Tag Archives: David Kaplan

Frankenturtles released

This really is a ‘Frankenstein’ story complete with turtle cadavers. From a June 14, 2016 news item on ScienceDaily,

It was a dark and stormy night in the laboratory, and jagged bolts of lightning lit the sky as Dr. Kaplan and his assistant Bianca stitched the pieces of the lifeless creature back together.

Actually, it was a sunny day on the shores of Chesapeake Bay, but recent sea turtle research by Assistant Professor David Kaplan of the Virginia Institute of Marine Science and graduate student Bianca Santos easily brings to mind the classic tale of Dr. Frankenstein and his makeshift monster.

Santos, a master’s student in William & Mary’s School of Marine Science at VIMS, is working with Kaplan to reduce sea turtle mortality by trying to pinpoint where the hundreds of dead loggerhead sea turtles that wash up on Chesapeake Bay beaches each summer may have succumbed. With that knowledge, researchers could hone in on likely causes of sea-turtle death, while wildlife authorities could map out safe zones for these imperiled marine reptiles. One of Kaplan’s research specialties is the spatial management of marine ecosystems.


David Kaplan examines the Frankenturtles before their deployment. Also visible are the bucket drifters that more closely follow Bay currents. Courtesy: VIMS

David Kaplan examines the Frankenturtles before their deployment. Also visible are the bucket drifters that more closely follow Bay currents. Courtesy: VIMS

A June 14, 2016 Virginia Institute of Marine Science news release by David Malmquist, which originated the news item, expands on the theme,

The pair’s approach to the problem is ingenious if somewhat morbid: obtain dead sea turtles (from the Virginia Aquarium’s Stranding Response Program), replace the turtles’ inner organs with buoyant Styrofoam, “sew” their shells back together with zip ties, and then attach GPS units to track the path of the “Frankenturtles” as winds and currents disperse them from a mid-Bay release site.

“It might seem sort of gross, but it’s a good way to reuse a dead turtle that would otherwise be buried,” says Kaplan. “And hopefully, the deployment of our two Frankenturtles will ultimately help lower the number of turtle deaths in the future.”

Santos explains that the team is actually releasing three different types of drifters: the two Frankenturtles, two wooden-Styrofoam turtle models, and a pair of bucket drifters. By observing how the wind differentially affects the highly buoyant, sail-like wooden models; the partly emergent Frankenturtles; and the mostly submerged buckets, the researchers hope to better understand how a wind-driven carcass might deviate from the more predictable current patterns traced by the Bay’s surface waters. Sea turtles initially sink after dying, but quickly float back to the surface buoyed by gases from decomposing tissues.

“Our plan is to deploy the drifters on several different occasions—under a variety of wind and wave conditions—and in locations where mortality events could occur during the spring peak in strandings,” says Santos. “We’ll then use the separation rate between our bucket drifters, which closely track water movement, and our turtle carcasses to determine the amount of wind forcing to apply to simulated carcasses in our computer model.”

They initiated their field trials on June 13th [2016], deploying the drifters in open Bay waters about halfway between the mouth of the York River and Cape Charles on Virginia’s bayside Eastern Shore. One Frankenturtle comprises the remains of a 15-20 year old loggerhead killed by a boat strike. The other is a younger turtle whose mode of death remains a mystery despite a necropsy. Deploying these creatures wasn’t an easy job: in addition to the unforgettable and growing aroma of thawing turtle, the creatures are both heavy and unwieldy. The larger Frankenturtle weighs in at 150 pounds, the smaller at 70 pounds.

Modeling turtle movement

Once data from the Frankenturtle trials have allowed the researchers to properly configure their “turtle carcass drift model,” they’ll feed the model with historical records of stranding locations provided by the Virginia Aquarium’s Stranding Response Team. The team is the Commonwealth’s official entity for responding to reports of dead and injured sea turtles and other marine life in Bay and nearby coastal waters.

“If our model can accurately simulate how winds and currents act on a dead sea turtle, we should be able to backtrack from a stranding site to the place where the turtle likely died,” says Santos. “By knowing the ‘where,’” she adds, “we can better look at the ‘why.’”

The researchers plan to track the Frankenturtles and other drifters released on June 13th for 3-4 days before retrieving the GPS units for future use. Earlier experiments by Santos show that’s about how long dead turtles remain intact before they are dismembered and consumed by waves, birds, crabs, and fish. The public can view the motion of the drifters in real-time via the VIMS website at www.vims.edu/frankenturtle.

Sea turtle mortality

Mortality of loggerhead turtles in Chesapeake Bay is of continuing concern. “Strandings peaked in the early 2000s at around 200-400 per year,” says Kaplan. “Modifications to the pound-net fishery likely reduced the number to the current 100-300 per year, and it is these we’re trying to understand.” He adds that scientists don’t really don’t have a good idea what percentage of dead turtles these strandings represent. “The actual number could be much higher,” Kaplan says.

Evidence that strandings may represent only a small percentage of actual deaths comes from Santos’ decay experiments as well as the low odds of finding every dead turtle. “Bianca’s decay study shows that turtles remain intact for only 3-5 days after death, decreasing the likelihood that they might last long enough to wash up on a beach,” says Kaplan. “And of those that do wash ashore, many probably strand in remote or marshy areas where they are unlikely to be observed and reported by a beachgoer.”

Potential sources of mortality in the Bay include accidental capture in fishing gear, strikes by boat propellers, entanglement in plastic trash, and sudden drops in temperature.

Although loggerheads are the most common sea turtles in the Chesapeake, with 5,000-10,000 entering Bay waters each summer to feed, they are listed as “threatened” in U.S. waters under the Endangered Species Act due to the perils they face across their range, including loss of nesting habitat, disorientation of hatchlings by beachfront lighting, nest predation, and incidental capture in dredges and coastal fisheries. Measures to protect against these threats are enforced by NOAA Fisheries and the U.S. Fish and Wildlife Service.

Producing stronger silk musically

Markus Buehler and his interdisciplinary team (my previous posts on their work includes Gossamer silk that withstands hurricane force winds and Music, math, and spiderwebs) have synthesized a new material based on spider silk. From the Nov. 28, 2012 news item on ScienceDaily,

Pound for pound, spider silk is one of the strongest materials known: Research by MIT’s [Massachusetts Institute of Technology] Markus Buehler has helped explain that this strength arises from silk’s unusual hierarchical arrangement of protein building blocks.

Now Buehler — together with David Kaplan of Tufts University and Joyce Wong of Boston University — has synthesized new variants on silk’s natural structure, and found a method for making further improvements in the synthetic material.

And an ear for music, it turns out, might be a key to making those structural improvements.

Here’s Buehler describing the work in an MIT video clip,

The Nov. 28, 2012 MIT news release by David Chandler provides more details,

Buehler’s previous research has determined that fibers with a particular structure — highly ordered, layered protein structures alternating with densely packed, tangled clumps of proteins (ABABAB) — help to give silk its exceptional properties. For this initial attempt at synthesizing a new material, the team chose to look instead at patterns in which one of the structures occurred in triplets (AAAB and BBBA).

Making such structures is no simple task. Kaplan, a chemical and biomedical engineer, modified silk-producing genes to produce these new sequences of proteins. Then Wong, a bioengineer and materials scientist, created a microfluidic device that mimicked the spider’s silk-spinning organ, which is called a spinneret.

Even after the detailed computer modeling that went into it, the outcome came as a bit of a surprise, Buehler says. One of the new materials produced very strong protein molecules — but these did not stick together as a thread. The other produced weaker protein molecules that adhered well and formed a good thread. “This taught us that it’s not sufficient to consider the properties of the protein molecules alone,” he says. “Rather, [one must] think about how they can combine to form a well-connected network at a larger scale.”

The different levels of silk’s structure, Buehler says, are analogous to the hierarchical elements that make up a musical composition — including pitch, range, dynamics and tempo. The team enlisted the help of composer John McDonald, a professor of music at Tufts, and MIT postdoc David Spivak, a mathematician who specializes in a field called category theory. Together, using analytical tools derived from category theory to describe the protein structures, the team figured out how to translate the details of the artificial silk’s structure into musical compositions.

The differences were quite distinct: The strong but useless protein molecules translated into music that was aggressive and harsh, Buehler says, while the ones that formed usable fibers sound much softer and more fluid.

Combining materials modeling with mathematical and musical tools, Buehler says, could provide a much faster way of designing new biosynthesized materials, replacing the trial-and-error approach that prevails today. Genetically engineering organisms to produce materials is a long, painstaking process, he says, but this work “has taught us a new approach, a fundamental lesson” in combining experiment, theory and simulation to speed up the discovery process.

Materials produced this way — which can be done under environmentally benign, room-temperature conditions — could lead to new building blocks for tissue engineering or other uses, Buehler says: scaffolds for replacement organs, skin, blood vessels, or even new materials for use in civil engineering.

It may be that the complex structures of music can reveal the underlying complex structures of biomaterials found in nature, Buehler says. “There might be an underlying structural expression in music that tells us more about the proteins that make up our bodies. After all, our organs — including the brain — are made from these building blocks, and humans’ expression of music may inadvertently include more information that we are aware of.”

“Nobody has tapped into this,” he says, adding that with the breadth of his multidisciplinary team, “We could do this — making better bio-inspired materials by using music, and using music to better understand biology.”

At the end of Chandler’s news release there’s a notice about a summer course with Markus Buehler,

For those interested in the work Professor Buehler is doing, you may also be interested to know that he is offering a short course on campus this summer called Materials By Design.

Materials By Design
June 17-20, 2013

Through lectures and hands-on labs, participants will learn how materials failure, studied from a first principles perspective, can be applied in an effective “learning-from-failure approach” to design and make novel materials. Participants will also learn how superior material properties in nature and biology can be mimicked in bioinspired materials for applications in new technology. This course will be of interest to scientists, engineers, managers, and policy makers working in the area of materials design, development, manufacturing, and testing. [emphasis mine]

I wasn’t expecting to see managers and policy makers as possible students for this course.

By the way, Buehler is not the only scientist to make a connection between music and biology (although he seems to be the only person using the concept for applications), there’s also geneticist and biophysicist, Mae Wan Ho and her notion of quantum jazz. From the Quantum Jazz Biology* article by David Reilly in the June 23, 2010 Isis Report,

I use the analogy of ‘quantum jazz’ to express the quantum coherence of the organism. It goes through a fantastic range of space and time scales, from the tiniest atom or subatomic particle to the whole organism and beyond. Organisms communicate with other organisms, and are attuned to natural rhythms, so they have circadian rhythms, annual rhythms, and so on. At the other extreme, you have very fast reactions that take place in femtoseconds. And all these rhythms are coordinated, there is evidence for that.

Tooth tattoos at Tufts University

In spring 2012, there was a fluttering in the blogosphere about tooth tattoos with the potential for monitoring dental health. As sometimes happens, I put off posting about the work until it seemed everyone else had written about it (e.g. Mar. 30, 2012 posting by Dexter Johnson for his Nanoclast blog on the IEEE website) and there was nothing left for me to say.  Happily, the researchers at Tufts University (where part of this research [Princeton University is also involved] is being pursued) have released more information in a Nov. 1, 2012 news article by David Levin,

The sensor, dubbed a “tooth tattoo,” was developed by the Princeton nanoscientist Michael McAlpine and Tufts bioengineers Fiorenzo Omenetto, David Kaplan and Hu Tao. The team first published their research last spring in the journal Nature Communications.

The sensor is relatively simple in its construction, says McAlpine. It’s made up of just three layers: a sheet of thin gold foil electrodes, an atom-thick layer of graphite known as graphene and a layer of specially engineered peptides, chemical structures that “sense” bacteria by binding to parts of their cell membranes.

“We created a new type of peptide that can serve as an intermediary between bacteria and the sensor,” says McAlpine. “At one end is a molecule that can bond with the graphene, and at the other is a molecule that bonds with bacteria,” allowing the sensor to register the presence of bacteria, he says.

Because the layers of the device are so thin and fragile, they need to be mounted atop a tough but flexible backing in order to transfer them to a tooth. The ideal foundation, McAlpine says, turns out to be silk—a substance with which Kaplan and Omenetto have been working for years.

By manipulating the proteins that make up a single strand of silk, it’s possible to create silk structures in just about any shape, says Omenetto, a professor of biomedical engineering at Tufts. Since 2005, he’s created dozens of different structures out of silk, from optical lenses to orthopedic implants. Silk is “kind of like plastic, in that we can make [it] do almost anything,” he says. “We have a lot of control over the material. It can be rigid. It can be flexible. We can make it dissolve in water, stay solid, become a gel—whatever we need.”

Omenetto, Kaplan and Tao created a thin, water-soluble silk backing for McAlpine’s bacterial sensor—a film that’s strong enough to hold the sensor components in place, but soft and pliable enough to wrap easily around the irregular contours of a tooth.

To apply the sensor, McAlpine says, you need only to wet the surface of the entire assembly—silk, sensor and all—and then press it onto the tooth. Once there, the silk backing will dissolve within 15 or 20 minutes, leaving behind the sensor, a rectangle of interwoven gold and black electrodes about half the size of a postage stamp and about as thick as a sheet of paper. The advantage of being attached directly to a tooth means that the sensor is in direct contact with bacteria in the mouth—an ideal way to monitor oral health.

Because the sensor doesn’t carry any onboard batteries, it must be both read and powered simultaneously through a built-in antenna. Using a custom-made handheld device about the size of a TV remote, McAlpine’s team can “ping” that antenna with radio waves, causing it to resonate electronically and send back information that the device then uses to determine if bacteria are present.

The sensor (A), attached to a tooth (B) and activated by radio signals (C), binds with certain bacteria (D). Illustration: Manu Mannoor/Nature Communications (downloaded from http://now.tufts.edu/articles/tooth-tattoo)

In addition to its potential for  monitoring dental health, the tooth tattoo could replace some of the more invasive health monitoring techniques (e.g., drawing blood), from the Tufts University article,

In addition to monitoring oral health, Kugel [Gerard Kugel, Tufts professor of prosthodontics and operative dentistry and associate dean for research at Tufts School of Dental Medicine] believes the tooth tattoo might be useful for monitoring a patient’s overall health. Biological markers for many diseases—from stomach ulcers to AIDS—appear in human saliva, he says. So if a sensor could be modified to react to those markers, it potentially could help dentists identify problems early on and refer patients to a physician before a condition becomes serious.

“The mouth is a window to the rest of the body,” Kugel says. “You can spot a lot of potential health problems through saliva, and it’s a much less invasive way to do diagnostic tests than drawing blood.”

Before monitoring of any type can take place, there is at least one major hurdle still be overcome. Humans are quite sensitive to objects being placed in their mouths. According to one of the researchers, we can sense objects that are 50 to 60 microns wide, about the thickness piece of paper, and that may be too uncomfortable to bear.

H/T Nov. 9, 2012 news item on Nanowerk for pointing me towards the latest information about these tooth tattoos.

Gossamer silk that withstands hurricane force winds

I’ve written about spiderwebs before (mostly recently in my Dec. 9, 2011 posting titled, Music, math, and spiderwebs. Researcher, Markus J. Buehler, was featured in the Dec. 2011 posting and he is featured in this one too. I imagine he’s the ‘go to’ spiderweb researcher at MIT (Massachusetts Institute of Technology).

The most discussed characteristic of spiderwebs is their strength, a topic of endless fascination. The Feb. 1, 2012 news item on physorg.com offers a new take on this phenomenon,

While researchers have long known of the incredible strength of spider silk, the robust nature of the tiny filaments cannot alone explain how webs survive multiple tears and winds that exceed hurricane strength.

Now, a study that combines experimental observations of spider webs with complex computer simulations has shown that web durability depends not only on silk strength, but on how the overall web design compensates for damage and the response of individual strands to continuously varying stresses.

Reporting in the cover story of the Feb. 2, 2012, issue of Nature, researchers from the Massachusetts Institute of Technology (MIT) [team leader Markus Buehler, associate professor of civil and environmental engineering at MIT] and the Politecnico di Torino [team leader Nicola Pugno, Professor of Solid and Structural Mechanics at the Politecnico di Torino] in Italy show how spider web-design localizes strain and damage, preserving the web as a whole.

Very simply, two of the types of spider silk that give the webs their strength were examined separately and together. From the news item,

Viscid silk is stretchy, wet and sticky, and it is the silk that winds out in increasing spirals from the web center. Its primary function is to capture prey. Dragline silk is stiff and dry, and it serves as the threads that radiate out from a web’s center, providing structural support. Dragline silk is crucial to the mechanical behavior of the web.

If you’re a weaver, that description will like remind you of warp and weft. The warp threads provide the strength and remain immobile while the the weft threads are the ones you weave in and out and use to create patterns, etc. if you are so inclined.

These observations about viscid and dragline silk have practical applications (from the news item),

The concept of selective, localized failure for spider webs is interesting since it is a distinct departure from the structural principles that seem to be in play for many biological materials and components,” adds Dennis Carter, the NSF program director for biomechanics and mechanobiology who helped support the study. [emphasis mine]

“For example, the distributed material components in bone spread stress broadly, adding strength. There is no ‘wasted’ material, minimizing the weight of the structure. While all of the bone is being used to resist force, bone everywhere along the structure tends to be damaged prior to failure.”

In contrast, a spider’s web is organized to sacrifice local areas so that failure will not prevent the remaining web from functioning, even if in a diminished capacity, says Carter. “This is a clever strategy when the alternative is having to make an entire, new web!,” he adds. “As Buehler suggests, engineers can learn from nature and adapt the design strategies that are most appropriate for specific applications.”

According to David Kaplan’s Feb. 2, 2012 article for MIT News, the spiderweb’s localized failure was a considered a sign of weakness,

It turns out that a key property of spider silk that helps make webs robust is something previously considered a weakness: the way it can stretch and soften at first when pulled, and then stiffen again as the force of the pulling increases.

This stiffening response is crucial to the way spider silk resists damage. Buehler and his team analyzed how materials with different properties, arranged in the same web pattern, respond to localized stresses. They found that materials with other responses — those that either behave as a simple linear spring as they’re pulled, or start out stretchy and then become more “plastic” — perform much less effectively.

Spider webs, it turns out, can take quite a beating without failing. Damage tends to be localized, affecting just a few threads — the place where a bug got caught in the web and flailed around, for example. This localized damage can simply be repaired, rather than replaced, or even left alone if the web continues to function as before. “Even if it has a lot of defects, the web actually still functions mechanically virtually the same way,” Buehler says. “It’s a very flaw-tolerant system.”

Here’s an image that illustrates how spiderwebs react to stress,

Images show the successive deformation states as loading is increased on a spider web, with red marking high stresses. Simulation picture by S. Cranford & M.J. Buehler/MIT, photographic image by Francesco Tomasinelli & Emanuele Biggi.

The researchers’ article in Nature, Nonlinear material behaviour of spider silk yields robust webs by Steven W. Cranford, Anna Tarakanova, Nicola M. Pugno & Markus J. Buehler is available behind a paywall.

Note: I’m pretty sure I searched to find out if it should be spiderwebs or spider webs. I will investigate further but do not have time now. Meanwhile, I committed to spiderwebs in Dec. 2011.