A research team from Yale, the American Museum of Natural History, the University of Brussels, and the University of Bonn announced the discovery Nov. 9 in the journal Nature Communications.

Fossil soft tissue in dinosaur bones has been a controversial topic among researchers for quite some time. Hard tissues, such as bones, eggs, teeth, and enamel scales, are able to survive fossilization extremely well. Soft tissues, such as blood vessels, cells, and nerves — which are stored inside the hard tissue — are more delicate and thought to decay rapidly after death. These soft tissues are composed mainly of proteins, which are believed to completely degrade within about four million years.

Yet dinosaur bones are much older, roughly 100 million years old, and they occasionally preserve organic structures similar to cells and blood vessels. Various attempts to resolve this paradox have failed to provide a conclusive answer.

“We took on the challenge of understanding protein fossilization,” said Yale paleontologist Jasmina Wiemann, the study’s lead author. “We tested 35 samples of fossil bones, eggshells, and teeth to learn whether they preserve proteinaceous soft tissues, find out their chemical composition, and determine under what conditions they were able to survive for millions of years.”

The researchers discovered that soft tissues are preserved in samples from oxidative environments such as sandstones and shallow, marine limestones. The soft tissues were transformed into Advanced Glycoxidation and Lipoxidation end products (AGEs and ALEs), which are resistant to decay and degradation. They’re also structurally comparable to chemical compounds that stain the dark crust on toast.

AGEs and ALEs are characterized by a brownish color that stains fossil bones and teeth that contain them. The compounds are hydrophobic, which means they are resistant to the normal effects of water, and have properties that make it difficult for bacteria to consume them.

Wiemann and her colleagues made their discovery by decalcifying fossils and imaging the released soft tissue structures. They applied Raman microspectroscopy — a non-destructive method for analyzing both the inorganic and organic contents of a sample — to the extracted fossil soft tissues. During this process, laser energy directed at the tissue causes molecular vibrations that carry spectral fingerprints for the chemicals that are present.

Co-author Derek Briggs, Yale’s G. Evelyn Hutchinson Professor of Geology and Geophysics and a curator at the Yale Peabody Museum of Natural History, said the study points to localities where soft tissue may be found in fossil bones, including sandstones deposited from rivers, dune sands, and shallow marine limestones.

“Our results show how chemical alteration explains the fossilization of these soft tissues and identifies the types of environment where this process occurs,” Briggs said. “The payoff is a way of targeting settings in the field where this preservation is likely to occur, expanding an important source of evidence of the biology and ecology of ancient vertebrates.”

Additional co-authors of the study are Matteo Fabbri from Yale, Martin Sander and Tzu-Ruei Yang from the University of Bonn, Koen Stein from the University of Brussels, and Mark Norell from the American Museum of Natural History.

Story Source:

Materials provided by Yale University. Original written by Jim Shelton. Note: Content may be edited for style and length.

“These huge marine heatwaves, which are being exacerbated by global warming, are equivalent to an atomic bomb in terms of impact on coral reefs — they kill millions of corals across huge areas of ocean in a very short time” says WHOI scientist Anne Cohen, who was principal investigator on the work. “We’ve seen this play out now globally for the past 30-40 years, and bleaching events have become more frequent and more severe.”

When water temperatures rise even slightly, symbiotic algae that live inside the cells of the live coral start to create toxic substances and are ejected by the corals. The algae normally provide the corals with food and energy, as well as their bright colors. Without them, the corals appear to be “bleached” white, then starve and die.

In their study, Cohen’s team traveled to Jarvis Island, a tiny, unpopulated coral reef island 1,400 miles south of Hawaii, to study the effects of extreme climate on the corals there. Because Jarvis is both remote and part of a marine protected area, it has been home to stunningly rich coral reefs — but with its location in the middle of the Pacific, it also experiences more extreme heat waves caused by periodic El Nino events than coral reefs elsewhere.

“The fact that it’s placed right at the equator in the central Pacific puts it at epicenter of El Niño dynamics.” says NOAA researcher Hannah Barkley, who was a graduate student and later a postdoctoral fellow in Cohen’s lab at the time of the study, and is the paper’s lead author. “It’s subject to incredible variability and extremes in temperature..”

Because there is no observational record of bleaching on the reef at Jarvis before 2015, Cohen and Barkley turned to massive old corals that had lived on the reef for more than 100 years. They took core samples from the corals, creating a sort of skeletal biopsy that records the history of the reef. After running the cores through a CT scanner, they found for the first time evidence of multiple bleaching events preserved in the physical structure of the reef. The longest cores revealed bleaching as far back as 1912.

“We found that when the reef bleaches, these big old corals lay down “stress bands,” or a dense layer of calcium carbonate, the bonelike material that make up the structure of corals. Those bands appear clearly in the CT scan, and correspond with historical heat waves,” says Cohen. The memory of past bleaching events on Jarvis is locked into these corals — they can tell us what has been going even though we weren’t there to see it for ourselves.”

Jarvis has experienced above-average temperatures every four to seven years, going back decades or even centuries. The team discovered that with each heat wave, the reef experienced severe bleaching, yet seems to have bounced back fairly quickly each time.

Based on their samples, the group thinks that one major reason for the reef’s recovery is the currents nearby. The topography of the ocean floor, combined with the force of trade winds on the surface, brings cold, nutrient-rich water up from the deep. That upwelling feeds a dense array of fish and other aquatic life around the reef, which in turn eat away grassy algae that compete with the corals. In the process, they leave room for new, young coral polyps to eventually settle.

“These reefs are resilient, having bleached and recovered many times, ” says Dan Thornhill, program director in the National Science Foundation’s Division of Ocean Sciences, which funded the research. “But the 2015-2016 bleaching event was particularly severe, so the island is providing us with new insights into how some of the world’s most resilient corals are faring in the face of severe bleaching stress.”

Understanding how coral reefs like Jarvis are able to recover after extensive bleaching will be essential for understanding how other reef ecosystems may grow back in the future, says Barkley.

But the 2015 Super El Nino caused Jarvis to heat up more than it ever did before, and the bleaching that ensued was the worst on record. 95 percent of island’s corals died.

“The big question for us is whether the reef can bounce back at all this time,” says Barkley. “Even reefs like Jarvis that have regrown in the past have a threshold beyond which they may not recover. What happens over next few years will really help us understand severe bleaching.”

Still, she’s guardedly optimistic. “It’s easy to look at a place like Jarvis after the 2015 bleaching event and feel depressed. But the historical record we got from our core samples says we’re not beyond hope. Jarvis is just one example: even though we are seeing signs of accelerated bleaching and mortality worldwide, we have a narrow window to address the effects of climate change on corals. Some reefs may be able to persist through huge stress events.”

“The initial signs of recovery are there,” says Cohen. “Now we wait, watch and learn.”

Also collaborating on the study was Kathryn R. Pietro and Pat Lohmann of WHOI, Cohen Lab graduate students Nathaniel R. Mollica, Hanny E. Rivera, Thomas M. DeCarlo, Elizabeth J. Drenkard, and Alice E. Alpert of the MIT-WHOI Joint Program in Oceanography; Russell E. Brainard and Thomas A. Oliver of the NOAA Pacific Islands Fisheries Science Center; Charles W. Young, Bernardo Vargas-Angel, and Kevin C. Lino of NOAA and the University of Hawaii at Manoa; and Victoria H. Luu of Princeton University. Funding for the study was provided by National Science Foundation awards OCE 1537338, OCE 1605365, and OCE 1031971 to A.L. Cohen, and the Robertson Foundation to A.L. Cohen; National Science Foundation Graduate Research Fellowships to T.M DeCarlo and A.E. Alpert; and a National Defense Science and Engineering Graduate Fellowship to H.E. Rivera.

“In the last five years, there has been a huge gold rush where researchers figured out we could make 2D materials that are naturally only one molecule thick but can have many different electronic properties, and by stacking them on top of each other, we could engineer nearly any electronic device at molecular sizes,” said Arend van der Zande, professor of mechanical science and engineering.

“The challenge was, though we could make these structures down to a few molecules thick, we couldn’t pattern them,” he said.

At any scale of electronic device, layers are etched away in precise patterns to control how the current flows. “This concept underlies many technologies, like integrated circuits. However, the smaller you go, the harder this is to do,” said van der Zande.

“For example, how do you make electrical contact on molecular layer three and five, but not on layer four at the atomic level?”

A serendipitous discovery led to a method for doing just that.

As a new postdoctoral researcher in van der Zande’s lab, Jangyup Son was running some experiments on single layers of graphene using Xenon difluoride, XeF2, when he happened to “throw in” another material on hand: hexagonal Boron Nitride (hBN), an electrical insulator.

“Jangyup shoved both materials into the etching chamber at the same time, and what he saw was that a single layer of graphene was still there, but a thick piece of hBN was completely etched away by the Xenon difluoride.”

This accidental discovery led the team to see where they could apply graphene’s ability to withstand the etching agent.

“This discovery allowed us to pattern two-dimensional structures by placing layers of graphene between other materials, such as hexagonal boron nitride (hBN), transition metal dichalcogenides (TMDCs), and black phosphorus (BP), to selectively and precisely etch one layer without etching the layer underneath.”

Graphene, when exposed to the etching agent XeF2, retains its molecular structure and masks, or protects, the layer below and actually stops the etch.

“What we’ve discovered is a way to pattern complicated structures down to a molecular and atomic scale,” he said.

To explore the strengths of the new technique, the group created a simple graphene transistor to test its performance relative to traditionally made graphene transistors, which are currently patterned in a way that induces disorder in the material, degrading their performance.

“Because these molecules are all surface, if you have it sitting on anything with any disorder at all, it messes up the ability for the electrons to move through the material and thus the electronic performance,” said van der Zande. “In order to make the best device possible, you need to encapsulate the graphene molecule in another two-dimensional material such as insulating hBN to keep it super flat and clean.”

This is where the new technique is so useful. The graphene molecule can remain encapsulated and pristine, while withstanding the etching needed to make contact with the material, thereby preserving the material’s properties.

As proof of concept, the transistors made using the new technique out-performed all other transistors, “making them the best graphene transistors so far demonstrated in the literature.”

The next steps, said van der Zande, are to see how scalable the technique is and whether it will enable previously impossible devices. Can we take advantage of the self-arresting nature of this technique to make a million identical transistors rather than just one? Can we pattern devices down to the nanoscale in all three dimensions at the same time to make nanoribbons without any disorder?

“Now that we have a way of minimizing the disorder within the material, we are exploring ways to make smaller features because we can do encapsulation and patterning at the same time,” he said. “Normally, when you try to make smaller features like nanoribbons of 2D materials the disorder begins to dominate, so the devices do not work properly.”

“The graphene etch stop, as the technique is called, will make the entire process of building devices easier.”

The research involved a multi-disciplinary collaboration of people and shared facilities equipment from the Materials Research Laboratory and the Micro & Nanotechnology Lab. Expert faculty include: Associate Professor of Physics and Director of the Illinois Materials Research Science and Engineering Center (MRSEC), Nadya Mason, for electronic transport; Associate Professor of Mechanical Science and Engineering, Elif Ertekin, for modeling interfaces; and Assistant Professor of Materials Science and Engineering, Pinshane Huang, for electron microscopy. MRSEC provided the primary funding for this research.