Chapter 3: Genomics, Proteomics, and Related Approaches to Physiology

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Imagine this,

a fish with blood as clear as ice.

Seriously, almost ghost -like.

That's where we're starting this deep dive.

Today, it's a journey into, well, the real cutting edge of animal physiology, genetics, and just the incredible ways life adapts.

We're getting our info straight from a really key text in the field, our mission, to unpack the story of the Antarctic icefish.

How does it survive extreme cold without red blood?

You know, the very thing we link with oxygen.

And we'll also explore the powerful scientific tools we have now that let us understand these biological marvels.

How scientists tackle these huge questions.

Yeah, and what's really fascinating, I think, is how this icefish, I mean,

its physiology is completely unique, right?

But it still functions like a pretty ordinary fish in its own world.

Gives us this amazing lens to look at fundamental physiological ideas from tiny cell stuff right up to the whole animal and, you know, how scientists use comparisons, genetics, experiments, all that stuff to figure out why these adaptations matter.

Okay, let's get into it then.

How did these incredible creatures end up being so, so different?

Right, the icefish.

That ghostly look.

There are actually 16 species we know of.

And like you said, clear blood.

It's because they don't have hemoglobin.

Not at all.

Which is, you know, what usually makes blood red in fish.

And well, us, theirs is more translucent, whitish even.

The discovery story is pretty cool too.

Back in the 1920s and then again in the 50s, this Norwegian biologist, Johan Rude, he heard reports from whalers about these bloodless fish they said their gills were white and if you cut them just this whitish liquid came out.

So Rude checked it out, confirmed they do have blood, just, you know, no hemoglobin, no red cells that really put them on the biological map.

Wow, that's just mind -bending.

I mean, you'd think losing hemoglobin, something so basic, would be crippling, wouldn't it?

But you're saying they're not rare or tiny.

Not at all.

Some species were even fished commercially for a while and several get pretty big, like up to half a meter long.

Some are even quite active swimmers moving up and down the water column daily.

So how do they pull it off?

How do they survive what looks like this massive disadvantage?

It really comes down to where they live.

The Antarctic seas, they are persistently cold, like minus 1 .9 degrees Celsius cold.

And that cold does two key things.

First, it slows down their metabolism, so they just don't need as much oxygen.

And second, and this is crucial, cold water holds a lot more dissolved oxygen, both the seawater and their own body fluids.

So oxygen can just dissolve directly into their blood plasma and get transported around that way.

No hemoglobin needed.

They evolved around 30 million years ago after the Antarctic got isolated and way colder.

That created this very specific niche.

Okay, that makes sense, adapting to the extreme cold.

But it still begs the question for me, how did they actually lose the ability to make hemoglobin?

Was it just gone one day?

Yeah, good question.

To get that, we need a quick look at hemoglobin itself, the protein part.

In vertebrates, it's usually made of two alpha chains, or globins, and two beta globins.

These globin genes are ancient, really ancient.

Part of a gene family you find even in bacteria and yeast,

deep evolutionary roots.

In fish, these alpha and beta genes are typically pretty close together on the same chromosome.

Right, and this is where the modern tools come in, yeah?

Like molecular genetics using things like PCR.

Exactly.

PCR, polymerase chain reaction lets scientists take tiny bits of DNA and make millions of copies.

Yeah.

Like a molecular photocopier.

So they could finally zoom right in on the icefish globin genes.

What did they see?

It was, well, astonishing.

In 15 out of the 16 icefish species, the DNA is changed in exactly the same way.

The gene for beta globin, completely gone, deleted, and the alpha globin gene, it's missing key parts, so it's non -functional.

A big chunk of DNA just vanished during their evolution.

15 out of 16, the same way, that's specific.

It is, and when scientists mapped this onto an evolutionary tree, you know, one they built using mitochondrial DNA, which is totally separate from globin genes, it showed something really clearly.

This big deletion happened once,

just once, in a common ancestor to all the modern icefish we see today.

So every icefish species out there basically inherited this same single loss event.

Okay, only happened once.

So,

was losing hemoglobin actually good for them, or was it bad?

Like, was it some weird advantage or just a defect they had to deal with?

The consensus is, it was probably a disadvantage at first.

The fact it only happened once really points that way.

If it were beneficial, you might expect it to pop up independently multiple times, but usually natural selection gets rid of harmful mutations like this.

And the strongest evidence is their physiology.

Icefish have huge hearts, like noticeably bigger compared to red -blooded fish of the same size.

And they pump blood way, way faster.

Their whole circulatory system is ramped up.

These are pretty dramatic changes, suggesting they're compensating, you know, making up for the poor oxygen transport without hemoglobin.

So it wasn't a benefit.

It was more like their bodies had to evolve a workaround for this historical kind of defect.

That's a great way to put it.

A workaround.

Life finds a way.

And, you know, the story gets even more complex when you look at myoglobin.

Ah, myoglobin.

That's the one in muscles, helps get oxygen into the muscle cells.

Exactly.

It helps oxygen diffuse in, and it acts as a little oxygen storage tank inside the muscle.

Most vertebrates have it, especially in heart muscle.

Yeah.

Many icefish have it too.

Their hearts look reddish because of it.

I remember reading some icefish have hearts that are cream colored, like no red tinge at all.

Right.

Those ones lack myoglobin entirely.

And here's the twist.

This loss of myoglobin happened multiple times,

independently.

Unlike the single loss of blood hemoglobin, the myoglobin just vanished on maybe four separate occasions in different icefish lineages.

Four times.

Wow.

So completely different evolutionary path for that protein.

Totally different.

It highlights how diverse evolution can be, even in closely related groups.

These myoglobin -free icefish, they're like natural knockouts.

Natural knockouts, like the lab experiments where scientists deliberately disable a gene.

Precisely.

Yeah.

And we can compare them to, say, lab mice where scientists have experimentally knocked out the myoglobin gene.

What happens in those mice?

They compensate.

They grow more capillaries in their heart muscle.

They circulate blood faster.

It kind of proves how important myoglobin normally is, physiologically,

but it also shows how adaptable the body is.

It finds ways to manage.

These comparisons are a great example of using experimental methods alongside studying natural variation.

That's fascinating.

Okay.

So they solved the oxygen problem with bigger hearts, faster pumping, maybe some lose myoglobin, but Antarctica isn't just about oxygen.

It's about freezing.

How do they not turn into fishicles?

Their body fluids should freeze before the seawater does.

Absolutely right.

Even if the seawater itself isn't frozen solid, it can be cold enough below the freezing point of typical fish blood to freeze them.

So Antarctic fish, including the icefish, have another trick up their sleeve.

Antifreeze glycoproteins, AFGPs, these are amazing molecules.

They basically latch onto any tiny ice crystals that might start to form in the body fluids, and they stop the crystals from growing.

They physically prevent the blood and tissues from freezing solid.

Okay.

Antifreeze proteins.

Makes sense.

And evolutionarily, where did these come from?

Did they evolve after they lost hemoglobin?

That's the interesting part.

These antifreeze genes, they're found in all the icefish, but also in their red -blooded relatives living in the Antarctic.

This tells us the antifreeze genes must have evolved before the icefish lineage split off and lost its hemoglobin.

It was a pre -existing advantage for surviving the cold.

And the origin of these antifreeze genes is pretty wild too, isn't it?

Oh yeah.

It's one of the classic examples of evolutionary innovation.

They're derived from genes that, in most ordinary fish, code for a digestive enzyme made in the pancreas.

Something like trypsinogen.

Seriously.

From a digestive enzyme to antifreeze?

Seriously.

A gene got duplicated, mutated, modified over time, and ended up performing this completely new, absolutely vital function.

It's just a fantastic illustration of how evolution tinkers and repurposes things.

Gene modification leading to totally new proteins.

This whole icefish story diving deep into their genes, their proteins, it really makes you think about how scientists figure all this out.

What are the tools?

What are these new frontiers allowing these kinds of insights?

Well, that brings us squarely into the omics era, starting with genomics.

That's the study of an organism's entire set of genes.

It's genome, all the DNA.

Genomics has sort of two big goals.

One is figuring out how genes and genomes evolved, looking at mechanisms like deletion, like we saw in the icefish, or gene duplication, and basically reconstructing evolutionary history.

The second goal is understanding how those genes function now, predicting what a gene does, often by comparing it to similar genes, homologous genes in other organisms where we already know the functions.

So it's way more than just getting the sequence, the letters of the DNA code.

Oh, absolutely.

You generate massive amounts of data, often using high throughput methods, robotics, computers.

It relies heavily on computational biology and bioinformatics to process it all.

Then comes annotation.

That's where humans interpret the data, adding meaning to the raw sequence.

And critically, all this info gets usually online through the World Wide Web.

It's hugely collaborative.

Can you give an example?

What has genomics shown us beyond the icefish?

Sure.

Take the purple sea urchin genome.

When they sequenced it, they found some really interesting things.

They seem to lack genes for certain common signaling molecules, neurotransmitters like epinephrine or melatonin that suggests maybe unusual ways their cells communicate.

But they had a huge number of genes related to immunity and detoxification, way more than expected.

That hints at really elaborate defense systems, which might maybe explain why they live so long.

Yeah.

And they found genes for making their skeleton that were different from how vertebrates do it.

Plus they found some genes that scientists thought were only found in vertebrates, suggesting our common ancestor had them too, much earlier than we realized.

That is incredible detail.

But hang on, you can't predict everything about the animal just from the genes, can you?

Does knowing the genome tell the whole story?

That's a really, really important point.

No, it doesn't tell the whole story.

Genomic predictions.

This gene probably does X.

They are essentially hypotheses.

They have to be tested.

You have to test them against the actual animal, its phenotype.

That means its observable traits, how it behaves, its biochemistry.

Right.

The blueprint isn't the building.

Exactly.

Knowing the genes is just step one.

You need direct study to see if they're actually turned on, when, where, and what they really do.

Sometimes the function isn't what you predicted based on sequence alone.

So the omics revolution isn't just about the blueprint.

It's about understanding the whole dynamic system, the whole orchestra playing together.

So thinking about research strategies.

Traditionally, physiology often use a top -down approach, right?

Like you see something happening in the animal, say, exercise makes muscles stronger, and then you work downwards.

You look at the tissues involved and the specific proteins, and eventually maybe identify the genes responsible.

Exactly.

Start with the function, drill down to the mechanism.

But now genomics gives us this powerful bottom -up approach, too.

You start with the genome, all the genes, then you look at which ones are being transcribed into RNA, predict the proteins being made from that RNA, and then try to build up a picture of how tissues and the whole animal function.

What's the advantage of starting from the bottom, from the genes?

Well, especially with these high -throughput methods that measure everything at once, it can be incredibly thorough,

unless biased.

You might uncover genes or proteins playing a role that you just wouldn't have thought to look for with a focused top -down approach, things that are completely unexpected.

But I guess the top -down approach still gives you that clear focus on a specific biological question.

Absolutely.

Neither approach replaces the other.

They're synergistic, they work together beautifully.

Top -down gives focus, bottom -up gives breath and discovery potential.

Both are super valuable.

Okay, let's get into some of those specific OMEX tools that let scientists do this bottom -up exploration.

What are we talking about?

Okay, so after genomics, which is the DNA blueprint, we have transcriptomics, some called transcription profiling.

This is all about studying which genes are actually being used or transcribed into messenger RNA, mRNA, at a particular time in a particular tissue, and how much.

So not just whether the gene exists, but whether it's switched on.

Exactly.

Is it active?

How active?

Tools like DNA microarrays are key here.

You can essentially get a snapshot, almost like a heat map, showing thousands of genes at once, which ones are ramped up, which are turned down under different conditions, say before and after exercise.

You mentioned exercise.

That's a good real -world example for transcriptomics.

Perfect example.

Studies show that even a single session of endurance exercise turns up the transcription of hundreds of genes in your muscles, things like genes for metabolic enzymes, enzymes in the mitochondria.

These proteins tend to last a while.

So even if the transcription boost each time is modest, doing it day after day builds up those crucial proteins.

That explains that cumulative training effect.

Okay, so it's the buildup.

Right, and we also see daily cycles in gene transcription for lots of things, in rat lungs, even in malaria mosquitoes, which might have implications for when they're most vulnerable to insecticides, for example.

It's all about timing and activity levels.

Okay, so transcriptomics is about the RNA messages.

What's next?

Next level up is proteomics.

This is the study of the actual proteins being made, the workhorses of the cell.

It's distinct from transcriptomics because, well, just because an mRNA message exists doesn't automatically mean a protein gets made or how much or for how long it lasts.

You need to look directly at the proteins.

And how do you do that?

Look at thousands of proteins at once.

A classic technique is called two -dimensional or 2D gel electrophoresis.

It's pretty neat.

You separate the proteins first based on their electrical charge, their isoelectric point in one direction.

Then you separate them by their size, their molecular weight.

In a second direction, perpendicular to the first, what you get is this gel with potentially thousands of spots where each spot is ideally a different protein.

You can compare patterns between different samples,

say muscle from trained versus untrained individuals.

And this has led to some cool discoveries.

Definitely, like the study on Tibetan Sherpas you mentioned.

Proteomics confirmed high myoglobin in their muscles, no surprise there.

But it also revealed unexpectedly high levels of an enzyme called glutathione S -transferase.

Which does what?

It's involved in dealing with oxidative stress.

So it gave a new clue about how their muscles might be adapted to function so well at high altitude, protecting against damage.

Another striking example, that weird hairworm parasite makes katydids jump into water so the worm can reproduce.

Proteomics showed the parasite actually alters specific proteins in the katydid's brain to manipulate its behavior.

That's slightly terrifying, but amazing science.

Okay, so we have genes, genomics, RNA transcripts, transcriptomics, proteins, proteomics.

The next layer is metabolomics.

This focuses on all the small organic molecules in cells or tissues, the metabolites.

Things like sugars, amino acids, fatty acids, intermediates, and metabolic pathways.

So the actual fuel and building blocks being used.

Exactly.

The goal is to get a comprehensive picture of the metabolic state to map out the pathways that are active.

Techniques like NMR spectroscopy and nuclear magnetic resonance can detect hundreds or even thousands of these small molecules simultaneously.

And an example here.

Fruit flies under heat stress.

Metabolomics showed lots of changes.

For instance, levels of alanine went up.

Alanine is often produced during anaerobic metabolism when oxygen is scarce.

So that suggests the heat stress was perhaps causing oxygen problems in the tissues.

Generating a new hypothesis to test.

Precisely.

Or levels of tyrosine went up.

Tyrosine is a precursor for certain hormones.

So maybe heat stress accelerates hormone synthesis.

Metabolomics provides this broad snapshot that generates many new testable ideas about what's happening biochemically.

It's incredible.

Genomics, transcriptomics, proteomics, metabolomics.

It's like peeling back layers of an onion to see how life works at these incredibly detailed levels.

It really is.

And alongside these comics approaches that observe the system, scientists also use experimental methods to actively manipulate genes to understand their function better.

Right.

Like the knockout mice you mentioned earlier.

Exactly.

Gene deletion, or knockout, is one tool.

You can also force a gene to be overexpressed to make more protein than usual.

There's RNA interference, RNAi, which lets you specifically silence a gene by targeting its mRNA message for destruction or blocking its translation.

And more recently, the CRISPR -Cas system has revolutionized things.

It allows for gene editing, deleting specific bits, inserting mutations, correcting defects.

It's incredibly powerful.

But you mentioned a challenge with interpreting these kinds of studies.

Something about compensation.

Yes.

That's a key consideration.

When you knock out or alter a gene, the rest of the biological system doesn't necessarily just sit there passively.

It often adapts.

It compensates.

Remember the myoglobin knockout mice?

They didn't just fail.

Their hearts grew more capillaries.

Blood circulation increased.

They compensated for the missing protein.

The final phenotype, what you observe in the knockout animal, might be a complex result of both the direct effect of the missing gene and the secondary compensatory changes.

It makes interpreting the results trickier, I imagine.

You can't just say gene X does Y because the animal found a way to do Y differently or cope without it.

Exactly.

It highlights how interconnected and robust biological systems often are.

They have backup plans, redundancy.

It doesn't invalidate the knockout approach, but it means you have to be sophisticated in your interpretation.

That really drives home how complex and resilient life is.

It's not just a simple machine where taking out one part breaks everything.

Well, this deep dive today into the ice fish, into the world of omics, it's really shown how powerful it is when you bring genetics and physiology together.

We've seen a creature lose something as basic as red blood and still thrive.

We've seen genes repurposed for totally new vital jobs like antifreeze and these amazing technologies that let us peek under the hood at the machinery of life itself.

If you step back and look at the bigger picture, it's all about this constant intricate dance between the genes an organism has and the environment it lives in.

That dance is what shapes life.

Studying omics using these comparative and experimental methods we've talked about helps us understand not just what the animals like now, but the how.

How did it get this way?

How dynamic are these systems?

It really deepens our understanding of physiological concepts and adaptation.

It definitely raises a big question for the future, doesn't it?

With all this genetic and molecular data pouring in, how might these high throughput omics methods change how we even think about what healthy means?

For any species, maybe even for us humans, could we start identifying these really subtle molecular signatures of adaptation,

of optimal function in a given environment?

Lots to think about there.

We really hope this deep talk has given you a shortcut to being well informed on this fascinating topic with maybe some surprising facts along the way.