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Blueprints of self-assembly

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Blueprints of self-assembly


Many biological structures of impressive beauty and sophistication arise through processes of self-assembly. Indeed, the natural world is teeming with intricate and useful forms that come together from many constituent parts, taking advantage of the built-in features of molecules.

Scientists hope to gain a better understanding of how this process unfolds and how such bottom-up construction can be used to advance technologies in computer science, materials science, medical diagnostics and other areas.

In new research, Arizona State University Assistant Professor Petr Sulc and his colleagues have taken a step closer to replicating nature’s processes of self-assembly. Their study describes the synthetic construction of a tiny, self-assembled crystal known as a “pyrochlore,” which bears unique optical properties.

The key to creating the crystal is the development of a new simulation method that can predict and guide the self-assembly process, avoiding unwanted structures and ensuring the molecules come together in just the right arrangement.

The advance provides a steppingstone to the eventual construction of sophisticated, self-assembling devices at the nanoscale — roughly the size of a single virus.

The new methods were used to engineer the pyrochlore nanocrystal, a special type of lattice that could eventually function as an optical metamaterial, “a special type of material that only transmits certain wavelengths of light,” Sulc says. “Such materials can then be used to produce so-called optical computers and more sensitive detectors, for a range of applications.”

Sulc is a researcher in the Biodesign Center for Molecular Design and Biomimetics, the School of Molecular Sciences and the Center for Biological Physics at Arizona State University.

The research appears in the current issue of the journal Science.

From chaos to complexity

Imagine placing a disassembled watch into a box, which you then shake vigorously for several minutes. When you open the box, you find an assembled, fully functional watch inside. Intuitively, we know that such an event is nearly impossible, as watches, like all other devices we manufacture, must be assembled progressively, with each component placed in its specific location by a person or a robotic assembly line.

Biological systems, such as bacteria, living cells or viruses, can construct highly ingenious nanostructures and nanomachines — complexes of biomolecules, like the protective shell of a virus or bacterial flagella that function similarly to a ship’s propeller, helping bacteria move forward.

These and countless other natural forms, comparable in size to a few dozen nanometers — one nanometer is equal to one-billionth of a meter, or roughly the length your fingernail grows in one second — arise through self-assembly. Such structures are formed from individual building blocks (biomolecules, such as proteins) that move chaotically and randomly within the cell, constantly colliding with water and other molecules, like the watch components in the box you vigorously shake.

Despite the apparent chaos, evolution has found a way to bring order to the unruly process.

Molecules interact in specific ways that lead them to fit together in just the right manner, creating functional nanostructures inside or on the cell’s surface. These include various intricate complexes inside cells, such as machinary that can replicate entire genetic material. Less intricate examples, but quite complex nevertheless, include self-assembly of the tough outer shells of viruses, whose assembly process Sulc also previously studied with his colleague, Banu Ozkan from ASU’s Department of Physics.

Crafting with DNA

For several decades, the field of bionanotechnology has worked to craft tiny structures in the lab, replicating the natural assembly process seen in living organisms. The technique generally involves mixing molecular components in water, gradually cooling them and hoping that when the solution reaches room temperature, all the pieces will fit together correctly.

One of the most successful strategies, known as DNA bionanotechnology, uses artificially synthesized DNA as the basic building block. This molecule of life is not only capable of storing vast troves of genetic information — strands of DNA can also be designed in the lab to connect with each other in such a way that a clever 3D structure is formed.

The resulting nanostructures, known as DNA origami, have a range of promising applications, from diagnostics to therapy, where, for example, they are being tested as a new method of vaccine delivery.

A significant challenge lies in engineering molecule interactions to form only the specific, pre-designed nanostructures. In practice, unexpected structures often result due to the unpredictable nature of particle collisions and interactions. This phenomenon, known as a kinetic trap, is akin to hoping for an assembled watch after shaking a box of its parts, only to find a jumbled heap instead.

Maintaining order

To attempt to overcome kinetic traps and ensure the proper structure self-assembles from the DNA fragments, the researchers developed new statistical methods that can simulate the self-assembly process of nanostructures.

The challenges for achieving useful simulations of such enormously complex processes are formidable. During the assembly phase, the chaotic dance of molecules can last several minutes to hours before the target nanostructure is formed, but the most powerful simulations in the world can only simulate a few milliseconds at most.

“Therefore, we developed a whole new range of models that can simulate DNA nanostructures with different levels of precision,” Sulc says. “Instead of simulating individual atoms, as is common in protein simulations, for example, we represent 12,000 DNA bases as one complex particle.”

This approach allows researchers to pinpoint problematic kinetic traps by combining computer simulations with different degrees of accuracy. Using their optimization method, researchers can fine-tune the blizzard of molecular interactions, compelling the components to assemble correctly into the intended structure.

The computational framework established in this research will guide the creation of more complex materials and the development of nanodevices with intricate functions, with potential uses in both diagnostics and treatment.

The research work was carried out in collaboration with researchers from Sapienza University of Rome, Ca’ Foscari University of Venice and Columbia University in New York.



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Are mixed emotions real? New research says yes

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Are mixed emotions real? New research says yes


In Pixar’s latest film, Inside Out 2, complex feelings like envy and embarrassment join the cast of characters. Nostalgia, however, is hurried out the door to cries of “too early!” when she appears.

If animators wish to give nostalgia more consideration in a future film, new data from researchers at the USC Dornsife College of Letters, Arts and Sciences could guide them in determining how to animate this sort of “mixed emotion.”

What’s new: In a recent study, the USC Dornsife neuroscientists found that brains display distinct neural activity when experiencing emotions such as bittersweetness.

  • The advance could help solve a longstanding scientific debate: whether “mixed emotions” arise from unique activity in the brain, or if we’re just flip-flopping back and forth between positive and negative feelings.

Why it matters: Mixed emotions are a common experience, but they’ve been understudied scientifically for several reasons.

  • Emotions are often thought to exist only on a spectrum from negative to positive.
  • It’s easier to study one feeling at a time.

In his words: “It’s hard to evoke these complex emotions in a realistic way inside the lab,” says Jonas Kaplan, associate professor (research) of psychology and co-author of the study, published in the journal Cerebral Cortex in April.

Key findings:

  • Mixed feelings elicited unique neural activity in the amygdala and nucleus accumbens areas of the brain.
  • This activity was different than the brain activity seen when a subject reported a purely positive or negative emotion.

What else? The researchers could predict when someone was going to shift emotions.

  • Particular regions of the brain, like the insular cortex, displayed significant changes as subjects reported an emotional transition.

“Not only did we find brain activity that was correlated with mixed emotions, but we found that it held steady over time,” says Anthony Vaccaro, lead author of the study and a postdoctoral researcher at the Neuroendocrinology of Social Ties Lab at USC Dornsife. Vaccaro recently completed his PhD in psychology at USC Dornsife. “You’re not ping-ponging between negative and positive. It’s a very unique, mixed emotion over a long period.”

Graphs show consistent brain activity during positive, negative and mixed emotions, demonstrating that mixed emotions are distinct from other feelings. (Image: Jonas Kaplan.)

How they did it: As study subjects watched a poignant animated short film, researchers monitored their brain activity using a magnetic resonance imaging (MRI) machine.· The researchers chose One Small Step by TAIKO Studios for its ability to evoke simultaneous happy and sad feelings. · After the first viewing, participants rewatched the video without MRI and indicated when they experienced positive, negative or mixed emotions. The researchers then compared these reports with the MRI imaging results.

Opportunity: The study lays out practical groundwork for future scientific research into this understudied phenomenon, research that Kaplan says would also be beneficial for understanding human psychology.

  • “There’s a certain sophistication that’s required to sit with a mixed emotion and to allow yourself to feel positive and negative at the same time. Looking into that more, exploring the benefits of being able to accept positive and negativity at the same time within yourself, is something we think is worth study,” he says.

What’s next: Kaplan and Vaccaro will next look at how emotional reactions fluctuate in group settings, such as watching a movie together in a cinema.



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Paleontology: New fossil fish genus discovered

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Paleontology: New fossil fish genus discovered


Gobies or Gobioidei are one of the most species-rich groups of marine and freshwater fish in Europe. Spending most of their lives on the bottom of shallow waterbodies, they make substantial contributions to the functioning of many ecosystems. With the identification of a new genus of a fossil freshwater goby, students of the international master program ‘Geobiology and Paleobiology’ at LMU and paleontologist Bettina Reichenbacher, professor at the Department of Earth and Environmental Sciences at LMU, have made a discovery that provides critical insights into the evolutionary history of these fish.

Measuring up to 34 mm, the small fish of the new genus †Simpsonigobius were discovered in 18-million-year-old rocks in Turkey and are marked by a distinct combination of morphological features, including otoliths (hearing stones) with a unique shape.

Modern research techniques elucidate position in family tree

To determine the relationships of †Simpsonigobius within the gobioid phylogenetic tree, the researchers utilized a “total-evidence” phylogenetic dataset, which they enhanced in order to combine a total of 48 morphological characters and genetic data from five genes for 48 living and 10 fossil species. In addition, the team employed “tip-dating” for fossil gobioid species for the first time. This is a phylogenetic method in which the age of the fossils (= tips) included in the phylogenetic tree is used to infer the timing of the evolutionary history of the entire group.

The results show that the new genus is the oldest skeleton-based member of the family Oxudercidae — which is classified among the “modern” gobies (families Gobiidae and Oxudercidae) — and the oldest freshwater goby within this modern group. The tip-dating analysis estimated the emergence of the Gobiidae at 34.1 million years ago and that of the Oxudercidae at 34.8 million years ago, which is consistent with previous dating studies using other methods. Moreover, stochastic habitat mapping, in which the researchers incorporated fossil gobies for the first time, revealed that the gobies probably possessed broad salinity tolerance at the beginning of their evolutionary history, which challenges previous assumptions.

“The discovery of †Simpsonigobius not only adds a new genus to the Gobioidei, but also provides vital clues about the evolutionary timeline and habitat adaptations of these diverse fishes. Our research highlights the importance of analyzing fossil records using modern methods to achieve a more accurate picture of evolutionary processes,” says Reichenbacher. First author Moritz Dirnberger, currently a doctoral candidate at the University of Montpellier, adds: “The findings are expected to pave the way for further studies on gobioid evolution and the role of environmental factors in shaping their diversity.”



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Ancient ocean slowdown warns of future climate chaos

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Ancient ocean slowdown warns of future climate chaos


When it comes to the ocean’s response to global warming, we’re not in entirely uncharted waters. A UC Riverside study shows that episodes of extreme heat in Earth’s past caused the exchange of waters from the surface to the deep ocean to decline.

This system has been described as the “global conveyer belt,” because it redistributes heat around the globe through the movement of the ocean waters, making large portions of the planet habitable.

Using tiny, fossilized shells recovered from ancient deep-sea sediments, the study in the Proceedings of the National Academy of Sciences demonstrates how the conveyor belt responded around 50 million years ago. At that time, Earth’s climate resembled conditions predicted by the end of this century, if significant action is not taken to reduce carbon emissions.

Oceans play a crucial role in regulating Earth’s climate. They move warm water from the equator toward the north and south poles, balancing the planet’s temperatures. Without this circulation system, the tropics would be much hotter and the poles much colder. Changes in this system are linked to significant and abrupt climate change.

Furthermore, the oceans serve a critical role in removing anthropogenic carbon dioxide from the atmosphere. “The oceans are by far the largest standing pool of carbon on Earth’s surface today,” said Sandra Kirtland Turner, vice-chair of UCR’s Department of Earth and Planetary Sciences and first author of the study.

“Today, the oceans contain nearly 40,000 billion tons of carbon — more than 40 times the amount of carbon in the atmosphere. Oceans also take up about a quarter of anthropogenic CO2 emissions,” Kirtland Turner said. “If ocean circulation slows, absorption of carbon into the ocean may also slow, amplifying the amount of CO2 that stays in the atmosphere.”

Previous studies have measured changes in ocean circulation in Earth’s more recent geologic past, such as coming out of the last ice age; however, those do not approximate the levels of atmospheric CO2 or warming happening to the planet today. Other studies provide the first evidence that deep ocean circulation, particularly in the North Atlantic, is already starting to slow.

To better predict how ocean circulation responds to greenhouse gas-driven global warming, the research team looked to the early Eocene epoch, between roughly 49 and 53 million years ago. Earth then was much warmer than today, and that high-heat baseline was punctuated by spikes in CO2 and temperature called hyperthermals.

During that period, the deep ocean was up to 12 degrees Celsius warmer than it is today. During the hyperthermals, the oceans warmed an additional 3 degrees Celsius.

“Though the exact cause of the hyperthermal events is debated, and they occurred long before the existence of humans, these hyperthermals are the best analogs we have for future climate change,” Kirtland Turner said.

By analyzing tiny fossil shells from different sea floor locations around the globe, the researchers reconstructed patterns of deep ocean circulation during these hyperthermal events. The shells are from microorganisms called foraminifera, which can be found living throughout the world’s oceans, both on the surface and on the sea floor. They are about the size of a period at the end of a sentence.

“As the creatures are building their shells, they incorporate elements from the oceans, and we can measure the differences in the chemistry of these shells to broadly reconstruct information about ancient ocean temperatures and circulation patterns,” Kirtland Turner said.

The shells themselves are made of calcium carbonate. Oxygen isotopes in the calcium carbonate are indicators of temperatures in the water the organisms grew in, and the amount of ice on the planet at the time.

The researchers also examined carbon isotopes in the shells, which reflect the age of the water where the shells were collected, or how long water has been isolated from the ocean surface. In this way, they can reconstruct patterns of deep ocean water movement.

Foraminifera can’t photosynthesize, but their shells indicate the impact of photosynthesis of other organisms nearby, like phytoplankton. “Photosynthesis occurs in the surface ocean only, so water that has recently been at the surface has a carbon-13 rich signal that is reflected in the shells when that water sinks to the deep ocean,” Kirtland Turner said.

“Conversely, water that has been isolated from the surface for a long time has built up relatively more carbon-12 as the remains of photosynthetic organisms sink and decay. So, older water has relatively more carbon-12 compared to ‘young’ water.”

Scientists often make predictions about ocean circulation today using computer climate models. They use these models to answer the question: ‘how is the ocean going to change as the planet keeps warming?’ This team similarly used models to simulate the ancient ocean’s response to warming. They then used the foraminifera shell analysis to help test results from their climate models.

During the Eocene, there were about 1,000 parts per million (ppm) of carbon dioxide in the atmosphere, which contributed to that era’s high temperatures. Today, the atmosphere holds about 425 ppm.

However, humans emit nearly 37 billion tons of CO2 into the atmosphere each year; if these emission levels continue, similar conditions to the Early Eocene could occur by the end of this century.

Therefore, Kirtland Turner argues it is imperative to make every effort to reduce emissions.

“It’s not an all-or-nothing situation,” she said. “Every incremental bit of change is important when it comes to carbon emissions. Even small reductions of CO2 correlate to less impacts, less loss of life, and less change to the natural world.”



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