Tag Archives: France

Congratulations to winners of 2020 Nobel Prize for Chemistry: Dr. Emmanuelle Charpentier & Dr. Jennifer A. Doudna (CRISPR-cas9)

It’s possible there’s a more dramatic development in the field of contemporary gene-editing but it’s indisputable that CRISPR (clustered regularly interspaced short palindromic repeats) -cas9 (CRISPR-associated 9 [protein]) ranks very highly indeed.

The technique, first discovered (or developed) in 2012, has brought recognition in the form of the 2020 Nobel Prize for Chemistry to CRISPR’s two discoverers, Emanuelle Charpentier and Jennifer Doudna.

An October 7, 2020 news item on phys.org announces the news,

The Nobel Prize in chemistry went to two researchers Wednesday [October 7, 2020] for a gene-editing tool that has revolutionized science by providing a way to alter DNA, the code of life—technology already being used to try to cure a host of diseases and raise better crops and livestock.

Emmanuelle Charpentier of France and Jennifer A. Doudna of the United States won for developing CRISPR-cas9, a very simple technique for cutting a gene at a specific spot, allowing scientists to operate on flaws that are the root cause of many diseases.

“There is enormous power in this genetic tool,” said Claes Gustafsson, chair of the Nobel Committee for Chemistry.

More than 100 clinical trials are underway to study using CRISPR to treat diseases, and “many are very promising,” according to Victor Dzau, president of the [US] National Academy of Medicine.

“My greatest hope is that it’s used for good, to uncover new mysteries in biology and to benefit humankind,” said Doudna, who is affiliated with the University of California, Berkeley, and is paid by the Howard Hughes Medical Institute, which also supports The Associated Press’ Health and Science Department.

The prize-winning work has opened the door to some thorny ethical issues: When editing is done after birth, the alterations are confined to that person. Scientists fear CRISPR will be misused to make “designer babies” by altering eggs, embryos or sperm—changes that can be passed on to future generations.

Unusually for phys.org, this October 7, 2020 news item is not a simple press/news release reproduced in its entirety but a good overview of the researchers’ accomplishments and a discussion of some of the issues associated with CRISPR along with the press release at the end.

I have covered some CRISPR issues here including intellectual property (see my March 15, 2017 posting titled, “CRISPR patent decision: Harvard’s and MIT’s Broad Institute victorious—for now‘) and designer babies (as exemplified by the situation with Dr. He Jiankui; see my July 28, 2020 post titled, “July 2020 update on Dr. He Jiankui (the CRISPR twins) situation” for more details about it).

An October 7, 2020 article by Michael Grothaus for Fast Company provides a business perspective (Note: A link has been removed),

Needless to say, research by the two scientists awarded the Nobel Prize in Chemistry today has the potential to change the course of humanity. And with that potential comes lots of VC money and companies vying for patents on techniques and therapies derived from Charpentier’s and Doudna’s research.

One such company is Doudna’s Editas Medicine [according to my search, the only company associated with Doudna is Mammoth Biosciences, which she co-founded], while others include Caribou Biosciences, Intellia Therapeutics, and Casebia Therapeutics. Given the world-changing applications—and the amount of revenue such CRISPR therapies could bring in—it’s no wonder that such rivalry is often heated (and in some cases has led to lawsuits over the technology and its patents).

As Doudna explained in her book, A Crack in Creation: Gene Editing and the Unthinkable Power to Control Evolution, cowritten by Samuel H. Sternberg …, “… —but we could also have woolly mammoths, winged lizards, and unicorns.” And as for that last part, she made clear, “No, I am not kidding.”

Everybody makes mistakes and the reference to Editas Medicine is the only error I spotted. You can find out more about Mammoth Biosciences here and while Dr. Doudna’s comment, “My greatest hope is that it’s used for good, to uncover new mysteries in biology and to benefit humankind,” is laudable it would seem she wishes to profit from the discovery. Mammoth Biosciences is a for-profit company as can be seen at the end of the Mammoth Biosciences’ October 7, 2020 congratulatory news release,

About Mammoth Biosciences

Mammoth Biosciences is harnessing the diversity of nature to power the next-generation of CRISPR products. Through the discovery and development of novel CRISPR systems, the company is enabling the full potential of its platform to read and write the code of life. By leveraging its internal research and development and exclusive licensing to patents related to Cas12, Cas13, Cas14 and Casɸ, Mammoth Biosciences can provide enhanced diagnostics and genome editing for life science research, healthcare, agriculture, biodefense and more. Based in San Francisco, Mammoth Biosciences is co-founded by CRISPR pioneer Jennifer Doudna and Trevor Martin, Janice Chen, and Lucas Harrington. The firm is backed by top institutional investors [emphasis mine] including Decheng, Mayfield, NFX, and 8VC, and leading individual investors including Brook Byers, Tim Cook, and Jeff Huber.

An October 7, 2029 Nobel Prize press release, which unleashed all this interest in Doudna and Charpentier, notes this,

Prize amount: 10 million Swedish kronor, to be shared equally between the Laureates.

In Canadian money that amount is $1,492,115.03 (as of Oct. 9, 2020 12:40 PDT when I checked a currency converter).

Ordinarily there’d be a mildly caustic comment from me about business opportunities and medical research but this is a time for congratulations to both Dr. Emanuelle Charpentier and Dr. Jennifer Doudna.

Get better protection from a sunscreen with a ‘flamenco dancing’ molecule?

Caption: illustrative image for the University of Warwick research on ‘Flamenco dancing’ molecule could lead to better-protecting sunscreen created by Dr. Michael Horbury. Credit:: created by Dr Michael Horbury

There are high hopes (more about why later) for a plant-based ‘flamenco dancing molecule’ and its inclusion in sunscreens as described in an October 18, 2019 University of Warwick press release (also on EurekAlert),

A molecule that protects plants from overexposure to harmful sunlight thanks to its flamenco-style twist could form the basis for a new longer-lasting sunscreen, chemists at the University of Warwick have found, in collaboration with colleagues in France and Spain. Research on the green molecule by the scientists has revealed that it absorbs ultraviolet light and then disperses it in a ‘flamenco-style’ dance, making it ideal for use as a UV filter in sunscreens.

The team of scientists report today, Friday 18th October 2019, in the journal Nature Communications that, as well as being plant-inspired, this molecule is also among a small number of suitable substances that are effective in absorbing light in the Ultraviolet A (UVA) region of wavelengths. It opens up the possibility of developing a naturally-derived and eco-friendly sunscreen that protects against the full range of harmful wavelengths of light from the sun.

The UV filters in a sunscreen are the ingredients that predominantly provide the protection from the sun’s rays. In addition to UV filters, sunscreens will typically also include:

Emollients, used for moisturising and lubricating the skin
Thickening agents
Emulsifiers to bind all the ingredients
Water
Other components that improve aesthetics, water resistance, etc.

The researchers tested a molecule called diethyl sinapate, a close mimic to a molecule that is commonly found in the leaves of plants, which is responsible for protecting them from overexposure to UV light while they absorb visible light for photosynthesis.

They first exposed the molecule to a number of different solvents to determine whether that had any impact on its (principally) light absorbing behaviour. They then deposited a sample of the molecule on an industry standard human skin mimic (VITRO-CORNEUM®) where it was irradiated with different wavelengths of UV light. They used the state-of-the-art laser facilities within the Warwick Centre for Ultrafast Spectroscopy to take images of the molecule at extremely high speeds, to observe what happens to the light’s energy when it’s absorbed in the molecule in the very early stages (millionths of millionths of a second). Other techniques were also used to establish longer term (many hours) properties of diethyl sinapate, such as endocrine disruption activity and antioxidant potential.

Professor Vasilios Stavros from the University of Warwick, Department of Chemistry, who was part of the research team, explains: “A really good sunscreen absorbs light and converts it to harmless heat. A bad sunscreen is one that absorbs light and then, for example, breaks down potentially inducing other chemistry that you don’t want. Diethyl sinapate generates lots of heat, and that’s really crucial.”

When irradiated the molecule absorbs light and goes into an excited state but that energy then has to be disposed of somehow. The team of researchers observed that it does a kind of molecular ‘dance’ a mere 10 picoseconds (ten millionths of a millionth of a second) long: a twist in a similar fashion to the filigranas and floreos hand movements of flamenco dancers. That causes it to come back to its original ground state and convert that energy into vibrational energy, or heat.

It is this ‘flamenco dance’ that gives the molecule its long-lasting qualities. When the scientists bombarded the molecule with UVA light they found that it degraded only 3% over two hours, compared to the industry requirement of 30%.

Dr Michael Horbury, who was a Postgraduate Research Fellow at The University Warwick when he undertook this research (and now at the University of Leeds) adds: “We have shown that by studying the molecular dance on such a short time-scale, the information that you gain can have tremendous repercussions on how you design future sunscreens.
Emily Holt, a PhD student in the Department of Chemistry at the University of Warwick who was part of the research team, said: “The next step would be to test it on human skin, then to mix it with other ingredients that you find in a sunscreen to see how those affect its characteristics.”

Professor Florent Allais and Dr Louis Mouterde, URD Agro-Biotechnologies Industrielles at AgroParisTech (Pomacle, France) commented: “What we have developed together is a molecule based upon a UV photoprotective molecule found in the surface of leaves on a plant and refunctionalised it using greener synthetic procedures. Indeed, this molecule has excellent long-term properties while exhibiting low endocrine disruption and valuable antioxidant properties.”

Professor Laurent Blasco, Global Technical Manager (Skin Essentials) at Lubrizol and Honorary Professor at the University of Warwick commented: “In sunscreen formulations at the moment there is a lack of broad-spectrum protection from a single UV filter. Our collaboration has gone some way towards developing a next generation broad-spectrum UV filter inspired by nature. Our collaboration has also highlighted the importance of academia and industry working together towards a common goal.”

Professor Vasilios Stavros added, “Amidst escalating concerns about their impact on human toxicity (e.g. endocrine disruption) and ecotoxicity (e.g. coral bleaching), developing new UV filters is essential. We have demonstrated that a highly attractive avenue is ‘nature-inspired’ UV filters, which provide a front-line defence against skin cancer and premature skin aging.”

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

Towards symmetry driven and nature inspired UV filter design by Michael D. Horbury, Emily L. Holt, Louis M. M. Mouterde, Patrick Balaguer, Juan Cebrián, Laurent Blasco, Florent Allais & Vasilios G. Stavros. Nature Communications volume 10, Article number: 4748 (2019) DOI: https://doi.org/10.1038/s41467-019-12719-z

This paper is open access.

Why the high hopes?

Briefly (the long story stretches over 10 years), the most recommended sunscreens today (2020) are ‘mineral-based’. This is painfully amusing because civil society groups (activists) such as Friends of the Earth (in particular the Australia chapter under Georgia Miller’s leadership) and Canada’s own ETC Group had campaigned against these same sunscreen when they were billed as being based on metal oxide nanoparticles such zinc oxide and/or titanium oxide. The ETC Group under Pat Roy Mooney’s leadership didn’t press the campaign after an initial push. As for Australia and Friend of the Earth, their anti-metallic oxide nanoparticle sunscreen campaign didn’t work out well as I noted in a February 9, 2012 posting and with a follow-up in an October 31, 2012 posting.

The only civil society group to give approval (very reluctantly) was the Environmental Working Group (EWG) as I noted in a July 9, 2009 posting. They had concerns about the fact that these ingredients are metallic but after a thorough of then available research, EWG gave the sunscreens a passing grade and noted, in their report, that they had more concerns about the use of oxybenzone in sunscreens. That latter concern has since been flagged by others (e.g., the state of Hawai’i) as noted in my July 6, 2018 posting.

So, rebranding metallic oxides as minerals has allowed the various civil society groups to support the very same sunscreens many of them were advocating against.

In the meantime, scientists continue work on developing plant-based sunscreens as an improvement to the ‘mineral-based’ sunscreens used now.

The latest math stars: honeybees!

Understanding the concept of zero—I still remember climbing that mountain, so to speak. It took the teacher quite a while to convince me that representing ‘nothing’ as a zero was worthwhile. In fact, it took the combined efforts of both my parents and the teacher to convince me to use zeroes as I was prepared to go without. The battle is long since over and I have learned to embrace zero.

I don’t think bees have to be convinced but they too may have a concept of zero. More about that later, here’s the latest abut bees and math from an October 10, 2019 news item on phys.org,

Start thinking about numbers and they can become large very quickly. The diameter of the universe is about 8.8×1023 km and the largest known number—googolplex, 1010100—outranks it enormously. Although that colossal concept was dreamt up by brilliant mathematicians, we’re still pretty limited when it comes to assessing quantities at a glance. ‘Humans have a threshold limit for instantly processing one to four elements accurately’, says Adrian Dyer from RMIT University, Australia; and it seems that we are not alone. Scarlett Howard from RMIT and the Université de Toulouse, France, explains that guppies, angelfish and even honeybees are capable of distinguishing between quantities of three and four, although the trusty insects come unstuck at finer differences; they fail to differentiate between four and five, which made her wonder. According to Howard, honeybees are quite accomplished mathematicians. ‘Recently, honeybees were shown to learn the rules of “less than” and “greater than” and apply these rules to evaluate numbers from zero to six’, she says. Maybe numeracy wasn’t the bees’ problem; was it how the question was posed? The duo publishes their discovery that bees can discriminate between four and five if the training procedure is correct in Journal of Experimental Biology.

An October 10, 2019 The Company of Biologists’ press release on EurekAlert, which originated the news item, refines the information with more detail,

Dyer explains that when animals are trained to distinguish between colours and objects, some training procedures simply reward the animals when they make the correct decision. In the case of the honeybees that could distinguish three from four, they received a sip of super-sweet sugar water when they made the correct selection but just a taste of plain water when they got it wrong. However, Dyer, Howard and colleagues Aurore Avarguès-Weber, Jair Garcia and Andrew Greentree knew there was an alternative strategy. This time, the bees would be given a bitter-tasting sip of quinine-flavoured water when they got the answer wrong. Would the unpleasant flavour help the honeybees to focus better and improve their maths?

‘[The] honeybees were very cooperative, especially when I was providing sugar rewards’, says Howard, who moved to France each April to take advantage the northern summer during the Australian winter, when bees are dormant. Training the bees to enter a Y-shaped maze, Howard presented the insects with a choice; a card featuring four shapes in one arm and a card featuring a different number of shapes (ranging from one to 10) in the other. During the first series of training sessions, Howard rewarded the bees with a sugary sip when they alighted correctly before the card with four shapes, in contrast to a sip of water when they selected the wrong card. However, when Howard trained a second set of bees she reproved them with a bitter-tasting sip of quinine when they chose incorrectly, rewarding the insects with sugar when they selected the card with four shapes. Once the bees had learned to pick out the card with four shapes, Howard tested whether they could distinguish the card with four shapes when offered a choice between it and cards with eight, seven, six or – the most challenging comparison – five shapes.

Not surprisingly, the bees that had only been rewarded during training struggled; they couldn’t even differentiate between four and eight shapes. However, when Howard tested the honeybees that had been trained more rigorously – receiving a quinine reprimand – their performance was considerably better, consistently picking the card with four shapes when offered a choice between it and cards with seven or eight shapes. Even more impressively, the bees succeeded when offered the more subtle choice between four and five shapes.

So, it seems that honeybees are better mathematicians than had been credited. Unlocking their ability was simply a matter of asking the question in the right way and Howard is now keen to find out just how far counting bees can go.

I’ll get to the link to and citation for the paper in a minute but first, I found more about bees and math (including zero) in this February 7, 2019 article by Jason Daley for The Smithsonian (Note: Links have been removed),

Bees are impressive creatures, powering entire ecosystems via pollination and making sweet honey at the same time, one of the most incredible substances in nature. But it turns out the little striped insects are also quite clever. A new study suggests that, despite having tiny brains, bees understand the mathematical concepts of addition and subtraction.

To test the numeracy of the arthropods, researchers set up unique Y-shaped math mazes for the bees to navigate, according to Nicola Davis at the The Guardian. Because the insects can’t read, and schooling them to recognize abstract symbols like plus and minus signs would be incredibly difficult, the researchers used color to indicate addition or subtraction. …

Fourteen bees spent between four and seven hours completing 100 trips through the mazes during training exercises with the shapes and numbers chosen at random. All of the bees appeared to learn the concept. Then, the bees were tested 10 times each using two addition and two subtraction scenarios that had not been part of the training runs. The little buzzers got the correct answer between 64 and 72 percent of the time, better than would be expected by chance.

Last year, the same team of researchers published a paper suggesting that bees could understand the concept of zero, which puts them in an elite club of mathematically-minded animals that, at a minimum, have the ability to perceive higher and lower numbers in different groups. Animals with this ability include frogs, lions, spiders, crows, chicken chicks, some fish and other species. And these are not the only higher-level skills that bees appear to possess. A 2010 study that Dyer [Adrian Dyer of RMIT University in Australia] also participated in suggests that bees can remember human faces using the same mechanisms as people. Bees also use a complex type of movement called the waggle dance to communicate geographical information to one other, another sophisticated ability packed into a brain the size of a sesame seed.

If researchers could figure out how bees perform so many complicated tasks with such a limited number of neurons, the research could have implications for both biology and technology, such as machine learning. …

Then again, maybe the honey makers are getting more credit than they deserve. Clint Perry, who studies invertebrate intelligence at the Bee Sensory and Behavioral Ecology Lab at Queen Mary University of London tells George Dvorsky at Gizmodo that he’s not convinced by the research, and he had similar qualms about the study that suggested bees can understand the concept of zero. He says the bees may not be adding and subtracting, but rather are simply looking for an image that most closely matches the initial one they see, associating it with the sugar reward. …

If you have the time and the interest, definitely check out Daley’s article.

Here’s a link to and a citation for the latest paper about honeybees and math,

Surpassing the subitizing threshold: appetitive–aversive conditioning improves discrimination of numerosities in honeybees by Scarlett R. Howard, Aurore Avarguès-Weber, Jair E. Garcia, Andrew D. Greentree, Adrian G. Dyer. Journal of Experimental Biology 2019 222: jeb205658 doi: 10.1242/jeb.205658 Published 10 October 2019

This paper is behind a paywall.

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.

Structure of tunneling nanotubes (TNTs) challenges the dogma of the cell

There is a video that accompanies the news but I strongly advise reading the press release first, unless you already know a lot about cells and tunneling nanotubes.

A January 30, 2019 Institut Pasteur press release (also on EurekAlert but published Jan.31, 2019) announces the work,

Cells in our bodies have the ability to speak with one another much like humans do. This communication allows organs in our bodies to work synchronously, which in turn, enables us to perform the remarkable range of tasks we meet on a daily basis. One of this mean of communication is ‘tunneling nanotubes’ or TNTs. In an article published in Nature Communications, researchers from the Institut Pasteur leaded by Chiara Zurzolo discovered, thanks to advanced imaging techniques, that the structure of these nanotubes challenged the very concept of cell.

As their name implies, TNTs are tiny tunnels that link two (or more cells) and allow the transport of a wide variety of cargoes between them, including ions, viruses, and entire organelles. Previous research by the same team (Membrane Traf?c and Pathogenesis Unit) at the Institut Pasteur have shown that TNTs are involved in the intercellular spreading of pathogenic amyloid proteins involved in Alzheimer and Parkinson’s disease. This led researchers to propose that they serve as a major avenue for the spreading of neurodegenerative diseases in the brain and therefore represent a novel therapeutic target to stop the progression of these incurable diseases. TNTs also appear to play a major role in cancer resistance to therapy. But as scientists still know very little about TNTs and how they relate or differ from other cellular protrusions such as filopodia, they decided to pursue their research to deal with these tiny tubular connections in depth.

The dogma of cell unit questioned

A better understanding of these tiny tubular connections is therefore required as TNTs might have tremendous implications in human health and disease. Addressing this issue has been very difficult due to the fragile and transitory nature of these structures, which do not survive classical microscopic techniques. In order to overcome these obstacles, researchers combined various state-of-the-art electron microscopy approaches, and imaged TNTs at below-freezing temperatures.

Using this imaging strategy, researchers were able to decipher the structure of TNTs in high detail. Specifically, they show that most TNTs – previously shown to be single connections – are in fact made up of multiple, smaller, individual tunneling nanotubes (iTNTs). Their images also show the existence of thin wires that connect iTNTs, which could serve to increase their mechanical stability. They demonstrate the functionality of iTNTs by showing the transport of organelles using time-lapse imaging. Finally, researchers employed a type of microscopy known as ‘FIB-SEM’ to produce 3D images with sufficient resolution to clearly identify that TNTs are ‘open’ at both ends, and thus create continuity between two cells. “This discovery challenges the dogma of cells as individual units, showing that cells can open up to neighbors and exchange materials without a membrane barrier” explains Chiara Zurzolo, head of the Membrane Traf?c and Pathogenesis Unit at the Institut Pasteur.

A news step in cell-to-cell communication decoding

By applying an imaging work-flow that improves upon, and avoids, previous limitations of tools used to study the anatomy of TNTs, researchers provide the first structural description of TNTs. Importantly, they provide the absolute demonstration that these are novel cellular organelles with a defined structure, very different from known cell protrusions. “The description of the structure allows the understanding of the mechanisms involved in their formation and provides a better comprehension of their function in transferring material directly between (the cytosol of) two connected cells” says Chiara Zurzolo. Furthermore, their strategy, which preserves these delicate structures, will be useful for studying the role TNTs play in other physiological and pathological conditions

This work is an essential step toward understanding cell-to-cell communication via TNTs and lays the groundwork for investigations into their physiological functions and their role in spreading of particles linked to diseases such as viruses, bacteria, and misfolded proteins.

The researchers have kindly produced a version of the video in English,

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

Correlative cryo-electron microscopy reveals the structure of TNTs in neuronal cells by Anna Sartori-Rupp, Diégo Cordero Cervantes, Anna Pepe, Karine Gousset, Elise Delage, Simon Corroyer-Dulmont, Christine Schmitt, Jacomina Krijnse-Locker & Chiara Zurzolo. Nature Communications volume 10, Article number: 342 (2019) DOI https://doi.org/10.1038/s41467-018-08178-7 Published 21 January 2019

This paper is open access.

Human lung enzyme can degrade graphene

Caption: A human lung enzyme can biodegrade graphene. Credit: Fotolia Courtesy: Graphene Flagship

The big European Commission research programme, Grahene Flagship, has announced some new work with widespread implications if graphene is to be used in biomedical implants. From a August 23, 2018 news item on ScienceDaily,

Myeloperoxidase — an enzyme naturally found in our lungs — can biodegrade pristine graphene, according to the latest discovery of Graphene Flagship partners in CNRS, University of Strasbourg (France), Karolinska Institute (Sweden) and University of Castilla-La Mancha (Spain). Among other projects, the Graphene Flagship designs based like flexible biomedical electronic devices that will interfaced with the human body. Such applications require graphene to be biodegradable, so our body can be expelled from the body.

An August 23, 2018 Grapehene Flagship press release (mildly edited version on EurekAlert), which originated the news item, provides more detail,

To test how graphene behaves within the body, researchers analysed how it was broken down with the addition of a common human enzyme – myeloperoxidase or MPO. If a foreign body or bacteria is detected, neutrophils surround it and secrete MPO, thereby destroying the threat. Previous work by Graphene Flagship partners found that MPO could successfully biodegrade graphene oxide.

However, the structure of non-functionalized graphene was thought to be more resistant to degradation. To test this, the team looked at the effects of MPO ex vivo on two graphene forms; single- and few-layer.

Alberto Bianco, researcher at Graphene Flagship Partner CNRS, explains: “We used two forms of graphene, single- and few-layer, prepared by two different methods in water. They were then taken and put in contact with myeloperoxidase in the presence of hydrogen peroxide. This peroxidase was able to degrade and oxidise them. This was really unexpected, because we thought that non-functionalized graphene was more resistant than graphene oxide.”

Rajendra Kurapati, first author on the study and researcher at Graphene Flagship Partner CNRS, remarks how “the results emphasize that highly dispersible graphene could be degraded in the body by the action of neutrophils. This would open the new avenue for developing graphene-based materials.”

With successful ex-vivo testing, in-vivo testing is the next stage. Bengt Fadeel, professor at Graphene Flagship Partner Karolinska Institute believes that “understanding whether graphene is biodegradable or not is important for biomedical and other applications of this material. The fact that cells of the immune system are capable of handling graphene is very promising.”

Prof. Maurizio Prato, the Graphene Flagship leader for its Health and Environment Work Package said that “the enzymatic degradation of graphene is a very important topic, because in principle, graphene dispersed in the atmosphere could produce some harm. Instead, if there are microorganisms able to degrade graphene and related materials, the persistence of these materials in our environment will be strongly decreased. These types of studies are needed.” “What is also needed is to investigate the nature of degradation products,” adds Prato. “Once graphene is digested by enzymes, it could produce harmful derivatives. We need to know the structure of these derivatives and study their impact on health and environment,” he concludes.

Prof. Andrea C. Ferrari, Science and Technology Officer of the Graphene Flagship, and chair of its management panel added: “The report of a successful avenue for graphene biodegradation is a very important step forward to ensure the safe use of this material in applications. The Graphene Flagship has put the investigation of the health and environment effects of graphene at the centre of its programme since the start. These results strengthen our innovation and technology roadmap.”

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

Degradation of Single‐Layer and Few‐Layer Graphene by Neutrophil Myeloperoxidase by Dr. Rajendra Kurapati, Dr. Sourav P. Mukherjee, Dr. Cristina Martín, Dr. George Bepete, Prof. Ester Vázquez, Dr. Alain Pénicaud, Prof. Dr. Bengt Fadeel, Dr. Alberto Bianco. Angewandte Chemie https://doi.org/10.1002/anie.201806906 First published: 13 July 2018

This paper is behind a paywall.

Carbon nanotube optics and the quantum

A US-France-Germany collaboration has led to some intriguing work with carbon nanotubes. From a June 18, 2018 news item on ScienceDaily,

Researchers at Los Alamos and partners in France and Germany are exploring the enhanced potential of carbon nanotubes as single-photon emitters for quantum information processing. Their analysis of progress in the field is published in this week’s edition of the journal Nature Materials.

“We are particularly interested in advances in nanotube integration into photonic cavities for manipulating and optimizing light-emission properties,” said Stephen Doorn, one of the authors, and a scientist with the Los Alamos National Laboratory site of the Center for Integrated Nanotechnologies (CINT). “In addition, nanotubes integrated into electroluminescent devices can provide greater control over timing of light emission and they can be feasibly integrated into photonic structures. We are highlighting the development and photophysical probing of carbon nanotube defect states as routes to room-temperature single photon emitters at telecom wavelengths.”

A June 18, 2018 Los Alamos National Laboratory (LANL) news release (also on EurekAlert), which originated the news item, expands on the theme,

The team’s overview was produced in collaboration with colleagues in Paris (Christophe Voisin [Ecole Normale Supérieure de Paris (ENS)]) who are advancing the integration of nanotubes into photonic cavities for modifying their emission rates, and at Karlsruhe (Ralph Krupke [Karlsruhe Institute of Technology (KIT]) where they are integrating nanotube-based electroluminescent devices with photonic waveguide structures. The Los Alamos focus is the analysis of nanotube defects for pushing quantum emission to room temperature and telecom wavelengths, he said.

As the paper notes, “With the advent of high-speed information networks, light has become the main worldwide information carrier. . . . Single-photon sources are a key building block for a variety of technologies, in secure quantum communications metrology or quantum computing schemes.”

The use of single-walled carbon nanotubes in this area has been a focus for the Los Alamos CINT team, where they developed the ability to chemically modify the nanotube structure to create deliberate defects, localizing excitons and controlling their release. Next steps, Doorn notes, involve integration of the nanotubes into photonic resonators, to provide increased source brightness and to generate indistinguishable photons. “We need to create single photons that are indistinguishable from one another, and that relies on our ability to functionalize tubes that are well-suited for device integration and to minimize environmental interactions with the defect sites,” he said.

“In addition to defining the state of the art, we wanted to highlight where the challenges are for future progress and lay out some of what may be the most promising future directions for moving forward in this area. Ultimately, we hope to draw more researchers into this field,” Doorn said.

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

Carbon nanotubes as emerging quantum-light sources by X. He, H. Htoon, S. K. Doorn, W. H. P. Pernice, F. Pyatkov, R. Krupke, A. Jeantet, Y. Chassagneux & C. Voisin. Nature Materials (2018) DOI: https://doi.org/10.1038/s41563-018-0109-2 Published online June 18, 2018

This paper is behind a paywall.

Revising history with science and art

Caption: The 2000-year-old pipe sculpture’s bulging neck is evidence of thyroid disease as a result of iodine deficient water and soil in the ancient Ohio Valley. Credit: Kenneth Tankersley

An October 4, 2018 news item on ScienceDaily describes the analytic breakthrough,

Art often imitates life, but when University of Cincinnati anthropologist and geologist Kenneth Tankersley investigated a 2000-year-old carved statue on a tobacco pipe, he exposed a truth he says will rewrite art history.

Since its discovery in 1901, at the Adena Burial Mound in Ross County, Ohio, archaeologists have theorized that the the 8-inch pipe statue—carved into the likeness of an Ohio Valley Native American—represented an achondroplastic dwarf (AD). People with achondroplasia typically have short arms and legs, an enlarged head, and an average-sized trunk, the same condition as Emmy Award-winning actor Peter Dinklage from HBO’s “Game of Thrones.”

“During the early turn of the century, this theory was consistent with actual human remains of a Native American excavated in Kentucky, also interpreted by archaeologists as being an achondroplastic dwarf,” says Tankersley.

This theory flourished in the scientific literature until the turn of the 21st century when Tankersley looked closer.

“Here we have a carved statue and human remains, both of achondroplasia from the same time period,” says Tankersley. “But what caught my eye on this pipe statue was an obvious tumor on the neck that looked remarkably like a goiter [or goitre] or thyroid tumor.”

An October 2, 2018 University of Cincinnati (UC) news release (also on EurekAlert but published Oct. 3, 2018), reveals more details,

Tankersley collaborated with Frederic Bauduer, a visiting biological anthropologist and paleopathologist from the University of Bordeaux, UC’s sister university in France, to ultimately dispel previous academic literature claiming the sculpture as portraying achondroplasia.

“In archaeological science, flesh does not survive, so many ancient maladies go unnoticed and are almost always impossible to get at from an archaeological standpoint,” says Tankersley. “So what struck me was how remarkably Bauduer was using ancient art from various periods of antiquity to argue for the paleopathology he presented.”

Using radiocarbon dating on textile and bark samples surrounding the pipe at the site, the Adena pipe dates to approximately 2000 years ago, to the earliest evidence of tobacco.

Traditionally, tobacco is considered a sacred plant to Native Americans in this region, and smoking tobacco played an important role in their ceremonies, but he points to tobacco smoking as being long associated with an increased prevalence of goiter in low iodine intake zones worldwide.

From a medical perspective, Bauduer found the physical characteristics, such as the short forehead and long bones of the upper and lower limbs, simply not adding up as an achondroplastic dwarf.

“We found the tumor in the neck, as well as the figure’s squatted stance — not foreshortened legs as was formerly documented in the literature — were both signs and symptoms of thyroid disease,” says Tankersley.

“We already know that iodine deficiencies can lead to thyroid tumors, and the Ohio Valley area, where this artifact was found, has historically had iodine depleted soils and water relative to the advance of an Ice Age glacier about 300,000 years ago.”

Students in a university lab look through microscopes.

Tankersley (top center) teaches archaeology students to date soil, bones and textiles using radiocarbon science.

Profile of ancient tobacco pipe sculpture portraying a Native American wearing ceremonial regalia.

The figure’s bulging neck (goiter) and appearance of short stature are actually results of iodine deficient thyroid disease. The legs are bent in a tilted squat likely during a Native American ceremonial dance.

Tankersley says the Ohio Valley region, before the introduction of iodized salt in the 1920s,
was part of the so-called U.S. “goiter belt” where goiter frequency was relatively high —  five to 15 incidences per thousand.

The lower limbs on the statue, previously documented in the literature as short in stature, are actually normal size in bone length, according to Bauduer. Upon closer inspection, both Bauduer and Tankersley agree that the figure is also portrayed in a tilted squat, a common gait anomaly found in people with hypothyroidism.

The figure has what appears to be an abdominal six-pack, but both researchers say the detailed physical features indeed portray a normal physique except for the telltale signs of thyroid disease.

“The fact that the bones of the figure are all normal size leads us to believe the squat portrays more of an abnormal gait while likely in the stance of a typical Native American ritual dance,” says Tankersley, who is one-quarter Native American himself and regularly attends ceremonial events throughout Ohio and Kentucky.

“The regalia the figure is wearing is also strongly indicative of ancient Native Ohio Valley Shawnee, Delaware and Ojibwa to the north and Miami Nation tribes in Indiana.

“The traditional headdress, pierced ears with expanded spool earrings and loincloth with serpentine motif on the front and feathered bustle on back are also still worn by local Native tribes during ceremonial events today.”

Artistic clues

Portrait of Dr. Frederic Bauduer, biological pathologist from University of Bordeaux in France, on an ancient architectural balcony.

Frederic Bauduer, biological anthropologist, paleopathologist and critical collaborator on this research from the University of Bordeaux, UC’s sister university in France. photo/Frederic Bauduer

In addition to figures found in South America and Mesoamerica, Tankersley says the Adena pipe is the first known example of a goiter depicted in ancient Native North American art and one of the oldest from the Western Hemisphere.

“The other real take here is that a lot of people ask, ‘What is the value of ancient art?’” asserts Tankersley. “Well, here’s an example of ancient art that tells a deeper story. And similar indigenous art representations found in South America and Mesoamerica strengthen our hypothesis.”

Tankersley is interested in looking deeper for pathologies and maladies portrayed on other ancient artifacts from Native Americans thousands of years ago here in the Ohio Valley and elsewhere.

“Art history is beginning to help substantiate many scientific hypotheses,” says Tankersley. “Because artists are such keen students of anatomy, artisans such as this ancient Adena pipe sculptor could portray physical maladies with great accuracy, even before they were aware of what the particular disease was.”

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

Medical Hypotheses Evidence of an ancient (2000 years ago) goiter attributed to iodine deficiency in North America by F. Bauduer, K. Barnett Tankersley. Medical Hypotheses Volume 118, September 2018, Pages 6-8 DOI: https://doi.org/10.1016/j.mehy.2018.06.011

This paper looks like it’s behind a paywall.