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Cometeer is 100% brewed coffee, flash frozen and delivered to your door. Head to cometeer.com and use code “SCISHOW30” and you’ll get 30% off your first order plus free shipping! [ intro ] When we talk about DNA as a code, this can obscure a basic fact: working with genetic material in the lab is complicated.

I mean on a physical level. It’s a long, twisty, sticky molecule. And working up from there, cells are full of stuff that gets in the way.

Meaning scientists need to be crafty to develop techniques for studying genetics in different living things. And you might be surprised by where they have needed such strategies. Like, birds.

As in, all of them, in general. So today we’re going to talk about a few surprising ways that genetics and genetic engineering have been, like hard. And it goes to show how studying genetics involves a little more than reading off a sequence of letters.

But first, a quick refresher on

DNA: At the smallest level, DNA is made of building blocks called nucleotides. These make up DNA’s four-letter code: A for adenine, T for thymine, G for guanine, and C for cytosine. Nucleotides buddy up in a predictable pattern: A with T and G with C, called ‘base pairs’ when they’re together. A portion of DNA that has a function is called a gene.

All of the DNA that codes for a living thing, together, is called a genome. And almost every cell has at least one copy of the genome packed into it. To study a genome, first, scientists need to break the DNA out of a cell.

Then they need to isolate the DNA, and get rid of the cell gunk. Then they can sequence the genome, which means detecting and listing billions of base pairs in the right order. And bird genomes present a special challenge.

The chicken genome was the first bird genome sequenced, in 2004. And scientists were surprised by the apparent absence of genes that they expected a chicken to have. Even though the chicken genome sequence has been updated since then, researchers still haven’t been able to find over two thousand genes that we know are needed in humans, mice, and zebrafish.

And if these genes look similar in other vertebrates, we have to explain why they’re not showing up the same way in chickens. And not just chickens. A paper published in 2021 scoured eight bird genomes for 15,000 common vertebrate genes.

From what we know about evolution, birds should have these genes. But scientists have struggled to find about 1,000 of them in any of the eight genomes. Maybe birds have evolved new genes to replace the ones scientists expect.

But there’s another explanation: maybe the chemical composition of bird DNA makes us bad at reading it. Bases are in the middle of the double helix, so you need to separate the base pairs if you want to read the DNA. That means unzipping the intermolecular interactions called hydrogen bonds that connect base pairs.

A-T pairs have two bonds, but G-C pairs have three, so it takes more energy to separate G-C pairs. So strands with a lot of A-T pairs would ideally be unzipped in different conditions than those with a lot of G-C pairs. Standard sequencing techniques work best for genomes with an even mix of base pairs.

Unfortunately, that means DNA sequences with a lot of AT or a lot of GC base pairs don’t come out so well. And research has shown that birds have really important genes with a ton of GC base pairs. Genes involved in flight muscle metabolism, that birds need in life-or-death scenarios, were once considered ‘missing’ genes.

By using creative techniques to reduce GC bias and look at other genetic material, scientists have finally found those genes in chicken DNA. Chickens can’t hide their secrets forever. GC content is a technical problem that stems from the level of base pairs.

But DNA is organized into enormous molecules called chromosomes, and they introduce their own set of headaches. Since the 1950s, scientists have altered rice and wheat to increase yields and feed more people. But potatoes?

Not so much. Only in March 2022 did scientists finally publish a full potato genome sequence. The reason it took so long is because of how potato chromosomes work.

Humans have 23 pairs of chromosomes, so 46 total. The term for this is diploid, meaning two copies of each chromosome is the rule. Since 2011, scientists have relied on diploid reference genomes for potatoes.

That’s basically a genome sequence uploaded to a database for researchers to work from. But potatoes are actually tetraploid. That means they have four copies of each of their 12 chromosomes.

What’s more, there appear to be some shenanigans as far as what genes appear where. Genes are written backwards, located on unexpected parts of a chromosome, found multiple times on one chromosome, or aren’t present on all four chromosomes. It’s like the world’s worst word search, where first, you have to extract the puzzle board from a potato.

Repetition, in particular, is the worst enemy of the most commonly used sequencing methods. They rely on breaking many copies of the genome into much smaller pieces, and then putting them back together by matching up the overlapping ends. So sorting out sets of four is way more of a nightmare than sets of two.

Because each chromosome in a set of four looked a little different, the researchers needed to be sure that they reconstructed the correct code for each one. So they took a clever approach using potato pollen grains. Pollen grains, being reproductive cells, have pairs of chromosomes, instead of sets of four.

They looked at one pollen grain at a time so they could be absolutely sure they had only two chromosomes. This allowed them to finally assemble a proper draft sequence. This is a necessary tool to help researchers understand how potatoes grow, and how to make them better food crops.

Lastly, even once you have a good way to handle chromosomes, DNA still comes in cells. And some cells make Fort Knox look easy to get into. In February 2022, researchers published the first successful methods for genetically modifying ticks.

Ticks carry nasty illnesses like Lyme disease. So why has it taken so long to get in there and edit some DNA to stop them? DNA editing needs to happen while an animal is still a young embryo.

Tick embryos develop in eggs, and eggs are designed to protect embryos. Tick eggs are covered in wax, and they have high internal pressure. Plus, the embryo has a hard outer membrane called a chorion.

All of these factors made it tricky for scientists to put a tiny syringe through the egg and into the embryo to inject new DNA. So how do you change tick eggs if you can’t yet edit the genes? The old fashioned way: with some Tick surgery.

Scientists removed the wax-producing organ from momma ticks, and a day later, they had wax-free eggs. The team treated those eggs with a salt solution to remove the chorion and reduce the internal pressure. Then they could inject the DNA for the gene editing tool CRISPR/Cas9, and edited in a gene for bigger mouthparts to provide visual proof that it worked.

This breakthrough means we can start doing genetic work in ticks to make progress preventing tick-borne disease. So while we can’t just snap our fingers and edit DNA, scientists are pretty handy at finding workarounds. Molecular biologists are still biologists, and biologists know they have to deal with the beautiful, glorious messiness of living things.

So on every scale that genetics can make itself a nuisance, there’s a solution that furthers our understanding of life. Tricky experiments like these require a lot of patience, a lot of skill… and, we’re willing to bet, a lot of coffee. Maybe some of these scientists would appreciate today’s sponsor, Cometeer.

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