Researchers from the 91̽�� have discovered a new way to help liquid flow in only one direction — but without flaps. In a published Sept. 24 in the Proceedings of the National Academy of Sciences, they report that a flexible pipe — with an interior helical structure inspired by shark intestines — can keep fluid flowing in one direction without the flaps that engines and anatomy rely upon.

Human intestines are essentially a hollow tube. But for sharks and rays, their intestines feature a network of spirals surrounding an interior passageway. In a 2021 , a different team proposed that this unique structure promoted one-way flow of fluids — also known as flow asymmetry — through the digestive tracts of sharks and rays without flaps or other aids to prevent backup. That claim caught the attention of 91̽��postdoctoral researcher , lead author on the new paper.

“Flow asymmetry in a pipe with no moving flaps has tremendous technological potential, but the mechanism was puzzling,” says Levin. “It was not clear which parts of the shark’s intestinal structure contributed to the asymmetry and which served only to increase the surface area for nutrient uptake.”

To answer these questions, Levin led a team that included co-authors and , both 91̽��professors of chemistry, and Naroa Sadaba, a fellow 91̽��postdoctoral researcher. They 3D-printed a series of “biomimetic pipes,” all with interior helices inspired by the layout of shark intestines. They varied the geometrical parameters among these prototype pipes, such as the pitch angle of the helix or the number of turns. Their first pipes were printed from rigid materials, and they found that some showed a strong preference for unidirectional flow.

“The first measurement of flow asymmetry was a ‘Eureka’ moment,” said Levin. “Until that instant, we didn’t know if our idealized structures could reproduce the flow effects seen in sharks.”

By further tuning the geometrical parameters and printing new designs, the researchers increased the flow asymmetry until it rivaled and even exceeded designs of famed inventor Nikola Tesla, who more than a century ago the Tesla valve, a with no moving parts.

“You don’t get to beat Tesla every day!” said Levin.

But shark intestines — like human intestines — aren’t rigid. The team suspected that so-called “deformable structures,” which are made from more flexible materials, might perform even better as Tesla valves. They 3D-printed a second series of prototypes made from the softest polymer that is both printable and commercially available. These flexible pipe designs, which are better mimics for shark intestines through both their “deformability” and their interior helices, performed at least seven times better compared to all previously measured Tesla valves.

“Chemists were already motivated to develop polymers that are simultaneously soft, strong and printable,” said Nelson, an expert in developing new types of polymers. “The potential use of these polymers to control flow in applications ranging from engineering to medicine strengthens that motivation.”

“Actual intestines are still about 100 times softer than our soft material, so there is plenty of room for improvement,” said Sadaba.

Keller credits the project’s success to the team’s interdisciplinary ideas from biology, chemistry and physics, and to the sharks themselves.

“Biomimicry is a powerful way of discovering new designs,” said Keller. “We never would have thought of the structures ourselves.”

The research was funded by the National Science Foundation, the Washington Research Foundation and the Fulbright Foundation.

For more information, contact Keller at slkeller@uw.edu, Nelson at alshakim@uw.edu and Levin at idolevin@uw.edu.

Membranes are crucial to our cells. Every cell in your body is enclosed by one. And each of those cells contains specialized compartments, or organelles, which are also enclosed by membranes.

Membranes help cells carry out tasks like breaking down food for energy, building and dismantling proteins, keeping track of environmental conditions, sending signals and deciding when to divide.

Biologists have long struggled to understand precisely how membranes accomplish these different types of jobs. The primary components of membranes — large, fat-like molecules called lipids and compact molecules like cholesterol — make great barriers. In all but a few cases, it’s unclear how those molecules help proteins within membranes do their jobs.

In a published Jan. 25 in the Proceedings of the National Academy of Sciences, a team at the 91̽�� looked at phase separation in budding yeast — the same single-celled fungus of baking and brewing fame — and reports that living yeast cells can actively regulate a process called phase separation in one of their membranes. During phase separation, the membrane remains intact but partitions into multiple, distinct zones or domains that segregate lipids and proteins. The new findings show for the first time that, in response to environmental conditions, yeast cells precisely regulate the temperature at which their membrane undergoes phase separation. The team behind this discovery suggests that phase separation is likely a “switch” mechanism that these cells use to govern the types of work that membranes do and the signals they send.

“Previous work showed that these domains can be seen in the membranes of living yeast cells,” said lead author Chantelle LeveilIe, a 91̽��doctoral student in chemistry. “We asked: If it’s important for a cell to have these domains, then if we change the cell’s environment — by growing them at different temperatures — would the cell ‘care’ and devote energy to maintaining phase separation in its membranes? The clear answer is yes, it does!”

Past research has shown that when sugar is plentiful, the yeast cell’s vacuole — an important organelle for storage and signaling — grows large and its membrane appears uniform under a microscope. But when food supplies dwindle, the vacuole undergoes phase separation, with many round zones appearing in the organelle’s membrane.

In this new study, Leveille and her co-authors — 91̽��chemistry professor , 91̽��biochemistry professor and Caitlin Cornell, previously a 91̽��doctoral student in chemistry — sought to understand whether yeast can actively regulate phase separation. Leveille grew yeast at their typical laboratory temperature of 86 F with plenty of food. After the food dwindled, the yeast cell vacuole membranes underwent phase separation, as expected. When Leveille briefly raised the temperature in the yeast’s environment by about 25 degrees Fahrenheit, the domains disappeared. Then Leveille grew yeast at a cooler temperature — 77 F instead of the normal 86 F — and discovered that the domains disappeared about 25 degrees above this new temperature. When she grew yeast in still colder conditions, at 68 F, phase separation yet again disappeared about 25 degrees higher than their growth temperature.

These experiments showed that the yeast cells always maintained phase separation in the vacuole membrane until the temperature rose about 25 degrees above their growth temperature.

“We think this is a clear sign that yeast cells are engineering the vacuole membrane in different environmental conditions to maintain this consistent state of phase separation,” said Leveille.

Phase separation in the vacuole membrane likely serves an important purpose in yeast, she added.

“This result suggests that membrane phase separation for yeast is likely a two-way door,” said Leveille. “For example, if the cells ever found food again, they would want to go back to their original state. Yeast do not want to get too far away from the transition.”

Future research could identify other membrane components that affect the vacuole membrane’s ability to phase separate, as well as the consequences of its phase separation. Biologists have known that, when the domains appear in the yeast vacuole’s membrane, the cell stops dividing. These two events may be linked because the yeast vacuole’s membrane contains two complexes of proteins that are important for cell division. When the complexes are far apart, cell division stops.

“Phase separation in the vacuole occurs right when the yeast cell needs to stop dividing because its food supply has run out,” said Merz. “One idea is that phase separation is the mechanism that the yeast cell ‘uses’ to separate these two protein complexes and stop cell division.”

In cells from yeast to humans, protein complexes embedded in membranes affect cell behavior. If additional research shows that phase separation in the yeast vacuole regulates cell division, it would likely be the first rigorous example of cell regulation through this once-overlooked property of membranes.

“Phase separation could be a common, reversible mechanism to modulate many, many types of cellular properties,” said Keller.

Cornell is now a postdoctoral researcher at the University of California, Berkeley. The research was funded by the National Institutes of Health and the National Science Foundation.

For more information, contact Keller at slkeller@uw.edu and Merz at merza@uw.edu.

These cells faced a chemical conundrum. They needed particular ions from the soup in order to perform basic functions. But those charged ions would have disrupted the simple membranes that encapsulated the cells.

A team of researchers at the 91̽�� has solved this puzzle using only molecules that would have been present on the early Earth. Using cell-sized, fluid-filled compartments surrounded by membranes made of fatty acid molecules, the team discovered that amino acids, the building blocks of proteins, can stabilize membranes against magnesium ions. Their results set the stage for the first cells to encode their genetic information in RNA, a molecule related to DNA that requires magnesium for its production, while maintaining the stability of the membrane.

The findings, Aug. 12 in the , go beyond explaining how amino acids could have stabilized membranes in unfavorable environments. They also demonstrate how the individual building blocks of cellular structures — membranes, proteins and RNA — could have co-localized within watery environments on the ancient Earth.

“Cells are made up of very different types of structures with totally different types of building blocks, and it has never been clear why they would come together in a functional way,” said co-corresponding author Roy Black, a 91̽��affiliate professor of chemistry and bioengineering. “The assumption was just that — somehow — they did come together.”

Black after a career at Amgen for the opportunity to fill in the crucial, missing details behind that “somehow.” He teamed up with , a 91̽��professor of chemistry and an expert on membranes. Black had been inspired by the observation that fatty acid molecules can self-assemble to form membranes, and hypothesized that these membranes could act as a favorable surface to assemble the building blocks of RNA and proteins.

“You can imagine different types of molecules moving within the primordial soup as fuzzy tennis balls and hard squash balls bouncing around in a big box that is being shaken,” said Keller, who is also co-corresponding author on the paper. “If you line one surface inside the box with Velcro, then only the tennis balls will stick to that surface, and they will end up close together. Roy had the insight that local concentrations of molecules could be enhanced by a similar mechanism.”

The team that the building blocks of RNA preferentially attach to fatty acid membranes and, surprisingly, also stabilize the fragile membranes against detrimental effects of salt, a common compound on Earth past and present.

The team hypothesized that amino acids might also stabilize membranes. They used a variety of experimental techniques — including light microscopy, electron microscopy and spectroscopy — to test how 10 different amino acids interacted with membranes. Their experiments revealed that certain amino acids bind to membranes and stabilize them. Some amino acids even triggered large structural changes in membranes, such as forming concentric spheres of membranes — much like layers of an onion.

“Amino acids were not just protecting vesicles from disruption by magnesium ions, but they also created multilayered vesicles — like nested membranes,” said lead author Caitlin Cornell, a 91̽��doctoral student in the Department of Chemistry.

The researchers also discovered that amino acids stabilized membranes through changes in concentration. Some scientists have hypothesized that the first cells may have formed within shallow basins that went through cycles of high and low concentrations of amino acids as water evaporated and as new water washed in.

The new findings that amino acids protect membranes — as well as prior results showing that RNA building blocks can play a similar role — indicate that membranes may have been a site for these precursor molecules to co-localize, providing a potential mechanism to explain what brought together the ingredients for life.

Keller, Black and their team will turn their attention next to how co-localized building blocks did something even more remarkable: They bound to each other to form functional machines.

“That is the next step,” said Black.

Their ongoing efforts are also forging ties across disciplines at the UW.

“The 91̽�� is an unusually good place to make discoveries because of the enthusiasm of the scientific community to work collaboratively to share equipment and ideas across departments and fields,” said Keller. “Our collaborations with the Drobny Lab and the Lee Lab were essential. No single laboratory could have done it all.”

Co-authors are , 91̽��professor of chemistry; , 91̽��associate professor of medicinal chemistry; 91̽��postdoctoral researchers Mengjun Xue and Helen Litz in the Department of Chemistry, and James Williams in the Department of Medicinal Chemistry; 91̽��graduate students Zachary Cohen in the Department of Chemistry and Alexander Mileant in the Biological Structure, Physics and Design Graduate Program; and 91̽��undergraduate alumni Andrew Ramsay and Moshe Gordon. The research was funded by NASA, the National Institutes of Health and the National Science Foundation.

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For more information, contact Black at blackr5@uw.edu or 206-713-4603 and Keller at slkeller@uw.edu or 206-543-9613.

Grant numbers: NNX17AK86G, R01-GM0999989, T32GM008268, T32GM007750, MCB-1402059

Cells — the building blocks of our bodies — are encapsulated by membranes. The same goes for the specialized compartments within our cells.

These membranes are extremely thin, oily films, containing proteins and fatty molecules called lipids. For decades, scientists have argued about how cell membranes organize and maintain distinct regions enriched in particular protein and lipid types. These regions are thought to influence cellular activities, such as the signaling that controls both normal cellular growth and the growth of cancerous cells.

In a paper in the , scientists at the 91̽�� show for the first time that the complex distribution of molecules within a membrane of a living yeast cell arises through demixing. Also known as phase separation, demixing is a simple physical process that is similar to the action that causes droplets of oil to separate from vinegar in a salad dressing.

“Cells have a toolbox with a variety of resources to help them complete a variety of tasks,” said senior author , a 91̽��professor of chemistry. “By teaming up with , a 91̽��professor of biochemistry and a yeast expert, we’ve shown that phase separation is one of those tools to shape membranes and their functions within a living system.”

The 91̽��researchers were inspired by pictures of a genetically engineered strain of yeast in which membrane proteins fluorescently glowed. The proteins lit up intracellular, membrane-bound compartments called vacuoles. The vacuoles looked like miniature green balls patterned with dark polka dots. Those polka dots, the researchers realized, looked nearly identical to membrane regions that arise from phase separation in two types of non-living systems: simple, artificial membranes created in a lab and membranes shed from cells under severe stress.

“The membranes of living systems contain many different types of fats, proteins and other molecules,” said co-lead author , a lecturer at 91̽��Tacoma who conducted this research when he was a 91̽��doctoral student in chemistry. “Each of these types of molecules harbors different physical and chemical properties with the potential to affect the properties of the membrane as a whole. We and other groups have hypothesized that this variety of molecules would allow membranes to phase separate by composition into discrete regions.”

First, the team discovered that the polka dots that appear on vacuole membranes can merge quickly. This behavior is consistent with fluid phases, just as droplets in a recently-shaken oil and vinegar salad dressing quickly coalesce when they collide. Next, the team found that phase separation in the membranes of yeast vacuoles depends on temperature. When the researchers warmed the yeast above 90 degrees Fahrenheit, the two liquid phases merged into one — the polka dots vanished. As the yeast cells were cooled back to room temperature, the phase-separated regions reappeared.

“Scientists had never previously shown that phase-separated liquids can co-exist in the membranes of living cells,” said co-lead author , a 91̽��doctoral student in chemistry. “To show that phase separation occurs, we had to reliably track the distribution of proteins within membranes, show that they formed regions like in artificial systems and that these regions would merge in response to changing environmental conditions.”

Now that the researchers have shown that living membranes can undergo phase separation, future work is needed to show how cells regulate phase separation. This could be through the action of genes, environmental conditions or a combination of factors.

“Our finding that phase separation can drive membrane organization in yeast suggests that similar processes may operate in other cells, including human cells,” said Merz. “Again, we see the power of model systems such as yeast, fruit flies and worms in our exploration of fundamental physiology. 91̽��has been at the forefront of yeast genetics and cell biology for over 60 years.”

“There is incredible potential here to unlock how different types of cells form and maintain unique structures — and how different structures are formed even within the same cell,” said Keller.

Caitlin Cornell, a 91̽��doctoral student in chemistry, is a co-author. The research was funded by the National Science Foundation and the National Institutes of Health.

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For more information, contact Keller at skeller@chem.washington.edu or 206-543-9613 and Merz at merza@uw.edu or 206-616-8308.

Grant numbers: DGE-1256082, MCB-1402059, T32GM008268, GM077349.

It could mean a simpler scenario for how that first spark of life came about on the planet, according to , 91̽��professor of , and Roy Black, 91̽��affiliate professor of bioengineering, co-authors of a published online July 29 in the Proceedings of the National Academy of Sciences.

Scientists have long thought that life started when the right combination of bases and sugars produced self-replicating ribonucleic acid, or RNA, inside a rudimentary “cell” composed of fatty acids. Under the right conditions, fatty acids naturally form into bag-like structures similar to today’s cell membranes.

In testing one of the fatty acids representative of those found before life began – decanoic acid – the scientists discovered that the four bases in RNA bound more readily to the decanoic acid than did the other seven bases tested.

By concentrating more of the bases and sugar that are the building blocks of RNA, the system would have been primed for the next steps, reactions that led to RNA inside a bag.

“The bag is the easy part. Making RNA from scratch is very hard,” Keller said. “If the parts that come together to make RNA happen to preferentially stick to the surfaces of bags, then everything gets easier.”

The scientists also discovered a second, mutually reinforcing mechanism: The same bases of RNA that preferentially stuck to the fatty acid also protected the bags from disruptive effects of salty seawater. Salt causes the fatty acid bags to clump together instead of remaining as individual “cells.”

The researchers found that several sugars also give protective benefit but the sugar from RNA, ribose, is more effective than glucose or even xylose, a sugar remarkably similar to ribose, except its components are arranged differently.

The ability of the building blocks of RNA to stabilize the fatty acid bags simplifies one part of the puzzle of how life started, Keller said.

“Taken together, these findings yield mutually reinforcing mechanisms of adsorption, concentration and stabilization that could have driven the emergence of primitive cells,” she said.

Black, lead author of the paper, originated the ideas behind the work. A retired biochemist with Amgen Inc., Black contributed funding for the work to Keller’s lab – the work also received National Science Foundation funding – and became a 91̽��affiliate professor volunteering in the Keller lab.

“I think that a pretty common story is that some young hotshot comes to 91̽��to start her or his career and does a risky experiment that uncovers new fundamental science,” Keller said.  “Here we have an older hotshot who came to 91̽��at the end of his Amgen career to do a risky experiment that uncovers new fundamental science.

“I think the story also emphasizes that people don’t become scientists just because it is a good job – they do it because they love it,” she said. “Roy worked for a year and a half straight, volunteering his time to 91̽��on something he didn’t get paid for, just for the joy and the curiosity.”

The paper’s other co-authors are Matthew Blosser at the UW, at Augsburg College in Minneapolis, at the University of Minnesota, and at the University of California, Santa Cruz.

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For more information:
Keller, keller@chem.washington.edu, 206-543-9613

Permission to use image, with credit:
http://commons.wikimedia.org/wiki/File:Computer_rna.jpg