Sunday, February 24, 2019

A Genetic Code update.

Scientists Just Added Four New Letters to the Genetic Code

Feb 24, 2019

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A four-letter alphabet might seem limited, but it’s all nature needed to write the instructions for all life on the planet. News that researchers have added four letters to the genetic alphabet opens the door to new possibilities in synthetic biology, data storage, and even the search for life beyond our planet.

The genetic code at the heart of all living things is elegantly simple. Each half of the famous double helix structure is built from four small molecules called bases: adenine, thymine, cytosine and guanine (ATCG). The order in which they appear determines what the DNA codes for, just like series of zeros and ones at the hearts of computers do.

But now scientists at the Foundation for Applied Molecular Evolution in Florida have successfully added four new bases to create what they are calling “hachi-moji DNA” (eight-letter DNA in Japanese), doubling the potential information density of genetic code.

This isn’t the first attempt at expanding the genetic code. In 2014, scientists at the Scripps Research Institute in California unveiled DNA with two extra bases, and in 2017 they showed that they could get bacteria to use this code to build proteins that don’t exist in nature. But the new work not only adds an extra two bases, it also sticks more closely to the blueprint used by nature.

The double helix of DNA is held together by hydrogen bonds between complementary bases—A pairs with T and C pairs with G. The Scripps research used water-repelling molecules that stick together but repel the other bases. These bases need to be sandwiched between natural bases, so it’s not possible to have extended stretches of unnatural bases limiting what they can code for.

Hachi-moji DNA, however, uses hydrogen bonds just like natural DNA to link its two new pairs—S with B and P with Z—and the bases are also capable of appearing next to each other. Because DNA is read in triplets of bases called codons, each of which codes for a particular amino acid, this significantly increases the number of potential codons compared to the previous approach: 4,096 compared to conventional DNA’s 64.

The experiments also suggest hachi-moji DNA preserves all the key characteristics required to support Darwinian evolution, crucial for supporting life. The bases pair reliably, the structure remains stable regardless of the sequence of bases, and they’ve demonstrated that it can be copied into RNA.

That’s crucial, because while DNA holds the blueprints for an organism, in order for cells to do anything with that information it has to be converted into the mobile, single-stranded molecule RNA, which can act as instructions for protein factories called ribosomes or can help regulate genes.

In terms of potential uses for the new letters, the possibilities are broad. All of nature’s complexity has been created from the 20 amino acids conventional DNA can produce (multiple codons code for the same amino acid). New codons make it possible to code for new amino acids with novel properties, which could enable everything from more powerful medicines and industrial catalysts to more outlandish ideas, like electrically-conducting proteins.

That will require a huge amount of work on tools that can take advantage of the new code, though, the scientists behind the research admitted to Wired. A potentially nearer-term goal might be to take advantage of the extra information density to boost efforts to see DNA as a super-compact and stable form of long-term data storage.

Perhaps the biggest contribution of the research is the window it gives us into the potential forms life could take. The new code is a long way from supporting self-sustaining organisms—the researchers have yet to demonstrate that the code can be replicated by cells, and it is reliant on supplies of lab-created building blocks that aren’t available in nature.

But the fact that you can replicate the form and function of DNA with very different constituent parts suggests that life beyond Earthmay be unlike anything we have seen before. The research was funded by NASA, and representatives told CNN that they hope it will help them expand the scope of their search for extraterrestrial life.

Saturday, February 23, 2019

No Nuclear missiles in space, please!

Gentle People:

I do not appreciate a potential for nuclear explosions in outer space polluting the atmosphere that protects life on Earth! Thanks to Donald Trump and his new space force, the possibility of nuclear explosions in space ripping away and polluting our thin layer of atmosphere now becomes a U.S. Republican political reality. I doubt if anybody else on Earth will take the U.S. president seriously because the consequences of a race to arm space with deadly Nukes or Lasers will be disasterous to the co-operation presently existing between technological nations. The International Space Station is a good example of the de-tente existing between countries interested in developing outer space for the benefit of humanity. It is basically a United Nations in space and its neutrality must be protected from political megalomaniacs and dictators back down on Earth.

It is possible to ring the Earth with dangerous satelites capable of destroying each other and possibly harboring a Nuclear war head or Two and that possibility must be banned here and now! We must create another international Non-Proliferation Treaty with outer space included in the treaty.

We only have approximately Three miles of atmosphere between us and the dark cold void of space and destroying that atmosphere won't take long if we allow it to happen! The good news is that World Scientists and every Astronaut connected with the International Space Program have bonded in friendship and believe that space is a good place for creating science experiments aimed at helping humanity. For decades the I.S.S. has housed Astronaut Scientists from around the world working together without fear of political interference from dominating governments. That will continue long after dictators have been removed from office.

The Nuclear Non-Proliferation Treaty (NPT), 1968

The Nuclear Non-Proliferation Treaty was an agreement signed in 1968 by several of the major nuclear and non-nuclear powers that pledged their cooperation in stemming the spread of nuclear technology. Although the NPT did not ultimately prevent nuclear proliferation, in the context of the Cold War arms race and mounting international concern about the consequences of nuclear war, the treaty was a major success for advocates of arms control because it set a precedent for international cooperation between nuclear and non-nuclear states to prevent proliferation.

After the United States and the Soviet Union signed the Limited Test Ban Treaty in 1963, leaders of both nations hoped that other, more comprehensive agreements on arms control would be forthcoming. Given the excessive costs involved in the development and deployment of new and more technologically advanced nuclear weapons, both powers had an interest in negotiating agreements that would help to slow the pace of the arms race and limit competition in strategic weapons development. Four years after the first treaty, the two sides agreed to an Outer Space Treaty that prevented the deployment of nuclear weapons systems as satellites in space. Of far greater import, Soviet and U.S. negotiators also reached a settlement on concluding an international non-proliferation treaty.

By the beginning of the 1960s, nuclear weapons technology had the potential to become widespread. The science of exploding and fusing atoms had entered into public literature via academic journals, and nuclear technology was no longer pursued only by governments, but by private companies as well. Plutonium, the core of nuclear weapons, was becoming easier to obtain and cheaper to process. As a result of these changes, by 1964 there were five nuclear powers in the world: in addition to the United States, the Soviet Union, and the United Kingdom, all of which obtained nuclear capability during or shortly after the Second World War, France exploded its first nuclear bomb in 1960, and the People's Republic of China was not far behind in 1964. There were many other countries that had not yet tested weapons, but which were technologically advanced enough that should they decide to build them, it was likely that they could do so before long.

The spread of nuclear weapons technology meant several things for international lawmakers. While the only countries that were capable of nuclear strike were the United States, its close ally Britain, and the Soviet Union, the doctrine of deterrence could be reasonably maintained. Because both sides of the Cold War had vast stocks of weapons and the capability of striking back after being attacked, any strike would likely have led to mutually assured destruction, and thus there remained a strong incentive for any power to avoid starting a nuclear war. However, if more nations, particularly developing nations that lay on the periphery of the balance of power between the two Cold War superpowers, achieved nuclear capability, this balance risked being disrupted and the system of deterrence would be threatened. Moreover, if countries with volatile border disputes became capable of attacking with nuclear weapons, then the odds of a nuclear war with truly global repercussions increased. This also caused the nuclear states to hesitate in sharing nuclear technology with developing nations, even technology that could be used for peaceful applications. All of these concerns led to international interest in a nuclear non-proliferation treaty that would help prevent the spread of nuclear weapons.

Although the benefits to be derived from such a treaty were clear, its development was not without controversy. A ban on the distribution of nuclear technology was first proposed by Ireland in a meeting of the General Assembly of the United Nations in 1961. Although the members approved the resolution, it took until 1965 for negotiations to begin in earnest at the Geneva disarmament conference. At that time, U.S. negotiators worked to strike a delicate balance between the interest in preventing further transfer of the technology that it shared with the Soviet Union and the desire to strengthen its NATO allies by giving several Western European nations some measure of control over nuclear weapons. The plan for a nuclear NATO threatened to scuttle the talks altogether, and the United States eventually abandoned it in favor of reaching a workable treaty. A more difficult problem involved the question of bringing non-nuclear nations into line with the planned treaty. Nations that had not yet developed nuclear weapons technology were essentially being asked to give up all intentions to ever develop the weapons. Without this agreement on the part of the non-nuclear powers, having the nuclear powers vow never to transfer the technology would likely not result in any real limitation on the number of worldwide nuclear powers. After two years of negotiations, the nuclear powers managed to make enough concessions to induce many non-nuclear powers to sign.

The final treaty involved a number of provisions all aimed at limiting the spread of nuclear weapons technology. First, the nuclear signatories agreed not to transfer either nuclear weapons or nuclear weapons technology to any other state. Second, the non-nuclear states agreed that they would not receive, develop or otherwise acquire nuclear weapons. All of the signatories agreed to submit to the safeguards against proliferation established by the International Atomic Energy Agency (IAEA). Parties to the treaty also agreed to cooperate in the development of peaceful nuclear technology and to continue negotiations to help end the nuclear arms race and limit the spread of the technology. The treaty was given a 25-year time limit, with the agreement that it would be reviewed every 5 years.

The Nuclear Non-Proliferation Treaty was, and continues to be, heralded as an important step in the ongoing efforts to reduce or prevent the spread of nuclear weapons. Still, it had one major drawback in that two nuclear powers, France and the People's Republic of China, did not sign the agreement, nor did a number of non-nuclear states. Of the non-nuclear states refusing to adhere, and thereby limit their own future nuclear programs, of particular importance were Argentina, Brazil, India, Israel, Pakistan, Saudi Arabia and South Africa, because these powers were close to being capable of the technology. In fact, in 1974, India joined the "nuclear club" by exploding its first weapon. Pakistan tested its first atomic bomb in 1983.

Wednesday, February 20, 2019

Juan Enriquez has a genius level intelligence.

https://www.ted.com/talks/juan_enriquez_the_age_of_genetic_wonder_feb_2019?utm_source=newsletter_daily&utm_campaign=daily&utm_medium=email&utm_content=button__2019-02-15#t-1073878
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https://www.ted.com/talks/juan_enriquez_the_age_of_genetic_wonder_feb_2019?utm_source=newsletter_daily&utm_campaign=daily&utm_medium=email&utm_content=button__2019-02-15#t-1073878
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Des outils d'édition de gènes tels que CRISPR nous permettent de programmer la vie à son niveau le plus fondamental. Mais cela soulève des questions pressantes: si nous pouvons générer de nouvelles espèces à partir de rien, que devrions-nous construire? Devrions-nous redéfinir l'humanité telle que nous la connaissons? Juan Enriquez prévoit les futurs possibles de l'édition génétique, explorant l'immense incertitude et les opportunités de cette nouvelle frontière.

Cette conférence a été présentée à un public local à TEDxCERN , un événement indépendant. Les éditeurs de TED ont choisi de le présenter pour vous.

A PROPOS DU CONFÉRENCIER

Juan Enriquez · Futuriste

Juan Enriquez réfléchit et écrit sur les profonds changements que la génomique et la recherche sur le cerveau apporteront dans les domaines des affaires, de la technologie, de la politique et de la société.

PLUS DE RESSOURCES

Nous évoluer: redéfinir l'avenir de l'humanité - un gène à la fois

Juan Enriquez et Steve Gullans

Portefeuille (2016)

Thursday, February 14, 2019

Shelly Xuelai Fan is a neuroscientist at U. of C.

5 Discoveries That Made 2018 a Huge Year for Neuroscience

Shelly Fan

Jan 17, 2019

19,008

2018 was when neuroscience made the impossible possible.

There was the dazzling array of crazy neurotech: paralyzed patients shopped and texted using an Android tablet with just their brain waves; BrainNet let three people collaboratively play a Tetris-like game using their thoughts; a first memory prosthesis boosted recall in humans; and brain-controlled robotic limbs could know their location in space or even add a “third arm” in able-bodied people.

There was the new lineup of exquisitely detailed brain maps that further unveiled the brain’s nooks and crannies: a digital museum, constructed with the help of a quarter million gamers, that showcases every bend and turn of neurons in the mouse’s retina, or a map in which billions of synapses in the mouse brain light up like the starry night.

It was the year that human brain organoids—“mini-brains” that loosely resemble the real thing during fetal development—grew their own blood supply, thrived for months inside mouse brains, and shocked the world by producing electrical patterns that resemble those seen in premature babies, launching a debate on their ethical use.

But that’s not all. Here are five neuroscience findings from 2018 that still blow our minds as we kick off the new year.

1. An infectious side to Alzheimer’s disease

Potential new drugs for Alzheimer’s have all ended up in its notorious graveyard of dreams. Despite best efforts, drugs that target two proteins that build up in Alzheimer’s disease—beta-amyloid and mutant tau—have consistently failed human drug trails.

This year, scientists are beginning to think outside the box, and new theories of how the disease is triggered and progresses are gaining steam.

In October, several studies presented some of the strongest evidence yet that herpes simplex virus type I (HSV1)—the annoying virus responsible for cold sores—may be a potential trigger. Scientists have known since the 1990s that HSV1 confers a large risk for Alzheimer’s in people who carry a specific variant of a gene called APOE4.

Most people get infected with HSV1 as children, and the virus then remains dormant until external cues such as stress reactivate it. The new theory suggests that repeated activation of the virus in adulthood in the brain could cause cumulative damage, particularly in the elderly with declined immune function. If the theory holds water, it means that anti-viral drugs may be a new avenue of treatment.

What’s more, beta-amyloid itself may be transmissible. Using cadaver-derived growth hormones (eww) prepared in the 1980s, a team in Britain injected the sample into mice and found extensive beta-amyloid clumps in their brains. While this doesn’t mean that Alzheimer’s itself is contagious, it does raise concern that medical procedures such as brain surgery could pose a risk for shuttling toxic forms of the protein from one brain to another.

2. Electrical implant restores walking in paralyzed patients

2018 was, without doubt, a breakthrough year for restoring mobility in paralyzed patients.

The technology is several years in the making, with initial positive results in monkeys. It works by implanting a neuroprosthesis into the spinal cord to bypass the site of injury by artificially stimulating remaining nerves.

In September, the Mayo Clinic reported the extraordinary case of Jered Chinnock, who was paralyzed at the waist in 2013. After getting the implant, he walked half the length of a football field. Another report showed that electrical stimulation in four cases was able to help some paralyzed patients go home and get around with only a walker.

Less than a month later, yet another team reported that electrical stimulation using a wireless implant helped three paralyzed patients walk with the aid of crutches or a walker. After a few months of training, the patients could more easily move around even when the stimulation was off, suggesting that the regime had helped remaining healthy nerves rework their connections to adapt and heal.

Electrical stimulation isn’t the only treatment in the works. Another study found that human stem cells, when implanted into monkeys, could synapse with the recipient’s own neurons and restore natural movement after spinal cord injury. These therapies—although expensive and in their infancy—lay a promising road ahead for returning mobility to paralyzed patients.

3. CRISPR barcodes map brain development in exquisite detail

The developing mammalian brain consists of an intricately-choreographed dance of newborn neurons, with each adopting its specific identity and migrating to its home base in the brain. Scientists have long hoped to examine the process in detail, which could help uncover secrets of brain development—and how it goes wrong.

Perhaps unsurprisingly, tracing the history of every single one of the billions of developing cells in the brain has been impossible—until CRISPR came along.

Last August, a team used CRISPR to generate a unique genetic barcode for every single cell in the mouse brain. By reading the barcodes, scientists were able to retrace a cell’s entire history in the developing brain. Like genetic sleuths, the scientists reconstructed entire cellular family trees to show how cells relate to one another.

It’s a technical tour-de-force, and a “holy grail” for developmental biology, earning Science’s Breakthrough of the Year title. The trove of technologies and data are poised to uncover how human cells mature with age, how tissues regenerate, and how the processes go wrong in disease.

4. A new type of neuron in the cortex that’s potentially uniquely human

Perhaps shockingly, even today neuroscientists are still uncovering new cellular components that make up our mighty brains. Last year saw the discovery of giant neurons within the claustrum, a thin sheet of cells that some believe is the seat of consciousness.

This year, the Allen Institute in Seattle is back at it with another finding: rosehip neurons, each containing dense bundles of processes around the cell’s center that make it look like a rose after shedding its petals.

These neurons make up nearly 15 percent of neurons in the outermost layer of the brain that supports high-level cognitive functions. Remarkably, rosehip neurons have never before been seen in mice or other well-studied lab animals. Although the team can’t yet fully conclude that they’re specific to humans, their scarcity within the animal kingdom is intriguing.

The next step is figuring out the functions of these rose-like neurons—in particular, are they partly why our brains are special?—and whether they are linked to neuropsychiatric disorders.

5. Gut-brain connection grows stronger with direct anatomical link

One of the hottest research trends in neuroscience is the link between the brain and the gut—often dubbed the “little brain.”

The human gut is lined with over 100 million nerve cells that allow it to talk to the brain, letting us know when we’re hungry or when we’ve over-indulged. But it’s not all digestion: scientists are increasingly realizing that the gut could contribute to anxiety, depression, or more controversially, cognition.

Last year scientists found a new set of informational highways that directly link the gut to the brain. Within the gut, enteroendocrine cells pump out hormones that kick off digestion and suppress hunger. These cells have little foot-like protrusions that look remarkably like synapses—the structure that neurons use to talk to each other using chemicals.

With the help of a glow-in-the-dark rabies virus, which can jump from synapse to synapse, the team found that enteroendocrine cells directly link to neurons in the vagus nerve—a giant nerve that runs from the brain to vital organs such as the heart and lungs. What’s more, they chat with their partners using classical neurotransmitters including glutamate and serotonin, which work much faster than hormones.

Another study found that the gut directly links to the brain’s reward centers through the vagus nerve. Using lasers to zap sensory neurons in the gut of mice, the scientists found increased levels of mood-boosting dopamine in their brains.

These new connections could explain why vagus nerve stimulation is potentially helpful for those with severe depression. More relevant to the holiday season, it also could explain why eating makes us feel warm and fuzzy.

Uncovering the gut-brain connection is gaining steam as a research field. Eventually, the findings could lead to new treatments for disorders linked to a malfunctioning gut—for example, obesity, eating disorders, depression, or even autism.

Image Credit: wowow / Shutterstock.com

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