The discovery of sirtuins, part 2

Unless you're a biologist who's already familiar with the ins and outs of research into sirtuin proteins, you might want to have a look (if you haven't already) at the previous note in this series, where I describe a lot of important background and provide various other references.

But if you're ready to forge ahead, in this note I'm going to write about a gene found in the nematode Caenorhabditis elegans. The gene is called sir2-1, and it's a homologue of the yeast SIR2 gene. (I. e. the two genes have very similar DNA sequences.)

C. elegans and some of its genes (like sir2-1 and several others affected by it, as mentioned here and here) has been studied by many investigators, because it's an easily-grown model organism for many biological processes that occur in multicellular creatures. And that's in spite of its simplicity – adults have a grand total of only 959 somatic cells.

Sydney Brenner began research into the detailed biology of C. elegans in 1974. Brenner had already earned his scientific spurs for helping decipher the 3-letter DNA code in the 1960s. But the Nobel Prize he shared in 2002 was awarded for his work with worms – which is an impressive statement about the importance of that work. Other prominent names associated with research into C. elegans include Cynthia Kenyon and Gary Ruvkun.

However, for the initial study of SIR2-like genes in C. elegans, we can return to the laboratory of Leonard Guarente. Soon after he and others at the lab had begun to appreciate the importance of SIR2 for longevity in yeast, Guarente suggested to a postdoc in his lab, Heidi Tissenbaum, that it might be very rewarding to figure out whether there were similar genes in the nematode that played a role in longevity. Tissenbaum was a pretty natural choice for this project, since she'd just recently done her thesis work in Gary Ruvkun's lab.

Despite the simplicity of C. elegans, following up on this suggestion was more easily said than done. Some idea of the complexity involved can be gained from the fact that there are about 20,000 genes in the worm's genome, as had only very recently been realized, since C. elegans was the first animal to have its whole genome figured out. The worm has almost 90% as many different genes as a human.

Among these 20,000 or so genes were four that were like SIR2. Which, if any, of those might have longevity-prolonging effects? Guarente and Tissenbaum set about trying to answer the question. So as not to miss any genes that might affect longevity even though unlike SIR2, they did experiments that could turn up others among the 20,000. They did this by considering different strains of C. elegans, each of which had one random section of its DNA duplicated. Since a eukaryotic organism already has two copies of each gene, this meant each strain would have 50% more copies (3 instead of 2) of the genes on the duplicated segment.

They found only one out of the 40 strains they tested that had a significantly longer life span. And the duplicated section of DNA contained only one of the 4 known SIR2-like genes – sir2-1, which was also the one closest in sequence to SIR2. Talk about "things that make you go hmmmmmm..."

To further strengthen the evidence that sir2-1 was somehow responsible for the increased life span, Tissenbaum produced a strain of C. elegans whose only extra gene was one or more extra copies of sir2-1. Lo and behold, these worms indeed lived much longer.

That's all well and good, of course. But how does sir2-1 bring about this increased life span? It certainly couldn't be much like the way SIR2 works in yeast to raise longevity. As you recall, longevity in a yeast cell is measured by how many times it is capable of budding off daughter cells. Normally, this is about 20 times. But this number can be substantially increased in a yeast strain with extra copies of SIR2.

However, the biology of C. elegans is quite different. The life span of these worms is manifested in a very different way than by how often cells are capable of dividing. In fact, the cells of an adult nematode do not divide at all – they have reached a state known as "senescence", all 959 of the somatic cells. All the difference in life span of a nematode occurs after its cells become senescent.

Initially, life span of the worms was measured simply by how long it took before the creature stopped wriggling, about 20 days. Later, more careful observation showed that aging could actually be noticed visibly (under a microscope). Old worms looked wrinkled and exhibited other visible signs of decrepitude. This is of importance, because an alternative hypothesis about how sir2-1 promoted longevity was that it somehow blocked a disease state that could kill the worm. But in fact, it was found that extra sir2-1 genes indeed slowed the rate of visible aging.

So there still remained to find an account of how sir2-1 extended life span. There were several other worm genes that were already known to affect longevity. I noted two of these (daf-2 and daf-16) here. Some of this information was already known to Guarente and Tissenbaum. In fact, the latter herself had participated in some of the relevant research while working in Ruvkun's lab. This 1997 press release describes some of that research:

Inactivation Of Key Gene Allows Worms To Develop Without Insulin (10/29/97)

The team — which also includes first author Scott Ogg, PhD, Suzanne Paradis, Shoshanna Gottlieb, PhD, Garth Patterson, PhD, Linda Lee, and Heidi Tissenbaum, PhD — discovered that insulin may control metabolism via inactivation of a second gene, daf-16. The researchers found that, although insulin normally is required to regulate metabolism in the worm C. elegans, as in humans, the animal no longer needs insulin if it also carries a mutation in daf-16. This gene encodes a DNA-binding protein that passes along insulin signals within the cell to control the production of enzymes that metabolize sugars and fats. The team proposes that in the absence of insulin, the DAF-16 protein becomes unregulated, and that its runaway activity may be the key cause of metabolic disease in diabetes. In support of this model, the research team shows that metabolic defects in worms with defective insulin signaling are "cured" by the inactivation of the daf-16 gene.

(If you're confused by the capitalization of daf-16 and DAF-16, note that the former refers to the gene, and the latter to the corresponding protein. But you're not alone, since the opposite convention is sometimes used.)

I suppose that, at this point, the suspense is killing you, or at least delivering a credible threat to curtail your life span, so I'll just summarize what has been learned over the years about daf-2, daf-16, related genes, and how sir2-1 fits into the picture.

The hormone insulin plays an important role. In mammals insulin has a signaling function that stimulates cells to take up glucose and metabolize it. However, its role in C. elegans is somewhat simpler. There it doesn't directly affect glucose metabolism, but it still acts as a signal, as a trigger of the so-called "insulin-signaling pathway". This pathway keeps the daf-16 gene turned off as long as a cell-surface receptor detects insulin.

The protein coded for by daf-16, namely DAF-16 (duh), is a transcription factor, which means it enables the expression of other genes. When this happens in an immature worm, the result is an alternative developmental path, in which the worm enters a larval state, called a "dauer" (German for "enduring"). (The name "daf" is short for "dauer formation".) A dauer will eventually, after some delay, develop into a normal adult anyhow. But evolution has provided this dauer stage in case times are lean, and a delay will allow the organism to survive a little longer, on the hope that better times will come soon.

Under normal conditions, when sufficient nutrients are available, insulin is produced. A cell surface receptor (DAF-2, coded for by daf-2) detects the insulin and initiates a signaling cascade within the cell, and this in turn keeps daf-16 inactive. This does no harm to the organism, and in fact worms get along just fine even without a daf-16 gene, assuming adequate nutrition.

However, assuming insufficient nutrients, insulin levels drop. If that happens early enough in the nematode's life, daf-16 becomes active and triggers the dauer state. But what occurs after the nematode reaches adulthood and daf-16 becomes active (due to low insulin level) is perhaps even more interesting: the worm's aging slows down, and total life span increases. So this is a second way that the worm, even after it reaches adulthood, may be able to survive when food runs low, in the hope for better times.

Why isn't this second scenario simply the normal one? Why bother with the dauer stage at all? The answer is probably that nature has found this "live fast and die young" strategy the most successful in the long run, just as with small rodents. After all, a C. elegans is pretty small – 959 cells and about 1 mm in length. It's easy prey to larger predators that can enjoy a nematode meal. On the other hand, in cases there's not enough food for the worm to "live fast", it's nice to have not one but two backup strategies.

So where does sir2-1 fit in to all of this? Well, just as with SIR2, the worm homologue produces a deacetylase enzyme that inhibits the production of other proteins. One or more of these proteins is a necessary part of the signaling cascade that insulin initiates to keep daf-16 inactive. So extra sir2-1 protein interferes with the insulin signaling and, in effect, activates daf-16, which slows down aging, and extends life span – even when adequate amounts of nutrients are available.

Pretty neat, eh? That's evolution for you – always coming up with the Rube Goldberg schemes.

OK, that's how sirtuins work in nematodes. What about mammals, like us? As you might suppose, since mammals have far more than 959 cells in their bodies, things are a lot more complicated. There are even (at least) seven different homologues of SIR2. But the fact that in worms sir2-1 messes with insulin signaling and metabolism is a clue. Those are pretty important processes in mammals too.

To be continued.


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Further reading:

daf-16: An HNF-3/forkhead Family Member That Can Function to Double the Life-Span of Caenorhabditis elegans (11/14/97)

Reproductive Signals Affect Lifespan In Roundworm C. Elegans, Offering Possible Insight Into Human Aging Process (5/27/99)

Smell, Taste May Influence Lifespan Of The Roundworm C. Elegans (12/17/99)

Long-Lived Worms (3/8/01)

University Of Colorado Researchers Identify Switch That Controls Aging In Worms (12/11/01)

Stem Cells For Eggs And Sperm Also Control Aging In Roundworm (1/18/02)

DAF-16 Target Genes That Control C. elegans Life-Span and Metabolism (4/25/03)

Scientists Find What Type Of Genes Affect Longevity (7/1/03)

Old Worms, New Aging Genes (8/2/03)

Methuselah Worm Remains Energetic for Life (10/27/03)

Signs Of Aging: Scientists Evaluate Genes Associated With Longevity (4/18/05)

For The First Time: Longevity Modulated Without Disrupting Life-sustaining Function (3/11/06)

Eat Less, Live Longer? Gene Links Calorie Restriction To Longevity (5/2/07)

Genes That Both Extend Life And Protect Against Cancer Identified (10/15/07)

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Tags: sirtuins, aging, longevity, calorie restriction, caloric restriction

The discovery of sirtuins, part 1

There's a lot more to the story of sirtuin proteins beyond what I've barely touched on here and here. Perhaps the best way to proceed is to rewind the tape (now, there's a metaphor on it's way out if there ever was one) to the point where biologists initially recognized what the story was about and where it might be going.

The best reference for this is Leonard Guarente's 2003 book Ageless Quest. Since Guarente seems to have played the largest role in the initial understanding of sirtuins, this reference is pretty much definitive. This book is short and readable, but packed with information. It seems to be rather underappreciated. However, if you don't happen to have it at hand, a few more brief references are listed at the end of this note.

Guarente isn't especially explicit about the dates of various milestones, so one has to infer a bit, but his memoir begins roughly in 1987, with the most important results it discusses coming out around 2000. The story begins after Guarente has received tenure in MIT's biology department and has begun to assume responsibility for a laboratory of his own. Until 1991 the lab's primary focus was gene transcription, but then (as now, and for good reason) that was a crowded field.

Gradually Guarente decided that investigation of the process of biological aging, and in particular the study of genes that regulate aging, was both less crowded and more interesting. Of course, the field was uncrowded for a reason – most biologists at the time considered the problem of aging to be too hard, and out of reach of serious scientific research. Guarente, however, succumbed to the challenge.

In 1991 he decided that yeast (genus Saccharomyces), a single-celled eukaryote, was the right model organism to begin with. It was simple enough to make research practical, but complex enough to exhibit the characteristic phenomena of aging seen in much more complicated multicellular organisms. Yeast cells reproduce by budding off copies of themselves. This process typically repeats through 20 to 40 iterations before any given cell becomes unable to reproduce, and eventually dies. (This is different from what happens with bacteria, which are prokaryotes and are able to continue dividing indefinitely.)

A newly-budded yeast cell is at a peak of generative vigor. This is regardless of the age of its mother cell – an important clue, as we'll see later. The new yeast cell may start budding daughter cells once an hour, but gradually slows down. At between 1 to 4 hours per iteration, 20 iterations typically occur in 40 to 60 hours. However, an intriguing fact is that different yeast strains are capable of continuing to reproduce for a variable number of iterations, up to a maximum of about 40. So the scientific problem is to figure out what accounts for the difference. Presumably, it's some small difference in the genes found in different strains of yeast. But what genes?

To keep the narrative brief, I'll leave out most of the details. Suffice it to say that the first clues came when a lab worker came across one batch of yeast with exceptional longevity. So what was different about its genes? Suspicion quickly focused on variants of a particular gene, which had already been named SIR4. SIR is an acronym for Silent Information Regulator, and SIR4 was already known to be a regulatory gene that silences the expression of other genes.

In yeast, SIR4 is frequently found in association with other SIR genes – SIR2 and SIR3, although these don't have similar amino acid sequences. So the question became, what other genes does SIR4 (and its associates) regulate, when, and why?

Initially suspicion focused on the possibility that the longevity effect of SIR4 was related to chromosome teleomeres. These structures, which occur at the ends of chromosomes, were already known to have an effect on the ability of a eukaryotic cell to divide. This clue turned out to be a red herring, as was eventually realized. But before enlightenment fully dawned, Guarente and some of his collaborators in the lab published a paper in the prestigious journal Cell, in 1995, reporting that the gene triple of SIR2, SIR3, and SIR4 affected some as-yet not well determined part of the yeast genome in such a way as to extend longevity under some circumstances.

The important question, then, was to determine exactly how this came about. Other labs besides Guarente's were also studying yeast and the SIR genes, and they made significant contributions. But to keep this simple, I'll continue to focus on the Guarente lab. The next advance, after the 1995 paper, involved certain curious DNA structures called "rDNA circles".

A new postdoc named David Sinclair, who Guarente recruited to join the lab in 1995, had some of the crucial insights, which involved rDNA. That is the name given to a certain part of the yeast genome that codes for RNA sequences used in building the cell structures known as ribosomes.

In the overall process of replicating chromosomes during cell division, a subprocess called recombination occurs. Normally, a strand of DNA in one chromosome of a pair is broken at a certain place, and "recombined" with a strand of DNA from the other member of a pair of chromosomes. The way that the process "ought" to work is that the DNA is broken and recombined at exactly the same place in the two strands, as determined by the sequence of genes within the DNA. However, rDNA happens to contain multiple copies of the same gene, in order to produce enough corresponding RNA needed to make ribosomes. So it's possible for mistakes to be made in which some copies of the ribosomal DNA genes are deleted from the resulting recombined DNA strands. The leftover rDNA genes float away in little rings of DNA called rDNA circles.

This circumstance is somewhat unique to yeast, due to the way the rDNA genes are laid out in yeast genome. So if all this was part of an aging mechanism, it wouldn't necessarily be applicable except in yeast. What is really surprising is that relevant mechanisms for other species were eventually found, but that's getting ahead of the story.

One result of the production of rDNA circles in yeast is that after awhile fewer genes remain in the chromosomal DNA to produce ribosomes for the cell's needs. Perhaps eventually there doesn't remain an adequate number of these genes, and this fact is responsible for yeast aging. But there's another possibility. Perhaps an increasing number of these rDNA circles accumulate in yeast cells, and eventually this is what gums up the cellular works and causes aging.

It was Sinclair who came up with this idea, and one clue which led to it is, as mentioned before, that newly budded daughter yeast cells have the maximum life expectancy that normally occurs with yeast cells of their lineage. They did not seem to inherit any premature aging from a mother cell that could already have budded many times before. This would indeed be a problem if too many rDNA genes became lost in the process of repeated recombination, to be sloughed off into rDNA circles. Instead, Sinclair suspected that what was happening was that the rDNA circles were themselves being cloned repeatedly by the process of recombination. And further, that all such cloned rDNA circles remained in the mother cell, instead of any being passed along to daughter cells. He managed to show, in a series of experiments, that this latter scenario was what was actually happening, and did cause aging in yeast.

In late December of 1997 Guarente and Sinclair published a paper in Cell, described at length in this press release, which reported these results. The paper attracted a considerable amount of attention, including a long front-page article in the New York Times, by science writer Nicholas Wade. (I mention Wade specifically, because he has remained interested in the topic, and wrote a perceptive article for the Times in November 2006 on resveratrol, which I discussed here.)

In spite of all this progress, one important part of the puzzle remained to be solved. That is, what exactly is the role, if any, that the SIR genes play in the whole process? It was already clear that they did affect the longevity and rate of aging of yeast cells, but how?

It turned out that it wasn't actually SIR4 that affected yeast cell longevity, as initially suspected, but instead its associate SIR2. And the mechanism for this that was discovered has profound implications for aging in many eukaryotic species, not just yeast.

The importance of SIR2 instead of the other SIR genes in yeast was recognized when it was found that permanently deactivating SIR2 drastically reduced yeast lifespan, but deactivating SIR3 and SIR4 had little effect on lifespan. So investigation quickly focused on SIR2. What was it doing? Sinclair moved on to become a professor at the Harvard medical school in 1999 and continued to study the problem. But Guarente and others in his lab, as well as many others outside the lab, also pressed on.

So SIR2 was the critical gene, but why? SIR2 was already known as a silencing gene, meaning it inhibits the expression of other genes. It turned out that in yeast, one thing SIR2 does is to suppress the process of recombination that produces all those rDNA circles. And how does it do that? (A new question seems to arise every time another one is answered.)

SIR2 does its work, at least in this case, because its enzymatic action (or rather, the action of the protein – Sir2 – encoded by SIR2) is to remove acetyl groups from other proteins. That's why Sir2 is called a deacetylase enzyme. The presence, or absense, of acetyl groups on a protein can determine whether or not the protein performs a specific function. So acetylation can by itself alter the expression of the gene that encodes the affected protein.

However, Sir2 doesn't act on just any old proteins, but specifically on histone proteins. You recall, of course, that a histone is a type of protein that comes together in groups of eight to make up a nucleosome. A nucleosome, in turn, is like a spool around which 146 base pairs of a DNA strand are wound, as one of many beads on a string that make up the chromatin constituting a chromosome. So Sir2 is actually a histone deacetylase enzyme (HDAC), such as described here. And when a histone is deacetylated, it becomes impossible for the gene whose base pairs are affected to be expressed, quite effectively silencing the gene.

And that's still not all. It turns out that Sir2 can perform this deacetylation only with the help of a relatively small molecule, called nicotinamide adenine dinucleotide, or NAD for short. (Such a helper molecule is called a coenzme.) NAD turns out to be critically important here, because it is centrally involved in cell metabolism.

When a cell is starved for nutrients, the levels of NAD will be high, enabling Sir2 to perform the deacetylase function. And as it happens, in yeast the genes that are consequently silenced are the very ones that cause the production of the rDNA circles. Putting this all together, a yeast cell that is starved for nutrients will cut back the process that plays a key role in cellular aging.

It's very clever of evolution to have come up with this Rube Goldberg mechanism. The net result is that yeast cells that are ill-nourished automatically cut back their rate of aging, so that they may survive until adequate nutrients may become available. Of course, evolution wouldn't have needed to be so clever if it hadn't also allowed aging to occur in the first place, because of (in this case) the production of inconveniently many rDNA circles. This all illustrates the unplanned, rather haphazard result of evolutionary processes.

Guarente and some of his lab associates published a paper describing all this in a February 2000 technical paper in Nature. That paper is announced here. A couple of months later, he composed a review, described here. That description began by noting

Caloric restriction, which is the reduction of caloric intake without malnutrition, is a time proven method for extending the life span of mammals and postponing the manifestations of aging, including both functional decline and age-related diseases. Much is know about the physiological changes that occur in animals subjected to caloric restriction, but molecular mechanisms involved in this phenomenon are poorly understood because of the lack of workable experimental models.

That press release continued to say

Dr. Leonard Guarente of the Massachusetts Institute of Technology announced that his lab has identified a gene, SIR2, which regulates the life span of yeast. The gene is responsible for the production of a protein, Sir2, and the higher the level of this protein, the longer the life span of yeast cells. Sir2 is responsible for a process called genomic silencing that Dr. Guarente believes helps slow the aging process. However, it requires help of another compound, the level of which is determined by metabolic rate, to do this.

"Our findings thus provide a model for aging that is universal and explains how calorie restriction extends life span," says Dr. Guarente. "We believe that these studies could lead to the development of a drug that intervenes to strengthen the Sir2-silencing process and provides the benefits of calorie restriction without the extreme difficulty of the regimen itself."

Of course, all he was claiming here is a possible model for the longevity-enhancing effects of calorie restriction. At best the model had experimental support in the case of yeast. What about more complex organisms, such as, for example, the nematode Caenorhabditis elegans?

C. elegans was next on the agenda, and surprisingly enough (or maybe not), a nematode gene very like SIR2 was also implicated in extending lifespan, though through a rather different mechanism. However, we'll have to tell that story later.

To be continued.


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Further reading:

Unlocking the Secrets of Longevity Genes – Article by Guarente and Sinclair published in Scientific American in 2006, discussing the state of knowledge at the time of the relationships between sirtuins, calorie restriction, and aging.

SIR2 and aging: an historical perspective – A very brief sketch of the subject.

Gaurente Lab – A brief overview of relevant discoveries made at the lab.

Guarente research summary – Very brief summary of Guarente's own research and short list of publications.

Genes Linking Aging and Cancer – A recent blog post that discusses recent findings about the role of sitruins in both aging and cancer.


Tags: sirtuins, aging, longevity, calorie restriction, caloric restriction

Sirtuin proteins

What's a sirtuin protein? Perhaps this will jog your memory. Not quite two months ago I wrote about resveratrol – the trace ingredient in red wine that may (or may not) have longevity-extending effects. See the article for plenty of details, but there are a few summary points to repeat here.

First, resveratrol may not occur in sufficiently high concentrations in red wine to offer practical health benefits to humans. Second, there are other compounds in red wine (and red or purple grape skins) which may play a larger role than resveratrol in the reported health benefits of red wine. Third, it is suspected that some of the health benefits observed in experiments with mice fed diets having high concentrations of resveratrol may be a result of its activation of a gene that produces the enzyme called SIRT1, which is a "sirtuin" protein. But, fourth, the observed health benefits of resveratrol may also be due to other effects. In summary, that situation with red wine and resveratrol is still not very clear.

However, it's specifically the sirtuin protein SIRT1 (and some closely related variants) we're interested in here, for reasons we'll get to in a moment. But to set the stage a little further, SIRT1 itself (and related proteins) has been of interest to biologists for over ten years because SIRT1 and its relatives appear to affect the longevity (usually in a positive way) of individuals belonging to several diverse eukaryotic species, ranging from yeast and nematodes to mammals. And this effect seems to be closely related to the observed beneficial effects on longevity of calorie restriction – effects that have been observed for many decades.

There's a little history behind the name of the protein SIRT1. It begins with certain proteins, which were observed in yeast, and which seemed to have something to do with the longevity of yeast cells. There were several of these proteins, which were called Silent Information Regulators. Three of them, in particular, known as SIR2, SIR3, and SIR4, seemed to be implicated in the longevity effect, although they are not structurally similar. Ultimately SIR2 proved to be the most important, and remarkably, a gene in the nematode Caenorhabditis elegans turned out not only to be a close analogue of SIR2 but also to have similar longevity-enhancing effects.

Because of their interesting effects, such proteins became known as "sirtuins" (get it?). It turns out that there are at least seven similar human proteins, named SIRT1 through SIRT7. Of these, it is SIRT1 that has (for good reason) attracted the most attention. It is an enzyme, in particular a histone deacetylase enzyme. Such enzymes are able to efficiently silence the expression of a variety of genes, so they are involved in a wide diversity of biological processes, as I've written about before. (And as I hope to write much more about.)

There are all sorts of interesting things to note about the human sirtuins, but the most notable recent finding, which is very relevant to calorie restriction and was announced at almost the same time as my resveratrol post, is this:

Eat Less To Live Longer: Calorie Restriction Linked To Long Healthy Lives (9/26/07)

Now, reporting in the September 21 issue of the journal Cell, researchers from Harvard Medical School, in collaboration with scientists from Cornell Medical School and the National Institutes of Health, have discovered two genes in mammalian cells that act as gatekeepers for cellular longevity. When cells experience certain kinds of stress, such as caloric restriction, these genes rev up and help protect cells from diseases of aging.

"We've reason to believe now that these two genes may be potential drug targets for diseases associated with aging," says David Sinclair, associate professor of pathology at Harvard Medical School and senior author on the paper.

The new genes that Sinclair's group have discovered, in collaboration with Anthony Sauve of Cornell Medical School and Rafael de Cabo of NIH, are called SIRT3 and SIRT4. They are members of a larger class of genes called sirtuins. (Another gene belonging to this family, SIRT1, was shown last year to also have a powerful impact on longevity when stimulated by the red-wine molecule resveratrol.)

David Sinclair, of course, has been heavily involved in research on SIRT1 and resveratrol, as discussed here. He is also co-founder of Sirtris Pharmaceuticals, which is investigating drugs that target sirtuins. Sinclair is a former student of Leonard Guarente, who is also very prominent in sirtuin research, and who had a great deal to do with investigation of the analogous proteins in yeast and nematodes.

One of the most interesting things about the longevity-enhancing effects of sirtuin proteins in yeast and nematodes is that they seem to achieve their effects by rather different means. In yeast, one cause of aging is the formation of "ribosomal DNA circles", and SIR2 (under appropriate conditions) can inhibit this. In C. elegans, on the other hand, the biological effect that retards aging is the inhibition of "insulin signaling". So what is it that SIRT3 and SIRT4 do in the cells of humans (and other mammals)?

In this paper, the newly discovered role of SIRT3 and SIRT4 drives home something scientists have suspected for a long time: mitochondria are vital for sustaining the health and longevity of a cell.

Mitochondria, a kind of cellular organ that lives in the cytoplasm, are often considered to be the cell's battery packs. When mitochondria stability starts to wane, energy is drained out of the cell, and its days are numbered. In this paper, Sinclair and his collaborators discovered that SIRT3 and SIRT4 play a vital role in a longevity network that maintains the vitality of mitochondria and keeps cells healthy when they would otherwise die.

When cells undergo caloric restriction, signals sent in through the membrane activate a gene called NAMPT. As levels of NAMPT ramp up, a small molecule called NAD begins to amass in the mitochondria. This, in turn, causes the activity of enzymes created by the SIRT3 and SIRT4 genes--enzymes that live in the mitochondria--to increase as well. As a result, the mitochondria grow stronger, energy-output increases, and the cell's aging process slows down significantly.

Other news stories on this research:

• Researchers Pinpoint Link Between Caloric Restriction and Longevity (9/20/07)
  
• New Clue To Why Eating Fewer Calories Can Help You Live Longer (9/21/07)
  
• Eat (Less) to Live (Longer) (9/20/07)
  
• U.S. study finds potential new ways to fight aging (9/20/07)
  

Tags: resveratrol, sirtuins, aging, longevity, calorie restriction, caloric restriction, SIRT1

Readings, 5 August 2007

I'm trying a new approach to this, so we have a bumper crop of readings this week. Don't count on as much every time, but have fun with the current list.

The text following each item is quoted material, except for editorial comments, which are in color.

General and physical science

Open Access and the Progress of Science

The power to transform research communication may be at each scientist's fingertips.

Open access publishing seems very important to me. It's quite frustrating – for both the writer and the reader – to present an overview of some important scientific research, yet have the actual research publication be inaccessible to most readers, and at best accessible to a few only by jumping through hoops. This is especially frustrating in the case of research that may have personal importance to certain readers, as with health and medical issues. It's also a major barrier to raising the scientific literacy of the public when there is no practical way for the public to gain a better understanding of a subject – by going to the original research papers – than provided by the mass media.

The chemistry of space grows more complex

The chemistry of outer space continues to amaze astronomers. After several decades of doubt, they know that chemical processes around and between stars produce complex molecules including precursors of organic life. But recent discoveries with a new observing technique show they have barely glimpsed what's really going on.

Space station's future in doubt

NASA has only a slim margin of error for completing construction of the international space station before the space shuttle is retired -- and more concerns about supplying it after that date....

And even if no unforeseen scheduling issues arise, experts said NASA faces problems dealing with changes to its work force as the agency moves to a future moon-Mars exploration program. And there is a shortage of science being done on the space station, conceived as a 200-mile-high floating laboratory.

In order to support real scientific research, NASA should be provided with a little of the hundreds of billions of $$ now being squandered on military boondoggles. Failing that, it would be a blessing if funding for real science came from savings that would result if the space station were simply abandoned, or at least mothballed for a few years. For comments regarding better use by NASA of its budget, see this and this.

The Great Global Warming Swindle Swindle

With all those other endangered species going extinct it's nice to know there's still a handful of global warming skeptics kicking around. ABC Science Online's Bernie Hobbs looks at the facts behind the vitriol in the film that's got everyone looking up the word 'polemic'.

Nice exposé of a propaganda film put out by global warming skeptics.

Self Assembly

Hofstadter's new book, deeply thought-provoking though it is, is less engaging than either Gödel, Escher, Bach or Le Ton Beau de Marot. Yet I Am a Strange Loop carries the high hopes of its author, not just those of its readers. Hofstadter feels that his first book, despite its massive popularity, has been widely misunderstood. Its fundamental message seems not to have been noticed: "It sometimes feels as if I had shouted a deeply cherished message out into an empty chasm and nobody heard me." This new volume is his attempt to set the record straight.

The core intellectual claim, then, is much the same as that of Gödel, Escher, Bach: namely, that a proper understanding of Gödel's proof helps us to see that life, mind and self are all constituted not by biochemistry but by the higher-level patterns that biochemistry makes possible. In particular, human selves are abstract self-referential (reflexively looping) patterns that arise spontaneously out of the meaningless base of neural activity.

Margaret Boden's review of Douglas Hofstadter's new book is brief, but should not be missed.

Do Loops Explain Consciousness? Review of I Am a Strange Loop

Another review of Hofstadter's book, by no less than Martin Gardner, who opines on its place in the philosophy of consciousness.

Mathematics

Poincaré, Perelman and proof

This is a review of Donal O'Shea's The Poincaré Conjecture: In Search of the Shape of the Universe. Both author and reviewer (Nigel Hitchin) are professional mathematicians, so the indications are this book is a must-have if you're even vaguely interested in the subject. The review itself nicely summarizes both the technical issues and the personal story of Grigori Perelman, who proved the Poincaré conjecture.

GEOMETRY AND THE IMAGINATION: Pricey Proof Keeps Gaining Support

No report on advances in topology is complete these days without an update on Russian mathematician Grigory Perelman's proof of Thurston's Geometrization Conjecture and its million-dollar corollary, the Poincaré conjecture (Science, 22 December 2006, p. 1848). After poring over Perelman's papers for 4 years, topologists are confident of the result, says John Morgan of Columbia University, who gave an overview of the proof at the Thurston conference.

There were other interesting results presented at the conference in honor of William Thurston. You can access accounts of these results here (subscription required for full access).

Tom Lehrer's Derivative Ditties

Should you be not old enough for the name Tom Lehrer even to ring a bell for you, Ivars Peterson offers a summary of the mathematician-songwriter's work having special appeal to the mathematically inclined. Such as "New Math". Somehow, he neglects to mention "Lobachevsky". Or perhaps you'd just like to know of a catchy little tune that's a hilarious send-up of Catholicism: "The Vatican Rag". (Needs to be heard sung to be really appreciated.) And for chemistry devotees there's "The Elements".

Technology

Building an Immersive Web

Early virtual worlds such as ­Second Life demonstrate that highly visual, 3-D online environments hold the potential to transform the way humans interact not only with computers but with each other .... Hyped as they are, these immersive environments address two fundamental aspects of being human: our visual and social natures.

A Smarter Web

New technologies will make online search more intelligent--and may even lead to a "Web 3.0."

This longish article may be for you if you have ever puzzled over questions like "What comes after Web 2.0?" or "What the heck is this 'Semantic Web' thing?"

At last, semiconductor industry begins embracing nano

Even though the conservative semiconductor industry, with its extreme performance and manufacturing demands, has done much of its manufacturing in nanoscale dimensions for years, it hasn’t yet had much use for the unique properties of nanoparticles, fullerenes, nanowires, quantum dots, etc.-the technologies usually considered “true” nanotech. Nor have the nanoscale patterning processes developed by the chip makers been of much use to the rest of the nanotechnology world.

But the old ways are starting to change.

A bot's life

Robotic designs based upon natural organisms are as diverse as the animal world itself. There are devices in the works that mimic caterpillars, spiders, dogs and octopuses. Their goals and purposes are equally varied, from new medical treatments to space labor to being a soldier's best friend.

Life sciences

What Do Mirror Neurons Mean?

The discovery of mirror neurons in the frontal lobes of macaques and their implications for human brain evolution is one of the most important findings of neuroscience in the last decade. Mirror neurons are active when the monkeys perform certain tasks, but they also fire when the monkeys watch someone else perform the same specific task. There is evidence that a similar observation/action matching system exists in humans.

This is a symposium comprising several papers on mirror neurons published in the last three years. I wrote about the subject here and here. These papers are technical but worth a look.

Genetic Engineers Who Don’t Just Tinker

FORGET genetic engineering. The new idea is synthetic biology, an effort by engineers to rewire the genetic circuitry of living organisms.

The ambitious undertaking includes genetic engineering, the now routine insertion of one or two genes into a bacterium or crop plant. But synthetic biologists aim to rearrange genes on a much wider scale, that of a genome, or an organism’s entire genetic code. Their plans include microbes modified to generate cheap petroleum out of plant waste, and, further down the line, designing whole organisms from scratch.

Can Adult Stem Cells Do It All?

Scientists may have turned mouse skin cells into embryolike stem cells, but prior claims for the power of adult cells have yet to stand the test of time.

Don't believe everything you read by opponents of embryonic stem cell research, such as the supposed power of adult stem cells to do whatever ESCs can.

An Elegant Molecular Dance

Her team's strategy is to spy on biological machines in action, watching as individual molecules fold, interact with one another, and do their work. They use sensitive optical imaging techniques to collect extraordinarily detailed pictures of this activity—watching, for example, as a single molecule of RNA folds into its functional shape or a tiny polio virus invades a mammalian cell. Combining those images with findings from their experiments in molecular biology and biochemistry, the scientists are revealing how the structural dynamics and movements of molecules drive biological processes. ...

One of the lab's most recent successes, however, is developing a precise portrait of the molecular dance that creates telomerase, a complex of molecules that protects the ends of chromosomes during DNA replication. Michael Stone, a postdoctoral fellow in Zhuang's lab, led the study published in the March 22 issue of Nature. The enzyme is essential for rapidly dividing cells, such as those in a developing embryo, but is usually shut off in healthy adult human cells. Upregulating the enzyme's activity allows adult cells to achieve a dangerous immortality. The enzyme is inappropriately active in the vast majority of human cancers, making it a potential target for new cancer therapies. ...

With experiments like these, Zhuang says biophysicists and biologists are steadily moving their field toward the kind of fundamental and quantitative ways of explaining the world that first attracted her to science.

Arresting developments

Dr Harel has been working on a computer model of C. elegans. He hopes this will reveal exactly how pluripotent stem cells—those capable of becoming any sort of mature cell—decide which speciality they will take on. He thinks that a true understanding of the processes involved will be demonstrated only when it is possible to build a simulation that does exactly—but artificially—what happens in nature.

There are interesting ideas in this short piece, the nature of which you would never guess from the dreadfully useless title. For example, the idea of computer modeling of entire, albeit simple, organisms. Inevitably, with the ever-increasing power of supercomputers, it will be possible before long to model more complex animals, like, say, jellyfish. This will enable zoologists who study such critters to gauge the quality of their understanding by observing how lifelike their computer models are.

Brain Boosters

Two days from now I'm planning to further tweak my mind by taking a brain-boost pill. Called Provigil, it differs from its predecessors in that it is believed to home in on a section of the brain that helps govern alertness and memory. The pill is manufactured by ­Cephalon of Frazer, PA, and its active ingredient is called modafinil. The drug's targeted delivery is supposed to prevent the side effects of stimulants that diffuse throughout the brain and rev up everything.

In addition to the Provigil the writer discusses electrical stimulation devices for the brain, which supposedly enhance performance, however slightly. Personally, I find caffeine works pretty well, and abundant evidence that's pretty well-known to all suggests I'm hardly alone. But did you know that the caffeine, plus exercise, may lower risk of skin cancer too?

Health and medicine

Gene therapy trial on hold

As the US Food and Drug Administration prepares to investigate the death of a patient in a phase I/II gene therapy trial for inflammatory arthritis, researchers in the field say the treatment's delivery vector, an adeno-associated virus (AAV), was unlikely to be the culprit.

It will be very good news if these researchers are correct, as a number of mainstream media accounts are portraying this gene therapy trial problem as yet another black eye for the whole concept of gene therapy.

Obesity: A Link to Rare Gene Variations

Sometimes, the rarest of the rare can still have an impact. A multi-institutional team of scientists led by Berkeley Lab geneticist Len Pennacchio has found that extremely uncommon gene variations likely contribute to obesity.

How and why — and to what extent — remain a mystery, but the research adds another clue to the problem of obesity, which is reaching epidemic proportions in developed nations. Overeating and lack of exercise loom as the chief culprits. But heredity and gene defects are implicated too, and now scientists have a better understanding of their role.

AIDS Abated: Genome scans illuminate immune control of HIV

Some people who contract HIV, the virus that causes AIDS, maintain low amounts of the virus in their bodies for years. These long-term nonprogressors—so called because a decade or more can pass before they develop full-blown AIDS—have attracted great attention from researchers.

Now, using powerful, whole-genome scans, researchers have identified three genetic variations that partially explain why some HIV-infected people develop AIDS quickly while others keep it at bay.

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

Longevity genes and cancer

Scientists have identified a number of genes that seem to have some effect on an animal's longevity. Mostly they have been found in small, short-lived creatures whose longevity is easily studied, such as mice, fruit flies, or roundworms (C. elegans), though they frequently have analogues in humans. See here for an earlier discussion.

Of course, any gene which is important for inhibiting cancer, such as the well-known p53, will tend to improve longevity, for obvious reasons. But surprisingly, there are some longevity genes which don't have such an obvious relation to cancer, and may lengthen expected life span even when cancer is present.

Longevity genes fight cancer at its source

Over the years, biologists have discovered a handful of genes in roundworms, mice and flies that bestow a dramatic increase in lifespan on the organism that carries it – sometimes up to twice their normal life expectancy.

These genes are involved in diverse biochemical pathways including those for growth hormones, insulin, food intake and caloric restriction. But it is thought that they are all have a role in how the body responds to stress.

Julie Pinkston at the University of California in San Francisco, US, and colleagues, wondered if these longevity genes had something else in common: the power to fight cancer – a notoriously age-related disease.

Pinkston manipulated a C. elegans gene to make the worm more susceptible to cancer, and she also introduced a mutated version of the daf-2 insulin-like receptor gene, known to be longevity-enhancing. Worms with both mutations, even though they developed tumors, still lived twice as long as unmutated worms. Apparently the mutated daf-2 was doing something in addition to preventing tumors from forming.

The something else seems to be related to apoptosis:

Daf-2 seemed to protect against the lethal cancer by stimulating apoptosis – programmed cell death – which tumour cells usually avoid, the researchers say.

It's understandable that a gene which stimulates apoptosis helps fight cancer. The question is whether stimulating apoptosis also has harmful side effects. Apparently not so much in this case, if longevity is doubled anyhow.

But there's more to it than that:

One hallmark of cancerous growth is a rapid acceleration of cell division. Daf-2 also decreased the number of cell divisions in the roundworms by 50% compared to what was expected for those with the gld-1 gene, Pinkston says.

Other longevity-releated gene mutations are known in C. elegans, and when these mutations were present, the longevity effect also occurred:

The team then used the same process to test three other known longevity genes in turn against the life-shortening gld-1 gene. These three double-mutant worms also lived longer than normal roundworms. Each of the three genes (eat-2, isp-1 and clk-1) suppressed cell division, even though they did not appear to increase apoptosis.

Again, it would seem that suppressing cell division with these mutations is a net benefit for longevity, despite the need for some cell division outside of tumors. Perhaps they simply cause an animal's life cycle to proceed at a slower pace.

But roundworms are rather simple animals. One wonders how such an effect would play out in a human...

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Other references:

Longevity genes fight back at cancer - subscription required

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Tags: cancer, longevity, lifespan, medicine, aging

Modulating the lifespan of Caenorhabditis elegans

For The First Time: Longevity Modulated Without Disrupting Life-sustaining Function

Within a hormone-triggered cascade of molecular signals that plays a crucial for a wide range of physiological functions, researchers for the very first time have identified a protein that functions specifically to extend lifespan and youthfulness -- without disrupting fertility, immunity or the organism's response to stress.

In mammals there is a pathway associated with insulin and IGF-1 (insulin-like growth factor-1) which (among other things) affects individual growth and development. But messing around with this pathway can have very undesirable side effects, such as diabetes. In C. elegans there is a cell surface receptor (DAF-2) analogous to the insulin/IGF-1 receptor in mammals. It is known that altering the signaling pathway associated with DAF-2 can extend the worm's lifespan, but there are also undesirable side effects. Now the protein associated with the Smk-1 gene has been found to modulate changes to the DAF-2 pathway so as to avoid the side effects. This suggests that the mammalian insulin/IGF-1 pathway can also be better controlled to enhance lifespan without harming other critical processes.

Related article: Our cousin, Caenorhabditis elegans

Tags: biology, aging, longevity, lifespan

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