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MORE unintended effects of CRISPR: Gene-edited plants could be toxic

Claire Robinson
GM Watch
Sat, 11 Jan 2020 00:00 UTC
One-third of gene knockouts via CRISPR are not knockouts at all - and there are serious implications for gene-edited food plants
CRISPR
© Wiki Commons under the Creative Commons Attribution 3.0 Unported license.
CRISPR (= Clustered Regularly Interspaced Short Palindromic Repeats) + DNA fragment, E.Coli, by Mulepati, S., Bailey, S.
A new study reveals yet another major unintended effect from the CRISPR-Cas9 gene editing tool - with potentially serious implications for the food safety of gene-edited plants. The study found that CRISPR-Cas9 edits intended to knockout the function of a gene fail to do so. Instead, proteins are still produced from the damaged genes, many of which are still functional. The result could be the production of gene-edited plants that are toxic or allergenic.

This suggests existing CRISPR-edited plants with gene knockouts, such as the non-browning mushroom that has been de-regulated in the US, should be subjected to extensive safety checks, as they could contain new proteins or compounds that pose a food safety risk.

Comment: More 'uh-oh's' in gene-editing:
Unintended consequences: CRISPR gene editing can backfire

According to a newly released scientific paper, the biologists used CRISPR on the cassava plant, hoping the technology would make it resistant to the mosaic virus.

However, the method, which lets researchers precisely delete genes in a plant's DNA, didn't make cassava resistant, instead causing viruses to mutate and be passed down to the next generation.

Devang Mehta, who was part of the cassava study and is a postdoctoral fellow with the biological sciences department at the University of Alberta, said he believes the mutated virus propagated because it was genetically selected.

He said that when they used CRISPR to delete a gene, the technology also caused viruses to evolve.
See also:

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Biohazard

Japan bans gene editing of human DNA amid calls for a moratorium from international scientists

F. William Engdahl
New Eastern Outlook
Sun, 12 Jan 2020 00:00 UTC
Scientist He Jiankui
© REUTERS/Stringer
Scientist He Jiankui attends the International Summit on Human Genome Editing at the University of Hong Kong in Hong Kong, China November 28, 2018.
Japan has banned gene-edited human embryos and international scientists are increasing the call to ban the highly uncertain and risky practice of gene-editing of human DNA. The growing opposition comes as details of a Chinese biologist's attempt to gene-edit embryos to resist HIV led to massive criticism of the flawed experiment. While the technology of altering DNA of humans, plants, animals is still in its infancy, the rate at which it is spreading worldwide with little oversight gives cause for alarm.

In December, 2019 the Japanese Health Ministry recommended a ban on implanting genetically modified human embryos. They warned such procedures could lead to a market for 'designer babies.' They follow recommendations of a panel of experts who warned that allowing gene-edited human embryos to be placed in the uterus for gestation held very serious health risks for both the infant and for future generations. In 2018 the Japanese government had moved to permit gene-editing of human embryos.

The latest decision by Japan to call for a ban on using the gene-edited embryos to give birth to gene-altered babies is a clear reaction to worldwide protest against a Chinese biologist who reported he had gene edited twins to be immune to HIV. It was the first report of babies born who had been genetically edited with CRISPR. Since then a growing number of scientists have called for a moratorium on gene editing of humans. Feng Zhang, a member of the Broad Institute of MIT and Harvard and the co-inventor of CRISPR/Cas9, has called for a moratorium on gene-edited babies. Nobel laureate David Baltimore said the He human experiment showed "there has been a failure of self-regulation in the scientific community."

Comment: More information on the risks inherent in gene-editing:

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Galaxy

Meteorite contains the oldest material on Earth: 7-billion-year-old stardust

Field Museum
Phys.org
Mon, 13 Jan 2020 22:54 UTC
Egg Nebula
© NASA, W. Sparks (STScI) and R. Sahai (JPL). Inset: SiC grain with ~8 micrometers in its longest dimension. Inset image courtesy of Janaína N. Ávila.
Dust-rich outflows of evolved stars similar to the pictured Egg Nebula are plausible sources of the large presolar silicon carbide grains found in meteorites like Murchison.
Stars have life cycles. They're born when bits of dust and gas floating through space find each other and collapse in on each other and heat up. They burn for millions to billions of years, and then they die. When they die, they pitch the particles that formed in their winds out into space, and those bits of stardust eventually form new stars, along with new planets and moons and meteorites. And in a meteorite that fell fifty years ago in Australia, scientists have now discovered stardust that formed 5 to 7 billion years ago-the oldest solid material ever found on Earth.

"This is one of the most exciting studies I've worked on," says Philipp Heck, a curator at the Field Museum, associate professor at the University of Chicago, and lead author of a paper describing the findings in PNAS. "These are the oldest solid materials ever found, and they tell us about how stars formed in our galaxy."

The materials Heck and his colleagues examined are called presolar grains-minerals formed before the Sun was born. "They're solid samples of stars, real stardust," says Heck. These bits of stardust became trapped in meteorites where they remained unchanged for billions of years, making them time capsules of the time before the solar system..

Comment: Regarding the statement above that "7 billion years ago, there was apparently a bumper crop of new stars forming-a sort of astral baby boom", there was another interesting and related discovery recently described in the article Mysterious 'wave' of star-forming gas that may be the largest structure in the galaxy:
Spanning about 9,000 light-years (or about 9% of the galaxy's diameter), the unbroken wave of stars begins near Orion in a trough about 500 light-years below the Milky Way's disk. The wave swoops upward through the constellations of Taurus and Perseus, then finally crests near the constellation Cepheus, 500 light-years above the galaxy's middle. The entire undulating structure also stretches about 400 light-years deep, includes some 800 million stars and is dense with active star-forming gas (known in more delightful terms as "stellar nurseries").


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Binoculars

10 new songbird species and subspecies found on Indonesian islands

Natalie Parletta
Cosmos Magazine
Mon, 13 Jan 2020 13:00 UTC
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Peleng
© Philippe Verbelen
A bird paradise: hill forest on the remote Indonesian island of Peleng.
Tucked away in three of the most geographically isolated Indonesian islands of Wallacea, known for their unique and rich biodiversity, researchers have discovered 10 new species and subspecies of songbirds.

Found on the remote isles of Taliabu, Peleng and Batudaka off the north-eastern coast of the larger island Sulawesi, and described in the journal Science, it's the largest number of new species named in a region of that size in more than a century.

"Birds are so well-known as compared to other animals, so it was a major surprise to find five new species and five subspecies in such a limited geographic area," says lead author Frank Rheindt, from the National University of Singapore.

Comment: See also:

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Microscope 1

Chromatin organizes itself into 3D 'forests' in single cells

Megan Fellman
Northwestern Now
Fri, 10 Jan 2020 08:30 UTC
chromatin forest

A 3D forest of chromatin predicted by the researchers’ model. Tree domains are colored from red to green according to their sizes.
A single cell contains the genetic instructions for an entire organism. This genomic information is managed and processed by the complex machinery of chromatin -- a mix of DNA and protein within chromosomes whose function and role in disease are of increasing interest to scientists.

A Northwestern University research team -- using mathematical modeling and optical imaging they developed themselves -- has discovered how chromatin folds at the single-cell level. The researchers found chromatin is folded into a variety of tree-like domains spaced along a chromatin backbone. These small and large areas are like a mixed forest of trees growing from the forest floor. The overall structure is a 3D forest at microscale.

Chromatin is responsible for packing DNA into the cell nucleus. In humans, that's about six feet of DNA in each cell. The new work suggests that chromatin is more structured and hierarchical in single cells than previously thought. Learning how chromatin correctly operates will help scientists understand what goes wrong with it in cancer and other diseases.

Comment: See also:

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Rose

Plants found to speak roundworm's language

Boyce Thompson Institute
Phys.org
Sun, 12 Jan 2020 21:47 UTC
nematodes
© BTI/Murli Manohar
These tomato roots have been infected with southern root-knot nematodes (Meloidogyne incognita). The microscopic roundworms form galls or "knots" where they feed, ultimately stunting the plants and reducing yield.
Nematodes are tiny, ubiquitous roundworms that infect plant roots, causing more than $100 billion in crop damage worldwide each year. New research has found that plants manipulate the worms' pheromones to repel infestations, providing insights into how farmers could fight these pests.

Led by Boyce Thompson Institute faculty member Frank Schroeder, the group studied a group of chemicals called ascarosides, which the worms produce and secrete to communicate with each other. As described in a paper published in Nature Communications on January 10, the researchers have shown that plants also "talk" to nematodes by metabolizing ascarosides and secreting the metabolites back into the soil.

"It's not only that the plant can 'sense' or 'smell' a nematode," Schroeder said. "It's that the plant learns a foreign language, and then broadcasts something in that language to spread propaganda that 'this is a bad place'. Plants mess with nematodes' communications system to drive them away."

Comment: See also:

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Better Earth

The 'desert' in the middle of the Pacific Ocean

Peter Dockrill
Science Alert
Sun, 12 Jan 2020 12:00 UTC
South Pacific Gyre
© (MPI Marine Microbiology/YouTube)
South Pacific Gyre
In the centre of the South Pacific, there's a place as far away from land as anyone on Earth could ever hope to get. The ocean is different there.

These distant waters lie at the heart of the South Pacific Gyre, the centre of which holds the 'oceanic pole of inaccessibility': the ocean's remotest extreme, aka Point Nemo (a name meaning 'no-one'), famous otherwise for being a spacecraft cemetery.

But aside from the ghosts of burnt-up satellites, what dwells under these far-off waves?

Not much, scientists have long thought. Despite taking up 10 percent of the ocean's surface, the South Pacific Gyre (SPG) - the largest of Earth's five giant ocean-spanning current systems - is generally considered a 'desert' in terms of marine biology.

Comment: See also:

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Microscope 1

You're as old as your microbiome? The bacteria in your gut may reveal your true age

Emily Mullin
Science
Sat, 11 Jan 2020 14:44 UTC
bacteria
© Dennis Kunkel Microscopy/Science Source
Bacteroides are the most common bacteria species found in the human intestinal tract.
The billions of bacteria that call your gut home may help regulate everything from your ability to digest food to how your immune system functions. But scientists know very little of how that system, known as the microbiome, changes over time — or even what a "normal" one looks like. Now, researchers studying the gut bacteria of thousands of people around the globe have come to one conclusion: The microbiome is a surprisingly accurate biological clock, able to predict the age of most people within years.

To discover how the microbiome changes over time, longevity researcher Alex Zhavoronkov and colleagues at InSilico Medicine, a Rockville, Maryland-based artificial intelligence startup, examined more than 3600 samples of gut bacteria from 1165 healthy individuals living across the globe. Of the samples, about a third were from people aged 20 to 39, another third were from people aged 40 to 59, and the final third were from people aged 60 to 90.

Comment:

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Chalkboard

Scientists have built a miniature particle accelerator on a silicon chip

Sophie Bushwick
Scientific American
Sat, 04 Jan 2020 01:02 UTC
miniature particle accelerator
© Neil Sapra
As electrons flow through this channel etched in a silicon chip, laser light (shown in yellow and purple) accelerates the particles to high speeds.
The device uses lasers to accelerate electrons along an etched channel

In a full-scale particle accelerator, electrons fly along a kilometers-long path as microwaves bombard them, boosting the particles to near light speed. Such a high-energy electron beam, produced at facilities such as California's SLAC National Accelerator Laboratory, enables a variety of experiments, including capturing extremely detailed images and probing the structures of molecules. But particle accelerators are expensive, require scientists to travel from locations all over the world and cannot accommodate all the researchers who submit requests to book time. To make these devices more accessible, a team at Stanford University developed a laser-driven particle accelerator that fits on a tiny silicon chip — and that could eventually be scaled up to produce a beam with as much energy as SLAC's.

"The idea of using lasers in accelerators goes all the way back to the year the laser was invented, 1960," says Robert Byer, a Stanford researcher who has been working on this concept since 1974. Lasers produce electromagnetic waves with much shorter wavelengths than the microwaves used in a full-scale accelerator, which means they can accelerate electrons moving through a much smaller space. "The size of these devices is uncannily small," Byer says. The electrons in the new accelerator, for example, travel along a channel that is about three one-thousandths of a millimeter wide — around half the width of a human red blood cell.
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X

Russian journals retract more than 800 papers after 'bombshell' investigation

Dalmeet Singh Chawla
Science Magazine
Wed, 08 Jan 2020 17:34 UTC
russian academy sciences
© ISTOCK.COM/MORDOLFF
The Russian Academy of Sciences is trying to improve ethical standards in publishing.
Academic journals in Russia are retracting more than 800 papers following a probe into unethical publication practices by a commission appointed by the Russian Academy of Sciences (RAS). The moves come in the wake of several other queries suggesting the vast Russian scientific literature is riddled with plagiarism, self-plagiarism, and so-called gift authorship, in which academics become a co-author without having contributed any work.

The RAS commission's preliminary report documenting the problems and journals' responses to them is "a bombshell," says Gerson Sher, a former staffer at the U.S. National Science Foundation and the author of a recent book on U.S.-Russia science cooperation. The report, released yesterday, "will reinforce the suspicions and fears of many — that their country is not going down the right path in science and that it's damaging its own reputation," says Sher, who applauds RAS for commissioning the investigation.

Russia's roughly 6000 academic journals, the vast majority published in Russian, are popular among the country's academics. A 2019 study found that Russian authors publish far more in domestic journals than, for instance, their counterparts in Poland, Germany, or Indonesia. But standards are often low. In March 2018, for instance, Dissernet, a network aimed at cleaning up the Russian literature, identified more than 4000 cases of plagiarism and questionable authorship among 150,000 papers in about 1500 journals.

Comment: And it's not just Russia. Science fraud is a major industry everywhere you find scientists. Kudos to the RAS commission for putting in the time and effort to make the science scene a bit cleaner.

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