On the heels of yesterday’s When the rocks sing “I got rhythm” (my December 18, 2023 posting), I received (via email) a media notice/reminder/update about a Northwestern University (Chicago, Illinois, US) app that allows you to listen,
As seismic activity intensifies ahead of an impending eruption of a fissure near Iceland’s Fagradalsfjall volcano, the island’s Reykjanes Peninsula is experiencing hundreds of earthquakes per day.
Now, listeners can follow along through Northwestern University’s Earthtunes app. Developed in 2019, the app transforms seismic frequencies into audible pitches. Whereas a classic seismometer records motions in the Earth’s surface as squiggly lines scratched across a page, Earthtunes enables users to hear, rather than see, activity.
So far, Iceland’s recent, ongoing seismic activity sounds like a jarring symphony of doors slamming, hail pelting against a tin roof or window and people cracking trays of ice cubes.
By listening to activities recorded by the Global Seismographic Network station (named BORG), located to the north-northeast of Reykjavik, people can hear how the seismic activity has changed around the Fagradalsfjall area.
In this audio clip, listeners can hear 24 hours of activity recorded from Friday, Nov. 10, into Saturday, Nov. 11. Peppered with a cacophony of sharp knocking noises, it sounds like someone is insistently banging on a door.
“The activity is formidable, exciting and scary,” said Northwestern seismologist Suzan van der Lee, who co-developed Earthtunes. “Iceland did the right thing by evacuating residents in nearby Grindavik and the nearby Svartsengi geothermal power plant, one of the world’s oldest geothermal power plants, which was the first to combine electricity generation with hot water for heating in the region.”
Van der Lee is the Sarah Rebecca Roland Professor of Earth and Planetary Sciences at Northwestern’s Weinberg College of Arts and Sciences. In her research, she applies data science to millions of records of seismic waves in order to decode seismic signals, which harbor valuable information about the Earth’s interior dynamics.
As hundreds of earthquakes shake the ground, Van der Lee says the impending eruption is reminiscent of the 1973 eruption of Heimaey on Iceland’s Vestmannaeyjar archipelago.
“This level of danger is unprecedented for this area of Iceland, but not for Iceland as a whole,” said van der Lee, who hiked Fagradalsfjall in June. “While most Icelandic volcanoes erupt away from towns and other infrastructure, Icelanders share the terrible memory of an eruption 50 years ago on the island Vestmannaeyjar, during which lava covered part of that island’s town, Heimaey. The residents felt very vulnerable, as the evacuated people of Grindavik feel now. In a few days or weeks, they might no longer have their jobs, homes and most possessions, while still having to feed their families and pay their mortgages. However, partially resulting from that eruption on Vestmannaeyjar, Icelanders are well prepared for the current situation in the Fagradallsfjall-Svartsengi-Grindavik area.”
Accelerated audio
This audio clip presents the same data, with the pitch increased by 10 octaves. Listeners will hear a long, low rumbling sound, punctuated by an occasional slamming door.
“What you’re hearing is 24 hours of seismic data — filled with earthquake signals,” van der Lee said. “The vast majority of these quakes are associated with the magma intrusion into the crust of the Fagradallsfjall-Svartsengi-Grindavik area of the Reykjanes Peninsula. Seismic data are not audible; their frequencies are too low. So, the 24 hours of data are compressed into approximately 1.5 minutes of audio data. You can hear an unprecedented intensity of earthquakes during the night from last Friday into Saturday and related to a new magma intrusion into the crust area.”
In a third audio clip, the same data is less compressed, with the pitch increased by just seven octaves
“One can hear frequent earthquakes happening at this point,” van der Lee said. “Icelandic seismologists have been monitoring these quakes and their increasing vigor and changing patterns. They recognized similar patterns to earthquake swarms that preceded the 2021-2023 eruptions of the adjacent Fagradallsfjall volcano.”
Earthtunes is supported by the American Geophysical Union and Northwestern’s department of Earth and planetary sciences. Seismic data is obtained from the Earthscope Consortium. The app was designed and developed by van der Lee, Helio Tejedor, Melanie Marzen, Igor Eufrasio, Josephine Anderson, Liam Toney, Cooper Barth, Michael Ji and Leonicio Cabrera.
Jennifer Ouellette’s November 16, 2023 article for Ars Tecnica draws heavily from the news release while delving into the topic of data sonification (making sounds from data), Note: Links have been removed,
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Sonification of scientific data is an area of growing interest in many different fields. For instance, several years ago, a project called LHCSound built a library of the “sounds” of a top quark jet and the Higgs boson, among others. The project hoped to develop sonification as a technique for analyzing the data from particle collisions so that physicists could “detect” subatomic particles by ear. Other scientists have mapped the molecular structure of proteins in spider silk threads onto musical theory to produce the “sound” of silk in hopes of establishing a radical new way to create designer proteins. And there’s a free app for Android called the Amino Acid Synthesizer that enables users to create their own protein “compositions” from the sounds of amino acids.
One last thing, there are a number of postings about data sonification here; many but not all scientists and/or communication practitioners think to include audio files.
I stumbled across a very interesting US Defense Advanced Research Projects Agency (DARPA) project (from an August 30, 2021 posting on Northwestern University’s Rivnay Lab [a laboratory for organic bioelectronics] blog),
Our lab has received a cooperative agreement with DARPA to develop a wireless, fully implantable ‘living pharmacy’ device that could help regulate human sleep patterns. The project is through DARPA’s BTO (biotechnology office)’s Advanced Acclimation and Protection Tool for Environmental Readiness (ADAPTER) program, meant to address physical challenges of travel, such as jetlag and fatigue.
The device, called NTRAIN (Normalizing Timing of Rhythms Across Internal Networks of Circadian Clocks), would control the body’s circadian clock, reducing the time it takes for a person to recover from disrupted sleep/wake cycles by as much as half the usual time.
The project spans 5 institutions including Northwestern, Rice University, Carnegie Mellon, University of Minnesota, and Blackrock Neurotech.
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Prior to the Aug. 30, 2021 posting, Amanda Morris wrote a May 13, 2021 article for Northwestern NOW (university magazine), which provides more details about the project, Note: A link has been removed,
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The first phase of the highly interdisciplinary program will focus on developing the implant. The second phase, contingent on the first, will validate the device. If that milestone is met, then researchers will test the device in human trials, as part of the third phase. The full funding corresponds to $33 million over four-and-a-half years.
Nicknamed the “living pharmacy,” the device could be a powerful tool for military personnel, who frequently travel across multiple time zones, and shift workers including first responders, who vacillate between overnight and daytime shifts.
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Combining synthetic biology with bioelectronics, the team will engineer cells to produce the same peptides that the body makes to regulate sleep cycles, precisely adjusting timing and dose with bioelectronic controls. When the engineered cells are exposed to light, they will generate precisely dosed peptide therapies.
“This control system allows us to deliver a peptide of interest on demand, directly into the bloodstream,” said Northwestern’s Jonathan Rivnay, principal investigator of the project. “No need to carry drugs, no need to inject therapeutics and — depending on how long we can make the device last — no need to refill the device. It’s like an implantable pharmacy on a chip that never runs out.”
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Beyond controlling circadian rhythms, the researchers believe this technology could be modified to release other types of therapies with precise timing and dosing for potentially treating pain and disease. The DARPA program also will help researchers better understand sleep/wake cycles, in general.
“The experiments carried out in these studies will enable new insights into how internal circadian organization is maintained,” said Turek [Fred W. Turek], who co-leads the sleep team with Vitaterna [Martha Hotz Vitaterna]. “These insights will lead to new therapeutic approaches for sleep disorders as well as many other physiological and mental disorders, including those associated with aging where there is often a spontaneous breakdown in temporal organization.”
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For those who like to dig even deeper, Dieynaba Young’s June 17, 2021 article for Smithsonian Magazine (GetPocket.com link to article) provides greater context and greater satisfaction, Note: Links have been removed,
In 1926, Fritz Kahn completed Man as Industrial Palace, the preeminent lithograph in his five-volume publication The Life of Man. The illustration shows a human body bustling with tiny factory workers. They cheerily operate a brain filled with switchboards, circuits and manometers. Below their feet, an ingenious network of pipes, chutes and conveyer belts make up the blood circulatory system. The image epitomizes a central motif in Kahn’s oeuvre: the parallel between human physiology and manufacturing, or the human body as a marvel of engineering.
An apparatus in the embryonic stage of development at the time of this writing in June of 2021—the so-called “implantable living pharmacy”—could have easily originated in Kahn’s fervid imagination. The concept is being developed by the Defense Advanced Research Projects Agency (DARPA) in conjunction with several universities, notably Northwestern and Rice. Researchers envision a miniaturized factory, tucked inside a microchip, that will manufacture pharmaceuticals from inside the body. The drugs will then be delivered to precise targets at the command of a mobile application. …
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The implantable living pharmacy, which is still in the “proof of concept” stage of development, is actually envisioned as two separate devices—a microchip implant and an armband. The implant will contain a layer of living synthetic cells, along with a sensor that measures temperature, a short-range wireless transmitter and a photo detector. The cells are sourced from a human donor and reengineered to perform specific functions. They’ll be mass produced in the lab, and slathered onto a layer of tiny LED lights.
The microchip will be set with a unique identification number and encryption key, then implanted under the skin in an outpatient procedure. The chip will be controlled by a battery-powered hub attached to an armband. That hub will receive signals transmitted from a mobile app.
If a soldier wishes to reset their internal clock, they’ll simply grab their phone, log onto the app and enter their upcoming itinerary—say, a flight departing at 5:30 a.m. from Arlington, Virginia, and arriving 16 hours later at Fort Buckner in Okinawa, Japan. Using short-range wireless communications, the hub will receive the signal and activate the LED lights inside the chip. The lights will shine on the synthetic cells, stimulating them to generate two compounds that are naturally produced in the body. The compounds will be released directly into the bloodstream, heading towards targeted locations, such as a tiny, centrally-located structure in the brain called the suprachiasmatic nucleus (SCN) that serves as master pacemaker of the circadian rhythm. Whatever the target location, the flow of biomolecules will alter the natural clock. When the solider arrives in Okinawa, their body will be perfectly in tune with local time.
The synthetic cells will be kept isolated from the host’s immune system by a membrane constructed of novel biomaterials, allowing only nutrients and oxygen in and only the compounds out. Should anything go wrong, they would swallow a pill that would kill the cells inside the chip only, leaving the rest of their body unaffected.
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If you have the time, I recommend reading Young’s June 17, 2021 Smithsonian Magazine article (GetPocket.com link to article) in its entirety. Young goes on to discuss, hacking, malware, and ethical/societal issues and more.
Both of these news bits are concerned with light for one reason or another.
Rice University (Texas, US) and breaking fluorocarbon bonds
The secret to breaking fluorocarbon bonds is light according to a June 22, 2020 news item on Nanowerk,
Rice University engineers have created a light-powered catalyst that can break the strong chemical bonds in fluorocarbons, a group of synthetic materials that includes persistent environmental pollutants.
In a study published this month in Nature Catalysis, Rice nanophotonics pioneer Naomi Halas and collaborators at the University of California, Santa Barbara (UCSB) and Princeton University showed that tiny spheres of aluminum dotted with specks of palladium could break carbon-fluorine (C-F) bonds via a catalytic process known as hydrodefluorination in which a fluorine atom is replaced by an atom of hydrogen.
The strength and stability of C-F bonds are behind some of the 20th century’s most recognizable chemical brands, including Teflon, Freon and Scotchgard. But the strength of those bonds can be problematic when fluorocarbons get into the air, soil and water. Chlorofluorocarbons, or CFCs, for example, were banned by international treaty in the 1980s after they were found to be destroying Earth’s protective ozone layer, and other fluorocarbons were on the list of “forever chemicals” targeted by a 2001 treaty.
“The hardest part about remediating any of the fluorine-containing compounds is breaking the C-F bond; it requires a lot of energy,” said Halas, an engineer and chemist whose Laboratory for Nanophotonics (LANP) specializes in creating and studying nanoparticles that interact with light.
Over the past five years, Halas and colleagues have pioneered methods for making “antenna-reactor” catalysts that spur or speed up chemical reactions. While catalysts are widely used in industry, they are typically used in energy-intensive processes that require high temperature, high pressure or both. For example, a mesh of catalytic material is inserted into a high-pressure vessel at a chemical plant, and natural gas or another fossil fuel is burned to heat the gas or liquid that’s flowed through the mesh. LANP’s antenna-reactors dramatically improve energy efficiency by capturing light energy and inserting it directly at the point of the catalytic reaction.
In the Nature Catalysis study, the energy-capturing antenna is an aluminum particle smaller than a living cell, and the reactors are islands of palladium scattered across the aluminum surface. The energy-saving feature of antenna-reactor catalysts is perhaps best illustrated by another of Halas’ previous successes: solar steam. In 2012, her team showed its energy-harvesting particles could instantly vaporize water molecules near their surface, meaning Halas and colleagues could make steam without boiling water. To drive home the point, they showed they could make steam from ice-cold water.
The antenna-reactor catalyst design allows Halas’ team to mix and match metals that are best suited for capturing light and catalyzing reactions in a particular context. The work is part of the green chemistry movement toward cleaner, more efficient chemical processes, and LANP has previously demonstrated catalysts for producing ethylene and syngas and for splitting ammonia to produce hydrogen fuel.
Study lead author Hossein Robatjazi, a Beckman Postdoctoral Fellow at UCSB who earned his Ph.D. from Rice in 2019, conducted the bulk of the research during his graduate studies in Halas’ lab. He said the project also shows the importance of interdisciplinary collaboration.
“I finished the experiments last year, but our experimental results had some interesting features, changes to the reaction kinetics under illumination, that raised an important but interesting question: What role does light play to promote the C-F breaking chemistry?” he said.
The answers came after Robatjazi arrived for his postdoctoral experience at UCSB. He was tasked with developing a microkinetics model, and a combination of insights from the model and from theoretical calculations performed by collaborators at Princeton helped explain the puzzling results.
“With this model, we used the perspective from surface science in traditional catalysis to uniquely link the experimental results to changes to the reaction pathway and reactivity under the light,” he said.
The demonstration experiments on fluoromethane could be just the beginning for the C-F breaking catalyst.
“This general reaction may be useful for remediating many other types of fluorinated molecules,” Halas said.
Caption: An artist’s illustration of the light-activated antenna-reactor catalyst Rice University engineers designed to break carbon-fluorine bonds in fluorocarbons. The aluminum portion of the particle (white and pink) captures energy from light (green), activating islands of palladium catalysts (red). In the inset, fluoromethane molecules (top) comprised of one carbon atom (black), three hydrogen atoms (grey) and one fluorine atom (light blue) react with deuterium (yellow) molecules near the palladium surface (black), cleaving the carbon-fluorine bond to produce deuterium fluoride (right) and monodeuterated methane (bottom). Credit: H. Robatjazi/Rice University
Called “robotic soft matter by the Northwestern team,” the materials move without complex hardware, hydraulics or electricity. The researchers believe the lifelike materials could carry out many tasks, with potential applications in energy, environmental remediation and advanced medicine.
“We live in an era in which increasingly smarter devices are constantly being developed to help us manage our everyday lives,” said Northwestern’s Samuel I. Stupp, who led the experimental studies. “The next frontier is in the development of new science that will bring inert materials to life for our benefit — by designing them to acquire capabilities of living creatures.”
The research will be published on June 22 [2020] in the journal Nature Materials.
Stupp is the Board of Trustees Professor of Materials Science and Engineering, Chemistry, Medicine and Biomedical Engineering at Northwestern and director of the Simpson Querrey Institute He has appointments in the McCormick School of Engineering, Weinberg College of Arts and Sciences and Feinberg School of Medicine. George Schatz, the Charles E. and Emma H. Morrison Professor of Chemistry in Weinberg, led computer simulations of the materials’ lifelike behaviors. Postdoctoral fellow Chuang Li and graduate student Aysenur Iscen, from the Stupp and Schatz laboratories, respectively, are co-first authors of the paper.
Although the moving material seems miraculous, sophisticated science is at play. Its structure comprises nanoscale peptide assemblies that drain water molecules out of the material. An expert in materials chemistry, Stupp linked the peptide arrays to polymer networks designed to be chemically responsive to blue light.
When light hits the material, the network chemically shifts from hydrophilic (attracts water) to hydrophobic (resists water). As the material expels the water through its peptide “pipes,” it contracts — and comes to life. When the light is turned off, water re-enters the material, which expands as it reverts to a hydrophilic structure.
This is reminiscent of the reversible contraction of muscles, which inspired Stupp and his team to design the new materials.
“From biological systems, we learned that the magic of muscles is based on the connection between assemblies of small proteins and giant protein polymers that expand and contract,” Stupp said. “Muscles do this using a chemical fuel rather than light to generate mechanical energy.”
For Northwestern’s bio-inspired material, localized light can trigger directional motion. In other words, bending can occur in different directions, depending on where the light is located. And changing the direction of the light also can force the object to turn as it crawls on a surface.
Stupp and his team believe there are endless possible applications for this new family of materials. With the ability to be designed in different shapes, the materials could play a role in a variety of tasks, ranging from environmental clean-up to brain surgery.
“These materials could augment the function of soft robots needed to pick up fragile objects and then release them in a precise location,” he said. “In medicine, for example, soft materials with ‘living’ characteristics could bend or change shape to retrieve blood clots in the brain after a stroke. They also could swim to clean water supplies and sea water or even undertake healing tasks to repair defects in batteries, membranes and chemical reactors.”
Fascinating, eh? No batteries, no power source, just light to power movement. For the curious, here’s a link to and a citation for the paper,
Supramolecular–covalent hybrid polymers for light-activated mechanical actuation by Chuang Li, Aysenur Iscen, Hiroaki Sai, Kohei Sato, Nicholas A. Sather, Stacey M. Chin, Zaida Álvarez, Liam C. Palmer, George C. Schatz & Samuel I. Stupp. Nature Materials (2020) DOI: https://doi.org/10.1038/s41563-020-0707-7 Published: 22 June 2020
This* story actually started in 2018 with an August 1, 2018 Harvard University news release (h/t Aug. 1, 2018 news item on phys.org) by Leslie Brownell announcing molecular and synthetic biology educational kits that been tested in the classroom. (In 2019, a new kit was released but more about that later.)
As biologists have probed deeper into the molecular and genetic underpinnings of life, K-12 schools have struggled to provide a curriculum that reflects those advances. Hands-on learning is known to be more engaging and effective for teaching science to students, but even the most basic molecular and synthetic biology experiments require equipment far beyond an average classroom’s budget, and often involve the use of bacteria and other substances that can be difficult to manage outside a controlled lab setting.
Now, a collaboration between the Wyss Institute at Harvard University, MIT [Massachusetts Institute of Technology], and Northwestern University has developed BioBits, new educational biology kits that use freeze-dried cell-free (FD-CF) reactions to enable students to perform a range of simple, hands-on biological experiments. The BioBits kits introduce molecular and synthetic biology concepts without the need for specialized lab equipment, at a fraction of the cost of current standard experimental designs. The kits are described in two papers published in Science Advances [2018].
“The main motivation in developing these kits was to give students fun activities that allow them to actually see, smell, and touch the outcomes of the biological reactions they’re doing at the molecular level,” said Ally Huang, a co-first author on both papers who is an MIT graduate student in the lab of Wyss Founding Core Faculty member Jim Collins, Ph.D. “My hope is that they will inspire more kids to consider a career in STEM [science, technology, engineering, and math] and, more generally, give all students a basic understanding of how biology works, because they may one day have to make personal or policy decisions based on modern science.”
Synthetic and molecular biology frequently make use of the cellular machinery found in E. coli bacteria to produce a desired protein. But this system requires that the bacteria be kept alive and contained for an extended period of time, and involves several complicated preparation and processing steps. The FD-CF reactions pioneered in Collins’ lab for molecular manufacturing, when combined with innovations from the lab of Michael Jewett, Ph.D. at Northwestern University, offer a solution to this problem by removing bacteria from the equation altogether.
“You can think of it like opening the hood of a car and taking the engine out: we’ve taken the ‘engine’ that drives protein production out of a bacterial cell and given it the fuel it needs, including ribosomes and amino acids, to create proteins from DNA outside of the bacteria itself,” explained Jewett, who is the Charles Deering McCormick Professor of Teaching Excellence at Northwestern University’s McCormick School of Engineering and co-director of Northwestern’s Center for Synthetic Biology, and co-corresponding author of both papers. This collection of molecular machinery is then freeze-dried into pellets so that it becomes shelf-stable at room temperature. To initiate the transcription of DNA into RNA and the translation of that RNA into a protein, a student just needs to add the desired DNA and water to the freeze-dried pellets.
An expansion of the BioBits Bright kit, called BioBits Explorer, includes experiments that engage the senses of smell and touch and allow students to probe their environment using designer synthetic biosensors. In the first experiment, the FD-CF reaction pellets contain a gene that drives the conversion of isoamyl alcohol to isoamyl acetate, a compound that produces a strong banana odor. In the second experiment, the FD-CF reactions contain a gene coding for the enzyme sortase, which recognizes and links specific segments of proteins in a liquid solution together to form a squishy, semi-solid hydrogel, which the students can touch and manipulate. The third module uses another Wyss technology, the toehold switch sensor, to identify DNA extracted from a banana or a kiwi. The sensors are hairpin-shaped RNA molecules designed such that when they bind to a “trigger” RNA, they spring open and reveal a genetic sequence that produces a fluorescent protein. When fruit DNA is added to the sensor-containing FD-CF pellets, only the sensors that are designed to open in the presence of each fruit’s RNA will produce the fluorescent protein.
The researchers tested their BioBits kits in the Chicago Public School system, and demonstrated that students and teachers were able to perform the experiments in the kits with the same success as trained synthetic biology researchers. In addition to refining the kits’ design so that they can one day provide them to classrooms around the world, the authors hope to create an open-source online database where teachers and students can share their results and ideas for ways to modify the kits to explore different biological questions.
“Synthetic biology is going to be one of the defining technologies of the century, and yet it has been challenging to teach the fundamental concepts of the field in K-12 classrooms given that such efforts often require expensive, complicated equipment,” said Collins, who is a co-corresponding author of both papers and also the Termeer Professor of Medical Engineering & Science at MIT. “We show that it is possible to use freeze-dried, cell-free extracts along with freeze-dried synthetic biology components to conduct innovative educational experiments in classrooms and other low-resource settings. The BioBits kits enable us to expose young kids, older kids, and even adults to the wonders of synthetic biology and, as a result, are poised to transform science education and society.
“All scientists are passionate about what they do, and we are frustrated by the difficulty our educational system has had in inciting a similar level of passion in young people. This BioBits project demonstrates the kind of out-of-the-box thinking and refusal to accept the status quo that we value and cultivate at the Wyss Institute, and we all hope it will stimulate young people to be intrigued by science,” said Wyss Institute Founding Director Donald Ingber, M.D., Ph.D., who is also the Judah Folkman Professor of Vascular Biology at Harvard Medical School (HMS) and the Vascular Biology Program at Boston Children’s Hospital, as well as Professor of Bioengineering at Harvard’s John A. Paulson School of Engineering and Applied Sciences (SEAS). “It’s exciting to see this project move forward and become available to biology classrooms worldwide and, hopefully some of these students will pursue a path in science because of their experience.”
Additional authors of the papers include Peter Nguyen, Ph.D., Nina Donghia, and Tom Ferrante from the Wyss Institute; Melissa Takahashi, Ph.D. and Aaron Dy from MIT; Karen Hsu and Rachel Dubner from Northwestern University; Keith Pardee, Ph.D., Assistant Professor at the University of Toronto; and a number of teachers and students in the Chicago school system including: Mary Anderson, Ada Kanapskyte, Quinn Mucha, Jessica Packett, Palak Patel, Richa Patel, Deema Qaq, Tyler Zondor, Julie Burke, Tom Martinez, Ashlee Miller-Berry, Aparna Puppala, Kara Reichert, Miriam Schmid, Lance Brand, Lander Hill, Jemima Chellaswamy, Nuhie Faheem, Suzanne Fetherling, Elissa Gong, Eddie Marie Gonzales, Teresa Granito, Jenna Koritsaris, Binh Nguyen, Sujud Ottman, Christina Palffy, Angela Patel, Sheila Skweres, Adriane Slaton, and TaRhonda Woods.
This research was supported by the Army Research Office, the National Science Foundation, the Air Force Research Laboratory Center of Excellence Grant, The Defense Threat Reduction Agency Grant, the David and Lucile Packard Foundation, the Camille Dreyfus Teacher-Scholar Program, the Wyss Institute at Harvard University, the Paul G. Allen Frontiers Group, The Air Force Office of Scientific Research, and the Natural Sciences and Engineering Council of Canada. [emphases mine]
Well, that list of funding agencies is quite interesting. The US Army and Air Force but not the Navy? As for what the Natural Sciences and Engineering Council of Canada is doing on that list, I can only imagine why.
This is what they were doing in 2018,
Now for the latest update, a May 7, 2019 news item on phys.org announces the BioBits Kits have been expanded,
How can high school students learn about a technology as complex and abstract as CRISPR? It’s simple: just add water.
A Northwestern University-led team has developed BioBits, a suite of hands-on educational kits that enable students to perform a range of biological experiments by adding water and simple reagents to freeze-dried cell-free reactions. The kits link complex biological concepts to visual, fluorescent readouts, so students know—after a few hours and with a single glance—the results of their experiments.
After launching BioBits last summer, the researchers are now expanding the kit to include modules for CRISPR [clustered regularly interspaced short palindromic repeats] and antibiotic resistance. A small group of Chicago-area teachers and high school students just completed the first pilot study for these new modules, which include interactive experiments and supplementary materials exploring ethics and strategies.
“After we unveiled the first kits, we next wanted to tackle current topics that are important for society,” said Northwestern’s Michael Jewett, principal investigator of the study. “That led us to two areas: antibiotic resistance and gene editing.”
Called BioBits Health, the new kits and pilot study are detailed in a paper published today (May 7 [2019]) in the journal ACS Synthetic Biology.
Jewett is a professor of chemical and biological engineering in Northwestern’s McCormick School of Engineering and co-director of Northwestern’s Center for Synthetic Biology. Jessica Stark, a graduate student in Jewett’s laboratory, led the study.
Test in a tube
Instead of using live cells, the BioBits team removed the essential cellular machinery from inside the cells and freeze-dried them for shelf stability. Keeping cells alive and contained for an extended period of time involves several complicated, time-consuming preparation and processing steps as well as expensive equipment. Freeze-dried cell-free reactions bypass those complications and costs.
“These are essentially test-tube biological reactions,” said Stark, a National Science Foundation graduate research fellow. “We break the cells open and use their guts, which still contain all of the necessary biological machinery to carry out a reaction. We no longer need living cells to demonstrate biology.”
This method to harness biological systems without intact, living cells became possible over the last two decades thanks to multiple innovations, including many in cell-free synthetic biology by Jewett’s lab. Not only are these experiments doable in the classroom, they also only cost pennies compared to standard high-tech experimental designs.
“I’m hopeful that students get excited about engineering biology and want to learn more,” Jewett said.
Conquering CRISPR
One of the biggest scientific breakthroughs of the past decade, CRISPR (pronounced “crisper”) stands for Clustered Regularly Interspaced Short Palindromic Repeats. The powerful gene-editing technology uses enzymes to cut DNA in precise locations to turn off or edit targeted genes. It could be used to halt genetic diseases, develop new medicines, make food more nutritious and much more.
BioBits Health uses three components required for CRISPR: an enzyme called the Cas9 protein, a target DNA sequence encoding a fluorescent protein and an RNA molecule that targets the fluorescent protein gene. When students add all three components — and water — to the freeze-dried cell-free system, it creates a reaction that edits, or cuts, the DNA for the fluorescent protein. If the DNA is cut, the system does not glow. If the DNA is not cut, the fluorescent protein is made, and the system glows fluorescent.
“We have linked this abstract, really advanced biological concept to the presence or absence of a fluorescent protein,” Stark said. “It’s something students can see, something they can visually understand.”
The curriculum also includes activities that challenge students to consider the ethical questions and dilemmas surrounding the use of gene-editing technologies.
“There is a lot of excitement about being able to edit genomes with these technologies,” Jewett said. “BioBits Health calls attention to a lot of important questions — not only about how CRISPR technology works but about ethics that society should be thinking about. We hope that this promotes a conversation and dialogue about such technologies.”
Reducing resistance
Jewett and Stark are both troubled by a prediction that, by the year 2050, drug-resistant bacterial infections could outpace cancer as a leading cause of death. This motivated them to help educate the future generation of scientists about how antibiotic resistance emerges and inspire them to take actions that could help limit the emergence of resistant bacteria. In this module, students run two sets of reactions to produce a glowing fluorescent protein — one set with an antibiotic resistance gene and one set without. Students then add antibiotics. If the experiment glows, the fluorescent protein has been made, and the reaction has become resistant to antibiotics. If the experiment does not glow, then the antibiotic has worked.
“Because we’re using cell-free systems rather than organisms, we can demonstrate drug resistance in a way that doesn’t create drug-resistant bacteria,” Stark explained. “We can demonstrate these concepts without the risks.”
A supporting curriculum piece challenges students to brainstorm and research strategies for slowing the rate of emerging antibiotic resistant strains.
Part of something cool
After BioBits was launched in summer 2018, 330 schools from around the globe requested prototype kits for their science labs. The research team, which includes members from Northwestern and MIT, has received encouraging feedback from teachers, students and parents.
“The students felt like scientists and doctors by touching and using the laboratory materials provided during the demo,” one teacher said. “Even the students who didn’t seem engaged were secretly paying attention and wanted to take their turn pipetting. They knew they were part of something really cool, so we were able to connect with them in a way that was new to them.”
“My favorite part was using the equipment,” a student said. “It was a fun activity that immerses you into what top scientists are currently doing.”
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The study, “BioBits Health: Classroom activities exploring engineering, biology and human health with fluorescent readouts,” was supported by the Army Research Office (award number W911NF-16-1-0372), the National Science Foundation (grant numbers MCB-1413563 and MCB-1716766), the Air Force Research Laboratory Center of Excellence (grant number FA8650-15-2-5518), the Defense Threat Reduction Agency (grant number HDTRA1-15-10052/P00001), the Department of Energy (grant number DE-SC0018249), the Human Frontiers Science Program (grant number RGP0015/2017), the David and Lucile Packard Foundation, the Office of Energy Efficiency and Renewable Energy (grant number DE-EE008343) and the Camille Dreyfus Teacher-Scholar Program. [emphases mine]
This is an image you’ll find in the abstract for the 2019 paper,
[downloaded from https://pubs.acs.org/doi/10.1021/acssynbio.8b00381]
Here are links and citations for the 2018 papers and the 2019 paper,
BioBits™ Explorer: A modular synthetic biology education kit by Ally Huang, Peter Q. Nguyen, Jessica C. Stark, Melissa K. Takahashi, Nina Donghia, Tom Ferrante, Aaron J. Dy, Karen J. Hsu, Rachel S. Dubner, Keith Pardee, Michael C. Jewett, and James J. Collins. Science Advances 01 Aug 2018: Vol. 4, no. 8, eaat5105 DOI: 10.1126/sciadv.aat5105
BioBits™ Bright: A fluorescent synthetic biology education kit by Jessica C. Stark, Ally Huang, Peter Q. Nguyen, Rachel S. Dubner, Karen J. Hsu, Thomas C. Ferrante, Mary Anderson, Ada Kanapskyte, Quinn Mucha, Jessica S. Packett, Palak Patel, Richa Patel, Deema Qaq, Tyler Zondor, Julie Burke, Thomas Martinez, Ashlee Miller-Berry, Aparna Puppala, Kara Reichert, Miriam Schmid, Lance Brand, Lander R. Hill, Jemima F. Chellaswamy, Nuhie Faheem, Suzanne Fetherling, Elissa Gong, Eddie Marie Gonzalzles, Teresa Granito, Jenna Koritsaris, Binh Nguyen, Sujud Ottman, Christina Palffy, Angela Patel, Sheila Skweres, Adriane Slaton, TaRhonda Woods, Nina Donghia, Keith Pardee, James J. Collins, and Michael C. Jewett. Science Advances 01 Aug 2018: Vol. 4, no. 8, eaat5107 DOI: 10.1126/sciadv.aat5107
BioBits Health: Classroom Activities Exploring Engineering, Biology, and Human Health with Fluorescent Readouts by Jessica C. Stark, Ally Huang, Karen J. Hsu, Rachel S. Dubner, Jason Forbrook, Suzanne Marshalla, Faith Rodriguez, Mechelle Washington, Grant A. Rybnicky, Peter Q. Nguyen, Brenna Hasselbacher, Ramah Jabri, Rijha Kamran, Veronica Koralewski, Will Wightkin, Thomas Martinez, and Michael C. Jewett. ACS Synth. Biol., Article ASAP DOI: 10.1021/acssynbio.8b00381 Publication Date (Web): March 29, 2019
Both of the 2018 papers appear to be open access while the 2019 paper is behind a paywall.
Should you be interested in acquiring a BioBits kit, you can check out the BioBits website. As for ‘conguering’ CRISPR, do we really need to look at it that way? Maybe a more humble appraoch could work just as well or even better, eh?
Caption: Novel nanolaser leverages the same color-changing mechanism that a chameleon uses to camouflage its skin. Credit: Egor Kamelev Courtesy: Northwestern University
I wish there was some detail included about how those colo(u)rs were achieved in that photograph. Strangely, Northwestern University (Chicago, Illinois, US) is more interested in describing the technology that chameleons have inspired. A June 20, 2018 news item on ScienceDaily announces the research,
As a chameleon shifts its color from turquoise to pink to orange to green, nature’s design principles are at play. Complex nano-mechanics are quietly and effortlessly working to camouflage the lizard’s skin to match its environment.
Inspired by nature, a Northwestern University team has developed a novel nanolaser that changes colors using the same mechanism as chameleons. The work could open the door for advances in flexible optical displays in smartphones and televisions, wearable photonic devices and ultra-sensitive sensors that measure strain.
“Chameleons can easily change their colors by controlling the spacing among the nanocrystals on their skin, which determines the color we observe,” said Teri W. Odom, Charles E. and Emma H. Morrison Professor of Chemistry in Northwestern’s Weinberg College of Arts and Sciences. “This coloring based on surface structure is chemically stable and robust.”
The same way a chameleon controls the spacing of nanocrystals on its skin, the Northwestern team’s laser exploits periodic arrays of metal nanoparticles on a stretchable, polymer matrix. As the matrix either stretches to pull the nanoparticles farther apart or contracts to push them closer together, the wavelength emitted from the laser changes wavelength, which also changes its color.
“Hence, by stretching and releasing the elastomer substrate, we could select the emission color at will,” Odom said.
The resulting laser is robust, tunable, reversible and has a high sensitivity to strain. These properties are critical for applications in responsive optical displays, on-chip photonic circuits and multiplexed optical communication.
Here’s a link to and a citation for the paper,
Stretchable Nanolasing from Hybrid Quadrupole Plasmons by Danqing Wang, Marc R. Bourgeois, Won-Kyu Lee, Ran Li, Dhara Trivedi, Michael P. Knudson, Weijia Wang, George C. Schatz, and Teri W. Odom. Nano Lett., Article ASAP DOI: 10.1021/acs.nanolett.8b01774 Publication Date (Web): June 18, 2018
