Tag Archives: Tufts University

A new generation of xenobots made with frog cells

I meant to feature this work last year when it was first announced so I’m delighted a second chance has come around so soon after. From a March 31, 2021 news item on ScienceDaily,

Last year, a team of biologists and computer scientists from Tufts University and the University of Vermont (UVM) created novel, tiny self-healing biological machines from frog cells called “Xenobots” that could move around, push a payload, and even exhibit collective behavior in the presence of a swarm of other Xenobots.

Get ready for Xenobots 2.0.

Here’s a video of the Xenobot 2.0. It’s amazing but, for anyone who has problems with animal experimentation, this may be disturbing,


The next version of Xenobots have been created – they’re faster, live longer, and can now record information. (Source: Doug Blackiston & Emma Lederer)

A March 31, 2021 Tufts University news release by Mike Silver (also on EurekAlert and adapted and published as Scientists Create the Next Generation of Living Robots on the University of Vermont website as a UVM Today story),

The same team has now created life forms that self-assemble a body from single cells, do not require muscle cells to move, and even demonstrate the capability of recordable memory. The new generation Xenobots also move faster, navigate different environments, and have longer lifespans than the first edition, and they still have the ability to work together in groups and heal themselves if damaged. The results of the new research were published today [March 31, 2021] in Science Robotics.

Compared to Xenobots 1.0, in which the millimeter-sized automatons were constructed in a “top down” approach by manual placement of tissue and surgical shaping of frog skin and cardiac cells to produce motion, the next version of Xenobots takes a “bottom up” approach. The biologists at Tufts took stem cells from embryos of the African frog Xenopus laevis (hence the name “Xenobots”) and allowed them to self-assemble and grow into spheroids, where some of the cells after a few days differentiated to produce cilia – tiny hair-like projections that move back and forth or rotate in a specific way. Instead of using manually sculpted cardiac cells whose natural rhythmic contractions allowed the original Xenobots to scuttle around, cilia give the new spheroidal bots “legs” to move them rapidly across a surface. In a frog, or human for that matter, cilia would normally be found on mucous surfaces, like in the lungs, to help push out pathogens and other foreign material. On the Xenobots, they are repurposed to provide rapid locomotion. 

“We are witnessing the remarkable plasticity of cellular collectives, which build a rudimentary new ‘body’ that is quite distinct from their default – in this case, a frog – despite having a completely normal genome,” said Michael Levin, Distinguished Professor of Biology and director of the Allen Discovery Center at Tufts University, and corresponding author of the study. “In a frog embryo, cells cooperate to create a tadpole. Here, removed from that context, we see that cells can re-purpose their genetically encoded hardware, like cilia, for new functions such as locomotion. It is amazing that cells can spontaneously take on new roles and create new body plans and behaviors without long periods of evolutionary selection for those features.”

“In a way, the Xenobots are constructed much like a traditional robot.  Only we use cells and tissues rather than artificial components to build the shape and create predictable behavior.” said senior scientist Doug Blackiston, who co-first authored the study with research technician Emma Lederer. “On the biology end, this approach is helping us understand how cells communicate as they interact with one another during development, and how we might better control those interactions.”

While the Tufts scientists created the physical organisms, scientists at UVM were busy running computer simulations that modeled different shapes of the Xenobots to see if they might exhibit different behaviors, both individually and in groups. Using the Deep Green supercomputer cluster at UVM’s Vermont Advanced Computing Core, the team, led by computer scientists and robotics experts Josh Bongard and Sam Kriegman, simulated the Xenbots under hundreds of thousands of random environmental conditions using an evolutionary algorithm.  These simulations were used to identify Xenobots most able to work together in swarms to gather large piles of debris in a field of particles

“We know the task, but it’s not at all obvious — for people — what a successful design should look like. That’s where the supercomputer comes in and searches over the space of all possible Xenobot swarms to find the swarm that does the job best,” says Bongard. “We want Xenobots to do useful work. Right now we’re giving them simple tasks, but ultimately we’re aiming for a new kind of living tool that could, for example, clean up microplastics in the ocean or contaminants in soil.” 

It turns out, the new Xenobots are much faster and better at tasks such as garbage collection than last year’s model, working together in a swarm to sweep through a petri dish and gather larger piles of iron oxide particles. They can also cover large flat surfaces, or travel through narrow capillary tubes.

These studies also suggest that the in silico [computer] simulations could in the future optimize additional features of biological bots for more complex behaviors. One important feature added in the Xenobot upgrade is the ability to record information.

Now with memory

A central feature of robotics is the ability to record memory and use that information to modify the robot’s actions and behavior. With that in mind, the Tufts scientists engineered the Xenobots with a read/write capability to record one bit of information, using a fluorescent reporter protein called EosFP, which normally glows green. However, when exposed to light at 390nm wavelength, the protein emits red light instead. 

The cells of the frog embryos were injected with messenger RNA coding for the EosFP protein before stem cells were excised to create the Xenobots. The mature Xenobots now have a built-in fluorescent switch which can record exposure to blue light around 390nm.
The researchers tested the memory function by allowing 10 Xenobots to swim around a surface on which one spot is illuminated with a beam of 390nm light. After two hours, they found that three bots emitted red light. The rest remained their original green, effectively recording the “travel experience” of the bots.

This proof of principle of molecular memory could be extended in the future to detect and record not only light but also the presence of radioactive contamination, chemical pollutants, drugs, or a disease condition. Further engineering of the memory function could enable the recording of multiple stimuli (more bits of information) or allow the bots to release compounds or change behavior upon sensation of stimuli. 

“When we bring in more capabilities to the bots, we can use the computer simulations to design them with more complex behaviors and the ability to carry out more elaborate tasks,” said Bongard. “We could potentially design them not only to report conditions in their environment but also to modify and repair conditions in their environment.”

Xenobot, heal thyself

“The biological materials we are using have many features we would like to someday implement in the bots – cells can act like sensors, motors for movement, communication and computation networks, and recording devices to store information,” said Levin. “One thing the Xenobots and future versions of biological bots can do that their metal and plastic counterparts have difficulty doing is constructing their own body plan as the cells grow and mature, and then repairing and restoring themselves if they become damaged. Healing is a natural feature of living organisms, and it is preserved in Xenobot biology.” 

The new Xenobots were remarkably adept at healing and would close the majority of a severe full-length laceration half their thickness within 5 minutes of the injury. All injured bots were able to ultimately heal the wound, restore their shape and continue their work as before. 

Another advantage of a biological robot, Levin adds, is metabolism. Unlike metal and plastic robots, the cells in a biological robot can absorb and break down chemicals and work like tiny factories synthesizing and excreting chemicals and proteins. The whole field of synthetic biology – which has largely focused on reprogramming single celled organisms to produce useful molecules – can now be exploited in these multicellular creatures

Like the original Xenobots, the upgraded bots can survive up to ten days on their embryonic energy stores and run their tasks without additional energy sources, but they can also carry on at full speed for many months if kept in a “soup” of nutrients. 

What the scientists are really after

An engaging description of the biological bots and what we can learn from them is presented in a TED talk by Michael Levin. In his TED Talk, professor Levin describes not only the remarkable potential for tiny biological robots to carry out useful tasks in the environment or potentially in therapeutic applications, but he also points out what may be the most valuable benefit of this research – using the bots to understand how individual cells come together, communicate, and specialize to create a larger organism, as they do in nature to create a frog or human. It’s a new model system that can provide a foundation for regenerative medicine.

Xenobots and their successors may also provide insight into how multicellular organisms arose from ancient single celled organisms, and the origins of information processing, decision making and cognition in biological organisms. 

Recognizing the tremendous future for this technology, Tufts University and the University of Vermont have established the Institute for Computer Designed Organisms (ICDO), to be formally launched in the coming months, which will pull together resources from each university and outside sources to create living robots with increasingly sophisticated capabilities.

The ultimate goal for the Tufts and UVM researchers is not only to explore the full scope of biological robots they can make; it is also to understand the relationship between the ‘hardware’ of the genome and the ‘software’ of cellular communications that go into creating organized tissues, organs and limbs. Then we can gain greater control of that morphogenesis for regenerative medicine, and the treatment of cancer and diseases of aging.

Here’s a link to and a citation for the paper,

A cellular platform for the development of synthetic living machines by Douglas Blackiston, Emma Lederer, Sam Kriegman, Simon Garnier, Joshua Bongard, and Michael Levin. Science Robotics 31 Mar 2021: Vol. 6, Issue 52, eabf1571 DOI: 10.1126/scirobotics.abf1571

This paper is behind a paywall.

Precision targeting of the liver for gene editing

Apparently the magic is in the lipid nanoparticles. A March 1, 2021 news item on Nanowerk announced research into lipid nanoparticles as a means to deliver CRISPR (clustered regularly interspaced short palindromic repeats) to specific organs (Note: A link has been removed),

The genome editing technology CRISPR has emerged as a powerful new tool that can change the way we treat disease. The challenge when altering the genetics of our cells, however, is how to do it safely, effectively, and specifically targeted to the gene, tissue and organ that needs treatment.

Scientists at Tufts University and the Broad Institute of Harvard [University] and MIT [Massachusetts Institute of Technology] have developed unique nanoparticles comprised of lipids — fat molecules — that can package and deliver gene editing machinery specifically to the liver.

In a study published in the Proceedings of the National Academy of Sciences [PNAS] (“Lipid nanoparticle-mediated codelivery of Cas9 mRNA and single-guide RNA achieves liver-specific in vivo genome editing of Angptl3”), they have shown that they can use the lipid nanoparticles (LNPs) to efficiently deliver the CRISPR machinery into the liver of mice, resulting in specific genome editing and the reduction of blood cholesterol levels by as much as 57% — a reduction that can last for at least several months with just one shot.

A March 2, 2021 Tufts University news release (also on EurekAlert but published March 1, 2021), which originated the news item, provides greater insight into and technical detail about the research,

The problem of high cholesterol plagues more than 29 million Americans, according to the Centers for Disease Control and Prevention. The condition is complex and can originate from multiple genes as well as nutritional and lifestyle choices, so it is not easy to treat. The Tufts and Broad researchers, however, have modified one gene that could provide a protective effect against elevated cholesterol if it can be shut down by gene editing.

The gene that the researchers focused on codes for the angiopoietin-like 3 enzyme (Angptl3). That enzyme tamps down the activity of other enzymes – lipases – that help break down cholesterol. If researchers can knock out the Angptl3 gene, they can let the lipases do their work and reduce levels of cholesterol in the blood. It turns out that some lucky people have a natural mutation in their Angptl3 gene, leading to consistently low levels of triglycerides and low-density lipoprotein (LDL) cholesterol, commonly called “bad” cholesterol, in their bloodstream without any known clinical downsides.

“If we can replicate that condition by knocking out the angptl3 gene in others, we have a good chance of having a safe and long term solution to high cholesterol,” said Qiaobing Xu, associate professor of biomedical engineering at Tufts’ School of Engineering and corresponding author of the study. “We just have to make sure we deliver the gene editing package specifically to the liver so as not to create unwanted side effects.”

Xu’s team was able to do precisely that in mouse models. After a single injection of lipid nanoparticles packed with mRNA coding for CRISPR-Cas9 and a single-guide RNA targeting Angptl3, they observed a profound reduction in LDL cholesterol by as much as 57% and triglyceride levels by about 29 %, both of which remained at those lowered levels for at least 100 days. The researchers speculate that the effect may last much longer than that, perhaps limited only by the slow turnover of cells in the liver, which can occur over a period of about a year. The reduction of cholesterol and triglycerides is dose dependent, so their levels could be adjusted by injecting fewer or more LNPs in the single shot, the researchers said.

By comparison, an existing, FDA [US Food and Drug Administration]-approved version of CRISPR mRNA-loaded LNPs could only reduce LDL cholesterol by at most 15.7% and triglycerides by 16.3% when it was tested in mice, according to the researchers.

The trick to making a better LNP was in customizing the components – the molecules that come together to form bubbles around the mRNA. The LNPs are made up of long chain lipids that have a charged or polar head that is attracted to water, a carbon chain tail that points toward the middle of the bubble containing the payload, and a chemical linker between them. Also present are polyethylene glycol, and yes, even some cholesterol – which has a normal role in lipid membranes to make them less leaky – to hold their contents better.

The researchers found that the nature and relative ratio of these components appeared to have profound effects on the delivery of mRNA into the liver, so they tested LNPs with many combinations of heads, tails, linkers and ratios among all components for their ability to target liver cells. Because the in vitro potency of an LNP formulation rarely reflects its in vivo performance, they directly evaluated the delivery specificity and efficacy in mice that have a reporter gene in their cells that lights up red when genome editing occurs. Ultimately, they found a CRISPR mRNA-loaded LNP that lit up just the liver in mice, showing that it could specifically and efficiently deliver gene-editing tools into the liver to do their work.

The LNPs were built upon earlier work at Tufts, where Xu and his team developed LNPs with as much as 90% efficiency in delivering mRNA into cells. A unique feature of those nanoparticles was the presence of disulfide bonds between the long lipid chains. Outside the cells, the LNPs form a stable spherical structure that locks in their contents. When they are inside a cell, the environment within breaks the disulfide bonds to disassemble the nanoparticles. The contents are then quickly and efficiently released into the cell. By preventing loss outside the cell, the LNPs can have a much higher yield in delivering their contents.

“CRISPR is one of the most powerful therapeutic tools for the treatment of diseases with a genetic etiology. We have recently seen the first human clinical trail for CRISPR therapy enabled by LNP delivery to be administered systemically to edit genes inside the human body. Our LNP platform developed here holds great potential for clinical translation,” said Min Qiu, post-doctoral researcher in Xu’s lab at Tufts.  “We envision that with this LNP platform in hand, we could now make CRISPR a practical and safe approach to treat a broad spectrum of liver diseases or disorders,” said Zachary Glass, graduate student in the Xu lab. Qiu and Glass are co-first authors of the study.

Here’s a link to and a citation for the paper,

Lipid nanoparticle-mediated codelivery of Cas9 mRNA and single-guide RNA achieves liver-specific in vivo genome editing of Angptl3 by Min Qiu, Zachary Glass, Jinjin Chen, Mary Haas, Xin Jin, Xuewei Zhao, Xuehui Rui, Zhongfeng Ye, Yamin Li, Feng Zhang, and Qiaobing Xu. PNAS March 9, 2021 118 (10) e2020401118 DOI: https://doi.org/10.1073/pnas.2020401118

This paper appears to be behind a paywall.

Fantastic Fungi Futures: a multi-night ArtSci Salon event in late November/early December 2019 in Toronto

In fact, I have two items about fungi and I’m starting with the essay first.

Giving thanks for fungi

These foods are all dependent on microorganisms for their distinctive flavor. Credit: margouillat photo/Shutterstock.com

Antonis Rokas, professor at Venderbilt University (Nashville, Tennessee, US), has written a November 25, 2019 essay for The Conversation (h/t phys.org Nov.26.19) featuring fungi and food, Note: Links have been removed),

I am an evolutionary biologist studying fungi, a group of microbes whose domestication has given us many tasty products. I’ve long been fascinated by two questions: What are the genetic changes that led to their domestication? And how on Earth did our ancestors figure out how to domesticate them?

The hybrids in your lager

As far as domestication is concerned, it is hard to top the honing of brewer’s yeast. The cornerstone of the baking, brewing and wine-making industries, brewer’s yeast has the remarkable ability to turn the sugars of plant fruits and grains into alcohol. How did brewer’s yeast evolve this flexibility?

By discovering new yeast species and sequencing their genomes, scientists know that some yeasts used in brewing are hybrids; that is, they’re descendants of ancient mating unions of individuals from two different yeast species. Hybrids tend to resemble both parental species – think of wholpins (whale-dolphin) or ligers (lion-tiger).

… What is still unknown is whether hybridization is the norm or the exception in the yeasts that humans have used for making fermented beverages for millennia.

To address this question, a team led by graduate student Quinn Langdon at the University of Wisconsin and another team led by postdoctoral fellow Brigida Gallone at the Universities of Ghent and Leuven in Belgium examined the genomes of hundreds of yeasts involved in brewing and wine making. Their bottom line? Hybrids rule.

For example, a quarter of yeasts collected from industrial environments, including beer and wine manufacturers, are hybrids.

The mutants in your cheese

Comparing the genomes of domesticated fungi to their wild relatives helps scientists understand the genetic changes that gave rise to some favorite foods and drinks. But how did our ancestors actually domesticate these wild fungi? None of us was there to witness how it all started. To solve this mystery, scientists are experimenting with wild fungi to see if they can evolve into organisms resembling those that we use to make our food today.

Benjamin Wolfe, a microbiologist at Tufts University, and his team addressed this question by taking wild Penicillium mold and growing the samples for one month in his lab on a substance that included cheese. That may sound like a short period for people, but it is one that spans many generations for fungi.

The wild fungi are very closely related to fungal strains used by the cheese industry in the making of Camembert cheese, but look very different from them. For example, wild strains are green and smell, well, moldy compared to the white and odorless industrial strains.

For Wolfe, the big question was whether he could experimentally recreate, and to what degree, the process of domestication. What did the wild strains look and smell like after a month of growth on cheese? Remarkably, what he and his team found was that, at the end of the experiment, the wild strains looked much more similar to known industrial strains than to their wild ancestor. For example, they were white in color and smelled much less moldy.

… how did the wild strain turn into a domesticated version? Did it mutate? By sequencing the genomes of both the wild ancestors and the domesticated descendants, and measuring the activity of the genes while growing on cheese, Wolfe’s team figured out that these changes did not happen through mutations in the organisms’ genomes. Rather, they most likely occurred through chemical alterations that modify the activity of specific genes but don’t actually change the genetic code. Such so-called epigenetic modifications can occur much faster than mutations.

Fantastic Fungi Futures (FFF) Nov. 29, Dec. 1, and Dec. 4, 2019 events in Toronto, Canada

The ArtSci Salon emailed me a November 23, 2019 announcement about a special series being presented in partnership with the Mycological Society of Toronto (MST) on the topic of fungi,

Fantastic Fungi Futures a discussion, a mini exhibition, a special screening, and a workshop revolving around Fungi and their versatile nature.

NOV 29 [2019], 6:00-8:00 PM Fantastic Fungi Futures (FFF): a roundtable discussion and popup exhibition.

Join us for a roundtable discussion. what are the potentials of fungi? Our guests will share their research, as well as professional and artistic practice dealing with the taxonomy and the toxicology, the health benefits and the potentials for sustainability, as well as the artistic and architectural virtues of fungi and mushrooms. The Exhibition will feature photos and objects created by local and Canadian artists who have been working with mushrooms and fungi.

This discussion is in anticipation of the special screening of Fantastic Fungi at the HotDocs Cinema on Dec 1 [2019] our guests:James Scott,Occupational & Environmental Health, Dalla Lana School of Public Health, UofT; Marshall Tyler, Director of Research, Field Trip, Toronto; Rotem Petranker, PhD student, Social Psychology, York University; Nourin Aman, PhD student, fungal biology and Systematics lab, Punjab University; Sydney Gram, PhD student, Ecology & Evolutionary Biology student researcher (UofT/ROM); [and] Tosca Teran, Interdisciplinary artist.

DEC. 1 [2019], 6:15 pm join us to the screening of Fantastic Fungi, at the HotDocs Cinemaget your tickets herehttps://boxoffice.hotdocs.ca/websales/pages/info.aspx?evtinfo=104145~fff311b7-cdad-4e14-9ae4-a9905e1b9cb0 afterward, some of us will be heading to the Pauper’s Pub, just across from the HotDocs Cinema

DEC. 4 [2019], 7:00-10:00PM Multi-species entanglements:Sculpting with Mycelium, @InterAccess, 950 Dupont St., Unit 1 

This workshop is a continuation of ArtSci Salon’s Fantastic Fungi Futures event and the HotDocs screening of Fantastic Fungi.this workshop is open to public to attend, however, pre-registration is required. $5.00 to form a mycelium bowl to take home.

During this workshop Tosca Teran introduces the amazing potential of Mycelium for collaboration at the intersection of art and science. Participants learn how to transform their kitchens and closets in to safe, mini-Mycelium biolabs and have the option to leave the workshop with a live Mycelium planter/bowl form, as well as a wide array of possibilities of how they might work with this sustainable bio-material. 

Bios

Nourin Aman is a PhD student at fungal biology and Systematics lab at Punjab University, Lahore, Pakistan. She is currently a visiting PhD student at the Mycology lab, Royal Ontario Museum. Her research revolves around comparison between macrofungal biodiversity of some reserve forests of Punjab, Pakistan.Her interest is basically to enlist all possible macrofungi of reserve forests under study and describe new species as well from area as our part of world still has many species to be discovered and named. She will be discussing factors which are affecting the fungal biodiversity in these reserve forests.

Sydney Gram is an Ecology & Evolutionary Biology student researcher (UofT/ROM)

Rotem Petranker- Bsc in psychology from the University of Toronto and a MA in social psychology from York University. Rotem is currently a PhD student in York’s clinical psychology program. His main research interest is affect regulation, and the way it interacts with sustained attention, mind wandering, and creativity. Rotem is a founding member oft the Psychedelic Studies Research Program at the University of Toronto, has published work on microdosing, and presented original research findings on psychedelic research in several conferences. He feels strongly that the principles of Open Science are necessary in order to do good research, and is currently in the process of starting the first lab study of microdosing in Canada.

James Scott– PhD, is a ARMCCM Professor and Head Division of Occupational & Environmental Health, Dalla Lana School of Public Health, University of TorontoUAMH Fungal Biobank: http://www.uamh.caUniversity Profile: http://www.dlsph.utoronto.ca/faculty-profile/scott-james-a/Research Laboratory: http://individual.utoronto.ca/jscottCommercial Laboratory: http://www.sporometrics.com

Marshall Tyler– Director of Research, Field Trip. Marshall is a scientist with a deep interest in psychoactive molecules. His passion lies in guiding research to arrive at a deeper understanding of consciousness with the ultimate goal of enhancing wellbeing. At Field Trip, he is helping to develop a lab in Jamaica to explore the chemical and biological complexities of psychoactive fungi.

Tosca Teran, aka Nanotopia, is an Multi-disciplinary artist. Her work has been featured at SOFA New York, Culture Canada, and The Toronto Design Exchange. Tosca has been awarded artist residencies with The Ayatana Research Program in Ottawa and The Icelandic Visual Artists Association through Sím, Reykjavik Iceland and Nes artist residency in Skagaströnd, Iceland. In 2019 she was one of the first Bio-Artists in residence at the Museum of Contemporary Art Toronto in partnership with the Ontario Science Centre as part of the Alien Agencies Collective. A recipient of the 2019 BigCi Environmental Award at Wollemi National Park within the UNESCO World Heritage site in the Greater Blue Mountains. Tosca started collaborating artistically with Algae, Physarum polycephalum, and Mycelium in 2016, translating biodata from non-human organisms into music.@MothAntler @nanopodstudio www.toscateran.com www.nanotopia.net8 

A trailer has been provided for the movie mentioned in the announcement (from the Fantastic Fungi screening webpage on the Mycological Society of Toronto website),

You can find the ArtSci Salon here and the Mycological Society of Toronto (MST) here.

Preprogramming silk protein-based materials

A new material based on silk proteins has been developed at Tufts University (US), according to a Dec. 26, 2016 news item on ScienceDaily,

Tufts University engineers have created a new format of solids made from silk protein that can be preprogrammed with biological, chemical, or optical functions, such as mechanical components that change color with strain, deliver drugs, or respond to light, according to a paper published online this week [Dec. 26 -30, 2016] in Proceedings of the National Academy of Sciences (PNAS).

Caption: This image shows examples of engineered 3-D silk constructs. Credit: Silklab, Department of Biomedical Engineering, School of Engineering, Tufts University

A Dec. 26, 2016 Tufts University news release (also on EurekAlert), which originated the news item, describes the research in more detail,

Using a water-based fabrication method based on protein self-assembly, the researchers generated three-dimensional bulk materials out of silk fibroin, the protein that gives silk its durability. Then they manipulated the bulk materials with water-soluble molecules to create multiple solid forms, from the nano- to the micro-scale, that have embedded, pre-designed functions.

For example, the researchers created a surgical pin that changes color as it nears its mechanical limits and is about to fail, functional screws that can be heated on demand in response to infrared light, and a biocompatible component that enables the sustained release of bioactive agents, such as enzymes.

Although more research is needed, additional applications could include new mechanical components for orthopedics that can be embedded with growth factors or enzymes, a surgical screw that changes color as it reaches its torque limits, hardware such as nuts and bolts that sense and report on the environmental conditions of their surroundings, or household goods that can be remolded or reshaped.

Silk’s unique crystalline structure makes it one of nature’s toughest materials. Fibroin, an insoluble protein found in silk, has a remarkable ability to protect other materials while being fully biocompatible and biodegradable.

Here’s a link to and a citation for the paper,

Programming function into mechanical forms by directed assembly of silk bulk materials by Benedetto Marelli, Nereus Patel, Thomas Duggan, Giovanni Perotto, Elijah Shirman, Chunmei Li, David L. Kaplan, and Fiorenzo G. Omenetto. PNAS 10.1073/pnas.1612063114 December 27, 2016

This paper is behind a paywall.

Sutures that can gather data wirelessly

Are sutures which gather data hackable? It’s a little early to start thinking about that issue as this seems to be brand new research. A July 18, 2016 news item on ScienceDaily tells more,

For the first time, researchers led by Tufts University engineers have integrated nano-scale sensors, electronics and microfluidics into threads — ranging from simple cotton to sophisticated synthetics — that can be sutured through multiple layers of tissue to gather diagnostic data wirelessly in real time, according to a paper published online July 18 [2016] in Microsystems & Nanoengineering. The research suggests that the thread-based diagnostic platform could be an effective substrate for a new generation of implantable diagnostic devices and smart wearable systems.

A July 18, 2016 Tufts University news release (also on EurekAlert), which originated the news item, provides more detail,

The researchers used a variety of conductive threads that were dipped in physical and chemical sensing compounds and connected to wireless electronic circuitry to create a flexible platform that they sutured into tissue in rats as well as in vitro. The threads collected data on tissue health (e.g. pressure, stress, strain and temperature), pH and glucose levels that can be used to determine such things as how a wound is healing, whether infection is emerging, or whether the body’s chemistry is out of balance. The results were transmitted wirelessly to a cell phone and computer.

The three-dimensional platform is able to conform to complex structures such as organs, wounds or orthopedic implants.

While more study is needed in a number of areas, including investigation of long-term biocompatibility, researchers said initial results raise the possibility of optimizing patient-specific treatments.

“The ability to suture a thread-based diagnostic device intimately in a tissue or organ environment in three dimensions adds a unique feature that is not available with other flexible diagnostic platforms,” said Sameer Sonkusale, Ph.D., corresponding author on the paper and director of the interdisciplinary Nano Lab in the Department of Electrical and Computer Engineering at Tufts School of Engineering. “We think thread-based devices could potentially be used as smart sutures for surgical implants, smart bandages to monitor wound healing, or integrated with textile or fabric as personalized health monitors and point-of-care diagnostics.”

Until now, the structure of substrates for implantable devices has essentially been two-dimensional, limiting their usefulness to flat tissue such as skin, according to the paper. Additionally, the materials in those substrates are expensive and require specialized processing.

Here’s a link to and a citation for the paper,

A toolkit of thread-based microfluidics, sensors, and electronics for 3D tissue embedding for medical diagnostics by Pooria Mostafalu, Mohsen Akbari, Kyle A. Alberti, Qiaobing Xu, Ali Khademhosseini, & Sameer R. Sonkusale. Microsystems & Nanoengineering 2, Article number: 16039 (2016) doi:10.1038/micronano.2016.39 Published online 18 July 2016

This paper is open access.

Coat fruit with silk to keep it fresh

A May 6, 2016 news item on ScienceDaily describes a way to keep fruit fresh without refrigeration,

Half of the world’s fruit and vegetable crops are lost during the food supply chain, due mostly to premature deterioration of these perishable foods, according to the Food and Agriculture Organization (FAO) of the United Nations.

Tufts University biomedical engineers have demonstrated that fruits can stay fresh for more than a week without refrigeration if they are coated in an odorless, biocompatible silk solution so thin as to be virtually invisible. The approach is a promising alternative for preservation of delicate foods using a naturally derived material and a water-based manufacturing process.

A May 6, 2016 Tufts University news release (also on EurekAlert), which originated the news item, describes the work,

Silk’s unique crystalline structure makes it one of nature’s toughest materials. Fibroin, an insoluble protein found in silk, has a remarkable ability to stabilize and protect other materials while being fully biocompatible and biodegradable.

For the study, researchers dipped freshly picked strawberries in a solution of 1 percent silk fibroin protein; the coating process was repeated up to four times.  The silk fibroin-coated fruits were then treated for varying amounts of time with water vapor under vacuum (water annealed) to create varying percentages of crystalline beta-sheets in the coating. The longer the exposure, the higher the percentage of beta-sheets and the more robust the fibroin coating. The coating was 27 to 35 microns thick.

The strawberries were then stored at room temperature. Uncoated berries were compared over time with berries dipped in varying numbers of coats of silk that had been annealed for different periods of time. At seven days, the berries coated with the higher beta-sheet silk were still juicy and firm while the uncoated berries were dehydrated and discolored.

Tests showed that the silk coating prolonged the freshness of the fruits by slowing fruit respiration, extending fruit firmness and preventing decay.

“The beta-sheet content of the edible silk fibroin coatings made the strawberries less permeable to carbon dioxide and oxygen. We saw a statistically significant delay in the decay of the fruit,” said senior and corresponding study author Fiorenzo G. Omenetto, Ph.D. Omenetto is the Frank C. Doble Professor in the Department of Biomedical Engineering and also has appointments in the Department of Electrical Engineering and in the Department of Physics in the School of Arts and Sciences.

Similar experiments were performed on bananas, which, unlike strawberries, are able to ripen after they are harvested. The silk coating decreased the bananas’ ripening rate compared with uncoated controls and added firmness to the fruit by preventing softening of the peel.

The thin, odorless silk coating did not affect fruit texture.  Taste was not studied.

“Various therapeutic agents could be easily added to the water-based silk solution used for the coatings, so we could potentially both preserve and add therapeutic function to consumable goods without the need for complex chemistries,” said the study’s first author, Benedetto Marelli, Ph.D., formerly a post-doctoral associate in the Omenetto laboratory and now at MIT.

Here’s a link to and a citation for the paper,

Silk Fibroin as Edible Coating for Perishable Food Preservation by B. Marelli, M. A. Brenckle, D. L. Kaplan & F. G. Omenetto. Scientific Reports 6, Article number: 25263 (2016) doi:10.1038/srep25263 Published online: 06 May 2016

This is an open access paper.

Green tech with single atom platinum catalyst?

There’s something mind boggling to me about the notion of a single atom catalyst. Luckily, an Oct. 5, 2015 news item on Nanowerk describes the research (Note: A link has been removed),

A new generation of platinum-copper catalysts that require very low concentrations of platinum in the form of individual atoms to cleanly and cheaply perform important chemical reactions is reported today by Tufts University researchers in the journal Nature Communications (“Selective hydrogenation of butadiene on platinum copper alloys at the single atom limit”).

An Oct. 9, 2015 Tufts University news release on EurekAlert, which originated the news item, describes the nature of the problem the researchers were trying to resolve and their solution,

Platinum is used as a catalyst in fuel cells, in automobile converters and in the chemical industry because of its remarkable ability to facilitate a wide range of chemical reactions. However, its future potential uses are significantly limited by scarcity and cost, as well as the fact that platinum readily binds with carbon monoxide, which “poisons” the desired reactions, for example in polymer electrolyte membrane (PEM) fuel cells, which are the leading contenders for small-scale and mobile power generation not based on batteries or combustion engines.

The Tufts researchers discovered that dispersing individual, isolated platinum atoms in much less costly copper surfaces can create a highly effective and cost-efficient catalyst for the selective hydrogenation of 1,3 butadiene, a chemical produced by steam cracking of naphtha or by catalytic cracking of gas oil. Butadiene is an impurity in propene streams that must be removed from the stream through hydrogenation in order to facilitate downstream polymer production. The current industrial catalyst for butadiene hydrogenation uses palladium and silver.

Like Sugar in Coffee

Copper, while a relatively cheap metal, is not nearly as catalytically powerful as platinum, noted Professor of Chemistry Charles Sykes, Ph.D., one of the senior authors on the paper. “We wanted to find a way to improve its performance.”

The researchers first conducted surface science experiments to study precisely how platinum and copper metals mix. “We were excited to find that the platinum metal dissolved in copper, just like sugar in hot coffee, all the way down to single atoms. We call such materials single atom alloys,” said Sykes.

The Tufts chemists used a specialized low temperature scanning tunneling microscope to visualize the single platinum atoms and their interaction with hydrogen. “We found that even at temperatures as low as minus 300 degrees F these platinum atoms were capable of splitting hydrogen molecules into atoms, indicating that the platinum atoms would be very good at activating hydrogen for a chemical reaction,” Sykes said.

With that knowledge, Sykes and his fellow chemists turned to long-time Tufts collaborator Maria Flytzani-Stephanopoulos, Ph.D., the Robert and Marcy Haber Endowed Professor in Energy Sustainability at the School of Engineering, to determine which hydrogenation reaction would be most significant for industrial applications. The answer, she said, was butadiene.

The model catalyst performed effectively for that reaction in vacuum conditions in the laboratory, so Flytzani-Stephanopoulos’s team took the study to the next level. They synthesized small quantities of realistic catalysts, such as platinum-copper single atom alloy nanoparticles supported on an alumina substrate, and then tested them under industrial pressure and temperatures.

“To our delight, these catalysts worked very well and their performance was steady for many days,” said Flytzani-Stephanopoulos. “While we had previously shown that palladium would do related reactions in a closed reactor system, this work with platinum is our first demonstration of operation in a flow reactor at industrially relevant conditions. We believe this approach is also applicable to other precious metals if added as minority components in copper.”

Further, the researchers found that the reaction actually became less efficient when they used more platinum, because clusters of platinum atoms have inferior selectivity compared with individual atoms. “In this case, less is more,” said Flytzani-Stephanopoulos, “which is a very good thing.”

Environmental Benefits

Because platinum is at the center of many clean energy and green chemicals production technologies, such as fuel cells, catalytic converters, and value-added chemicals from bio-renewable feedstocks, the new, less expensive platinum-copper catalysts could facilitate broader adoption of such environmentally friendly devices and processes, she added.

The news release goes on to describe this cross-disciplinary partnership,

The work is the latest fruit from a long cross-disciplinary partnership between Sykes and Flytzani-Stephanopoulos.

“Maria and I met more than seven years ago and talked regularly about how to combine our fairly different fields of research into an effective collaboration across the schools of Arts and Sciences and Engineering,” said Sykes. “I had a state-of-the-art microscope that could see and manipulate atoms and molecules, and I wanted to use its unique capabilities to gain insight into industrially important chemical reactions. In the early 2000s, Maria’s group had pioneered the single-atom approach for metals anchored on oxide supports as the exclusive active sites for the water-gas shift reaction to upgrade hydrogen streams for fuel cell use. Catalyst design know-how already existed in her lab. In retrospect, it seems obvious that combining forces would be a ‘natural’ development. Together we embarked on a new direction involving single atom alloys as catalysts for selective hydrogenation reactions. Our microscope was uniquely suited for characterizing the atomic composition of surfaces. We got funding from the National Science Foundation, U.S. Department of Energy and the Tufts Collaborates initiative to pursue this new area of research.”

Sykes and Flytzani-Stephanopoulos have used this approach to design a variety of single atom alloy catalysts that have, in the last two years, sparked international interest.

“Traditionally catalyst development happens by trial and error and screening many materials,” said Flytzani-Stephanopoulos. “In this study we took a fundamental approach to understanding the atomic scale structure and properties of single atom alloy surfaces and then applied this knowledge to develop a working catalyst. Armed with this knowledge, we are now ready to compare the stability of these single atom alloy catalysts to single atom catalysts supported on various oxide or carbon surfaces. This may give us very useful criteria for industrial catalyst design.”

Here’s a link to and a citation for the paper,

Selective hydrogenation of 1,3-butadiene on platinum–copper alloys at the single-atom limit by Felicia R. Lucci, Jilei Liu, Matthew D. Marcinkowski, Ming Yang, Lawrence F. Allard, Maria Flytzani-Stephanopoulos, & E. Charles H. Sykes. Nature Communications 6, Article number: 8550 doi:10.1038/ncomms9550 Published 09 October 2015

This is an open access paper.

Silk inks containing enzymes, antibiotics, antibodies, nanoparticles, and growth factors

There’s an almost euphoric tone to a June 16, 2015 Tufts University news release (also on EurekAlert) about research which has resulted in the ability to print silk-based inks,

Silk inks containing enzymes, antibiotics, antibodies, nanoparticles and growth factors could turn inkjet printing into a new, more effective tool for therapeutics, regenerative medicine and biosensing, according to new research led by Tufts University  biomedical engineers and published June 16 [2015] in the journal Advanced Materials online in advance of print.

Until now, heat used in the inkjet printing process made using silk a challenge (as it does for cellulose nanomaterials used in 3D printers, noted in my June 17, 2015 posting), from the Tufts news release,

Inkjet printing is one of the most immediate and accessible forms of printing technology currently available, according to the researchers, and ink-jet printing of biomolecules has been previously proposed by scientists. However, the heat-sensitive nature of these unstable compounds means printed materials rapidly lose functionality, limiting their use.

Enter purified silk protein, or fibroin, which offers intrinsic strength and protective properties that make it well-suited for a range of biomedical and optoelectronic applications. This natural polymer is an ideal “cocoon” that can stabilize compounds such as enzymes, antibodies and growth factors while lending itself to many different mechanically robust formats, said Fiorenzo Omenetto, Ph.D., senior author on the paper and associate dean for research and Frank C. Doble Professor of Engineering at Tufts School of Engineering.

“We thought that if we were able to develop an inkjet-printable silk solution, we would have a universal building block to generate multiple functional printed formats that could lead to a wide variety of applications in which inks remain active over time,” he said.

By using this simple approach and starting with the same base material, the research team created and tested a “custom library” of inkjet-printable, functional silk inks doped with a variety of components:

  • Bacterial-sensing polydiacetylenes (PDAs) printed on surgical gloves; the word “contaminated” printed on the glove changed from blue to red after exposure to E. coli
  • Proteins that stimulate bone growth (BMP-2) printed on a plastic dish to test topographical control of directed tissue growth
  • Sodium ampicillin printed on a bacterial culture to test the effectiveness of a topographical distribution of the antibiotic
  • Gold nanoparticles printed on paper, for possible application in photonics and biology (e.g., color engineering, surface plasmon resonance based sensing and bio-imaging)
  • Enzymes printed on paper to test the ability of the ink to entrain small functional biomolecules

The researchers, who included collaborators from the University of Illinois at Urbana-Champaign, foresee wide potential for future investigation and application of this technology.

For example, Omenetto envisions more work on the bio-sensing gloves, which he says could selectively react to different pathological agents. The ability to print antibiotics in topographical patterns could address the need for “smart” bandages, where therapeutics are incorporated and delivered to match a complex injury.

The published research was restricted to one ink cartridge, but the scientists believe it could extend to multi-cartridge printing combining complex functions.

Omenetto and Kaplan are pioneers in the use of silk as an alternative to plastics. Omenetto’s 2011 TED Talk called silk a “new old material” that could have a profound impact in many technical fields.

Here’s a link to and citation for the paper,

Inkjet Printing of Regenerated Silk Fibroin: From Printable Forms to Printable Functions by Hu Tao, Benedetto marelli, Miaomiao Yang, Bo An, Serdar Onses, John A. Rogers, David L. Kaplan, & Fiorenzo G. Omenetto. Advanced Materials DOI: 10.1002/adma.201501425 First published: 16 June 2015

This article is behind a paywall.

AI assistant makes scientific discovery at Tufts University (US)

In light of this latest research from Tufts University, I thought it might be interesting to review the “algorithms, artificial intelligence (AI), robots, and world of work” situation before moving on to Tufts’ latest science discovery. My Feb. 5, 2015 post provides a roundup of sorts regarding work and automation. For those who’d like the latest, there’s a May 29, 2015 article by Sophie Weiner for Fast Company, featuring a predictive interactive tool designed by NPR (US National Public Radio) based on data from Oxford University researchers, which tells you how likely automating your job could be, no one knows for sure, (Note: A link has been removed),

Paralegals and food service workers: the robots are coming.

So suggests this interactive visualization by NPR. The bare-bones graphic lets you select a profession, from tellers and lawyers to psychologists and authors, to determine who is most at risk of losing their jobs in the coming robot revolution. From there, it spits out a percentage. …

You can find the interactive NPR tool here. I checked out the scientist category (in descending order of danger: Historians [43.9%], Economists, Geographers, Survey Researchers, Epidemiologists, Chemists, Animal Scientists, Sociologists, Astronomers, Social Scientists, Political Scientists, Materials Scientists, Conservation Scientists, and Microbiologists [1.2%]) none of whom seem to be in imminent danger if you consider that bookkeepers are rated at  97.6%.

Here at last is the news from Tufts (from a June 4, 2015 Tufts University news release, also on EurekAlert),

An artificial intelligence system has for the first time reverse-engineered the regeneration mechanism of planaria–the small worms whose extraordinary power to regrow body parts has made them a research model in human regenerative medicine.

The discovery by Tufts University biologists presents the first model of regeneration discovered by a non-human intelligence and the first comprehensive model of planarian regeneration, which had eluded human scientists for over 100 years. The work, published in PLOS Computational Biology, demonstrates how “robot science” can help human scientists in the future.

To mine the fast-growing mountain of published experimental data in regeneration and developmental biology Lobo and Levin developed an algorithm that would use evolutionary computation to produce regulatory networks able to “evolve” to accurately predict the results of published laboratory experiments that the researchers entered into a database.

“Our goal was to identify a regulatory network that could be executed in every cell in a virtual worm so that the head-tail patterning outcomes of simulated experiments would match the published data,” Lobo said.

The paper represents a successful application of the growing field of “robot science” – which Levin says can help human researchers by doing much more than crunch enormous datasets quickly.

“While the artificial intelligence in this project did have to do a whole lot of computations, the outcome is a theory of what the worm is doing, and coming up with theories of what’s going on in nature is pretty much the most creative, intuitive aspect of the scientist’s job,” Levin said. “One of the most remarkable aspects of the project was that the model it found was not a hopelessly-tangled network that no human could actually understand, but a reasonably simple model that people can readily comprehend. All this suggests to me that artificial intelligence can help with every aspect of science, not only data mining but also inference of meaning of the data.”

Here’s a link to and a citation for the paper,

Inferring Regulatory Networks from Experimental Morphological Phenotypes: A Computational Method Reverse-Engineers Planarian Regeneration by Daniel Lobo and Michael Levin. PLOS (Computational Biology) DOI: DOI: 10.1371/journal.pcbi.1004295 Published: June 4, 2015

This paper is open access.

It will be interesting to see if attributing the discovery to an algorithm sets off criticism suggesting that the researchers overstated the role the AI assistant played.

Synthesizing spider silk

Most of the research on spider silk and spider webs that’s featured here is usually from the Massachusetts Institute of Technology (MIT) and, more specifically, from professor Markus J. Buehler. This May 28, 2015 news item on ScienceDaily, which heralds the development of synthetic spider silk, is no exception,

After years of research decoding the complex structure and production of spider silk, researchers have now succeeded in producing samples of this exceptionally strong and resilient material in the laboratory. The new development could lead to a variety of biomedical materials — from sutures to scaffolding for organ replacements — made from synthesized silk with properties specifically tuned for their intended uses.

The findings are published this week in the journal Nature Communications by MIT professor of civil and environmental engineering (CEE) Markus Buehler, postdocs Shangchao Lin and Seunghwa Ryu, and others at MIT, Tufts University, Boston University, and in Germany, Italy, and the U.K.

The research, which involved a combination of simulations and experiments, paves the way for “creating new fibers with improved characteristics” beyond those of natural silk, says Buehler, who is also the department head in CEE. The work, he says, should make it possible to design fibers with specific characteristics of strength, elasticity, and toughness.

The new synthetic fibers’ proteins — the basic building blocks of the material — were created by genetically modifying bacteria to make the proteins normally produced by spiders. These proteins were then extruded through microfluidic channels designed to mimic the effect of an organ, called a spinneret, that spiders use to produce natural silk fibers.

A May 28, 2015 MIT news release (also on EurekAlert), which originated the news item, describes the work in more detail,

While spider silk has long been recognized as among the strongest known materials, spiders cannot practically be bred to produce harvestable fibers — so this new approach to producing a synthetic, yet spider-like, silk could make such strong and flexible fibers available for biomedical applications. By their nature, spider silks are fully biocompatible and can be used in the body without risk of adverse reactions; they are ultimately simply absorbed by the body.

The researchers’ “spinning” process, in which the constituent proteins dissolved in water are extruded through a tiny opening at a controlled rate, causes the molecules to line up in a way that produces strong fibers. The molecules themselves are a mixture of hydrophobic and hydrophilic compounds, blended so as to naturally align to form fibers much stronger than their constituent parts. “When you spin it, you create very strong bonds in one direction,” Buehler says.

The team found that getting the blend of proteins right was crucial. “We found out that when there was a high proportion of hydrophobic proteins, it would not spin any fibers, it would just make an ugly mass,” says Ryu, who worked on the project as a postdoc at MIT and is now an assistant professor at the Korea Advanced Institute of Science and Technology. “We had to find the right mix” in order to produce strong fibers, he says.

The researchers made use of computational modelling to speed up the process of synthesizing proteins for synthetic spider silk, from the news release,

This project represents the first use of simulations to understand silk production at the molecular level. “Simulation is critical,” Buehler explains: Actually synthesizing a protein can take several months; if that protein doesn’t turn out to have exactly the right properties, the process would have to start all over.

Using simulations makes it possible to “scan through a large range of proteins until we see changes in the fiber stiffness,” and then home in on those compounds, says Lin, who worked on the project as a postdoc at MIT and is now an assistant professor at Florida State University.

Controlling the properties directly could ultimately make it possible to create fibers that are even stronger than natural ones, because engineers can choose characteristics for a particular use. For example, while spiders may need elasticity so their webs can capture insects without breaking, those designing fibers for use as surgical sutures would need more strength and less stretchiness. “Silk doesn’t give us that choice,” Buehler says.

The processing of the material can be done at room temperature using water-based solutions, so scaling up manufacturing should be relatively easy, team members say. So far, the fibers they have made in the lab are not as strong as natural spider silk, but now that the basic process has been established, it should be possible to fine-tune the materials and improve its strength, they say.

“Our goal is to improve the strength, elasticity, and toughness of artificially spun fibers by borrowing bright ideas from nature,” Lin says. This study could inspire the development of new synthetic fibers — or any materials requiring enhanced properties, such as in electrical and thermal transport, in a certain direction.

Here’s a link to and a citation for the paper,

Predictive modelling-based design and experiments for synthesis and spinning of bioinspired silk fibres by Shangchao Lin, Seunghwa Ryu, Olena Tokareva, Greta Gronau, Matthew M. Jacobsen, Wenwen Huang, Daniel J. Rizzo, David Li, Cristian Staii, Nicola M. Pugno, Joyce Y. Wong, David L. Kaplan, & Markus J. Buehler. Nature Communications 6, Article number: 6892 doi:10.1038/ncomms7892 Published 28 May 2015

This paper is behind a paywall.

My two most recent (before this one) postings about Buehler’s work are an August 5, 2014 piece about structural failures and a June 4, 2014 piece about spiderwebs and music.

Finally, I recognized one of the authors, Nicola Pugno from Italy. He’s been mentioned here more than once in regard to his biomimicry work which has often been focused on geckos and their adhesive qualities as per this April 3, 2014 post announcing his book ‘An Experimental Study on Adhesive or Anti-Adhesive, Bio-Inspired Experimental Nanomaterials‘ (co-authored with Emiliano Lepore).