Lawrence Tabak, D.D.S., Ph.D.
Science, Serendipity, and Art
Posted on by Lawrence Tabak, D.D.S., Ph.D.
Fractals are complex geometric patterns repeated at progressively smaller scales. You’ll find them throughout nature. That includes in the 3D structures and shapes of tissues throughout our bodies, from the bones in our skulls down to the blood vessels in our feet. But the fractal pattern above isn’t from a precisely patterned human tissue. It comes from some unexpected biochemistry that formed the stunning pattern on its own.
In fact, the exact source for this fractal pattern reminiscent of peacock feathers isn’t known. It turned up out of the blue (and green) in a sample that had been sitting around on the shelf for some time. The original image appeared in black and white, but the colors added post-collection help to highlight the fractal pattern of a sample including an essential hormone produced in the pancreas. The hormone is called islet amyloid polypeptide (IAPP).
Also known as amylin, IAPP plays many important roles in our bodies, including the feeling of fullness after a meal. But the amino acid chains that make up IAPP also are prone to forming abnormal clumps of misfolded polypeptides (a long name for proteins) known as amyloids. Much like the amyloid plaques in the brains of people with Alzheimer’s disease, misfolded IAPP amyloids in people with type 2 diabetes also can damage insulin-producing beta cells in the pancreas and make controlling their blood sugar levels even more difficult.
This unusual image comes from graduate students Bryan Bogin and Matthew Steinsaltz. They study the biophysics and biochemistry of protein folding and misfolding in the lab of Zachary Levine, Yale School of Medicine, New Haven, CT. The Levine lab recently moved to the Altos Labs San Diego Institute. However, Bogin and Steinsaltz continue to conduct their studies at Yale.
The two conduct in-solution experiments and molecular simulations to elucidate the precise conditions and triggers that can lead otherwise normal polypeptide chains to fold up incorrectly and wreak havoc as they do in diabetes and other diseases. When Steinsaltz was learning how to use transmission electron microscopy (TEM), a technique in which an electron beam captures images including detailed molecular-level structures, Bogin handed over an assortment of IAPP samples in different solution conditions from some of his past experiments for a look.
In those microscopy images, they expected to see long, linear fibrils consisting of IAPP polypeptides. While that’s indeed what they saw in most of the samples, this one was the exception. It was such a remarkable image that they submitted it in the Biophysical Society’s 2022 Art of Science Image Contest, where it took the top prize.
Bogin and Steinsaltz say they still can’t explain the source or meaning behind these unusual fractal patterns. But they do continue to conduct experiments to understand how various polypeptides implicated in health and disease misfold to form destructive aggregates. This striking image may not hold the answers they seek, but it is an inspiring reminder that the path to making groundbreaking biomedical discoveries will have many beautiful surprises along the way.
Links:
Type 2 Diabetes (National Institute of Diabetes and Digestive and Kidney Diseases/NIH)
Zachary Levine Lab (Yale School of Medicine, New Haven, CT)
Art of Science Image Contest (Biophysical Society, Rockville, MD)
NIH Support: National Institute on Aging
NIH Welcomes Visitors from OSTP
Posted on by Lawrence Tabak, D.D.S., Ph.D.
How Neurons Make Connections
Posted on by Lawrence Tabak, D.D.S., Ph.D.
For many people, they are tiny pests. These fruit flies that sometimes hover over a bowl of peaches or a bunch of bananas. But for a dedicated community of researchers, fruit flies are an excellent model organism and source of information into how neurons self-organize during the insect’s early development and form a complex, fully functioning nervous system.
That’s the scientific story on display in this beautiful image of a larval fruit fly’s developing nervous system. Its subtext is: fundamental discoveries in the fruit fly, known in textbooks as Drosophila melanogaster, provide basic clues into the development and repair of the human nervous system. That’s because humans and fruit flies, though very distantly related through the millennia, still share many genes involved in their growth and development. In fact, 60 percent of the Drosophila genome is identical to ours.
Once hatched, as shown in this image, a larval fly uses neurons (magenta) to sense its environment. These include neurons that sense the way its body presses against the surrounding terrain, as needed to coordinate the movements of its segmented body parts and crawl in all directions.
This same set of neurons will generate painful sensations, such as the attack of a parasitic wasp. Paintbrush-like neurons in the fly’s developing head (magenta, left side) allow the insect to taste the sweetness of a peach or banana.
There is a second subtype of neurons, known as proprioceptors (green). These neurons will give the young fly its “sixth sense” understanding about where its body is positioned in space. The complete collection of developing neurons shown here are responsible for all the fly’s primary sensations. They also send these messages on to the insect’s central nervous system, which contains thousands of other neurons that are hidden from view.
Emily Heckman, now a postdoctoral researcher at the Michigan Neuroscience Institute, University of Michigan, Ann Arbor, captured this image during her graduate work in the lab of Chris Doe, University of Oregon, Eugene. For her keen eye, she received a trainee/early-career BioArt Award from the Federation of American Societies for Experimental Biology (FASEB), which each year celebrates the art of science.
The image is one of many from a much larger effort in the Doe lab that explores the way neurons that will partner find each other and link up to drive development. Heckman and Doe also wanted to know how neurons in the developing brain interconnect into integrated neural networks, or circuits, and respond when something goes wrong. To find out, they disrupted sensory neurons or forced them to take alternate paths and watched to see what would happen.
As published in the journal eLife [1], the system has an innate plasticity. Their findings show that developing sensory neurons instruct one another on how to meet up just right. If one suddenly takes an alternate route, its partner can still reach out and make the connection. Once an electrically active neural connection, or synapse, is made, the neural signals themselves slow or stop further growth. This kind of adaptation and crosstalk between neurons takes place only during a particular critical window during development.
Heckman says part of what she enjoys about the image is how it highlights that many sensory neurons develop simultaneously and in a coordinated process. What’s also great about visualizing these events in the fly embryo is that she and other researchers can track many individual neurons from the time they’re budding stem cells to when they become a fully functional and interconnected neural circuit.
So, the next time you see fruit flies hovering in the kitchen, just remember there’s more to their swarm than you think. Our lessons learned studying them will help point researchers toward new ways in people to restore or rebuild neural connections after devastating disruptions from injury or disease.
Reference:
Presynaptic contact and activity opposingly regulate postsynaptic dendrite outgrowth. Heckman EL, Doe CQ. Elife. 2022 Nov 30;11:e82093.
Links:
Research Organisms (National Institute of General Medical Sciences/NIH)
Doe Lab (University of Oregon, Eugene)
Emily Heckman (University of Michigan, Ann Arbor)
BioArt Awards (Federation of American Societies for Experimental Biology, Rockville, MD)
NIH Support: Eunice Kennedy Shriver National Institute of Child Health and Human Development
3D Animation Captures Viral Infection in Action
Posted on by Lawrence Tabak, D.D.S., Ph.D.
With the summer holiday season now in full swing, the blog will also swing into its annual August series. For most of the month, I will share with you just a small sampling of the colorful videos and snapshots of life captured in a select few of the hundreds of NIH-supported research labs around the country.
To get us started, let’s turn to the study of viruses. Researchers now can generate vast amounts of data relatively quickly on a virus of interest. But data are often displayed as numbers or two-dimensional digital images on a computer screen. For most virologists, it’s extremely helpful to see a virus and its data streaming in three dimensions. To do so, they turn to a technological tool that we all know so well: animation.
This research animation features the chikungunya virus, a sometimes debilitating, mosquito-borne pathogen transmitted mainly in developing countries in Africa, Asia and the Americas. The animation illustrates large amounts of research data to show how the chikungunya virus infects our cells and uses its specialized machinery to release its genetic material into the cell and seed future infections. Let’s take a look.
In the opening seconds, you see how receptor binding glycoproteins (light blue), which are proteins with a carbohydrate attached on the viral surface, dock with protein receptors (yellow) on a host cell. At five seconds, the virus is drawn inside the cell. The change in the color of the chikungunya particle shows that it’s coated in a vesicle, which helps the virus make its way unhindered through the cytoplasm.
At 10 seconds, the virus then enters an endosome, ubiquitous bubble-like compartments that transport material from outside the cell into the cytosol, the fluid part of the cytoplasm. Once inside the endosome, the acidic environment makes other glycoproteins (red, blue, yellow) on the viral surface change shape and become more flexible and dynamic. These glycoproteins serve as machinery that enables them to reach out and grab onto the surrounding endosome membrane, which ultimately will be fused with the virus’s own membrane.
As more of those fusion glycoproteins grab on, fold back on themselves, and form into hairpin-like shapes, they pull the membranes together. The animation illustrates not only the changes in protein organization, but the resulting effects on the integrity of the membrane structures as this dynamic process proceeds. At 53 seconds, the viral protein shell, or capsid (green), which contains the virus’ genetic instructions, is released back out into the cell where it will ultimately go on to make more virus.
This remarkable animation comes from Margot Riggi and Janet Iwasa, experts in visualizing biology at the University of Utah’s Animation Lab, Salt Lake City. Their data source was researcher Kelly Lee, University of Washington, Seattle, who collaborated closely with Riggi and Iwasa on this project. The final product was considered so outstanding that it took the top prize for short videos in the 2022 BioArt Awards competition, sponsored by the Federation of American Societies for Experimental Biology (FASEB).
The Lee lab uses various research methods to understand the specific shape-shifting changes that chikungunya and other viruses perform as they invade and infect cells. One of the lab’s key visual tools is cryo-electron microscopy (Cryo-EM), specifically cryo-electron tomography (cryo-ET). Cryto-ET enables complex 3D structures, including the intermediate state of biological reactions, to be captured and imaged in remarkably fine detail.
In a study in the journal Nature Communications [1] last year, Lee’s team used cryo-ET to reveal how the chikungunya virus invades and delivers its genetic cargo into human cells to initiate a new infection. While Lee’s cryo-ET data revealed stages of the virus entry process and fine structural details of changes to the virus as it enters a cell and starts an infection, it still represented a series of snapshots with missing steps in between. So, Lee’s lab teamed up with The Animation Lab to help beautifully fill in the gaps.
Visualizing chikungunya and similar viruses in action not only makes for informative animations, it helps researchers discover better potential targets to intervene in this process. This basic research continues to make progress, and so do ongoing efforts to develop a chikungunya vaccine [2] and specific treatments that would help give millions of people relief from the aches, pains, and rashes associated with this still-untreatable infection.
References:
[1] Visualization of conformational changes and membrane remodeling leading to genome delivery by viral class-II fusion machinery. Mangala Prasad V, Blijleven JS, Smit JM, Lee KK. Nat Commun. 2022 Aug 15;13(1):4772. doi: 10.1038/s41467-022-32431-9. PMID: 35970990; PMCID: PMC9378758.
[2] Experimental chikungunya vaccine is safe and well-tolerated in early trial, National Institute of Allergy and Infectious Diseases news release, April 27, 2020.
Links:
Chikungunya Virus (Centers for Disease Control and Prevention, Atlanta)
Global Arbovirus Initiative (World Health Organization, Geneva, Switzerland)
The Animation Lab (University of Utah, Salt Lake City)
Video: Janet Iwasa (TED Speaker)
Lee Lab (University of Washington, Seattle)
BioArt Awards (Federation of American Societies for Experimental Biology, Rockville, MD)
NIH Support: National Institute of General Medical Sciences; National Institute of Allergy and Infectious Diseases
Cryo-EM Scores Again
Posted on by Lawrence Tabak, D.D.S., Ph.D.
Human neurons are long, spindly structures, but if you could zoom in on their surfaces at super-high resolution, you’d see surprisingly large pores. They act as gated channels that open and close for ions and other essential molecules of life to pass in and out the cell. This rapid exchange of ions and other molecules is how neurons communicate, and why we humans can sense, think, move, and respond to the world around us [1].
Because these gated channels are so essential to neurons, mapping their precise physical structures at high-resolution has profound implications for informing future studies on the brain and nervous system. Good for us in these high-tech times that structural biologists keep getting better at imaging these 3D pores.
In fact, as just published in the journal Nature Communications [2], a team of NIH-supported scientists imaged the molecular structure of a gated pore of major research interest. The pore is called calcium homeostasis modulator 1 (CALHM1). Pictured below, you can view its 3D structure at near atomic resolution [2]. Keep in mind, this relatively large neuronal pore still measures approximately 50,000 times smaller than the width of a hair.
The structure comes from a research team led by Hiro Furukawa, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY. He and his team relied on cryo-electron microscopy (cryo-EM) to produce the first highly precise 3D models of CALHM1.
Cryo-EM involves flash-freezing molecules in liquid ethane and bombarding them with electrons to capture their images with a special camera. When all goes well, cryo-EM can reveal the structure of intricate macromolecular complexes in a matter of weeks.
Furukawa’s team had earlier studied CALHM1 from chickens with cryo-EM [3], and their latest work reveals that the human version is quite similar. Eight copies of the CALHM1 protein assemble to form the circular channel. Each of the protein subunits has a flexible arm that allows it to reach into the central opening, which the researchers now suspect allows the channels to open and close in a highly controlled manner. The researchers have likened the channels’ eight flexible arms to the arms of an octopus.
The researchers also found that fatty molecules called phospholipids play a critical role in stabilizing and regulating the eight-part channel. They used simulations to demonstrate how pockets in the CALHM1 channel binds this phospholipid over cholesterol to shore up the structure and function properly. Interestingly, these phospholipid molecules are abundant in many healthy foods, such as eggs, lean meats, and seafood.
Researchers knew that an inorganic chemical called ruthenium red can block the function of the CALHM1 channel. They’ve now shown precisely how this works. The structural details indicate that ruthenium red physically lodges in and plugs up the channel.
These details also may be useful in future efforts to develop drugs designed to target and modify the function of these channels in helpful ways. For instance, on our tongues, the channel plays a role in our ability to perceive sweet, sour, or umami (savory) flavors. In our brains, studies show the abnormal function of CALHM1 may be implicated in the plaques that accumulate in the brains of people with Alzheimer’s disease.
There are far too many other normal and abnormal functions to mention here in this brief post. Suffice it to say, I’ll look forward to seeing what this enabling research yields in the years ahead.
References:
[1] On the molecular nature of large-pore channels. Syrjanen, J., Michalski, K., Kawate, T., and Furukawa, H. J Mol Biol. 2021 Aug 20;433(17):166994. DOI: 10.1016/j.jmb.2021.166994. Epub 2021 Apr 16. PMID: 33865869; PMCID: PMC8409005.
[2] Structure of human CALHM1 reveals key locations for channel regulation and blockade by ruthenium red. Syrjänen JL, Epstein M, Gómez R, Furukawa H. Nat Commun. 2023 Jun 28;14(1):3821. DOI: 10.1038/s41467-023-39388-3. PMID: 37380652; PMCID: PMC10307800.
[3] Structure and assembly of calcium homeostasis modulator proteins. Syrjanen JL, Michalski K, Chou TH, Grant T, Rao S, Simorowski N, Tucker SJ, Grigorieff N, Furukawa H. Nat Struct Mol Biol. 2020 Feb;27(2):150-159. DOI: 10.1038/s41594-019-0369-9. Epub 2020 Jan 27. PMID: 31988524; PMCID: PMC7015811.
Links:
Brain Basics: The Life and Death of a Neuron (National Institute of Neurological Disorders and Stroke/NIH)
Alzheimer’s Disease (National Institute on Aging/NIH)
Furukawa Lab (Cold Spring Harbor Lab, Cold Spring Harbor, NY)
NIH Support: National Institute of Neurological Disorders and Stroke; National Institute of Mental Health
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