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How can you write data to DNA without changing the base sequence?

29 October 2024 at 14:32

Zettabytes—that’s 1021 bytes—of data are currently generated every year. All of those cat videos have to be stored somewhere, and DNA is a great storage medium; it has amazing data density and is stable over millennia.

To date, people have encoded information into DNA the same way nature has, by linking the four nucleotide bases comprising DNA—A, T,  C, and G—into a particular genetic sequence. Making these sequences is time-consuming and expensive, though, and the longer your sequence, the higher chance there is that errors will creep in.

But DNA has an added layer of information encoded on top of the nucleotide sequence, known as epigenetics. These are chemical modifications to the nucleotides, specifically altering a C when it comes before a G. In cells, these modifications function kind of like stage directions; they can tell the cell when to use a particular DNA sequence without altering the “text” of the sequence itself. A new paper in Nature describes using epigenetics to store information in DNA without needing to synthesize new DNA sequences every time.

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Is accidentally stumbling across the unknown a key part of science?

7 September 2024 at 11:00
The First Combat of Gav and Talhand', Folio from a Shahnama (Book of Kings), ca. 1330–40, Attributed to Iran, probably Isfahan, Ink, opaque watercolor, gold, and silver on paper, Page: 8 1/16 x 5 1/4 in. (20.5 x 13.3 cm), Codices, Three battles between two Indian princes - half brothers contending for the throne - resulted in the invention of the game of chess, to explain the death of one of them to their grieving mother. The Persian word shah mat, or checkmate, indicating a position of no escape, describes the plight of Talhand at the end of the third battle. (Photo by: Sepia Times/Universal Images Group via Getty Images)

Enlarge / The First Combat of Gav and Talhand', Folio from a Shahnama (Book of Kings), ca. 1330–40, Attributed to Iran, probably Isfahan, Ink, opaque watercolor, gold, and silver on paper, Page: 8 1/16 x 5 1/4 in. (20.5 x 13.3 cm), Codices, Three battles between two Indian princes - half brothers contending for the throne - resulted in the invention of the game of chess, to explain the death of one of them to their grieving mother. The Persian word shah mat, or checkmate, indicating a position of no escape, describes the plight of Talhand at the end of the third battle. (Photo by: Sepia Times/Universal Images Group via Getty Images)

The three princes of Sarandib—an ancient Persian name for Sri Lanka—get exiled by their father the king. They are good boys, but he wants them to experience the wider world and its peoples and be tested by them before they take over the kingdom. They meet a cameleer who has lost his camel and tell him they’ve seen it—though they have not—and prove it by describing three noteworthy characteristics of the animal: it is blind in one eye, it has a tooth missing, and it has a lame leg.

After some hijinks the camel is found, and the princes are correct. How could they have known? They used their keen observational skills to notice unusual things, and their wit to interpret those observations to reveal a truth that was not immediately apparent.

It is a very old tale, sometimes involving an elephant or a horse instead of a camel. But this is the version written by Amir Khusrau in Delhi in 1301 in his poem The Eight Tales of Paradise, and this is the version that one Christopher the Armenian clumsily translated into the Venetian novel The Three Princes of Serendip, published in 1557; a publication that, in a roundabout way, brought the word “serendipity” into the English language.

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Nitrogen-using bacteria can cut farms’ greenhouse gas emissions 

1 June 2024 at 11:00
A tractor amidst many rows of small plants, with brown hills in the background.

Enlarge (credit: Timothy Hearsum)

Fritz Haber: good guy or bad guy? He won the Nobel Prize in Chemistry in 1918 for his part in developing the Haber-Bosch process, a method for generating ammonia using the nitrogen gas in air. The technique freed agriculture from the constraint of needing to source guano or manure for nitrogen fertilizer and is widely credited for saving millions from starvation. About half of the world’s current food supply relies on fertilizers made using it, and about half of the nitrogen atoms in our bodies can be traced back to it.

But it also allowed farmers to use this newly abundant synthetic nitrogen fertilizer with abandon. This has accentuated agriculture’s role as a significant contributor to global warming because the emissions that result from these fertilizers is a greenhouse gas—one that has a warming potential almost 300 times greater than that of carbon dioxide and remains in the atmosphere for 100 years. Microbes in soil convert nitrogen fertilizer into nitrous oxide, and the more nitrogen fertilizer they have to work with, the more nitrous oxide they make.

Agriculture also leaks plenty of the excess nitrogen into waterways in the form of nitrate, generating algal blooms that create low-oxygen ‘dead zones’ where no marine life can live.

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Mutations in a non-coding gene associated with intellectual disability

31 May 2024 at 17:30
Colored ribbons that represent the molecular structure of a large collection of proteins and RNAs.

Enlarge / The spliceosome is a large complex of proteins and RNAs. (credit: NCBI)

Almost 1,500 genes have been implicated in intellectual disabilities; yet for most people with such disabilities, genetic causes remain unknown. Perhaps this is in part because geneticists have been focusing on the wrong stretches of DNA when they go searching. To rectify this, Ernest Turro—a biostatistician who focuses on genetics, genomics, and molecular diagnostics—used whole genome sequencing data from the 100,000 Genomes Project to search for areas associated with intellectual disabilities.

His lab found a genetic association that is the most common one yet to be associated with neurodevelopmental abnormality. And the gene they identified doesn’t even make a protein.

Trouble with the spliceosome

Most genes include instructions for how to make proteins. That’s true. And yet human genes are not arranged linearly—or rather, they are arranged linearly, but not contiguously. A gene containing the instructions for which amino acids to string together to make a particular protein—hemoglobin, insulin, albumin, whatever protein you like—is modular. It contains part of the amino acid sequence, then it has a chunk of DNA that is largely irrelevant to that sequence, then a bit more of the protein’s sequence, then another chunk of random DNA, back and forth until the end of the protein. It’s as if each of these prose paragraphs were separated by a string of unrelated letters (but not a meaningful paragraph from a different article).

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