Category Archives: Uncategorized

Entanglement-based quantum network courtesy of Dutch researchers

Belated congratulations to the researchers at the Delft University of Technology! Very exciting news as an April 15, 2021 news item on ScienceDaily makes clear,

A team of researchers from QuTech in the Netherlands reports realization of the first multi-node quantum network, connecting three quantum processors. In addition, they achieved a proof-of-principle demonstration of key quantum network protocols. Their findings mark an important milestone towards the future quantum internet and have now been published in Science.

An April 15, 2021 Delft University of Technology (TU Delft) press release (also on EurekAlert), which originated the news item, describes the breakthrough in more detail, Note: QuTech is the research center for Quantum Computing and Quantum Internet, a collaboration between TU Delft and TNO is Nederlandse Organisatie voor Toegepast Natuurwetenschappelijk Onderzoek (English: Netherlands Organisation for Applied Scientific Research), an independent research organization),

The quantum internet

The power of the Internet is that it allows any two computers on Earth to be connected with each other, enabling applications undreamt of at the time of its creation decades ago. Today, researchers in many labs around the world are working towards first versions of a quantum internet – a network that can connect any two quantum devices, such as quantum computers or sensors, over large distances. Whereas today’s Internet distributes information in bits (that can be either 0 or 1), a future quantum internet will make use of quantum bits that can be 0 and 1 at the same time. ‘A quantum internet will open up a range of novel applications, from unhackable communication and cloud computing with complete user privacy to high-precision time-keeping,’ says Matteo Pompili, PhD student and a member of the research team. ‘And like with the Internet 40 years ago, there are probably many applications we cannot foresee right now.’

Towards ubiquitous connectivity

The first steps towards a quantum internet were taken in the past decade by linking two quantum devices that shared a direct physical link. However, being able to pass on quantum information through intermediate nodes (analogous to routers in the classical internet) is essential for creating a scalable quantum network. In addition, many promising quantum internet applications rely on entangled quantum bits, to be distributed between multiple nodes. Entanglement is a phenomenon observed at the quantum scale, fundamentally connecting particles at small and even at large distances. It provides quantum computers their enormous computational power and it is the fundamental resource for sharing quantum information over the future quantum internet. By realizing their quantum network in the lab, a team of researchers at QuTech – a collaboration between Delft University of Technology and TNO – is the first to have connected two quantum processors through an intermediate node and to have established shared entanglement between multiple stand-alone quantum processors.

Operating the quantum network

The rudimentary quantum network consists of three quantum nodes, at some distance within the same building. To make these nodes operate as a true network, the researchers had to invent a novel architecture that enables scaling beyond a single link. The middle node (called Bob) has a physical connection to both outer nodes (called Alice and Charlie), allowing entanglement links with each of these nodes to be established. Bob is equipped with an additional quantum bit that can be used as memory, allowing a previously generated quantum link to be stored while a new link is being established. After establishing the quantum links Alice-Bob and Bob-Charlie, a set of quantum operations at Bob converts these links into a quantum link Alice-Charlie. Alternatively, by performing a different set of quantum operations at Bob, entanglement between all three nodes is established.

Ready for subsequent use

An important feature of the network is that it announces the successful completion of these (intrinsically probabilistic) protocols with a “flag” signal. Such heralding is crucial for scalability, as in a future quantum internet many of such protocols will need to be concatenated. ‘Once established, we were able to preserve the resulting entangled states, protecting them from noise,’ says Sophie Hermans, another member of the team. ‘It means that, in principle, we can use these states for quantum key distribution, a quantum computation or any other subsequent quantum protocol.’

Quantum Internet Demonstrator

This first entanglement-based quantum network provides the researchers with a unique testbed for developing and testing quantum internet hardware, software and protocols. ‘The future quantum internet will consist of countless quantum devices and intermediate nodes,’ says Ronald Hanson, who led the research team. ‘Colleagues at QuTech are already looking into future compatibility with existing data infrastructures.’ In due time, the current proof-of-principle approach will be tested outside the lab on existing telecom fibre – on QuTech’s Quantum Internet Demonstrator, of which the first metropolitan link is scheduled to be completed in 2022.

Higher-level layers

In the lab, the researchers will focus on adding more quantum bits to their three-node network and on adding higher level software and hardware layers. Pompili: ‘Once all the high-level control and interface layers for running the network have been developed, anybody will be able to write and run a network application without needing to understand how lasers and cryostats work. That is the end goal.’

This news has likely lit some competitive fires in the research community. I think this is the first time I’ve featured news about the quantum internet since 2016 when, as it turns out, it was research from the University of Calgary that piqued my interest. See Teleporting photons in Calgary (Canada) is a step towards a quantum internet (a September 21, 2016 posting).

Here’s a link to and a citation for this latest work

Realization of a multinode quantum network of remote solid-state qubits by M. Pompili, S. L. N. Hermans, S. Baier, H. K. C. Beukers, P. C. Humphreys, R. N. Schouten, R. F. L. Vermeulen, M. J. Tiggelman, L. dos Santos Martins, B. Dirkse, S. Wehner, R. Hanson. Science 16 Apr 2021: Vol. 372, Issue 6539, pp. 259-264 DOI: 10.1126/science.abg1919

This paper is behind a paywall.

There is a video which introduces the concept of a quantum internet,

Beginner’s guide to folding DNA origami

I think this Aug. 6, 2010 post, Folding, origami, and shapeshifting and an article with over 50,000 authors is the first time I wrote about DNA (deoxyribonucleic acid) and origami (the Japanese art of paper folding).

Since then, the technique has become even more popular with the result that the US National Institute of Standards and Technology (NIST) has produced a beginner’s guide, according to a Jan. 8, 2021 news item on Nanowerk,

In a technique known as DNA origami, researchers fold long strands of DNA over and over again to construct a variety of tiny 3D structures, including miniature biosensors and drug-delivery containers. Pioneered at the California Institute of Technology in 2006, DNA origami has attracted hundreds of new researchers over the past decade, eager to build receptacles and sensors that could detect and treat disease in the human body, assess the environmental impact of pollutants, and assist in a host of other biological applications.

Although the principles of DNA origami are straightforward, the technique’s tools and methods for designing new structures are not always easy to grasp and have not been well documented. In addition, scientists new to the method have had no single reference they could turn to for the most efficient way of building DNA structures and how to avoid pitfalls that could waste months or even years of research.

That’s why Jacob Majikes and Alex Liddle, researchers at the National Institute of Standards and Technology (NIST) who have studied DNA origami for years, have compiled the first detailed tutorial on the technique. Their comprehensive report provides a step-by-step guide to designing DNA origami nanostructures, using state-of-the-art tools.

Here’s an image illustrating some of the techniques for DNA origami,

Caption: Collage shows some of the techniques and designs employed in DNA origami. Credit: K. Dill/NIST

A Jan. 8, 2021 US NIST news release (also on EurekAlert), which originated the news item, provide more detail as to the authors’ motivations, objectives, and future plans for their beginner’s guide,

“We wanted to take all the tools that people have developed and put them all in one place, and to explain things that you can’t say in a traditional journal article,” said Majikes. “Review papers might tell you everything that everyone’s done, but they don’t tell you how the people did it. “

DNA origami relies on the ability of complementary base pairs of the DNA molecule to bind to each other. Among DNA’s four bases — adenine (A), cytosine (C), guanine (G) and thymine (T) — A binds with T and G with C. This means that a specific sequence of As, Ts, Cs and Gs will find and bind to its complement.

The binding enables short strands of DNA to act as “staples,” keeping sections of long strands folded or joining separate strands. A typical origami design may require 250 staples. In this way, the DNA can self-assemble into a variety of shapes, forming a nanoscale framework to which an assortment of nanoparticles — many useful in medical treatment, biological research and environmental monitoring — can attach.

The challenges in using DNA origami are twofold, said Majikes. First, researchers are fabricating 3D structures using a foreign language — the base pairs A, G, T and C. In addition, they’re using those base-pair staples to twist and untwist the familiar double helix of DNA molecules so that the strands bend into specific shapes. That can be difficult to design and visualize. Majikes and Liddle urge researchers to strengthen their design intuition by building 3D mock-ups, such as sculptures made with bar magnets, before they start fabrication. These models, which can reveal which aspects of the folding process are critical and which ones are less important, should then be “flattened” into 2D to be compatible with computer-aided design tools for DNA origami, which typically use two-dimensional representations.

DNA folding can be accomplished in a variety of ways, some less efficient than others, noted Majikes. Some strategies, in fact, may be doomed to failure.

“Pointing out things like ‘You could do this, but it’s not a good idea’ — that type of perspective isn’t in a traditional journal article, but because NIST is focused on driving the state of technology in the nation, we’re able to publish this work in the NIST journal,” Majikes said. “I don’t think there’s anywhere else that would have given us the leeway and the time and the person hours to put all this together.”

Liddle and Majikes plan to follow up their work with several additional manuscripts detailing how to successfully fabricate nanoscale devices with DNA.

Here’s a link to and a citation for the beginner’s guide,

DNA Origami Design: A How-To Tutorial by Majikes, Jacob M. and Liddle, J. Alexander. Journal of Research of the National Institute of Standards and Technology Volume 126, Article No. 126001 (2021) Published online Jan. 8, 2021. DOI: 10.6028/jres.126.001

This is open access and it include such gems as this,

1.2 Education or Skill Level

Readers of this tutorial should be familiar with the physical properties of B-DNA, single-stranded DNA (ssDNA), and crossover junctions. In addition, once ready to create a structure for a specific application, the designer should determine the full list of functional requirements. This list includes answers to the following questions: What should the structure do? What specific properties are critical to the system’s performance?

1.3 Prerequisites

The designer should have either sufficient paper for manual design (not recommended) or a design program such as cadnano [1] (all versions sufficient), nanoengineer®, ParaboninSēquio®, or equivalent.1 A registered account with three-dimensional (3D) structure prediction servers such as CanDo [2, 3] is also recommended.

1.4Tools or Equipment

Equipment includes desktop or laptop computer equipment, craft supplies for macroscale models, and DNA nanotechnology computer-aided design (CAD) software.

Feel free to go forth and fold!

Merry Christmas/Joyeux Noël with/avec glass frogs, ghost shrimp, and more

Christmas Eve 2020: There haven’t been enough frog stories here this year and this December 21, 2020 essay by James B. Barnett, postdoctoral fellow inbBehavioural ecology at McMaster University (Ontario, Canada), for The Conversation helps fill that void,

Transparency may seem like the simplest form of camouflage, but in the last year, research has revealed new complexities behind what some animals do to vanish into their surroundings.

In my research, I have experienced first-hand how effective and sophisticated transparency really can be. That story begins on a dark night in the pouring rain in the thick of French Guiana’s tropical rainforest.

.. we had been searching for: a tiny glass frog (Teratohyla midas), only a couple of centimetres long. These bizarre frogs have transparent skin that lets us look directly at their intestines and bones — even at their beating hearts.

Here’s an image of a glass frog, from an October 11, 2011 posting by Lindsay on the amphibianrescue.org blog,

Glass frogs have such transparent skin that you can see their organs. (Photo by Mehgan Murphy, Smithsonian’s National Zoo)

Barnett’s December 21, 2020 essay explains why animals might find transparency a useful survival mechanism,

Glass frogs are an amazing sight but seeing one raises an interesting question: what’s the point of having transparent skin if your predators can still see you, or your internal organs?

… as light moves between transparent materials it can be bent and scattered. Think about how a straw in a glass of water appears to bend. This is refraction, and results from the different ways that light moves through air and water.

An animal’s body is made up of many organs and tissues, each with a different thickness, structure and chemical makeup. For the animal to be transparent, light must not be reflected, absorbed, scattered or refracted as it travels through each of these different layers.

On land, transparency is much rarer, but we are now learning that it can be very effective, sometimes in unexpected ways.

… [glass frogs’] transparency provides yet another form of camouflage. Unlike butterflies and moths with their transparent wings, these frogs have all of their internal organs on show, preventing true transparency. Instead, by combining their transparent underside with a green topside, the frogs become translucent: allowing some light through but not showing a clear image.

Their green colouring is a close match to that of a generic leaf, and the trick of translucency allows the frog to brighten or darken in keeping with the leaves around it. What’s more, the frogs’ legs are more translucent than their bodies, providing an extra advantage from a process called “edge diffusion,” further blending frog and leaf together in the eyes of its predators.

This is an interesting essay illustrated with images of ‘transparent’ species, including a ghost shrimp.

I have one hesitation, the banner image for Barnett’s essay features what’s identified as a glasswing butterfly but Barnett references clearwing butterflies in his text. I did a brief search to see if the names are interchangeable and the answer is often but not on Wikipedia.

The search ‘clearwing butterfiles’ will lead you to this Wikipedia entry on Cressida cressida, the clearwing swallowtail butterfly or big greasy, which is found in northern Australia, New Guinea, Maluku, and Timor,

Dorsal perspective of mounted Cressida cressida cressida male (above) and female (below). Date 24 July 2015, 16:44:45 Source Own work Author JKDw Courtesy: Wikipedia

Here’s the glasswing butterfly (Greta oto),

The clear wings make this South-American butterfly hard to see in flight, a successfull defense mechanism. Credit: Eddy Van 3000 from in Flanders fields – B – United Tribes ov Europe – the wings-become-windows butterfly. [downloaded from https://commons.wikimedia.org/wiki/Category:Greta_oto#/media/File:South-American_butterfly.jpg] First featured here in my Nov. 14, 2019 posting

You can find the Greta Oto Wikipedia entry here. The butterfly is found mainly in Central America and the northern region of South America.

To sum up, I think the term ‘clearwing’ is used to describe a lot of butterflies that have transparent or translucent wing qualities, as well as to a specific butterfly and ‘glasswing; is used only for the Greta oto. (If anyone knows more, please feel free to let me know with a blog comment.)

Just after I stumbled across Barnett’s essay, I came across some research involving transparent worms. I’ve included a link to the research but do note that this is not about their ‘transparent’ quality but about how scientists have used different types of light to observe various metabolic processes. Here’s the December 22, 2020 Rice University news release on EurekAlert.

Finally,Joyeux Noël!

Adisokan: Winter Solstice 2020 and storytelling; a December 2020 event

Ingenium (Canada’s Museums of Science and Innovation) is hosting the second in a series of Indigenous Star Knowledge Symposia. (There’s a more comprehensive description of the series in my Sept. 18, 2020 posting, which also features the Fall Equinox event (the first in the series) and information about a traveling exhibit. )

Adisokan: Winter Solstice, Stars and Storytelling will be held on December 21, 2020 (from the event page),

December 21, 2020 from 3 p.m. to 5 p.m. EST

Adisokan is the Algonquin word for storytelling with special cultural meaning. Join us for stories about the stars from three Indigenous nations – Mapuche (Chile), Algonquin  (Quebec), and Dene (Northwest Territories). Indigenous teachings, spirit, language, world views and an exploration of the word and role of stories in Indigenous culture. 

Anita Tenasco, Kitigan Zibi, Quebec (Algonquin)

Joan Tenasco, Kitigan Zibi, Quebec (Algonquin)

Chris Canon, University of Alaska (with Dene partners in the NWT)

Yasmin Catricheo, Chile (Mapuche)

Moderated by Wilfred Buck, Ininew, Manitoba

Anita Tenasco is an Anishinabeg from Kitigan Zibi. She has a Bachelor’s degree in history and teaching from the University of Ottawa, as well as a First Nations leadership certificate from Saint Paul’s University, in Ottawa. She has also taken courses in public administration at ENAP (The University of Public Administration). In Kitigan Zibi, she has held various positions in the field of education and, since 2005, is director of education in her community.

Anita was an active participant in the Honouring Our Ancestors project, in which the Anishinabeg Nation of Kitigan Zibi, under Gilbert Whiteduck’s direction, was successful in the restitution of the remains of ancestors conserved at the Canadian Museum of History, in Gatineau. Anita also participated in the organizing of a conference on repatriation, in Kitigan Zibi, in 2005. She plays an important role in this research project.

http://nikanishk.ca/en/blog/project-participants/anita-tenasco-2/

Chris Cannon is a Ph.D. student in cultural anthropology at the University of Alaska Fairbanks. His research interests are in Northern Dene (Athabaskan) language and culture with a particular emphasis on astronomical knowledge within and across Dene ethnolinguistic groups. He enjoys traveling the land with traditional knowledge bearers and has collaborated on several projects to transform his research into other materials and deliverables that are of greater use to Dene communities and the general public, including a poster-sized Gwich’in star chart (in press).

Arctic Research Consortium of the United States 

Yasmin Catricheo is the STEM Education Scholar at AUI’s Office of Education and Public Engagement. She is a physics educator from Chile, and of Mapuche origin. Yasmin is passionate about the teaching of science and more recently has focused in the area of astronomy and STEM. In her professional training she has taken a range of courses in science and science education, and researched the benefits of scientific argumentation in the physics classroom, earning a master’s degree in education from the University of Bío-Bío. Yasmín is also a member of the indigenous group “Mapu Trafun”, and she works closely with the Mapuche community to recover the culture and communicate the message of the Mapuche Worldview. In 2018 Yasmín was selected as the Chilean representative for Astronomy in Chile Educator Ambassador Program (ACEAP) founded by NSF.

Associated Universities Inc.

Wilfred Buck is a member of the Opaskwayak Cree Nation. He obtained his B.Ed. & Post Bacc. from the University of Manitoba.

As an educator Wilfred has had the opportunity and good fortune to travel to South and Central America as well as Europe and met, shared and listened to Indigenous people from all over the world.

He is a husband, father of four, son, uncle, brother, nephew, story-teller, mad scientist, teacher, singer, pipe-carrier, sweat lodge keeper, old person and sun dance leader.
Researching Ininew star stories Wilfred found a host of information which had to be interpreted and analyzed to identify if the stories were referring to the stars. The journey began… The easiest way to go about doing this, he was told, was to look up. 

“The greatest teaching that was ever given to me, other than my wife and children, is the ability to see the humor in the world”…Wilfred Buck

https://acakwuskwun.com/

The registration page is here.

Of puke, CRISPR, fruit flies, and monarch butterflies

I’ve never seen an educational institution use a somewhat vulgar slang term such as ‘puke’ before. Especially not in a news release. You’ll find that elsewhere online ‘puke’ has been replaced, in the headline, with the more socially acceptable ‘vomit’.

Since I wanted to catch this historic moment amid concerns that the original version of the news release will disappear, I’m including the entire news release as i saw it on EurekAlert.com (from an October 2, 2019 University of California at Berkeley news release),

News Release 2-Oct-2019

CRISPRed fruit flies mimic monarch butterfly — and could make you puke
Scientists recreate in flies the mutations that let monarch butterfly eat toxic milkweed with impunity

University of California – Berkeley

The fruit flies in Noah Whiteman’s lab may be hazardous to your health.

Whiteman and his University of California, Berkeley, colleagues have turned perfectly palatable fruit flies — palatable, at least, to frogs and birds — into potentially poisonous prey that may cause anything that eats them to puke. In large enough quantities, the flies likely would make a human puke, too, much like the emetic effect of ipecac syrup.

That’s because the team genetically engineered the flies, using CRISPR-Cas9 gene editing, to be able to eat milkweed without dying and to sequester its toxins, just as America’s most beloved butterfly, the monarch, does to deter predators.

This is the first time anyone has recreated in a multicellular organism a set of evolutionary mutations leading to a totally new adaptation to the environment — in this case, a new diet and new way of deterring predators.

Like monarch caterpillars, the CRISPRed fruit fly maggots thrive on milkweed, which contains toxins that kill most other animals, humans included. The maggots store the toxins in their bodies and retain them through metamorphosis, after they turn into adult flies, which means the adult “monarch flies” could also make animals upchuck.

The team achieved this feat by making three CRISPR edits in a single gene: modifications identical to the genetic mutations that allow monarch butterflies to dine on milkweed and sequester its poison. These mutations in the monarch have allowed it to eat common poisonous plants other insects could not and are key to the butterfly’s thriving presence throughout North and Central America.

Flies with the triple genetic mutation proved to be 1,000 times less sensitive to milkweed toxin than the wild fruit fly, Drosophila melanogaster.

Whiteman and his colleagues will describe their experiment in the Oct. 2 [2019] issue of the journal Nature.

Monarch flies

The UC Berkeley researchers created these monarch flies to establish, beyond a shadow of a doubt, which genetic changes in the genome of monarch butterflies were necessary to allow them to eat milkweed with impunity. They found, surprisingly, that only three single-nucleotide substitutions in one gene are sufficient to give fruit flies the same toxin resistance as monarchs.

“All we did was change three sites, and we made these superflies,” said Whiteman, an associate professor of integrative biology. “But to me, the most amazing thing is that we were able to test evolutionary hypotheses in a way that has never been possible outside of cell lines. It would have been difficult to discover this without having the ability to create mutations with CRISPR.”

Whiteman’s team also showed that 20 other insect groups able to eat milkweed and related toxic plants – including moths, beetles, wasps, flies, aphids, a weevil and a true bug, most of which sport the color orange to warn away predators – independently evolved mutations in one, two or three of the same amino acid positions to overcome, to varying degrees, the toxic effects of these plant poisons.

In fact, his team reconstructed the one, two or three mutations that led to each of the four butterfly and moth lineages, each mutation conferring some resistance to the toxin. All three mutations were necessary to make the monarch butterfly the king of milkweed.
Resistance to milkweed toxin comes at a cost, however. Monarch flies are not as quick to recover from upsets, such as being shaken — a test known as “bang” sensitivity.

“This shows there is a cost to mutations, in terms of recovery of the nervous system and probably other things we don’t know about,” Whiteman said. “But the benefit of being able to escape a predator is so high … if it’s death or toxins, toxins will win, even if there is a cost.”

Plant vs. insect

Whiteman is interested in the evolutionary battle between plants and parasites and was intrigued by the evolutionary adaptations that allowed the monarch to beat the milkweed’s toxic defense. He also wanted to know whether other insects that are resistant — though all less resistant than the monarch — use similar tricks to disable the toxin.

“Since plants and animals first invaded land 400 million years ago, this coevolutionary arms race is thought to have given rise to a lot of the plant and animal diversity that we see, because most animals are insects, and most insects are herbivorous: they eat plants,” he said.

Milkweeds and a variety of other plants, including foxglove, the source of digitoxin and digoxin, contain related toxins — called cardiac glycosides — that can kill an elephant and any creature with a beating heart. Foxglove’s effect on the heart is the reason that an extract of the plant, in the genus Digitalis, has been used for centuries to treat heart conditions, and why digoxin and digitoxin are used today to treat congestive heart failure.

These plants’ bitterness alone is enough to deter most animals, but a small minority of insects, including the monarch (Danaus plexippus) and its relative, the queen butterfly (Danaus gilippus), have learned to love milkweed and use it to repel predators.

Whiteman noted that the monarch is a tropical lineage that invaded North America after the last ice age, in part enabled by the three mutations that allowed it to eat a poisonous plant other animals could not, giving it a survival edge and a natural defense against predators.

“The monarch resists the toxin the best of all the insects, and it has the biggest population size of any of them; it’s all over the world,” he said.

The new paper reveals that the mutations had to occur in the right sequence, or else the flies would never have survived the three separate mutational events.

Thwarting the sodium pump

The poisons in these plants, most of them a type of cardenolide, interfere with the sodium/potassium pump (Na+/K+-ATPase) that most of the body’s cells use to move sodium ions out and potassium ions in. The pump creates an ion imbalance that the cell uses to its favor. Nerve cells, for example, transmit signals along their elongated cell bodies, or axons, by opening sodium and potassium gates in a wave that moves down the axon, allowing ions to flow in and out to equilibrate the imbalance. After the wave passes, the sodium pump re-establishes the ionic imbalance.

Digitoxin, from foxglove, and ouabain, the main toxin in milkweed, block the pump and prevent the cell from establishing the sodium/potassium gradient. This throws the ion concentration in the cell out of whack, causing all sorts of problems. In animals with hearts, like birds and humans, heart cells begin to beat so strongly that the heart fails; the result is death by cardiac arrest.

Scientists have known for decades how these toxins interact with the sodium pump: they bind the part of the pump protein that sticks out through the cell membrane, clogging the channel. They’ve even identified two specific amino acid changes or mutations in the protein pump that monarchs and the other insects evolved to prevent the toxin from binding.

But Whiteman and his colleagues weren’t satisfied with this just so explanation: that insects coincidentally developed the same two identical mutations in the sodium pump 14 separate times, end of story. With the advent of CRISPR-Cas9 gene editing in 2012, coinvented by UC Berkeley’s Jennifer Doudna, Whiteman and colleagues Anurag Agrawal of Cornell University and Susanne Dobler of the University of Hamburg in Germany applied to the Templeton Foundation for a grant to recreate these mutations in fruit flies and to see if they could make the flies immune to the toxic effects of cardenolides.

Seven years, many failed attempts and one new grant from the National Institutes of Health later, along with the dedicated CRISPR work of GenetiVision of Houston, Texas, they finally achieved their goal. In the process, they discovered a third critical, compensatory mutation in the sodium pump that had to occur before the last and most potent resistance mutation would stick. Without this compensatory mutation, the maggots died.

Their detective work required inserting single, double and triple mutations into the fruit fly’s own sodium pump gene, in various orders, to assess which ones were necessary. Insects having only one of the two known amino acid changes in the sodium pump gene were best at resisting the plant poisons, but they also had serious side effects — nervous system problems — consistent with the fact that sodium pump mutations in humans are often associated with seizures. However, the third, compensatory mutation somehow reduces the negative effects of the other two mutations.

“One substitution that evolved confers weak resistance, but it is always present and allows for substitutions that are going to confer the most resistance,” said postdoctoral fellow Marianna Karageorgi, a geneticist and evolutionary biologist. “This substitution in the insect unlocks the resistance substitutions, reducing the neurological costs of resistance. Because this trait has evolved so many times, we have also shown that this is not random.”

The fact that one compensatory mutation is required before insects with the most resistant mutation could survive placed a constraint on how insects could evolve toxin resistance, explaining why all 21 lineages converged on the same solution, Whiteman said. In other situations, such as where the protein involved is not so critical to survival, animals might find different solutions.

“This helps answer the question, ‘Why does convergence evolve sometimes, but not other times?'” Whiteman said. “Maybe the constraints vary. That’s a simple answer, but if you think about it, these three mutations turned a Drosophila protein into a monarch one, with respect to cardenolide resistance. That’s kind of remarkable.”

###

The research was funded by the Templeton Foundation and the National Institutes of Health. Co-authors with Whiteman and Agrawal are co-first authors Marianthi Karageorgi of UC Berkeley and Simon Groen, now at New York University; Fidan Sumbul and Felix Rico of Aix-Marseille Université in France; Julianne Pelaez, Kirsten Verster, Jessica Aguilar, Susan Bernstein, Teruyuki Matsunaga and Michael Astourian of UC Berkeley; Amy Hastings of Cornell; and Susanne Dobler of Universität Hamburg in Germany.

Robert Sanders’ Oct. 2, 2019′ news release for the University of California at Berkeley (it’s also been republished as an Oct. 2, 2019 news item on ScienceDaily) has had its headline changed to ‘vomit’ but you’ll find the more vulgar word remains in two locations of the second paragraph of the revised new release.

If you have time, go to the news release on the University of California at Berkeley website just to admire the images that have been embedded in the news release. Here’s one,

Caption: A Drosophila melanogaster “monarch fly” with mutations introduced by CRISPR-Cas9 genome editing (V111, S119 and H122) to the sodium potassium pump, on a wing of a monarch butterfly (Danaus plexippus). Credit & Ccpyright: Julianne Pelaez

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

Genome editing retraces the evolution of toxin resistance in the monarch butterfly by Marianthi Karageorgi, Simon C. Groen, Fidan Sumbul, Julianne N. Pelaez, Kirsten I. Verster, Jessica M. Aguilar, Amy P. Hastings, Susan L. Bernstein, Teruyuki Matsunaga, Michael Astourian, Geno Guerra, Felix Rico, Susanne Dobler, Anurag A. Agrawal & Noah K. Whiteman. Nature (2019) DOI: https://doi.org/10.1038/s41586-019-1610-8 Published 02 October 2019

This paper is behind a paywall.

Words about a word

I’m glad they changed the headline and substituted vomit for puke. I think we need vulgar and/or taboo words to release anger or disgust or other difficult emotions. Incorporating those words into standard language deprives them of that power.

The last word: Genetivision

The company mentioned in the new release, Genetivision, is the place to go for transgenic flies. Here’s a sampling from the their Testimonials webpage,

GenetiVision‘s service has been excellent in the quality and price. The timeliness of its international service has been a big plus. We are very happy with its consistent service and the flies it generates.”
Kwang-Wook Choi, Ph.D.
Department of Biological Sciences
Korea Advanced Institute of Science and Technology


“We couldn’t be happier with GenetiVision. Great prices on both standard P and PhiC31 transgenics, quick turnaround time, and we’re still batting 1000 with transformant success. We used to do our own injections but your service makes it both faster and more cost-effective. Thanks for your service!”
Thomas Neufeld, Ph.D.
Department of Genetics, Cell Biology and Development
University of Minnesota

You can find out more here at the Genetivision website.

Repairing brain circuits using nanotechnology

A July 30, 2019 news item on Nanowerk announces some neuroscience research (they used animal models) that could prove helpful with neurodegenerative diseases,

Working with mouse and human tissue, Johns Hopkins Medicine researchers report new evidence that a protein pumped out of some — but not all — populations of “helper” cells in the brain, called astrocytes, plays a specific role in directing the formation of connections among neurons needed for learning and forming new memories.

Using mice genetically engineered and bred with fewer such connections, the researchers conducted proof-of-concept experiments that show they could deliver corrective proteins via nanoparticles to replace the missing protein needed for “road repairs” on the defective neural highway.

Since such connective networks are lost or damaged by neurodegenerative diseases such as Alzheimer’s or certain types of intellectual disability, such as Norrie disease, the researchers say their findings advance efforts to regrow and repair the networks and potentially restore normal brain function.

A July 30, 2019 Johns Hopkins University School of Medicine news release (also on EurekAlert) provides more detail about the work (Note: A link has been removed),

“We are looking at the fundamental biology of how astrocytes function, but perhaps have discovered a new target for someday intervening in neurodegenerative diseases with novel therapeutics,” says Jeffrey Rothstein, M.D., Ph.D., the John W. Griffin Director of the Brain Science Institute and professor of neurology at the Johns Hopkins University School of Medicine.

“Although astrocytes appear to all look alike in the brain, we had an inkling that they might have specialized roles in the brain due to regional differences in the brain’s function and because of observed changes in certain diseases,” says Rothstein. “The hope is that learning to harness the individual differences in these distinct populations of astrocytes may allow us to direct brain development or even reverse the effects of certain brain conditions, and our current studies have advanced that hope.”

In the brain, astrocytes are the support cells that act as guides to direct new cells, promote chemical signaling, and clean up byproducts of brain cell metabolism.

Rothstein’s team focused on a particular astrocyte protein, glutamate transporter-1, which previous studies suggested was lost from astrocytes in certain parts of brains with neurodegenerative diseases. Like a biological vacuum cleaner, the protein normally sucks up the chemical “messenger” glutamate from the spaces between neurons after a message is sent to another cell, a step required to end the transmission and prevent toxic levels of glutamate from building up.

When these glutamate transporters disappear from certain parts of the brain — such as the motor cortex and spinal cord in people with amyotrophic lateral sclerosis (ALS) — glutamate hangs around much too long, sending messages that overexcite and kill the cells.

To figure out how the brain decides which cells need the glutamate transporters, Rothstein and colleagues focused on the region of DNA in front of the gene that typically controls the on-off switch needed to manufacture the protein. They genetically engineered mice to glow red in every cell where the gene is activated.

Normally, the glutamate transporter is turned on in all astrocytes. But, by using between 1,000- and 7,000-bit segments of DNA code from the on-off switch for glutamate, all the cells in the brain glowed red, including the neurons. It wasn’t until the researchers tried the largest sequence of an 8,300-bit DNA code from this location that the researchers began to see some selection in red cells. These red cells were all astrocytes but only in certain layers of the brain’s cortex in mice.

Because they could identify these “8.3 red astrocytes,” the researchers thought they might have a specific function different than other astrocytes in the brain. To find out more precisely what these 8.3 red astrocytes do in the brain, the researchers used a cell-sorting machine to separate the red astrocytes from the uncolored ones in mouse brain cortical tissue, and then identified which genes were turned on to much higher than usual levels in the red compared to the uncolored cell populations. The researchers found that the 8.3 red astrocytes turn on high levels of a gene that codes for a different protein known as Norrin.

Rothstein’s team took neurons from normal mouse brains, treated them with Norrin, and found that those neurons grew more of the “branches” — or extensions — used to transmit chemical messages among brain cells. Then, Rothstein says, the researchers looked at the brains of mice engineered to lack Norrin, and saw that these neurons had fewer branches than in healthy mice that made Norrin.

In another set of experiments, the research team took the DNA code for Norrin plus the 8,300 “location” DNA and assembled them into deliverable nanoparticles. When they injected the Norrin nanoparticles into the brains of mice engineered without Norrin, the neurons in these mice began to quickly grow many more branches, a process suggesting repair to neural networks. They repeated these experiments with human neurons too.

Rothstein notes that mutations in the Norrin protein that reduce levels of the protein in people cause Norrie disease — a rare, genetic disorder that can lead to blindness in infancy and intellectual disability. Because the researchers were able to grow new branches for communication, they believe it may one day be possible to use Norrin to treat some types of intellectual disabilities such as Norrie disease.

For their next steps, the researchers are investigating if Norrin can repair connections in the brains of animal models with neurodegenerative diseases, and in preparation for potential success, Miller [sic] and Rothstein have submitted a patent for Norrin.

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

Molecularly defined cortical astroglia subpopulation modulates neurons via secretion of Norrin by Sean J. Miller, Thomas Philips, Namho Kim, Raha Dastgheyb, Zhuoxun Chen, Yi-Chun Hsieh, J. Gavin Daigle, Malika Datta, Jeannie Chew, Svetlana Vidensky, Jacqueline T. Pham, Ethan G. Hughes, Michael B. Robinson, Rita Sattler, Raju Tomer, Jung Soo Suk, Dwight E. Bergles, Norman Haughey, Mikhail Pletnikov, Justin Hanes & Jeffrey D. Rothstein. Nature Neuroscience volume 22, pages741–752 (2019) DOI: https://doi.org/10.1038/s41593-019-0366-7 Published: 01 April 2019 Issue Date: May 2019

This paper is behind a paywall.

Printing metal on flowers or gelatin

Martin Thuo and his research group have developed heat-free technology that can print conductive, metallic lines and traces on just about anything, including a rose petal. Photo courtesy of Martin Thuo.

I’m not sure how I feel about an electrified rose but it is strangely fascinating. Here’s more from a July 29, 2019 news item on Nanowerk,

Martin Thuo of Iowa State University and the Ames Laboratory clicked through the photo gallery for one of his research projects.

How about this one? There was a rose with metal traces printed on a delicate petal.

Or this? A curled sheet of paper with a flexible, programmable LED display.

Maybe this? A gelatin cylinder with metal traces printed across the top.

Caption: Martin Thuo and his research group have printed electronic traces on gelatin. Credit: Martin Thuo/Iowa State University

A July 26, 2019 Iowa State University news release (also on EurekAlert but published on July 29, 2019), which originated the news item,

All those photos showed the latest application of undercooled metal technology developed by Thuo and his research group. The technology features liquid metal (in this case Field’s metal, an alloy of bismuth, indium and tin) trapped below its melting point in polished, oxide shells, creating particles about 10 millionths of a meter across.

When the shells are broken – with mechanical pressure or chemical dissolving – the metal inside flows and solidifies, creating a heat-free weld or, in this case, printing conductive, metallic lines and traces on all kinds of materials, everything from a concrete wall to a leaf.

That could have all kinds of applications, including sensors to measure the structural integrity of a building or the growth of crops. The technology was also tested in paper-based remote controls that read changes in electrical currents when the paper is curved. Engineers also tested the technology by making electrical contacts for solar cells and by screen printing conductive lines on gelatin, a model for soft biological tissues, including the brain.

“This work reports heat-free, ambient fabrication of metallic conductive interconnects and traces on all types of substrates,” Thuo and a team of researchers wrote in a paper describing the technology recently published online by the journal Advanced Functional Materials.

Thuo – an assistant professor of materials science and engineering at Iowa State, an associate of the U.S. Department of Energy’s Ames Laboratory and a co-founder of the Ames startup SAFI-Tech Inc. that’s commercializing the liquid-metal particles – is the lead author. Co-authors are Andrew Martin, a former undergraduate in Thuo’s lab and now an Iowa State doctoral student in materials science and engineering; Boyce Chang, a postdoctoral fellow at the University of California, Berkeley, who earned his doctoral degree at Iowa State Zachariah Martin, Dipak Paramanik and Ian Tevis, of SAFI-Tech; Christophe Frankiewicz, a co-founder of Sep-All in Ames and a former Iowa State postdoctoral research associate; and Souvik Kundu, an Iowa State graduate student in electrical and computer engineering.
The project was supported by university startup funds to establish Thuo’s research lab at Iowa State, Thuo’s Black & Veatch faculty fellowship and a National Science Foundation Small Business Innovation Research grant.

Thuo said he launched the project three years ago as a teaching exercise.

“I started this with undergraduate students,” he said. “I thought it would be fun to get students to make something like this. It’s a really beneficial teaching tool because you don’t need to solve 2 million equations to do sophisticated science.”

And once students learned to use a few metal-processing tools, they started solving some of the technical challenges of flexible, metal electronics.

“The students discovered ways of dealing with metal and that blossomed into a million ideas,” Thuo said. “And now we can’t stop.”

And so the researchers have learned how to effectively bond metal traces to everything from water-repelling rose petals to watery gelatin. Based on what they now know, Thuo said it would be easy for them to print metallic traces on ice cubes or biological tissue.

All the experiments “highlight the versatility of this approach,” the researchers wrote in their paper, “allowing a multitude of conductive products to be fabricated without damaging the base material.”

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

Heat‐Free Fabrication of Metallic Interconnects for Flexible/Wearable Devices by Andrew Martin, Boyce S. Chang, Zachariah Martin, Dipak Paramanik, Christophe Frankiewicz, Souvik Kundu, Ian D. Tevis, Martin Thuo. Advanced Functional Materials Online Version of Record before inclusion in an issue 1903687 DOI: https://doi.org/10.1002/adfm.201903687 First published online: 15 July 2019

This paper is behind a paywall.

Artificial nose for intelligent olfactory substitution

The signal transmitted into mouse brain can participate in mouse perception and act as the brain stimulator. (Image credit: Prof. ZHAN Yang)

I’m fascinated by the image. Are they suggesting putting implants into people’s brains that can sense dangerous gaseous molecules and convert that into data which can be read on a smartphone? And, are they harvesting bioenergy to supply energy to the implant?

A July 29, 2019 news item on Azonano was not as helpful in answering my questions as I’d hoped (Note: A link has been removed),

An artificial olfactory system based on a self-powered nano-generator has been built by Prof. ZHAN Yang’s team at the Shenzhen Institutes of Advanced Technology (SIAT) of the Chinese Academy of Sciences [CAS], together with colleagues at the University of Electronic Science and Technology of China.

The device, which can detect a variety of odor molecules and identify different odors, has been demonstrated in vivo in animal models. The research titled “An artificial triboelectricity-brain-behavior closed loop for intelligent olfactory substitution” has been reported in Nano Energy.

A July 25, 2019 CAS press release, which originated the news item, provides a little more information,

Odor processing is important to many species. Specific olfactory receptors located on the neurons are involved in odor recognition. These different olfactory receptors form patterned distribution.

Inspired by the biological receptors, the teams collaborated on formulating an artificial olfactory system. Through nano-fabrication on the soft materials and special alignment of material structures, the teams built a self-power device that can code and differentiate different odorant molecules.

This device has been connected to the mouse brain to demonstrate that the olfactory signals can produce appropriate neural stimulation. When the self-powered device generated the electric currents, the mouse displayed behavioral motion changes.

This study, inspired by the biological olfactory system, provides insights on novel design of neural stimulation and brain-machine interface. 

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

An artificial triboelectricity-brain-behavior closed loop for intelligent olfactory substitution by Tianyan Zhong, Mengyang Zhang, Yongming Fu, Yechao Han, Hongye Guan, Haoxuan He, Tianming Zhao, Lili Xing, Xinyu Xue, Yan Zhang, Yang Zhan.Nano Energy Volume 63, September 2019, 103884 DOI: https://doi.org/10.1016/j.nanoen.2019.103884

This paper is behind a paywall.

Animating a paper doll with a crystalline muscle

She does sit-ups!

I love those opening scenes (Hint: It was a dark and stormy night …). Now for the science, from a July 17, 2019 news item on Nanowerk,

Scary movies about dolls that can move, like Anabelle and Chucky, are popular at theaters this summer. Meanwhile, a much less menacing animated doll has chemists talking. Researchers have given a foil “paper doll” the ability to move and do sit-ups with a new material called polymer covalent organic frameworks (polyCOFs). …

A July 17, 2019 American Chemical Society (ACS) news release (also on EurekAlert), which originated the news item, provides technical detail,

Scientists make conventional COFs by linking simple organic building blocks, such as carbon-containing molecules with boric acid or aldehyde groups, with covalent bonds. The ordered, porous structures show great potential for various applications, including catalysis, gas storage and drug delivery. However, COFs typically exist as nano- or micro-sized crystalline powders that are brittle and can’t be made into larger sheets or membranes that would be useful for many practical applications. Yao Chen, Shengqian Ma, Zhenjie Zhang and colleagues wondered if they could improve COFs’ mechanical properties by using linear polymers as building blocks.

The researchers based their polyCOF on an existing COF structure, but during the compound’s synthesis, they added polyethylene glycol (PEG) to the reactants. The PEG chains bridged the pore space of the COF, making a more compact, cohesive and stable structure. In contrast to the original COF, the polyCOF could be incorporated into flexible membranes that were repeatedly bent, twisted or stretched without damage. To demonstrate how polyCOFs could be used as an artificial muscle, the team made a doll containing the membrane as the waist and aluminum foil as its other parts. Upon exposure to ethanol vapors, the doll sat up; when the vapors were withdrawn, it laid down. The researchers repeated these actions several times, making the doll do “sit-ups.” The expansion of polyCOF pores upon binding the gas likely explains the doll’s calisthenics, the researchers say.

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

PolyCOFs: A New Class of Freestanding Responsive Covalent Organic Framework Membranes with High Mechanical Performance by Zhifang Wang, Qi Yu, Yubo Huang. Hongde An, Yu Zhao, Yifan Feng, Xia Li, Xinlei Shi, Jiajie Liang, Fusheng Pan, Peng Cheng, Yao Chen, Shengqian Ma, Zhenjie Zhang. ACS Cent. Sci.2019XXXXXXXXXX-XXX DOI: https://doi.org/10.1021/acscentsci.9b00212 Publication Date: June 25, 2019 Copyright © 2019 American Chemical Society

This paper appears to be open access.

Aesthetics and Colour Research—a November 28, 2019 talk about the tools and technology in Toronto, Canada

From a November 19, 2019 ArtSci Salon announcement (received via email),\

I [Robin] am co-organizing a lecture on AESTHETICS AND COLOUR RESEARCH AT THE

UNIVERSITY OF TORONTO’S PSYCHOLOGICAL LABORATORY

by Erich Weidenhammer, PhD (University of Toronto)

The lecture is Thu Nov 28 [2019], 6-8pm at the Thomas Fisher Rare Book Library at U of T [University of Toronto]. There will also be colour-related artifacts from the library collection on display.

Full details are here, with an eventbrite registration link for the talk (Free).

HTTPS://WWW.COLOURRESEARCH.ORG/CRSC-EVENTS/2019/11/28/LECTURE-AESTHETICS-AND-COLOUR-RESEARCH-AT-THE-UNIVERSITY-OF-TORONTOS-PSYCHOLOGICAL-LABORATORY

If you follow the link above, you’ll find this description of the talk and more,

Aesthetics and Colour Research at the University of Toronto’s Psychological Laboratory

This talk focuses on the tools and technology of colour research used in Kirschmann’s Toronto laboratory, as well as their role in supporting Kirschmann’s belief in a renewed science of aesthetics. [Between 1893 and 1908, the German-born psychologist August Kirschmann (1860-1932), led the University of Toronto’s newly founded psychological laboratory.] The talk will include a display of surviving artifacts used in the Laboratory. It will also include some colour-related artifacts from the University of Toronto Archives and Records Management Services (UTARMS), and the Fisher Rare Books Library.

Erich Weidenhammer is Curator of the University of Toronto Scientific Instruments Collection (UTSIC.org), an effort to safeguard and catalogue the material culture of research and teaching at the University of Toronto. He is also an Adjunct Curator for Scientific Processes at Ingenium: Canada’s Museums of Science & Innovation in Ottawa. Erich received his PhD in 2014 from the Institute for the History and Philosophy of Science and Technology (IHPST) of the University of Toronto for a dissertation that explored the relationship between chemistry and medicine in late eighteenth-century Britain.

Courtesy University of Toronto Scientific Instruments Collection

It turns out that this talk at the University of Toronto is part of a larger series of talks being organized by the Colour Research Society of Canada (CRSC). Here’s more about the society from the CRSC’s About page,

The CRSC is a non-profit organisation for colour research, focused on fostering a cross-disciplinary sharing of colour knowledge. seeking to develop and support a national, cross-disciplinary network of artists and designers, scholars and practitioners, with an interest in engagements with colour, and to encourage discourse between arts, sciences and industry related to colour research and knowledge.

The Colour Research Society of Canada (CRSC) is the Canadian member organisation of the AIC (International Colour Association)

The Nov. 28, 2019 talk is part of the CRSC’s Kaleidoscope Lecture Series.