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Controlling the Shape-Shifting Skeletons of Cells

You know you have a skeleton, but did you know that your cells have skeletons, too? Cellular skeletons, or cytoskeletons, are shapeshifting networks of tiny protein filaments, enabling cells to propel themselves, carry cargo, and divide. Now, an interdisciplinary team of Caltech researchers has designed a way to study and manipulate the cytoskeleton in test tubes in the lab. Understanding how cells control movement could one day lead to tiny, bioinspired robots for therapeutic applications. The work also contributes to the development of new tools for manipulating fluids on very small scales relevant to molecular biology and chemistry.

The work is described in a paper appearing in the August 8 issue of the journal Nature.

The building blocks of the cellular cytoskeleton are thin, tube-like filaments called microtubules that can form together into three-dimensional scaffolds. Each microtubule is 1,000 times thinner than a human hair and only about 10 micrometers long (about 1,000 times smaller than a common black ant). Along with motor proteins that power movement, these incredibly small structures combine to propel the relatively large cell—like ants steering and powering a car.

An immune cell chases a bacterium

Originally taken by David Rogers at Vanderbilt University, this movie shows an immune cell chasing a bacterium. Cells like these use shape-shifting skeletons to move around.Credit: Vanderbilt University

In previous studies, researchers have taken these molecules out of the cell and put them into test tubes, where the tubules and motor proteins spontaneously group together to organize themselves into star-shaped structures called asters. How asters in a test tube are related to a cytoskeleton powering cell movement, however, is still unclear. Moreover, the collective microtubule organization demonstrated by aster formation involves interacting forces that are not entirely understood.

“What we wanted to know was: how do you get from these spontaneously forming aster structures in the lab, to a cell controlling its movement? And, how can we control these molecules the way a cell does?” says graduate student Tyler Ross, first author on the study.

Led by Ross, a team of Caltech researchers explored how to manipulate the component filaments and motor proteins outside of the cell’s natural environment. In test tubes, they linked motor proteins to light-activated proteins that are naturally found in plants, so that the tubules would only organize into asters when light was shining on them. In this way, the researchers could control when and where asters would form by projecting different patterns of light, enabling them to develop theories about the physical mechanisms underlying aster formation.

Two white asters merge together along a line

Two asters (white) form and are guided together with beams of light (dark yellow).Credit: Caltech

Controlling the asters not only allowed for the study of their formation but also enabled the team to build things out of the structures. Ross developed simple procedures of light patterns to place, move, and merge asters of various sizes. The technique offers a way to manipulate structures and study fluid dynamics at a miniscule length scale that is usually difficult to work at; fluids exhibit tricky behaviors at such small volumes.

“Generally, it’s really difficult to manipulate fluids and structures on this length scale. But this is the scale that we’re most interested in for studying cells and chemistry; all of molecular biology works on this scale,” says Ross. “Our light-based system allows us to dynamically manipulate our system. We could look through a microscope and say, ‘Okay we have enough over here, let’s start routing things over there,’ and change the light pattern accordingly. We could use aster structures in such a way that they could stir and mix solutions at very small length scales.”

Forming asters in a "plus" shape makes spiraling fluid flows around

This video illustrates how the formation of asters (white) can excite very small-scale fluid flows (black). Normally, fluids on these small scales are difficult to manipulate and characterize. Credit: Caltech

The research is a collaboration between the laboratories of Matt Thomson, assistant professor of computational biology and Heritage Medical Research Institute Investigator, and Rob Phillips, Fred and Nancy Morris Professor of Biophysics, Biology, and Physics. This collaboration, notes Thomson, enabled pivotal breakthroughs in the project, which Ross had begun in Thomson’s laboratory at UC San Francisco (UCSF) before the two came to Caltech in 2017. At Caltech, the pair teamed up with Heun Jin Lee, a staff scientist with extensive expertise in optics, to develop a specialized microscope with which they could view aster formation and direct precise patterns of light.

“This has been one of the great collaborations I’ve seen in my career,” says Thomson. “This story really speaks to the community, how you can do work across different fields and people will support and cultivate it. We had feedback from people who work in DNA nanotechnology and people who work in chemical engineering and fluid dynamics.”

The paper is titled, “Controlling Organization and Forces in Active Matter Through Optically-Defined Boundaries.” In addition to Ross, Thomson, Phillips, and Lee, other co-authors are postdoctoral scholar Zijie Qu and graduate student Rachel Banks. Funding was provided by the National Institutes of Health, the National Science Foundation, the John Templeton Foundation, the Foundational Questions Institute and the Fetzer Franklin Fund, the UCSF Center for Systems and Synthetic Biology, and the Heritage Medical Research Institute.

Materials provided by California Institute of Technology

Culture of rat brain cells

Researchers develop technology to control the brain cells with help of smartphone

A group of researchers in the United States and Korea have invented a device which can control neural circuits with the help of a small brain implant which is controlled by a smartphone. Scientists believe that this device can amplify the efforts to detect brain diseases like Alzheimer’s, Parkinson’s, migraine and depression. With the help of replaceable drug cartridges similar to LEGO and Bluetooth low-energy, this device can target the specific neurons for prolonged periods using drug and light. The study was published in Nature Biomedical Engineering journal.

Raza Qazi, a scientist with Korea Advanced Institute of Science and Technology (KAIST) and University of Colorado Boulder said that the wireless neural device enables optical and chemical neuromodulation which has been achieved for the first time. This technology overshadows the normal methods used by researchers which generally involve optical fibers and metal tubes for delivering light and drugs. It limits the subject’s movement due to physical connections with the heavy equipment and causes a lesion in soft brain tissue due to their rigid structure. Hence they are not suitable for long-term implantation. Efforts were put to mitigate the adverse tissue response with the incorporation of wireless platforms and soft probes however they could not deliver drugs for a prolonged time period.

For achieving chronic wireless drug delivery, researchers had to solve the challenge of evaporation and exhaustion of drugs. They invented a neural device having a replaceable drug cartridge that allowed to study the brain circuits without worrying about the factor of drug exhaustion. These drug cartridges were assembled for brain implantation in mice with an ultrathin probe which had microfluidic channels, LEDs for unlimited light delivery and drug doses.

Researchers controlled it with a user interface on a smartphone and could trigger any combination of light and drug deliveries in any implanted animal without being present in a laboratory. They could also set up automated animal studies where an animal’s behavior could affect other animals’ behavior due to the conditional triggering of drug and light delivery. This revolutionary equipment is possible due to complex electronics design and powerful nanoscale engineering. It would help scientists in several ways. It would also help to dissect the neural circuit basis of behavior and understand how neuromodulators control behavior in several ways. It would also help researchers develop therapeutics for emotional and addiction disorders.

KAIST researchers developed soft electronics for implantable devices and University of Washington scientists study brain circuits which are responsible for addiction, pain, stress. This global collaboration for three years made it possible to develop the powerful brain implant in mice which can speed up the detection of brain diseases. It was supported by grants from the National Research Foundation, Korea, National Institute of Health in the US, National Institute on Drug Abuse.

ELSI Scientists Discover New Chemistry That May Help Explain the Origins of Cellular Life

Scientists Discover New Chemistry That May Help Explain the Origins of Cellular Life

Before life began on Earth, the environment likely contained a massive number of chemicals that reacted with each other more or less randomly, and it is unclear how things as complex as cells could have emerged from such chemical chaos.

Now, a team led by Tony Z. Jia of the Earth-Life Science Institute (ELSI) at the Tokyo Institute of Technology and Kuhan Chandru of the National University of Malaysia, has shown that simple α-hydroxy acids, like glycolic and lactic acid (which is used in common store-bought facial peels), spontaneously polymerize and self-assemble into polyester microdroplets when dried at moderate temperatures followed by rehydration, as might have happened along primitive beaches and river banks or in drying puddles.

These form a new type of cell-like compartment which can trap and concentrate biomolecules like nucleic acids and proteins. These droplets, unlike most modern cells, are able to easily merge and reform and thus could have hosted versatile early genetic and metabolic systems potentially critical for the origins of life.

Figure 1. A team of scientists from the Earth-Life Science Institute have discovered that simple organic compounds like glycolic and lactic acid polymerize and self-assemble into cell-sized droplets when dried and rewetted, as might have happened along primitive beaches and drying puddles.

Figure 1. A team of scientists from the Earth-Life Science Institute have discovered that simple organic compounds like glycolic and lactic acid polymerize and self-assemble into cell-sized droplets when dried and rewetted, as might have happened along primitive beaches and drying puddles. Credit: Nerissa Escanlar, ELSI

Scientists from around the world are actively working to understand how life began. All modern Earth life, from bacteria to humans, is made up of cells. Cells are comprised of lipids, proteins, and nucleic acids, with the lipid forming the cell membrane, an enclosure that keeps the other components together and interfaces with the environment, exchanging food and waste. How molecular assemblages as complex as cells originally formed remains a mystery.

Most origins of life research focuses on how the molecules and structures present in contemporary life were produced by the environment, and then assembled into structures that led to the first cells. However, there were likely many other types of molecules that formed alongside biomolecules on early Earth, and it is possible that life started using very simple chemistry unrelated to modern biomolecules then evolved through increasingly complex stages to give rise to the structures found in modern cells.

Previous work conducted at ELSI showed that moderate temperature drying of the simple organic compounds known as alpha-hydroxyacids, which are found in meteorites and many simulations of prebiological chemistry, spontaneously polymerizes them into mixtures of long polyesters. Building on this work, Jia and colleagues took the next step and examined these reactions under the microscope, and found that these mixed polyester systems form a gel phase and spontaneously self-assemble when rewetted to form simple cell-like structures.

The most challenging aspect of this work was devising new methods to characterize the droplets’ properties and functions, as no one had analyzed such systems before. Jia noted that the team was fortunate to have such a diversity of multidisciplinary expertise including chemists, biochemists, materials scientists, and geologists. After determining their composition and showing their propensity to self-assemble, the next question was whether these cell-like structures might be able to do something chemically useful.

Modern cell membranes perform many crucial functions that help maintain the cell; for example, retaining macromolecules and metabolites in one place, as well as providing a constant internal environment, which can be very different from the one outside the cell. They first measured how stable these structures were and found they could persist for very long periods depending on the environmental conditions, but could also be made to merge and coalesce.

They then tested the ability of these structures to sequester molecules from the environment and found they accumulated large dye molecules to a remarkable degree. They then showed that these droplets could also host RNA and protein molecules and still permit them to be functionally catalytic. Further, the team showed that the droplets could assist in the formation of a lipid layer on their surface, suggesting they could have helped scaffold protocell formation.

Jia and colleagues are not certain these structures are the direct ancestors of cells, but they think it is possible such droplets could have enabled the assembly of protocells on Earth. The new compartmentalization system they have found is extremely simple, they note, and could form easily in primitive environments throughout the Universe.

Says Jia, “This allows us to imagine non-biological systems on early Earth that could have still had a hand in the origins of life on Earth. This suggests there may be many other non-biological systems that should be targets of future investigations of this type.” He thinks the development of these or similar model systems could allow better study of the evolution of diverse chemical systems representative of the complex chemistries likely to be found on primitive planetary bodies.

“The early Earth was certainly a messy place chemically,” Jia explains, “and often most origins of life studies focus on modern biomolecules under relatively “clean” conditions. Perhaps it is important to take these “messy” mixtures and see if there are interesting functions or structures that can arise from them spontaneously.” The authors now think that by systematically increasing the chemical complexity of such systems, they will be able to observe how they evolve over time and possibly discover divergent and emergent properties.

“We have this new experimental system we can now play with, so we can start to study phenomena like evolution and evolvability of these droplets. The possible combinations of structures or functions these droplets might have are almost endless. If the physical rules that govern the formation of droplets are fairly universal in nature, then we hope to study similar systems to discover whether they also can form microdroplets with novel properties,” adds Jia.

Finally, while the team is presently focused on understanding the origins of life they note this basic research could have applications in other areas, for example, drug delivery and personalized medicine. “This is just a wonderful example of the unexpected ways projects can develop when a team of diverse scientists from around the world come together to try and understand new and interesting phenomena,” said team member Jim Cleaves, also of ELSI.

Figure 2. Prebiotically synthesized heterogeneous polyester microdroplets containing a fluorescent dye, showing the capability of polyester microdroplets to act as primitive compartments.

Figure 2. Prebiotically synthesized heterogeneous polyester microdroplets containing a fluorescent dye, showing the capability of polyester microdroplets to act as primitive compartments. (Credit: Tony Jia, ELSI)

Figure 3. Alpha-hydroxy acid monomers are dried, resulting in the synthesis of a polyester gel. This gel is then rehydrated, resulting in the assembly of microdroplets.

Figure 3. Alpha-hydroxy acid monomers are dried, resulting in the synthesis of a polyester gel. This gel is then rehydrated, resulting in the assembly of microdroplets. (Credit: ELSI)

Journal Reference: PNAS

Materials provided by the Tokyo Institute of Technology