dna (8)

The Anatomy of Delta...

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A computer simulation of the structure of the coronavirus SARS-CoV-2.Credit: Janet Iwasa, University of Utah

Topics: Biology, Biotechnology, COVID-19, DNA, Existentialism, Research

The coronavirus sports a luxurious sugar coat. “It’s striking,” thought Rommie Amaro, staring at her computer simulation of one of the trademark spike proteins of SARS-CoV-2, which stick out from the virus’s surface. It was swathed in sugar molecules, known as glycans.

“When you see it with all the glycans, it’s almost unrecognizable,” says Amaro, a computational biophysical chemist at the University of California, San Diego.

Many viruses have glycans covering their outer proteins, camouflaging them from the human immune system like a wolf in sheep’s clothing. But last year, Amaro’s laboratory group and collaborators created the most detailed visualization yet of this coat, based on structural and genetic data and rendered atom-by-atom by a supercomputer. On 22 March 2020, she posted the simulation to Twitter. Within an hour, one researcher asked in a comment: what was the naked, uncoated loop sticking out of the top of the protein?

Amaro had no idea. But ten minutes later, structural biologist Jason McLellan at the University of Texas at Austin chimed in: the uncoated loop was a receptor-binding domain (RBD), one of three sections of the spike that bind to receptors on human cells (see ‘A hidden spike’).

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Source: Structural image from Lorenzo Casalino, Univ. California, San Diego (Ref. 1); Graphic: Nik Spencer/Nature

How the coronavirus infects cells — and why Delta is so dangerous, Megan Scudellari, Nature

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Elephants, Mice, and Clocks...

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Topics: Biology, DNA, Evolution, Research

In her laboratory in Barcelona, Spain, Miki Ebisuya has built a clock without cogs, springs, or numbers. This clock doesn’t tick. It is made of genes and proteins, and it keeps time in a layer of cells that Ebisuya’s team has grown in its lab. This biological clock is tiny, but it could help to explain some of the most conspicuous differences between animal species.

Animal cells bustle with activity, and the pace varies between species. In all observed instances, mouse cells run faster than human cells, which tick faster than whale cells. These differences affect how big an animal gets, how its parts are arranged, and perhaps even how long it will live. But biologists have long wondered what cellular timekeepers control these speeds, and why they vary.

A wave of research is starting to yield answers for one of the many clocks that control the workings of cells. There is a clock in early embryos that beats out a regular rhythm by activating and deactivating genes. This ‘segmentation clock’ creates repeating body segments such as the vertebrae in our spines. This is the timepiece that Ebisuya has made in her lab.

“I’m interested in biological time,” says Ebisuya, a developmental biologist at the European Molecular Biology Laboratory Barcelona. “But lifespan or gestation period, they are too long for me to study.” The swift speed of the segmentation clock makes it an ideal model system, she says.

These cellular clocks help explain why elephants are bigger than mice, Michael Marshall, Nature

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VOC...

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Inside the B.1.1.7 Coronavirus Variant, By Jonathan Corum and Carl ZimmerJan, The New York Times, January 18, 2021

Topics: Biology, COVID-19, DNA, Research

VariantReported cases in the USNumber of Jurisdictions Reporting
B.1.1.716,27552
B.1.35138636
P.135625
Source: CDC

Download Accessible Data [XLS – 738 B]

CDC is closely monitoring these variants of concern (VOC). These variants have mutations in the virus genome that alter the characteristics and cause the virus to act differently in ways that are significant to public health (e.g., causes more severe disease, spreads more easily between humans, requires different treatments, changes the effectiveness of current vaccines).

CDC: US COVID-19 Cases Caused by Variants

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Women's History Month, and CRISPR...

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Topics: Biology, Chemistry, DNA, Nobel Prize, Research, Women in Science

This year’s (2020) Nobel Prize in Chemistry has been awarded to two scientists who transformed an obscure bacterial immune mechanism, commonly called CRISPR, into a tool that can simply and cheaply edit the genomes of everything from wheat to mosquitoes to humans. 

The award went jointly to Emmanuelle Charpentier of the Max Planck Unit for the Science of Pathogens and Jennifer Doudna of the University of California, Berkeley, “for the development of a method for genome editing.” They first showed that CRISPR—which stands for clustered regularly interspaced short palindromic repeats—could edit DNA in an in vitro system in a paper published in the 28 June 2012 issue of Science. Their discovery was rapidly expanded on by many others and soon made CRISPR a common tool in labs around the world. The genome editor spawned industries working on making new medicines, agricultural products, and ways to control pests.

Many scientists anticipated that Feng Zhang of the Broad Institute, who showed 6 months later that CRISPR worked in mammalian cells, would share the prize. The institutions of the three scientists are locked in a fierce patent battle over who deserves the intellectual property rights to CRISPR’s discovery, which some estimate could be worth billions of dollars.

“The ability to cut DNA where you want has revolutionized the life sciences. The genetic scissors were discovered 8 years ago, but have already benefited humankind greatly,” Pernilla Wittung Stafshede, a chemical biologist at the Chalmers University of Technology, said at the prize briefing.

CRISPR was also used in one of the most controversial biomedical experiments of the past decade, when a Chinese scientist edited the genomes of human embryos, resulting in the birth of three babies with altered genes. He was widely condemned and eventually sentenced to jail in China, a country that has become a leader in other areas of CRISPR research.

Although scientists were not surprised Doudna and Charpentier won the prize, Charpentier was stunned. “As much as I have been awarded a number of prizes, it’s something you hear, but you don’t completely connect,” she said in a phone call with the Nobel Prize officials. “I was told a number of times that when it happens, you’re very surprised and feel that it’s not real.”

At a press briefing today, Doudna noted she was asleep and missed the initial calls from Sweden, only waking up to answer the phone finally when a Nature reporter called. "She wanted to know if I could comment on the Nobel and I said, Well, who won it? And she was shocked that she was the person to tell me."

CRISPR, the revolutionary genetic ‘scissors,’ honored by Chemistry Nobel, Jon Cohen, Science Magazine, AAAS

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Our Flexible Molecule...

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1 Soap, shampoo, and worm-like micelles Soaps and shampoos are made from amphiphilic molecules with water-loving (red) and water-hating (blue) parts that arrange themselves to form long tubes known as “worm-like micelles”. Entanglements between the tubes give these materials their pleasant, sticky feel. b The micelles can, however, disentangle themselves, just as entangled long-chain polymer molecules can slide apart too. In polymers, this process can be modeled by imagining the molecule sliding, like a snake, out of an imaginary tube formed by the surrounding spatial constraints. c Worm-like micelles can also morph their architecture by performing reconnections (left), breakages (down), and fusions (right). These operations occur randomly along the backbone, are in thermal equilibrium, and reversible. (Courtesy: Davide Michieletto)

Topics: Biology, DNA, Physics, Polymer Science, Research

DNA molecules are not fixed objects – they are constantly getting broken up and glued back together to adopt new shapes. Davide Michieletto explains how this process can be harnessed to create a new generation of “topologically active” materials.

Call me naïve, but until a few years ago I had never realized you can actually buy DNA. As a physicist, I’d been familiar with DNA as the “molecule of life” – something that carries genetic information and allows complex organisms, such as you and me, to be created. But I was surprised to find that biotech firms purify DNA from viruses and will ship concentrated solutions in the post. In fact, you can just go online and order DNA, which is exactly what I did. Only there was another surprise in store.

When the DNA solution arrived at my lab in Edinburgh, it came in a tube with about half a milligram of DNA per centimeter cube of water. Keen to experiment on it, I tried to pipette some of the solution out, but it didn’t run freely into my plastic tube. Instead, it was all gloopy and resisted the suction of my pipette. I rushed over to a colleague in my lab, eagerly announcing my amazing “discovery”. They just looked at me like I was an idiot. Of course, solutions of DNA are gloopy.

I should have known better. It’s easy to idealize DNA as some kind of magic material, but it’s essentially just a long-chain double-helical polymer consisting of four different types of monomers – the nucleotides A, T, C, and G, which stack together into base pairs. And like all polymers at high concentrations, the DNA chains can get entangled. In fact, they get so tied up that a single human cell can have up to 2 m of DNA crammed into an object just 10 μm in size. Scaled up, it’s like storing 20 km of hair-thin wire in a box no bigger than your mobile phone.

Make or break: building soft materials with DNA, Davide Michieletto is a Royal Society university research fellow in the School of Physics and Astronomy, University of Edinburgh

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ATCG Drive...

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MGM/VICTOR TANGERMANN

 

Topics: Biology, Computer Science, DNA

Why cannot we write the entire 24 volumes of the Encyclopedia Britannica on the head of a pin? Dr. Richard P. Feynman, "There's Plenty of Room at the Bottom," said to be the seminal talk that started the concept of atomic-level engineering, soon known as nanotechnology, (named by Professor Norio Taniguchi, 1974, of the Tokyo Science University).

The intricate arrangement of base pairs in our DNA encodes just about everything about us. Now, DNA contains the entirety of “The Wonderful Wizard of Oz” as well.

A team of University of Texas Austin scientists just vastly improved the storage capacity of DNA and managed to encode the entire novel — translated into the geek-friendly language of Esperanto — in a double strand of DNA far more efficiently than has been done before. DNA storage isn’t new, but this work could help finally make it practical.

Big tech companies like Microsoft are already exploring DNA-storage technology, as the biomolecule can encode several orders of magnitude more information per unit volume than a hard drive. But DNA is particularly error-prone. It can easily be damaged and erase whatever’s stored on it.

“The key breakthrough is an encoding algorithm that allows accurate retrieval of the information even when the DNA strands are partially damaged during storage,” molecular biologist Ilya Finkelstein said in a UT Austin press release.

Scientists Stored "The Wizard of Oz" on a Strand of DNA, Dan Robitzgi, Futurism

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Snake Oil...

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Image Source: Link below


Topics: Biology, DNA, Genetics


"Extraordinary claims require extraordinary evidence." Carl Sagan

I'm guessing "I did Ancestry" is going to become the "I used to do Amway" in the 21st Century?

I participated, thinking it was legitimate science. It did somewhat jive with my own experiences of being consistently identified by Nigerians as resembling someone from the Igbo. This again is pure conjecture, and likely only a polite guess.
 

I can see the desire to know about our roots, especially if you're a part of the African Diaspora is tempting as well as an opportunity for confidence rackets and quackery.

In the spring of 2017, a college student named Mary spit into a tube and sent it to the DNA testing company Ancestry, which analyzed it and sent back a breakdown of her family history.

But Mary wanted to know more. The human genome contains, in theory, an extraordinary wealth of pre-programmed information about who we are and who we might become: whether she was at risk for the same types of cancer that killed her parents, for instance, or if she had medical conditions she could unknowingly pass on to her children.

For that information, Mary — we’re withholding her last name to protect her privacy — turned to a dubious new sector of the genomics industry, in which startups claim to provide vastly greater insights than prominent companies like Ancestry and 23andMe do. She uploaded a copy of her raw genetic code, which Ancestry provided as a 17.6 megabyte text file, to a site called Genomelink, which advertises tests for everything from medical conditions and mental illnesses to ludicrously specific personality traits including “loneliness,” “social communication problems,” and “vulnerability to helicopter parenting.”

But when her results arrived, Mary immediately noticed that many were “wildly inaccurate.” Genomelink said she was “less easily depressed,” but Mary was diagnosed with clinical depression at a young age. The startup predicted that she had a peanut allergy, but Mary told Futurism that “peanut butter is one of the true loves of my life.” Other errors in Mary’s report included traits like blood iron levels, body fat measurements, hearing problems, height, and skin complexion.

“I felt that much of it was off-base and unhelpful,” she told Futurism, “as it didn’t fit me at all.”

Genomelink is just one of a growing number of shady DNA testing startups now operating in the regulatory Wild West of commercial genomics.

There’s GenePlaza, for instance, which sold a DNA test that claimed to predict users’ sexual preferences — and still sells tests that purport to measure intelligence and risk of depression. A company called Soccer Genomics claims to examine a child’s DNA to create a sports training regimen to turn them into the perfect soccer player. An outfit called GenoPalate told a Milwaukee Journal Sentinel reporter that their DNA demanded a diet of elk meat and passion fruit. A venture called Vinome claims it can recommend the perfect wine for each person based on their genetic code.

The problem, according to experts, is that these companies are promising information about DNA with a granularity that even scientists can’t deliver. Deanna Church, a geneticist at the biotech company Inscripta, told Futurism the tests are “all equally useless.”

“There is not a scientific basis for this sort of testing,” she said. “I certainly would not recommend anyone spend any money on this sort of thing.”

 

"Like Horoscope Readings!": The Scammy World of DNA Startups, Dan Robitzki, Futurism

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Distant Cousins...

Callao Cave, Luzon Island, The Philippines

Image credits:
Callao Cave Archaeology Project

 

Topics: Biology, DNA, Evolution, History, Research


(Inside Science) -- In a jungle cave in the Philippines, scientists have discovered fossils of what may be a new human species they call Homo luzonensis. The newfound teeth and bones combine primitive and modern traits in a way never previously seen together in one species, and suggest much remains to be discovered about human evolution outside Africa.
 
Image Source: Homo luzonensis

Although modern humans, Homo sapiens, are now the only surviving branch of the genus Homo, other species of humans once roamed across Earth. For example, previous research suggested Homo erectus, the most likely ancestor of modern humans, made its way out of Africa by at least 1.8 million years ago. In contrast, modern humans may have only begun dispersing from Africa roughly 200,000 years ago.

Fifteen years ago, scientists revealed an unusual extinct human species from the Indonesian island of Flores -- Homo floresiensis, often called "the hobbit" due to its diminutive size, which lived on Earth during the same time as modern humans. This finding hinted that other hominins -- any relatives of modern humans dating from after our ancestors split from those of chimpanzees -- might await discovery in Southeast Asia.
 

Researchers Find a New Ancient Human Species in the Philippines
Charles Q. Choi, Live Science

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