Qian Lab (Caltech, Pasadena, CA)
NIH Support: National Institute of General Medical Sciences
Posted on by Dr. Francis Collins
The herringbone motif is familiar as the classic, V-shaped patterned weave long popular in tweed jackets. But the nano-sized herringbone pattern seen here is much more than a fashion statement. It helps to solve a tricky design problem for a cancer-detecting “lab-on-a-chip” device.
A research team, led by Yong Zeng, University of Kansas, Lawrence, and Andrew Godwin at the University of Kansas Medical Center, Kansas City. previously developed a lab-on-a-chip that senses exosomes. They are tiny bubble-shaped structures that most mammalian cells secrete constantly into the bloodstream . Once thought of primarily as trash bags used by cells to rid themselves of waste products, exosomes carry important molecular information (RNA, protein, and metabolites) used by cells to communicate and influence the behavior of other cells.
What’s also interesting, tumor cells produce more exosomes than healthy cells. That makes these 30-to-150-nanometer structures (a nanometer is a billionth of a meter) potentially useful for detecting cancer. In fact, these NIH-funded researchers found that their microfluidic device can detect exosomes from ovarian cancer within a 2-microliter blood sample. That’s just 1/25th of a drop!
But there was a technical challenge. When such tiny samples are placed into microfluidic channels, the fluid and any particles within it tend to flow in parallel layers without any mixing between them. As a result, exosomes can easily pass through undetected, without ever touching the biosensors on the surface of the chip.
That’s where the herringbone comes in. As reported in Nature Biomedical Engineering, when fluid flows over those 3D herringbone structures, it produces a whirlpool-like effect . As a result, exosomes are more reliably swept into contact with the biosensors.
The team’s distinctive herringbone structures also increase the surface area within the chip. Because the surface is also porous, it allows fluid to drain out slowly to further encourage exosomes to reach the biosensors.
Zeng’s team put their “lab-on-a-chip” to the test using blood samples from 20 patients with ovarian cancer and 10 age-matched controls. The chip was able to detect rapidly the presence of exosomal proteins known to be associated with ovarian cancer.
The researchers report that their device is sensitive enough to detect just 10 exosomes in a 1-microliter sample. It also could be easily adapted to detect exosomal proteins associated with other cancers, and perhaps other conditions as well.
Zeng and colleagues haven’t mentioned whether they’re also looking into trying other geometric patterns in their designs. But the next time you see a tweed jacket, just remember that there’s more to its herringbone pattern than meets the eye.
 Ultrasensitive microfluidic analysis of circulating exosomes using a nanostructured graphene oxide/polydopamine coating. Zhang P, He M, Zeng Y. Lab Chip. 2016 Aug 2;16(16):3033-3042.
 Ultrasensitive detection of circulating exosomes with a 3D-nanopatterned microfluidic chip. Zhang P, Zhou X, He M, Shang Y, Tetlow AL, Godwin AK, Zeng Y. Nature Biomedical Engineering. February 25, 2019.
Ovarian, Fallopian Tube, and Primary Peritoneal Cancer—Patient Version (National Cancer Institute/NIH)
Extracellular RNA Communication (Common Fund/NIH)
Zeng Lab (University of Kansas, Lawrence)
Godwin Laboratory (University of Kansas Medical Center, Kansas City)
NIH Support: National Cancer Institute
Posted on by Dr. Francis Collins
Infrared vision often brings to mind night-vision goggles that allow soldiers to see in the dark, like you might have seen in the movie Zero Dark Thirty. But those bulky goggles may not be needed one day to scope out enemy territory or just the usual things that go bump in the night. In a dramatic advance that brings together material science and the mammalian vision system, researchers have just shown that specialized lab-made nanoparticles applied to the retina, the thin tissue lining the back of the eye, can extend natural vision to see in infrared light.
The researchers showed in mouse studies that their specially crafted nanoparticles bind to the retina’s light-sensing cells, where they act like “nanoantennae” for the animals to see and recognize shapes in infrared—day or night—for at least 10 weeks. Even better, the mice maintained their normal vision the whole time and showed no adverse health effects. In fact, some of the mice are still alive and well in the lab, although their ability to see in infrared may have worn off.
When light enters the eyes of mice, humans, or any mammal, light-sensing cells in the retina absorb wavelengths within the range of visible light. (That’s roughly from 400 to 700 nanometers.) While visible light includes all the colors of the rainbow, it actually accounts for only a fraction of the full electromagnetic spectrum. Left out are the longer wavelengths of infrared light. That makes infrared light invisible to the naked eye.
In the study reported in the journal Cell, an international research team including Gang Han, University of Massachusetts Medical School, Worcester, wanted to find a way for mammalian light-sensing cells to absorb and respond to the longer wavelengths of infrared . It turns out Han’s team had just the thing to do it.
His NIH-funded team was already working on the nanoparticles now under study for application in a field called optogenetics—the use of light to control living brain cells . Optogenetics normally involves the stimulation of genetically modified brain cells with blue light. The trouble is that blue light doesn’t penetrate brain tissue well.
That’s where Han’s so-called upconversion nanoparticles (UCNPs) came in. They attempt to get around the normal limitations of optogenetic tools by incorporating certain rare earth metals. Those metals have a natural ability to absorb lower energy infrared light and convert it into higher energy visible light (hence the term upconversion).
But could those UCNPs also serve as miniature antennae in the eye, receiving infrared light and emitting readily detected visible light? To find out in mouse studies, the researchers injected a dilute solution containing UCNPs into the back of eye. Such sub-retinal injections are used routinely by ophthalmologists to treat people with various eye problems.
These UCNPs were modified with a protein that allowed them to stick to light-sensing cells. Because of the way that UCNPs absorb and emit wavelengths of light energy, they should to stick to the light-sensing cells and make otherwise invisible infrared light visible as green light.
Their hunch proved correct, as mice treated with the UCNP solution began seeing in infrared! How could the researchers tell? First, they shined infrared light into the eyes of the mice. Their pupils constricted in response just as they would with visible light. Then the treated mice aced a series of maneuvers in the dark that their untreated counterparts couldn’t manage. The treated animals also could rely on infrared signals to make out shapes.
The research is not only fascinating, but its findings may also have a wide range of intriguing applications. One could imagine taking advantage of the technology for use in hiding encrypted messages in infrared or enabling people to acquire a temporary, built-in ability to see in complete darkness.
With some tweaks and continued research to confirm the safety of these nanoparticles, the system might also find use in medicine. For instance, the nanoparticles could potentially improve vision in those who can’t see certain colors. While such infrared vision technologies will take time to become more widely available, it’s a great example of how one area of science can cross-fertilize another.
 Mammalian Near-Infrared Image Vision through Injectable and Self-Powered Retinal Nanoantennae. Ma Y, Bao J, Zhang Y, Li Z, Zhou X, Wan C, Huang L, Zhao Y, Han G, Xue T. Cell. 2019 Feb 27. [Epub ahead of print]
 Near-Infrared-Light Activatable Nanoparticles for Deep-Tissue-Penetrating Wireless Optogenetics. Yu N, Huang L, Zhou Y, Xue T, Chen Z, Han G. Adv Healthc Mater. 2019 Jan 11:e1801132.
Diagram of the Eye (National Eye Institute/NIH)
Infrared Waves (NASA)
Visible Light (NASA)
Han Lab (University of Massachusetts, Worcester)
NIH Support: National Institute of Mental Health; National Institute of General Medical Sciences