Proto-eukaryotes and LUCA

LUCA stands for "last universal common ancestor". It refers to the presumed common ancestor of the three presently recognized "domains" of life – Archaea, Bacteria, and Eukarya.

This common ancestor must have been very primitive, of course. One is tempted to think it might resemble modern-day religious fundamentalists, but in fact it was probably even more primitive, if you can imagine such a thing.

It's not absolutely clear there was actually one common ancestor, but that's what evidence currently indicates. But assuming there was, it's fascinating to speculate about what this ancestor was like.

Here's a very detailed blog post that discusses the issue: Ur... Again (Sort of).

It's based on an original research paper: The origins of phagocytosis and eukaryogenesis. The paper is open access and appears to be great reading, though it's conjectural and requires a little familiarity with fundamental biochemistry and cellular biology. Probably a good excuse to learn some of the details if you need to. These are topics that everybody ought to know about, even though our public educational system is way too inadequate to have done a good job of that.

Try reading at least the blog post, with a copy of Wikipedia close at hand.

P53 and skin pigmentation

Since we just mentioned skin coloration (here, in passing), and we have previously discussed how the p53 protein is involved with it (here), it's interesting that there is now more news on the subject.

Protein Linked To Bone Marrow Failure In Humans Found Through Study Of Dark-skinned Mice (7/20/08)

McGowan, Barsh, and their colleagues found that skin from the feet of the mutant mice exhibited elevated levels of p53. This elevation, or "activation," of p53 stimulated the production of a protein called Kit ligand that stimulates the growth of pigment cells, which turned the mice's skin darker than normal. In contrast, mutant mice unable to express p53 had normal levels of Kit ligand. They also had light-colored feet and unaffected numbers of red blood cells. ...

The researchers hypothesize that increased activation of p53 affects different types of cells in the body in different ways. In skin cells, it increases the amount of Kit ligand and causes darker skin, whereas in bone marrow cells it causes anemia by causing the death of red blood cell precursors.

Is there some lesson in this? Well, p53 is generally regarded as a "good" protein, because it helps ward off cancer that would otherwise result from DNA damage. But it does this by promoting apoptosis of cells affected by the DNA mutation. Anemia is the result when too many red blood cells die.

And the skin darkening? Earlier studies indicate that is also a side effect of increased levels of p53. Such unexpected – and not always desirable – side effects are the reason that developing drugs to treat disease is so difficult. There is so much unexpected interconnection of our cellular machinery, adjusting something in one place can lead to problems in quite different places.

Tags: p53

Blue eyes

The question of eye color seems to interest quite a few people. Previous discussions (here, here) have been among the most popular.

The actual genetics behind eye color remained somewhat obscure until February of this year. Although it's no longer new news, the findings are worth mentioning.

Humans certainly aren't the only animals having variable eye color. But the surprising thing is that (according to the primary author of the new research), until just a few thousand years ago, blue-eyed humans would have been very rare, at best.

Blue-eyed Humans Have A Single, Common Ancestor (1/30/08)

New research shows that people with blue eyes have a single, common ancestor. A team at the University of Copenhagen have tracked down a genetic mutation which took place 6-10,000 years ago and is the cause of the eye colour of all blue-eyed humans alive on the planet today.

“Originally, we all had brown eyes”, said Professor Eiberg from the Department of Cellular and Molecular Medicine. “But a genetic mutation affecting the OCA2 gene in our chromosomes resulted in the creation of a “switch”, which literally “turned off” the ability to produce brown eyes”. The OCA2 gene codes for the so-called P protein, which is involved in the production of melanin, the pigment that gives colour to our hair, eyes and skin. The “switch”, which is located in the gene adjacent to OCA2 does not, however, turn off the gene entirely, but rather limits its action to reducing the production of melanin in the iris – effectively “diluting” brown eyes to blue.

Note what this is saying. It is melanin that produces brown eyes, and melanin production is controlled by the OCA2 gene. A person in whom melanin isn't produced because both copies of OCA2 are faulty will not only not have brown eyes, but will not have brown color anywhere in the skin. However, if there is a certain mutation in both copies of a gene (known as HERC2) adjacent to OCA2 – not in OCA2 itself, as some accounts incorrectly state – production of melanin due to OCA2 will be reduced enough to produce blue eyes, while in skin there is still enough melanin produced to allow some brown coloration.

The reasoning that all people who now have blue eyes descended from a single individual who lived 6-10,000 years ago is based on different evidence, but it's a little more speculative. Another account outlines the argument:

Don't It Make Your Brown Eyes Blue? (2/1/08)

[B]y comparing people with brown or blue eyes, including people from Jordan and Turkey, the researchers were able to pinpoint the exact mutation. It wasn't on the OCA gene but rather on a nearby gene called HERC2. ...

Because blue eye color is found almost exclusively in people of European descent, Eiberg's team speculates that the mutation traces back to the Neolithic expansion, when people in the Black Sea region migrated to northern Europe 6000 to 10,000 years ago.

Two other studies, both appearing in this month's issue of The American Journal of Human Genetics, examined blue eyes in different populations and found the same mutation. The researchers also suggested a common ancestor for all blue-eyed individuals. These teams, however, did not estimate an age for the mutation. Geneticist Richard Sturm of the University of Queensland in Brisbane, Australia, an author of one of the papers says that someday scientists may find additional mutations that cause blue eyes but for now, the signs point to a single change.

Further reading:

One Common Ancestor Behind Blue Eyes – 1/31/08 article at LiveScience

The Family Tree of Blue-Eyed Individuals (2/6/08) – blog article that gives a bit more of the genetic details

Blue eyed people have a single, common ancestor (2/3/08) – another article, which gets some of the details wrong

Tags: eye color, blue eyes

Choanoflagellates II

No sooner than we do an article on a topic that may seem esoteric to some – namely tyrosine kinase signaling in choanoflagellates – than new information comes along to add to the picture.

The previous discussion was about how remarkable it is that a complete set of sophisticated intercellular signaling proteins exists in a single-celled organism. The new research partially echoes the previous findings:

Primitive Single-Celled Microbe Expert In Cellular Communication Networks (7/7/08)

When it comes to cellular communication networks, a primitive single-celled microbe that answers to the name of Monosiga brevicollis has a leg up on animals composed of billions of cells. It commands a signaling network more elaborate and diverse than found in any multicellular organism higher up on the evolutionary tree, researchers at the Salk Institute for Biological Studies have discovered.

Their study, which will be published during the week of July 7-11 in the online edition of the Proceedings of the National Academy of Science, unearthed the remarkable count of 128 tyrosine kinase genes, 38 more than found in humans.

But it also points out that M. brevicollis actually has a more extensive tyrosine kinase system than metazoa do:

"We were absolutely stunned," says Manning. "Based on past work, we had expected maybe a handful of these kinases but instead discovered that this primitive organism has a record number of them. Two other essential parts of the tyrosine kinase network - PTP and SH2 genes - are also more numerous than in any other genome, showing that it is the whole network that is elaborated here." ...

The Monosiga kinases are more divergent than anything previously seen in animals, which may help scientists understand the fundamentals of how all tyrosine kinase signaling works. Despite their extreme diversity, Monosiga kinases time and again arrive at the same solution to a problem, as do animal kinases, but using a distinct method for instance to create a sensor structure that emerges from the cell, or to target a kinase to a specific part of the cell. "This convergent evolution suggests that there are only a limited number of ways build a functional network from these components," says Manning.

And as was pointed out before, this discovery merely suggests new questions that need to be answered:

With all this new information, one obvious question remains unanswered: what is a single-celled organism doing with all this communications gear? "We don't have a clue!" says Manning, "but this discovery is the first step in finding out."

A possible answer, though one for which no evidence exists, as far as I know, is that M. brevicollis actually developed from the type of cell it strongly resembles ("collar cells") found in sponges. Perhaps the tyrosine kinase signaling system actually evolved in sponges, but then some of the constituent cells decided to go it alone. It would still need to be explained why the kinases didn't disappear in subsequent evolution. Since they are still present, they must serve some useful purpose.

Further reading:

The protist, Monosiga brevicollis, has a tyrosine kinase signaling network more elaborate and diverse than found in any known metazoan – research article from PNAS that reports the research discussed (open access)

Tags: choanoflagellates, cell signaling, tyrosine kinases

Choanoflagellates

Choanoflagellates are single-celled eukaryotic organisms – like amoebae, yeasts, or slime molds, as opposed to prokaryotic organisms like bacteria. Eukaryotic cells are different from prokaryotic ones in having a variety of internal and external structures, including a cell nucleus that contains the organism's genome.

One distinctive feature of a choanoflagellate is its flagellum, a whiplike structure made up of microtubules, which a choanoflagellate uses to propel itself in water. A choanoflagellate rather resembles an animal sperm cell.

But the type of animal cell that a choanoflagellate most strongly resembles is called a choanocyte (meaning "collared cell") and is found in sponges. Modern sponges were, until quite recently, considered to be lineal descendants of the earliest type of multicellular animal (metazoan). (As discussed here and here, comb jellies may be descended from an even earlier metazoan.)

A metazoan is more than simply a collection of cells living together in a cohesive colony, such as slime molds and some choanoflagellates. The cells of a metazoan are of different types, and they communicate among themselves in order to effect whatever behavior the organism has evolved to sustain itself.

With that in mind, it is quite interesting that the genome of choanoflagellates contains genes for three proteins that are used ubiquitously in metazoa for intercellular communication:

New Evidence That Ancient Choanoflagellates' Form Evolutionary Link Between Single-celled And Multi-celled Organisms (7/1/08)

What do humans and single-celled choanoflagellates have in common? More than you'd think. New research into the choanoflagellate genome shows these ancient organisms have similar levels of proteins that cells in more complex organisms, including humans, use to communicate with each other.

According to a paper published in the Proceedings of the National Academies of Science, these findings help confirm choanoflagellates' role as an evolutionary link between single-celled and multi-celled organisms. They also contend that these insights into the organism's genome may mean that the proteins used to help cells communicate may have other roles as well. ...

Choanoflagellates, or at least their ancestors, have long been suspected as being the bridge between microorganisms with only one cell and metazoan, or multi-cellular organisms. There are many clues that lead to this conclusion, including the fact that choanoflagellates are similar to the individual cells in ocean sponges and unlike most other flagellates, they use their flagellate, or tail, to push themselves through water, rather than being pulled by it.

By analyzing the recently-sequenced choanoflagellate genome, the researchers discovered another similarity between choanoflagellates and most metazoans--their genetic code carries the markers of three types of molecules that cells use to achieve phospho-tyrosine signaling proteins.

The type of signaling in question here utilizes phosphorylation – the addition of a phosphate (PO₄) group to a protein at one or more of its constituent amino acids. It is tyrosine phosphorylation when the the phosphate is attached to a tyrosine unit. (Tyrosine is one of the 20 kinds of amino acids that make up proteins.)

This process is much like reading, writing, and erasing a single bit of information in a computer memory. It is the proteins that perform these operations that are found to be shared by choanoflagellates and most metazoa.

Animals depend on tyrosine phosphorylation to conduct a number of important communications between their cells, including immune system responses, hormone system stimulation and other crucial functions. These phospho-tyrosine signaling pathways utilize a three-part system of molecular components to make these communications possible.

Tyrosine kinases (TyrK) 'write' messages between cells by adding phospho-tyrosine modifications, protein tyrosine phosphatases (PTP) are molecules that modify or 'erase' these modifications, and Src Homology 2 (SH2) molecules 'read' these modifications so the recipient cell gets the message.

What is intriguing is that all three of these signaling proteins are found in choanoflagellates in significant amounts. Although the proteins exist in other single-celled organisms, they aren't found together or in the same amounts as they are in choanoflagellates. This is the sort of thing that makes a researcher think, "Hmmm, that's strange. Wonder what's up with that?"

The researchers conclude that the presence of the full three-component signaling system may have played a role in the development of metazoan organisms whose cells could communicate with each other in complex ways.

It would be interesting to find out whether choanoflagellates actually use the proteins to communicate among themselves, and if so, for what purposes. But those are questions that remain to be answered.

Further reading:

The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans – an earlier (2/08) journal article on the choanoflagellate genome, and possible links to metazoa (sub. rqd. for full access)

The Premetazoan Ancestry of Cadherins – companion research article to the preceding, from Science, 2/15/08 (sub. rqd. for full access)

Genome Of Marine Organism Tells Of Humans' Unicellular Ancestors (2/14/08) – press release that describes the preceding research

Tags: choanoflagellates, cell signaling, tyrosine kinases, phosphorylation

Selfish genes

News flash: "selfish" genes actually exist. They aren't simply a metaphor.

New Discovery Proves 'Selfish Gene' Exists (6/20/08)

A new discovery by a scientist from The University of Western Ontario provides conclusive evidence which supports decades-old evolutionary doctrines long accepted as fact.

Since renowned British biologist Richard Dawkins ("The God Delusion") introduced the concept of the 'selfish gene' in 1976, scientists the world over have hailed the theory as a natural extension to the work of Charles Darwin.

Although I think that the idea of the "selfish gene" was a nice way to conceptualize the situation, the above remarks seem to be a little hyperbolic. It's not clear that this theoretical insight was that Earth-shattering. And the adjective wasn't meant to be taken literally:

In studying genomes, the word 'selfish' does not refer to the human-describing adjective of self-centered behavior but rather to the blind tendency of genes wanting to continue their existence into the next generation. Ironically, this 'selfish' tendency can appear anything but selfish when the gene does move ahead for selfless and even self-sacrificing reasons.

Nobody seriously thinks that genes have psychological "wants" or "needs". It's just that the effect of a gene may resemble what might be conscious advantage-seeking behavior in a human.

Or then again, specific human behavior may have adaptive evolutionary value even if it's not consciously undertaken for personal advantage or evolutionary success. Indeed, many human motivators that might seem to be "wants" or "needs" may have beneficial evolutionary consequences that are different from the apparent immediate objective of the specific motivator. (Sex itself is the best example of this. Even though a few species succeed without sex.)

And on the other hand, behavior that outwardly appears altruistic can be undertaken for genuinely "selfish" reasons, such as the personal satisfaction that can be enjoyed, or perhaps even public and social acclaim. If such social reward reliably does ensue, the behavior may well have adaptive value for an individual and a social group. The literature is replete with discussions of such issues.

However all that may be, the research in focus here gives actual evidence of the existence of a gene in honey bees behaving selfishly. The gene (which still remains to be explicitly identfied) disadvantages ordinary worker bees by making them sterile, but at the same time contributes to the success of the colony by promoting reproductive success of the queen bee. The gene can be called "selfish" because it condemns most bees to a lifetime of drudgery, in order to promote its own survival through the success of the colony and its most elite member(s).

Because the 'selfish' gene controlling worker sterility has never been isolated by scientists, the understanding of how reproductive altruism can evolve has been entirely theoretical -- until now.

Working with Peter Oxley of the University of Sydney in Australia, Western biology professor Graham Thompson has, for the first time-ever, isolated a region on the honey bee genome that houses this 'selfish' gene in female workers bees.

This means that the 'selfish' gene does exist, not just in theory but in reality. "We don't know exactly which gene it is, but we're getting close."

Who ever suspected that Republican political philosophy existed among honey bees?

Tags: sociobiology, altruism

Comb jellies, again

Comb jellies were in the news back in April, and I discussed that here. They're a lot like jellyfish, only different. In particular, they are now thought to be the closest living relatives of the earliest animals on this planet.

The most recent news is that, although the bodies of these animals appear primitive, their genetic machinery has interesting resemblances to that of more modern animals, including humans.

Genes key to the development of modern animals' body plans show up in primitive-looking comb jellies (6/6/08)

No one suspected that the primitive comb jellies — watery, rotund and nearly invisible sea creatures — would rely on an intricate interplay of genes to design their rudimentary bodies. Yet researchers got a surprise when they looked at the comb jelly’s genes. Scientists found pattern-making genes that, in most animals, plot out the position of the head, brain, limbs and rear ends during development. These “homeobox” genes turned on in a specific pattern in the comb jellies, even though these ancient sea creatures are headless, brainless, limbless and rear end–less, scientists show in the June Development Genes and Evolution.

Homeobox genes are genes that have specific genetic code sequences. The sequences code for portions of proteins (called homeodomains) that are in turn able to bind to DNA, so that the proteins act as transcription factors. These transcription factors are especially important in the process of embryonic development, as they determine the overall body plan of the organism. Homeobox genes aren't unique to animals. They're also found in plants and fungi.

However, although comb jelly homeobox genes are similar to those of other animals, and they have functions in comb jellies that are vaguely similar to their functions in other animals, there are important differences too:

Certain genes expressed in the mouths of comb jellies and in the heads of other animals could indicate that the comb jellies’ mouths correspond to the front-end of all animals (except for amorphous sponges), Martindale says. And it implies that the mouth region of an ancestral headless animal is in the same area where the first head eventually arose. Although comb jellies are using the same basic toolkit as other animals, they might be doing so in an entirely different way, Martindale says. Genes involved with limb formation in other animals were expressed at seemingly random points along the comb jellies’ throat-like pharynx, for example.

“Mice, flies and even cnidarians [jellyfish and sea anenomes, mainly] seem to be built on the same basic plan, but the sponges and comb jellies don’t fall into that mold,” Martindale says.

Tags: Ctenophora, homeobox

Bdelloid rotifers

The bdelloid rotifers are certainly in the news a lot recently.

They may not be into sex very much, but it turns out they are world-class gene snarfers.

No sex, but plenty of gene transfer

Where do you get your genes? If you are an animal, you inherit them from your parents at the moment of conception, and that's about it. No later incorporation of environmental DNA for you, unless you become host to a parasite or an endosymbiont that somehow transfers bits of its genome into yours (which is a rarely documented event). Unless you are a bdelloid rotifer, that is.

This odd, microscopic, freshwater animal is making news once again, this time for the startling discovery of numerous chunks of foreign DNA in its genome. In a paper published this week in Science, evidence for massive horizontal gene transfer—from bacteria, fungi, even from plants—into the bdelloid rotifer genome is presented by Irina Arkhipova and Matthew Meselson. ...

While horizontal gene transfer is common in bacterial species, it was unheard of in the animal kingdom on such a massive scale – until this study.

"It is quite amazing that bdelloids are able to recruit foreign genes, which were acquired from remarkably diverse sources, to function in the new host," says Arkhipova. "Bdelloids may have the capacity for tapping into the entire environmental gene pool, which may be of (evolutionarily) adaptive significance during expansion into new ecological niches, and may even contribute to bdelloid speciation," she says.

So the first question one has is, how have all these genes from totally different species gotten into the bdelloid genome? The most likely answer is: as a direct consequence of how bdelloids are able to survive such traumatic events as complete dessication or levels of radiation deadly to almost all other species.

Apparently bdelloids are able to do this because of a nearly unique ability to reconstitute and repair heavily damaged DNA. Evidently, in the process, they sometimes incorporate foreign DNA from other creatures they have eaten, or which may simply be lying around. And since some of this reconstituted bdelloid DNA is included in bdelloid egg cells, which eventually become separate individual animals, it is passed on to subsequent generations.

(Something similar to this process, but on a much smaller scale, occurs in "higher" animals too, such as humans. Our genome is full of remnants of the DNA ("exogenous DNA") of viruses that infected our ancestors unknown millions of years ago.)

How bdelloids have been able to gobble up such a variety of genes from their environment and incorporate it into their genome is a good question. Typically in animals, the germ line–the heritable egg and sperm cells–are protected from environmental assaults, such as intrusion of foreign DNA, by the rest of the body cells, which are not heritable and serve to "sequester" the germ line. Ideas on why the bdelloids' germ line is so exposed to environmental exchange, Arkhipova says, "are all speculative. But we talk about this a lot!"

One clue is the unusual ability of bdelloids to survive total desiccation (drying out), which is fatal for most organisms. When water disappears from their environment, bdelloids enter a kind of suspended, dehydrated state, and can stay there for months or even years. But once water returns, they spring back to action, move around, eat things, and start reproducing again.

During the desiccation phase, Arkhipova says, "you would imagine there is potential for membrane damage and DNA damage in the rotifer. And not only the rotifer desiccates, but also everything it just consumed." If the DNA of both the rotifer and its food are broken up during desiccation, "this would provide an opportunity for the (foreign) DNA to enter the rotifer's germ line. During rehydration, the DNA breakage is somehow repaired, and the foreign DNA may get incorporated," she says.

From the details mentioned so far, there may be some other things you could be wondering about.

For instance, do any of these foreign genes actually work like normal genes once they've become part of the bdelloid genome? Generally, they do not. But there is evidence that a few foreign genes are sufficiently intact that they are transcribed into messenger RNA. And some of this RNA may even be used to make proteins, such as enzymes to catalyze basic metabolic processes.

Interestingly enough, some bacterial genes that have entered the bdelloid genome now have embedded introns, which is normal for eukaryotic genes, but unheard of in prokaryotic (bacterial) genes. (The introns are like punctuation marks that separate distinct segments of a gene, called exons. This makes it possible to construct a number of different proteins from a single gene, by the process of "alternative splicing".)

Another more general question that might occur to you is: why do asexual animals such as bdelloids have egg cells, like more normal sexual creatures? And how, exactly, do they reproduce, anyhow? The answer is probably that at some time back in the evolutionary history of bdelloids (estimated at 50 to 100 million years ago), bdelloids diverged from a rotifer ancestor species that was sexual, as are many species of rotifers today.

So bdelloids still have egg cells, with paired chromosomes that carry two separate copies of the genome, just as "normal" sexual animals do. However, bdelloid eggs do not undergo the process of meiosis, in which egg cells divide, and the paired chromosomes are separated, to be later combined with chromosomes from another individual during fertilization.

Instead, bdelloid eggs are eventually expelled from the mother's body, and go on to develop into a new individual by parthenogenesis, which also occurs occasionally in a few other species capable of asexual reproduction, such as some insects, fish, snakes, and lizards. (Or even sharks and komodo dragons.)

In case you enjoy thinking about sex, you probably have many other questions about what's up with bdelloids. Answers to a lot of these questions can be found in the following.

Further reading:

Common Aquatic Animal's Genome Can Capture Foreign DNA – another 5/29/08 press release about the research

Water creatures caught stealing DNA – 5/30/08 ABC/Reuters news story on the research

Who needs sex when you can steal DNA? – 5/29/08 Reuters news story

Scientists find promiscuous genes in an asexual animal – informative 5/29/08 article from Science News

Massive Horizontal Gene Transfer in Bdelloid Rotifers – 5/30/08 research article in Science (sub. rqd.)

The Weird Sisters – very informative 6/3/08 New York Times blog article, by Olivia Judson

An Evolutionary Scandal – 11/2000 Harvard Magazine article on bdelloid rotifers

Who Needs Sex (or Males) Anyway? – 3/20/07 PLOS Biology article on bdelloids

Tags: bdelloids, bdelloid rotifers

Is DNA Repair A Substitute For Sex?

Yeah, it's a trick question. The answer is clearly "no" – unless you're a bdelloid rotifer.

What's interesting, of course, about these minute but multi-cellular animals is that they are completely asexual, and apparently have been for millions of years. There are no males, and females reproduce entirely by parthenogenesis. Although that might seem to imply a rather joyless existence, it hasn't stopped the bdelloids from persisting, and even diversifying into more than 370 species.

The conventional evolutionary reason for the invention and predominance of sexual reproduction – apart from the recreational aspect – is that it provides a mechanism for a species to cope with the inevitability of sustaining damage to its DNA. So why do the bdelloids seem to think they have a better way?

Is DNA Repair A Substitute For Sex?

These hardy creatures somehow escape the usual drawback of asexuality – extinction – and the MBL’s David Mark Welch, Matthew Meselson, and their colleagues are finding out how.

In two related papers published recently in Proceedings of the National Academy of Sciences (PNAS), the team proposes an interesting hypothesis: Bdelloid rotifers have been able to give up sex and survive because they have evolved an extraordinary efficient mechanism for repairing harmful mutations to their DNA. ...

In animals that do have sex, DNA repair is accomplished during meiosis, when chromosomes pair up (one from the father, one from the mother) and “fit” genes on one chromosome can serve as templates to repair damaged genes on the other chromosome. The bdelloid, though, always seems to reproduce asexually, by making a clone of itself. How then, does it cope with deleterious mutations?

Before we come to the hypothesized answer, it must be noted that the bdelloids' ability to repair their DNA is not merely adequate. It's spectacularly good:

MBL adjunct scientist Matthew Meselson and Eugene Gladyshev, both of Harvard University, demonstrate the enormous DNA repair capacity of bdelloid rotifers by zapping them with ionizing radiation (gamma rays), which has the effect of shattering its DNA into many pieces. “We kept exposing them to more and more radiation, and they didn’t die and they didn’t die and they didn’t die,” says Mark Welch. Even at five times the levels of radiation that all other animals are known to endure, the bdelloids were able to continue reproducing.

“Because there is no source of such intense ionizing radiation on Earth, except if we make it, there is no way these organisms could have evolved to be radiation resistant,” says Mark Welch. Instead, they propose that bdelloids’ DNA repair capacity evolved due to a different environmental adaptation – tolerance of extreme dryness.

Bdelloids, which live in ephemeral aquatic habitats such as temporary freshwater pools and on mosses, are able to survive complete desiccation (drying out) at any stage of their life cycle. They just curl up and go dormant for weeks, months, or years, and when water becomes available, they spring back to life. Mark Welch and his colleagues showed that desiccation, like ionizing radiation, breaks up the rotifers’ DNA into many pieces. Presumably, the same mechanisms they use to survive desiccation as part of their life cycle also protect them from ionizing radiation.

Hmmmm. That sounds oddly familiar. Where have we heard about that sort of thing before? Oh yes, this is apparently exactly the same thing found in a bacterium (Deinococcus radiodurans), as discussed here. And in the closely related bacterial species, Deinococcus geothermalis, as discussed here.

But what the bdelloids do is much more impressive, since they are multicellular eukaryotes, not simple prokaryotic bacteria. In any case, what't the trick for bdelloids?

One feature that may confer exceptional DNA repair capacity on the bdelloids is described in the team’s second PNAS paper. Here, they give evidence that the bdelloid rotifer, like most animals, originally had two copies of each chromosome. But at some point in its evolution, it underwent a “whole-genome duplication,” giving it four copies of each chromosome and hence of each gene. Normally, lineages that undergo whole-genome duplication lose the duplicate genes over time. The bdelloid, though, has kept most of its duplicate genes throughout its evolutionary history.

“We believe they have kept most of their duplicate genes because they are serving as templates for DNA repair,” says Mark Welch.

Comb jellies

I just thought it was sort of fascinating that comb jellies (also known as Ctenophorae), which aren't true jellyfish but are closely related, are now thought to be the oldest extant linage of the animal kingdom, usurping the title from sponges.

What's especially strange (though hardly inexplicable) is that comb jellies have some features that sponges lack, such as differentiated tissues and a nervous system.

The First Animal On Earth Was Significantly More Complex Than Previously Believed

A new study mapping the evolutionary history of animals indicates that Earth's first animal -- a mysterious creature whose characteristics can only be inferred from fossils and studies of living animals--was probably significantly more complex than previously believed.

Using new high-powered technologies for analyzing massive volumes of genetic data, the study defined the earliest splits at the base of the animal tree of life. ...

Among the study's surprising findings is that the comb jelly split off from other animals and diverged onto its own evolutionary path before the sponge.

How could it be that comb jellies are notably more complex than sponges, in spite of having appeared earlier?

Dunn says that the comb jelly could only have achieved its apparent seniority over the simpler sponge via one of two new evolutionary scenarios:

1. the comb jelly evolved its complexity independently of other animals, after it branched off onto its own evolutionary path; or
2. the sponge evolved its simple form from more complex creatures -- a possibility that underscores the fact that "evolution is not necessarily just a march towards increased complexity," says Dunn. "This scenario would provide a particularly dramatic example of that principle."

The evidence that comb jellies emerged earlier than sponges comes from intensive analysis of genetic data. The general idea is that detailed computer analysis comparing the DNA of different species indicates which species emerged earlier or later. As the researcher explains:

"Even though we looked at fewer than 100 species, they were sampled in such a way that they inform the relationships of major groups of animals relative to each other. Therefore, this study, and others like it, will have implications for the placement of far more species than just those that are sampled."

A somewhat earlier announcement is slightly more specific about what the researchers did:

Tree Of Animal Life Has Branches Rearranged, By Evolutionary Biologists

A study led by Brown University biologist Casey Dunn uses new genomics tools to answer old questions about animal evolution. The study is the most comprehensive animal phylogenomic research project to date, involving 40 million base pairs of new DNA data taken from 29 animal species.

Speaking of jellyfish-like creatures, I highly recommend Jelly Music.

Further reading:

Shock: First Animal on Earth Was Surprisingly Complex – another news report of the research

Phylogenetic fallacies: "early branching equals primitive" – blog post that cautions against certains misinterpretations of genomic data

Genomicron: Phylogenetic fallacies: “early branching equals primitive” – another blog post, elaborating on the preceding one

Tags: Ctenophora

Our plant relatives

Humans aren't related merely to other animals – plants are kinfolk too. In fact, we share some genes with ancestors of both animals and plants, genes not found even in most modern plants.

Green Algae: The Nexus Of Plant-Animal Ancestry

Genes of a tiny, single-celled green alga called Chlamydomonas reinhardtii may contain scores more data about the common ancestry of plants and animals than the richest paleontological dig. This work is described in an article in Science.

A group of researchers, including Arthur Grossman of the Carnegie Institution, report on the results of a major effort to obtain the full library of genes, or the genome sequence, of Chamydomonas and to compare its ~15,000 genes to those of plants and animals, including humans. The research shows that this alga has maintained many genes that were lost during the evolution of land plants, has others that are associated with functions in humans, and has numerous genes of unknown function, but which are associated with critical metabolic processes.

In particular, cilia are important structures of some eukaryotic cells, are inherited from the common ancestor of plants and animals. Cilia are found in animal cells, analogous to flagella in Chamydomonas, but have no analogue in most plant cells.

Chlamydomonas, affectionately called Chlamy, is an alga of 10 micrometres in size that is present in soil and freshwater environments. It performs photosynthesis like plants, but it diverged evolutionarily from flowering land plants about 1 billion years ago. It is even more distantly related to animals (the split between animals and plants was ~1.6 billion years ago). Chlamy moves using two anterior, hair-like flagella that were lost by its cousins, the flowering land plants, after the evolutionary split of the two lineages. The flagella are equivalent to the cilia and centrioles in animal cells. Centrioles are structures involved in cell division; they form a spindle apparatus, which helps separate genetic material into two new cells during mitosis. Cilia are important to many animal functions.

More information:

The Chlamydomonas Genome Reveals the Evolution of Key Animal and Plant Functions (Sub. rqd.)

Study involving more than 100 scientists provides new insights on green algae

Scientists Sequence Genome of Soil-Dwelling Green Alga

Tags: Chlamydomonas, cilia

Origins of brains as sensory organs

Recently (well, not too long ago) I posted (here) a bit about how elements of the modern nervous system of vertebrates can be traced back to some of the most primitive animals – sea sponges.

Now it transpires that the origins of specific brain subsystems can also be found in invertebrates. In this case, the subsystem is the hypothalamus. One of the interesting things about the hypothalamus is that it is not only an important part of the central nervous system, but also part of the endocrine system. As such, it causes production of a number of important hormones itself, such as melatonin, oxytocin, and corticotropin-releasing hormone. It is further tied into the endocrine system via its direct connection to the nearby pituitary gland. Some of these hormones appear to have invertebrate origins the same as the hypothalamus itself:

Modern Brains Have An Ancient Core

Hormones control growth, metabolism, reproduction and many other important biological processes. In humans, and all other vertebrates, the chemical signals are produced by specialised brain centres such as the hypothalamus and secreted into the blood stream that distributes them around the body.

Researchers from the European Molecular Biology Laboratory [EMBL] now reveal that the hypothalamus and its hormones are not purely vertebrate inventions, but have their evolutionary roots in marine, worm-like ancestors. In this week's issue of the journal Cell they report that hormone-secreting brain centres are much older than expected and likely evolved from multifunctional cells of the last common ancestor of vertebrates, flies and worms.

The invertebrate in question here is the marine ragworm Platynereis dumerilii. And if the foregoing findings weren't interesting enough, it seems that not only vertebrates share a common ancestor (Urbilateria) with P. dumerilii, but so too do insects and other worms. Furthermore, P. dumerilii has two types of light-sensing cells – one type of which is found in insects, and the other is found in vertebrates.

Marine Worm Has Insectile and Vertebrate 'Eyes'

Scientists today believe that the eye could evolve from a single light-sensing cell. Scientists disagree over whether it evolved just once, or many times.

It turns out that Nature is both creative and generous with her gifts. Recent research has shown that the tiny marine worm Platynereis dumerilii has two types of light-sensing cells. The eyes of the worm have rhabdomeric photoreceptors, a compound lens formation that is seen almost exclusively in insect eyes. Rhabdomeric photoreceptors are covered in little finger-like protrusions. In its brain, however, it has a different kind of light-sensing cells - ciliary cells that are seen in vertebrate animals. Ciliary cells have hair-like cilia that extend outward and branch out like tiny umbrellas. Two different ways of sensing light in a single organism!

In light of this circumstance, the following, from the first-mentioned research announcement, is especially interesting:

Both of the cell types studied in Platynereis and fish are multifunctional: they secrete hormones and at the same time have sensory properties. The vasotocin-secreting cells contain a light-sensitive pigment, while RF-amide appears to be secreted in response to certain chemicals. The EMBL scientists now assume that such multifunctional sensory neurons are among the most ancient neuron types. Their role was likely to directly convey sensory cues from the ancient marine environment to changes in the animal's body. Over time these autonomous cells might have clustered together and specialised forming complex brain centres like the vertebrate hypothalamus.

"These findings revolutionise the way we see the brain," says Tessmar-Raible. "So far we have always understood it as a processing unit, a bit like a computer that integrates and interprets incoming sensory information. Now we know that the brain is itself a sensory organ and has been so since very ancient times."

Tags: hypothalamus, endocrine gland, hormones

Origins Of Nervous System Found In Genes Of Sea Sponge

One of the things that's always fascinating (or inspiring, astonishing, awe-inspiring – take your pick) about what we learn from the evolutionary history of living critters is how much very different sorts of living things have in common. This even reaches down to the level of single cells, where very similar genes can be found in mammals and yeast, even bacteria.

We also find complex subsystems with substantial similarities. So much so that the nervous system of the roundworm Caenorhabditis elegans, which has all of 302 neurons in its whole nervous system (hermaphrodite version), is routinely used as an experimental model for the nervous systems of much more complex animals.

Perhaps even more astonishing than that, however, is that it now appears some genes important for modern nervous systems existed even before there were nervous systems – in sea sponges, which are just about the most primitive animals known.

Origins Of Nervous System Found In Genes Of Sea Sponge

Scientists at the University of California, Santa Barbara have discovered significant clues to the evolutionary origins of the nervous system by studying the genome of a sea sponge, a member of a group considered to be among the most ancient of all animals.

And not only are some of the genes there, but the proteins they represent may have interacted similarly to the way that corresponding proteins interact in modern synapses.

"It turns out that sponges, which lack nervous systems, have most of the genetic components of synapses," said Todd Oakley, co-author and assistant professor in the Department of Ecology, Evolution and Marine Biology at UC Santa Barbara.

"Even more surprising is that the sponge proteins have 'signatures' indicating they probably interact with each other in a similar way to the proteins in synapses of humans and mice," said Oakley. "This pushes back the origins of these genetic components of the nervous system to at or before the first animals ---- much earlier than scientists had previously suspected."

Other blog articles: here

Original research paper: here

Tags: synapses, neuroscience

No Single Gene For Eye Color, Researchers Prove

Since I wrote a little about eye color before, I think I ought to clarify some things. The earlier article was really about how recessive and dominant genes can have an indirect effect on social behavior via evolution. But the truth about the genetics of eye color is actually somewhat more complicated:

No Single Gene For Eye Color, Researchers Prove

A study by researchers from The University of Queensland's Institute for Molecular Bioscience (IMB) and the Queensland Institute of Medical Research is the first to prove conclusively that there is no single gene for eye colour.

Instead, it found that several genes determine the colour of an individual's eyes, although some have more influence than others.

Update 8/3/08: There is more recent news on this subject here.

Tags: eye color, blue eyes

Clues to the origins of life

The question of how life originated on Earth is one of the really big open questions for science. Right up there with questions like how the universe itself started and how the human mind works.

Questions about how life began have been asked for a long time, of course. But only within roughly the last 50 years, since DNA and related biochemistry began to be understood, has it been possible to address such questions scientifically.

DNA, and its very close relative RNA, provide the framework for one essential of life: the storage of information, which allows for "blueprints" that describe a living organism to be conveniently encoded, so that individual organisms can be duplicated and, ultimately, evolve into more complex organisms. We now understand pretty well how DNA and RNA work, so one key question now is – how did DNA and RNA, the carriers of genetic information, come about?

DNA and RNA are made up of relatively simple organic molecules – sugars and phosphate groups that can polymerize to form a backbone, and a small number of bases which encode information by the way they are ordered in their attachment to the backbone. The information encoded in DNA details how to make proteins, which are also polymeric organic molelcules, consisting of amino acids attached to each other in a sequence specified (mostly) by the DNA. It is the proteins that make up the bulk of the cellular machinery that constitutes a stand-alone single-celled organism, or by grouping together makes a multi-celled organism. So a large part of the question of life's origins comes down to that of how these various organic chemicals came to exist.

In addition to the organic chemicals that make up an organism, another necessity of life is the ability to utilize energy that is ultimately obtained from the environment. In most cases, this energy is derived from sunlight, although in a few rare cases it can come from radioactive elements. Either way, an organism needs to tap into the environmental energy in order to drive chemical reactions which power cellular mechanisms that enable reproduction, locomotion, and (in multicellular organisms) growth. (More complex organisms can also derive their energy from "food", in the form of simpler organisms that have stored up environmental energy obtained more directly.) So another key question is: when and how did these energy-management processes come about?

There have been recent research findings that are relevant to various of these questions.

Let's consider the origins of organic compounds first. One line of thinking is that organic compounds were primarily synthesized from inorganic compounds in natural processes here on Earth. The names Aleksandr Oparin and J. B. S. Haldane are associate with this idea. The classic experiment testing the idea is known as the Miller-Urey experiment, after Stanley Miller and Harold Urey, and was first conducted in 1953, the same year that the structure of DNA was identified by Francis Crick and James Watson. As yet, this is still just a conjectural possibility.

An alternative scenario for the origins of organic compounds is that some simple ones formed in space, which is known to happen, and that some of the basic building blocks of life, such as amino acids, were introduced to Earth on meteorites. This possibility has gained more plausibility from the recently announced finding of apparent "organic materials" in a meteorite that fell in 2000.

NASA Scientists Find Primordial Organic Matter In Meteorite

In a paper published in the Dec. 1 issue of the journal Science, the team, headed by NASA space scientist Keiko Nakamura-Messenger, reports that the Tagish Lake meteorite contains numerous submicrometer hollow organic globules.

Because the meteorite immediately became frozen in ice after it landed, the possibility of contamination from terrestrial material was minimized. Further, the isotopic composition of hydrogen and nitrogen in the globules is quite unlike what is normally found on Earth. It also appears that the material in the meteorite formed at least 4.5 billion years ago – before the Earth and the other planets themselves.

"The isotopic ratios in these globules show that they formed at temperatures of about -260° C, near absolute zero," said Scott Messenger, NASA space scientist and co-author of the paper. "The organic globules most likely originated in the cold molecular cloud that gave birth to our Solar System, or at the outermost reaches of the early Solar System."

Additional references:

• Ancient Meteorites from Outer Solar System May Have Provided Raw Materials for Life
  
• Carbon globules in meteorite may have seeded Earth life
  
• An Ancient Building Block of Life
  
• Organic Globules in the Tagish Lake Meteorite: Remnants of the Protosolar Disk - original research article (Science sub. rqd. for full access)
  

Just about two weeks later, results from a completely different souce appeared that also showed the existence of organic compounds in primorial solar system material. This was from the Stardust mission to retrieve grains of matter from the comet 81P/Wild-2:

Comets hold life chemistry clues

Scientists studying the tiny grains of material recovered from Comet Wild-2 by Nasa's Stardust mission have found large, complex carbon-rich molecules.

They are of the type that could have been important precursor components of the initial reactions that gave rise to the planet's biochemistry.

Unlike the case with the Tagish Lake meteorite, it was possible to identify many of the organic compounds in the returned material:

These Wild-2 compounds lack the aromaticity, or carbon ring structures, frequently found in meteorite organics. They are very rich in oxygen and nitrogen, and they probably pre-date the existence of our Solar System.

"It's quite possible that what we're seeing is an organic population of molecules that were made when ices in the dense cloud from which our Solar System formed were irradiated by ultraviolet photons and cosmic rays," Dr Sandford explained.

"That's of interest because we know that in laboratory simulations where we irradiate ice analogues of types we know are out there, these same experiments produce a lot of organic compounds, including amino acids and a class of compounds called amphiphiles which if you put them in water will spontaneously form a membrane so that they make little cellular-like structures."

Additional information from the special Stardust issue of Science (December 15, 2006 – sub. rqd. for full access):

• Look into the Seeds of Time – introduction and summary
  
• Organics Captured from Comet 81P/Wild 2 by the Stardust Spacecraft
  

Although these results indicate that organic material formed in or before the earliest stages of the solar system might have seeded organic chemistry on Earth, there is as yet no evidence that this actually is how it happened. An even more radical possibility is that actual living carbon-based organisms that originated outside of our solar system "transplanted" life to Earth. This idea is known as panspermia, but so far, there's little or no credible evidence for it. Short of that, we know at least that the organic compounds for life either originated on Earth or arrived from outside.

So let's move on and turn to the question of how the earliest organisms managed energy supplies in order to reproduce and move. Every organism on Earth that produces energy from the chemical processing of carbohydrates, fats, and proteins uses, a complex series or reactions known as the citric acid cycle (also known as the Krebs cycle). (There are other energy-producing processes, of course, such as photosynthesis.) The question to be answered is how this complex series of reactions first arose:

New Insights Into The Origin Of Life On Earth

In an advance toward understanding the origin of life on Earth, scientists have shown that parts of the Krebs cycle can run in reverse, producing biomolecules that could jump-start life with only sunlight and a mineral present in the primordial oceans.

The Krebs cycle is a series of chemical reactions of central importance in cells -- part of a metabolic pathway that changes carbohydrates, fats and proteins into carbon dioxide and water to generate energy.

Since the cycle can run backwards, it is possible to identify an inorganic compound that may have kickstarted the process:

Nature's Jump-Starter

Reporting in next week's Journal of the American Chemical Society, researchers at Harvard University say they may have found at least one of the original players. Called sphalerite, the compound is a mix of zinc and sulfur ejected from hydrothermal vents and known to have been plentiful in Earth's early seas. Geochemist and co-author Scot Martin says the team's new lab experiments show that when immersed in sterile water and exposed to sunlight, sphalerite can create three of the five basic organic chemicals necessary to start the Krebs cycle in relatively quick fashion. Further research is needed to isolate the other compound or compounds that could have produced the remaining two Krebs ingredients, he notes. If scientists can find their sources, then they will know that the five chemical foundations of the Krebs cycle were being manufactured easily and routinely in Earth's early oceans.

In addition to relatively simple organic chemical building blocks and chemical reactions that can release energy to make an organism that is "alive", there is a third prerequisite for life: some method of storing information about an organism's composition and structure so that the organism can replicate itself, instead of simply disappearing after each generation. In other words, genetic material.

Today, that genetic material consists of DNA and RNA, which in turn are made up of a handful of bases that act as symbols encoding the genetic message and are arranged along a linear backbone of simple sugar and phosphate groups. But are these the only possible chemical entities that can perform this kind of function?

In the past, other possibilities have been suggested, such as peptide nucleic acids (PNAs). A PNA has a backbone formed of simple molecules consisting of carbon, nitrogen, hydrogen, and oxygen. These are liked together by peptide bonds, which form when H- and OH- units from two molecules combine to form H₂O, leaving the original molecules joined to each other. Such peptide bonds also form the backbone of proteins. But unlike proteins, PNAs have DNA-like bases attached to the backbone instead of amino acids. However, PNAs do not occur naturally, so they do not seem to have played a role in life on Earth.

If there are other ways of structuring a backbone, perhaps comparing them to what is actually used in RNA (the sugar known as ribose) and DNA (the sugar deoxyribose) would suggest why the latter proved to win out. That was the idea behind this research:

Uncovering DNA's 'Sweet' Secret

“These molecules are the result of evolution,” said Egli, professor of Biochemistry. “Somehow they have been shaped and optimized for a particular purpose.”

“For a chemist, it makes sense to analyze the origin of these molecules.”

One particular curiosity: how did DNA and RNA come to incorporate five-carbon sugars into their “backbone” when six-carbon sugars, like glucose, may have been more common? Egli has been searching for the answer to that question for the past 13 years.

Recently, Egli and colleagues solved a structure that divulges DNA's “sweet” secret. In a recent issue of the Journal of the American Chemical Society, Egli and colleagues report the X-ray crystal structure of homo-DNA, an artificial analog of DNA in which the usual five-carbon sugar has been replaced with a six-carbon sugar.

It was found that homo-DNA is more stable that DNA/RNA and it allows a wider variety of bases to be attached. So why didn't it prevail?

[D]espite homo-DNA's apparent versatility in base pairing and its thermodynamic stability, other features of the molecule's architecture probably preclude it from being a viable genetic system

For example, it cannot pair with other nucleic acids — unlike DNA and RNA which can and must pair with each other. Also the steep angle, or inclination, between the sugar backbone and the bases of homo-DNA requires that the pairing strands align strictly in an antiparallel fashion — unlike DNA which can adopt a parallel orientation. Finally, the irregular spaces between the “rungs” prevent homo-DNA from taking on the uniform structure DNA uses to store genetic information.

The findings suggest that fully hydroxylated six-carbon sugars probably would not have produced a stable base-pairing system capable of carrying genetic information as efficiently as DNA.

So that variation didn't work out. But what about the possibility of using a different set of bases than the purines and pyrimidines which actually occur? That was investigated in this study:

Origin Of Life: The Search For The First Genetic Material

To find the right track in searching for the origins of life, the team is trying to put together groups of potential building blocks from which primitive molecular information transmitters could have been made. The researchers have taken a pragmatic approach to their experiments. Compounds that they test do not need to fulfill specific chemical criteria; instead, they must pass their “genetic information” on to subsequent generations just as simply as the genetic molecules we know today—and their formation must have been possible under prebiotic conditions. Experiments with molecules related to the usual pyrimidine bases (pyrimidine is a six-membered aromatic ring containing four carbon and two nitrogen atoms), among others, seemed a good place to start. The team thus tried compounds with a triazine core (a six-membered aromatic ring made of three carbon and three nitrogen atoms) or aminopyridine core (which has an additional nitrogen- and hydrogen-containing side group). Imitating the structures of the normal bases, the researchers equipped these with different arrangements of nitrogen- and hydrogen- and/or oxygen-containing side groups.

Unlike the usual bases, these components can easily be attached to many different types of backbone, for example, a backbone made of dipeptides or other peptide-like molecules. In this way, the researchers did indeed obtain molecules that could form specific base pairs not only with each other, but also with complementary RNA and DNA strands. Interestingly, only one sufficiently strong pair was formed within both the triazine and aminopyridine families; however, for a four-letter system analogous to the ACGT code, two such strongly binding pairs are necessary.

The conclusion was that the critical factor affecting the composition of modern genetic material was the structure of the bases rather than the structure of the backbone. It was necessary to have only certain bases which are capable of pairing up in specific ways, as occurs in double-stranded DNA and DNA-RNA combinations.

Tags: origins of life, biology, biochemistry, Krebs cycle, citric acid cycle, Tagish Lake meteorite

What makes humans smarter than chimps?

Why have geneticists considered complete sequencing of the genomes of a variety of species so important? One reason (of many) is what we learn by comparing these other genomes with the human genome. And if you consider the genome of a close relative of humans, such as our closest relatives, chimpanzees, the comparison may be particularly enlightening.

The complete sequencing of the chimp genome was announced in August 2005. In May of this year, some results from comparing human and chimp genomes started to emerge:

Chimpanzee study reveals genome variation hotspots

Researchers believe that dynamic regions of the human genome - "hotspots" in terms of duplications and deletions - are potentially involved in the rapid evolution of morphological and behavioral characteristics that are genetically determined.

Now, an international team of researchers, including a graduate student and an associate professor from Arizona State University, are finding similar hotspots in chimpanzees, which has implications for the understanding of genomic evolution in all species.

That's an interesting clue, but it still doesn't tell us much about what accounts for the difference between human and chimp brains. More specifics about this came out three months ago, in August:

Scientists Find Brain Evolution Gene

Scientists believe they have found a key gene that helped the human brain evolve from our chimp-like ancestors. In just a few million years, one area of the human genome seems to have evolved about 70 times faster than the rest of our genetic code. It appears to have a role in a rapid tripling of the size of the brain's crucial cerebral cortex, according to an article published Thursday in the journal Nature.

Study co-author David Haussler, director of the Center for Biomolecular Science and Engineering at the University of California, Santa Cruz, said his team found strong but still circumstantial evidence that a certain gene, called HAR1F, may provide an important answer to the question: "What makes humans brainier than other primates?" Human brains are triple the size of chimp brains.

But that's only the beginning of the story:

Scientists Identify Gene Difference Between Humans and Chimps

Although this research does not definitively link this region to brain differences between humans and our closest relatives, it is intriguing. "We don't know what it does, and we don't know if it interacts with reelin, but the evidence is very suggestive that this gene is important in the development of the cerebral cortex, and that's exciting because the human cortex is three times as large as it was in our predecessors," notes team leader David Haussler of the University of California, Santa Cruz. "Something caused our brains to evolve to be much larger and have more function than the brains of other mammals."

And, of course, this is just the first of the 49 rapidly evolving regions to be studied. "Now we have to go through the other 48," Haussler says.

Sure enough, other interesting things are being found in other regions of the human genome that have evolved rapidly. This came out in October:

DNA trail points to human brain evolution

The human brain may have evolved beyond that of our primate cousins because our brain cells are better at sticking in place, researchers say.

A new study comparing the genomes of humans, chimps, monkeys and mice found an unexpectedly high degree of genetic difference in the human DNA regions that influence nerve cell adhesion, compared with the DNA of the other animals.

Accelerated evolution here allowed human brain cell connections to form with greater complexity, enabling us to grow bigger brains, the researchers suggest.

Ah ha. So enhanced adhesion between neurons facilitates bigger brains. That makes sense. But the story gets even more interesting, because apparently it's not only specific genes that play a role in this, but certain noncoding DNA regions between genes do also:

Looking for Smarts Between the Genes

The strongest evidence for accelerated evolution on the human line was found in noncoding sequences next to genes involved in helping neurons adhere to each other. The team found 69 such sequences, suggesting that changes in these regulatory elements may have contributed to the evolution of uniquely human cognitive talents.

Neuronal adhesion molecules play a major role in wiring the brain, Rubin says, such as the formation of connective synapses between nerve cells. These processes, he adds, are important in early brain development and also crucial for learning, memory, and cognition in adults. For example, Rubin says, one of the noncoding sequences is next to a gene called CNTN4, which appears to be involved in the development of both verbal and nonverbal communication abilities in humans, while another is adjacent to CHL1, which is linked to cognition in both humans and mice.

So this links up with another famously intriguing question: why is it that more than 90% of the human genome is made up of gaps between genes, gaps that don't seem to code for any proteins? Researchers have begun to suspect that some of this noncoding DNA consists of regulatory sequences that can affect, in different ways, when different genes are "expressed" and actually able to produce specific proteins. Looks like some of this noncoding DNA is important enough to help account for the rapid evolution of human brains.

I have the feeling we're just seeing the beginning of research findings in this area, and we're about to be hit by an avalanche of it. Here's another study reported just this week. It involves not just single genes, but entire networks of interconnected genes:

Unraveling where chimp and human brains diverge

By evaluating the correlated activity of thousands of genes, the UCLA team identified not just individual genes, but entire networks of interconnected genes whose expression patterns within the brains of humans varied from those in the chimpanzee.

"Genes don't operate in isolation – each functions within a system of related genes," said first author Michael Oldham, UCLA genetics researcher. "If we examined each gene individually, it would be similar to reading every fifth word in a paragraph – you don't get to see how each word relates to the other. So instead we used a systems biology approach to study each gene within its context."

The scientists identified networks of genes that correspond to specific brain regions. When they compared these networks between humans and chimps, they found that the gene networks differed the most widely in the cerebral cortex -- the brain's most highly evolved region, which is three times larger in humans than chimps.

Secondly, the researchers discovered that many of the genes that play a central role in cerebral cortex networks in humans, but not in the chimpanzee, also show significant changes at the DNA level.

Since there are probably scores of genes implicated in human-chimp brain differences, organized in different networks, I expect we're going to see research on this come out for some time to come.


------------------------------------

Additional information:

Accelerated Evolution of Conserved Noncoding Sequences in Humans

This is the abstract of the article in Science which describes the research about the importance of noncoding DNA for human brain evolution. (Subscription rqd for access to full text of the article.)

Scientists Explore Function of 'Junk DNA'

Via Evolution Research, this is a recent (like, last two days) news item on research into noncoding DNA that works by coding for microRNA.

Tags: biology, neuroscience, human evolution, noncoding DNA

Earliest Animals Had Human-like Genes

Earliest Animals Had Human-like Genes

Species evolve at very different rates, and the evolutionary line that produced humans seems to be among the slowest. The result, according to a new study by scientists at the European Molecular Biology Laboratory [EMBL], is that our species has retained characteristics of a very ancient ancestor that have been lost in more quickly-evolving animals.

What was surprising was this:

The genes of animals usually contain extra bits of DNA sequence, called introns – information which has to be removed as cells create new molecules. The number of introns in genes, however, varies greatly among animals. While humans have many introns in their genes, common animal models such as flies have fewer. From an evolutionary perspective, it was long assumed that the simpler fly genes would be more ancient. The current study reveals the opposite: early animals already had a lot of introns, and quickly-evolving species like insects have lost most of them.

Our cousins, Caenorhabditis elegans

Humans descended from worms? Sounds about right...

Evolutionary Conservation Of A Mechanism Of Longevity From Worms To Mammals

Though the study of aging in the nematode model organism C. elegans has provided much insight into this complex process, it is not yet clear whether genes involved in aging in the worm have a similar role in mammals. In a recent study, Dr. Hekimi and colleagues of McGill University (Canada) report that inactivation of the gene mclk1, the murine ortholog of the C. elegans gene clk-1, results in increased cellular fitness and prolonged lifespan in mice.

The gene clk-1 in the worm, as well as mclk1 in mice, encodes an enzyme necessary for the biosynhesis of ubiquinone, an essential cofactor in numerous redox reactions such as mitochondrial respiration. Though lack of the mclk1 gene results in embryonic lethality, the authors were able to study mclk1-/- embryonic stem (ES) cells and show that they are resistant to oxidative stress and exhibit reduced DNA damage when compared to ES cells in which this gene is active. ...

Though the aging process of different organisms will most likely differ due to different physiologies and environments, Dr. Hekimi summarizes the relevance of their findings by concluding that "... the longevity-promoting effect of reducing clk-1/mclk1 activity that was initially observed in C. elegans is conserved in mice, supporting the idea that some molecular mechanisms of aging are shared throughout the animal kingdom."

A number of other genes that affect aging in a wide range of species have also been found in research using the nematode worm C. elegans -- for example:

• daf-2, an insulin-like receptor gene (see Signs Of Aging: Scientists Evaluate Genes Associated With Longevity and Scientists Find What Type Of Genes Affect Longevity)
  
• the gene for enzyme age-1/PI3 kinase, which plays a role in muscle deterioration (see Researchers Seek Fountain Of Youth Among The Worms)
  
• DAF-16, also involved in an insulin/glucose pathway (see Researchers Identify Switch That Controls Aging In Worms)
  

Tags: longevity