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Induced pluripotent stem cells III

Sunday, August 31, 2008

There is still some news from here that we need to look at. It has to do with reducing the risk of tumorigenicity by using a signaling protein Wnt3a – a member of the Wnt family of proteins – in place of the c-Myc transcription factor for inducing pluripotency in differentiated adult cells.

This press release gives the executive summary:

Embryonic-like Stem Cells Can Be Created Without Cancer-causing Gene (8/6/08)
Currently, IPS cells can be created by reprogramming adult cells through the use of viruses to transfer four genes (Oct4, Sox2, c-Myc and Klf4) into the cells' DNA. The activated genes then override the adult state and convert the cells to embryonic-like IPS cells.

However, this method poses significant risks for potential use in humans.

First, the viruses employed in the process, called retroviruses, are associated with cancer because they insert DNA anywhere in a cell's genome, thereby potentially triggering the expression of cancer-causing genes, or oncogenes. Second, c-Myc is a known oncogene whose overexpression can also cause cancer. For IPS cells to be employed to treat human diseases such as Parkinson's, researchers must find safe alternatives to reprogramming with retroviruses and oncogenes.

Earlier research has shown that c-Myc is not strictly required for the generation of IPS cells. However, its absence makes the reprogramming process time-consuming and highly inefficient.

To bypass these obstacles, the Whitehead researchers replaced c-Myc and its retrovirus with a naturally occurring signaling molecule called Wnt3a. When added to the fluid surrounding the cells being reprogrammed, Wnt3a promotes the conversion of adult cells into IPS cells.

What amounts to a crude form of gene therapy has been used to make IPS cells. The idea is to insert extra copies of genes for 4 different transcription factors into a cell's DNA in order to raise the expression level of those factors. The problem is that every insertion of a gene into a cell's DNA risks damage to some other random gene in the DNA. Wnt3a, on the other hand, is a signaling protein that normally affects cells only by attaching to receptors on the cell surface.

So what has been accomplished here is that the number of transcription factor genes that need to be inserted into the DNA is reduced from 4 to 3. In addition, the factor that is eliminated, c-Myc, has tumorigenicity risks of its own. Therefore, this research represents a small but useful improvement. However, it is probably only a first step.

More about the present research: here

We discussed earlier research aimed at eliminating use of c-Myc in making IPS cells here.

In fact, just a little bit earlier than the research discussed above, a team from Germany reported, on July 31 in Nature, making IPS cells by adding just two transcription factors. However, they didn't start with adult somatic cells, but with neural stem cells that already had higher expression levels of Sox2 and c-Myc. Given that, they needed to add only Oct4 and either Klf4 or more c-Myc. Here's the abstract:

Pluripotent stem cells induced from adult neural stem cells by reprogramming with two factors
Here we show that adult mouse neural stem cells express higher endogenous levels of Sox2 and c-Myc than embryonic stem cells, and that exogenous Oct4 together with either Klf4 or c-Myc is sufficient to generate iPS cells from neural stem cells. These two-factor iPS cells are similar to embryonic stem cells at the molecular level, contribute to development of the germ line, and form chimaeras. We propose that, in inducing pluripotency, the number of reprogramming factors can be reduced when using somatic cells that endogenously express appropriate levels of complementing factors.

Keep in mind that there's a further variable that's important here: the efficiency of the process, i. e. the yield of IPS cells obtained as a percentage of original cells at the beginning. It should be obvious that a fair amount of work still needs to be done to find a method of making IPS cells that's both efficient and produces cells that are potentially safe to use in therapeutic applications (as opposed to pure research).

OK, enough of that. Let's move on to something new.

One of the interesting questions about IPS cells is about exactly how close they are to actual embryonic stem cells, which are pluripotent by definition. The best way to measure the degree of closeness is by comparing gene expression levels between embryonic stem cells and IPS cells.

The next research has done exactly that. In fact, it studies gene expression levels for stem-like cells obtained from a wide variety of sources:

A new test distinguishes embryonic stem cells and those with equal therapeutic potential (8/24/08)
To distinguish adult stem cells from pluripotent cells, Loring’s team compared the gene activity of about 150 stem cell samples of various types, including reprogrammed cells, embryonic stem cells and neural stem cells. Out of this comparison popped 299 interacting genes that form what the researchers call a pluripotency network, or PluriNet. Measuring the activity of these genes could reliably distinguish the different kinds of stem cells, the team reports.

Here's the abstract for this research:

Regulatory networks define phenotypic classes of human stem cell lines
We report here the creation and analysis of a database of global gene expression profiles (which we call the 'stem cell matrix') that enables the classification of cultured human stem cells in the context of a wide variety of pluripotent, multipotent and differentiated cell types. Using an unsupervised clustering method to categorize a collection of ∼150 cell samples, we discovered that pluripotent stem cell lines group together, whereas other cell types, including brain-derived neural stem cell lines, are very diverse. Using further bioinformatic analysis we uncovered a protein–protein network (PluriNet) that is shared by the pluripotent cells (embryonic stem cells, embryonal carcinomas and induced pluripotent cells). Analysis of published data showed that the PluriNet seems to be a common characteristic of pluripotent cells, including mouse embryonic stem and induced pluripotent cells and human oocytes. Our results offer a new strategy for classifying stem cells and support the idea that pluripotency and self-renewal are under tight control by specific molecular networks.

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Emotions and the insula

Saturday, August 30, 2008

I've been meaning for some time to write more about a brain region known as the insula. Looks like now is as good a time as any.

This is a big topic. We had one previous, tentative discussion here. It dealt with involvement of the insula in the "feeling" of fairness and how moral/ethical decisions are made.

Let's start with a review of what the insula actually is, anatomically. It is a part of the brain's cerebral cortex, the outermost layer of the brain, which in humans ranges from 2 to 4 mm in thickness. Although part of the cortex, the insula is located fairly deep within the brain, in an especially deep fold (or "sulcus") of the cortex, between the temporal lobe and the inferior parietal cortex.

Since the insula is adjacent to the temporal lobe on each side of the brain, it is made up of two separate parts, on the right and left sides of the brain. It is found that one side or the other, often the part on the right side, may be more important than the other in particular circumstances. Sometimes the critical area is even smaller, such as the anterior or posterior region of the insula on one side.

A good reason for considering the insula is that it seems to be deeply involved in mediating various emotions in humans. However, the evidence is somewhat indirect.

One important clue is that when a part of the brain including the insula is damaged due to disease or trauma, significant changes in emotions of the affected individual are observed. For example, smokers who experience damage to the insula suddenly cease to feel pleasure from smoking, and they are able to quickly give up the habit. (See here.)

Another clue is that fMRI brain scans show significantly increased activity in the insula when experimental subjects feel strong emotions. There are many example of this. In fact, the relationship seems so predictable that activity in the insula as revealed in fMRI scans is taken to be a marker for emotional experience.

However, there's a lot more we would like to know about exactly how the insula is involved with emotion. For instance, is there anything special about neurons found in the insula, some genes expressed in those neurons more than in neurons elsewhere? Or is the insula's role simply a matter of how it is connected to other parts of the brain? Are there particular hormones or neurotransmitters that are important for processing of emotions in the insula?

In order to even think about such questions, we need to look more closely at what is known about emotions themselves, from classical psychological studies.

To begin with, psychologists distinguish between different "levels" of emotion, not in the sense of intensity, but in the degree to which a particular emotion is more or less "fundamental" and related to basic instinctual needs or aversions. Fundametal emotions are such things as hunger, lust, craving, and fear. It is easily imagined that most animals with a developed central nervous system have such emotions.

Other emotions are a little more abstract, such as happiness, sadness, anger, disgust, anxiety, joy, surprise, delight, pleasure, and amusement. One supposes that substantially fewer animal species experience such "higher" emotions.

And then there are emotions which are pretty much limited to complex social animals that have a rich social life – for example, group loyalty, a sense of fairness or unfairness, altruism, trust, pride, shame, envy, jealousy, greed, grief, etc.

A whole lot more could be (and has been) said about such a categorization of emotions or alternative categorizations, but this will serve to provide an idea of what is meant by "emotion".

There are very good reasons for studying emotions per se. Here are some of them:

  • Emotions play a large role in making moral and ethical judgments. The sense of "fairness" and empathy, as well as various other emotions (especially social ones), come in here. This was discussed here.
  • Another special case of emotional involvement with decision making is found in politics. For instance, our attitudes towards particular candidates have a lot to do with our emotional reactions to the candidates as people – e. g., whether or not they give us a feeling of trust or security or empathy. (Some discussion here.)
  • Emotions play a significant role in economics. For instance, choices made about investments depend a lot on whether one has emotions of fear (in troubled times) or greed (when the economy seems to be doing well).
  • Emotions play a large role in decision making in general. Everyone understands the importance of "gut feelings" here. The emotions a person typically has in certain situations have a large effect on the decisions the person makes in such situations.
  • Critiques of artificial intelligence and certain forms of cognitive psychology assert that intelligent behavior is not simply a matter of algorithmically applying rules and heuristics to known facts. The idea is that computers in their present form are not capable of fully human intelligent behavior because they are not embodied in the way humans are, and in particular they lack emotions. Such critiques have been posed by many philosophers and cognitive scientists, such as Hubert Dreyfus, and George Lakoff. The latter is a representative of the viewpoint known as "embodied philosophy".

We're not going to address all those issues right away. They just serve to remind us of things where more knowledge of the insula and emotions might help our understanding.

As an example of very recently reported research on the insula and emotions, we have this:

Why An Exciting Book Is Just As Thrilling As A Hair-raising Movie (8/12/08)
We all know, however, that reading a book describing the same scene can be similarly gripping. This week, in a paper published in the online, open-access journal PLoS ONE, Mbemba Jabbi, Jojanneke Bastiaansen and Christian Keysers show us why.

At the NeuroImaging Center of the University Medical Center Groningen of the University of Groningen (the Netherlands), Jabbi and colleagues compared what happens in our brains when we view the facial expressions of other people with the brain activity as we read about emotional experiences. ...

"Our striking result," said Keysers, "is that in all three cases, the same location of the anterior insula lit up. The anterior insula is the part of the brain that is the heart of our feeling of disgust. Patients who have damage to the insula, because of a brain infection for instance, lose this capacity to feel disgusted. If you give them sour milk, they would drink it happily and say it tastes like soda."

Prof. Keysers continued, "What this means is that whether we see a movie or read a story, the same thing happens: we activate our bodily representations of what it feels like to be disgusted– and that is why reading a book and viewing a movie can both make us feel as if we literally feel what the protagonist is going through."

To summarize: the question was about similarities (and differences) in brain response to the emotion of disgust, which may be stimulated in three different ways: actual experience (tasting something very unpleasant), observation of facial expressions of others experiencing disgust, and subjective imagination of disgust.

It was already known that fMRI scans showed activity in the insula and an adjacent region (the frontal operculum) – collectively termed the IFO – as a result of experiencing or observing the emotion of disgust. The research showed that very similar activity occurred as a result of imagining disgust.

Further reading:

Why real and imagined disgust have the same effect (8/13/08) – New Scientist article about the research

Emotional Thrills From A Movie (or a Book) – blog post on this research

A Common Anterior Insula Representation of Disgust Observation, Experience and Imagination Shows Divergent Functional Connectivity Pathways – August 2008 research article in PLoS ONE

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Spitzer Reveals Stellar 'Family Tree'

Friday, August 29, 2008

Spitzer Reveals Stellar 'Family Tree' (8/22/08)
Generations of stars can be seen in this new infrared portrait from NASA's Spitzer Space Telescope. In this wispy star-forming region, called W5, the oldest stars can be seen as blue dots in the centers of the two hollow cavities (other blue dots are background and foreground stars not associated with the region). Younger stars line the rims of the cavities, and some can be seen as pink dots at the tips of the elephant-trunk-like pillars. The white knotty areas are where the youngest stars are forming. Red shows heated dust that pervades the region's cavities, while green highlights dense clouds.

W5 spans an area of sky equivalent to four full moons and is about 6,500 light-years away in the constellation Cassiopeia. The Spitzer picture was taken over a period of 24 hours.

Like other massive star-forming regions, such as Orion and Carina, W5 contains large cavities that were carved out by radiation and winds from the region's most massive stars. According to the theory of triggered star-formation, the carving out of these cavities pushes gas together, causing it to ignite into successive generations of new stars.

This image contains some of the best evidence yet for the triggered star-formation theory. Scientists analyzing the photo have been able to show that the ages of the stars become progressively and systematically younger with distance from the center of the cavities.

W5 star-forming region – click for 720×900 image

More: here, here, here

Hubble Unveils Colorful Star Birth Region on 100,000th Orbit

Wednesday, August 20, 2008

Hubble Unveils Colorful Star Birth Region on 100,000th Orbit (8/11/08)
Hubble peered into a small portion of the Tarantula nebula near the star cluster NGC 2074. The region is a firestorm of raw stellar creation, perhaps triggered by a nearby supernova explosion. It lies about 170,000 light-years away and is one of the most active star-forming regions in our local group of galaxies.

The image reveals dramatic ridges and valleys of dust, serpent-head "pillars of creation," and gaseous filaments glowing fiercely under torrential ultraviolet radiation. The region is on the edge of a dark molecular cloud that is an incubator for the birth of new stars.

The high-energy radiation blazing out from clusters of hot young stars is sculpting the wall of the nebula by slowly eroding it away. Another young cluster may be hidden beneath a circle of brilliant blue gas.

NGC 2074 – Click for 800×789 image

More: here, here

Evidence for dark energy accumulates

Sunday, August 17, 2008

Dark energy (in its most plausible form as a "cosmological constant") has been a hypothetical possibility almost since Einstein's publication of his general theory of relativity in 1916. (Check here for our previous discussions of dark energy.)

However, it has been just over 10 years (since late 1997) that there has been strong evidence for the existence of dark energy. This evidence came from the observation of Type 1a supernovae. Such supernovae are expected on theoretical grounds to have roughly the same absolute brightness in all cases. This is because they result from the accumulation of hydrogen on the surface of white dwarf stars. This hydrogen is "stolen" by the white dwarf from a larger companion star, and as soon as a sufficient amount accumulates, a thermonuclear explosion occurs, destroying the white dwarf and producing a supernova.

Because all Type 1a supernovae should have approximately the same absolute brightness, it is possible to compare their observed brightness with what would be expected as a result of the absolute brightness and their estimated distance. The distance of a Type 1a supernova can be estimated from the redshift of its spectral lines, and assumptions about how fast the universe is expanding.

Up until 1997 it had generally been assumed that the universe was expanding, but at a slowly decreasing rate. However, what was determined in 1997 was that distant Type 1a supernovae had an observed brightness that was dimmer than would be expected on the assumption that the expansion of the universe was decelerating. Instead, the most natural assumption was that the expansion was accelerating, which would mean that the distant supernovae were farther away than expected, and hence dimmer.

There was a lot of uncertainty in the initial measurements of supernova brightness, as well as questions about the suitability of assumptions made in order to calculate the expected brightness. However, there were two other lines of evidence that supported the idea of a cosmological constant (and hence, dark energy).

One line of evidence was obtained from observations of the angular size of hot and cold spots in the cosmic microwave background (CMB) radiation. The actual size of these fluctuation can be calculated theoretically based on certain reasonable assumptions. However, the size that we observe depends on the curvature of the universe. For instance, if the curvature is positive, like a convex lens, then the angular size of the fluctuations will be magnified and appear larger than calculations predict. But it turns out that the observed size is very close to what is predicted, meaning that the universe must be nearly flat. And from other considerations, the universe can be "flat" only if there is a much higher energy density than can be accounted for in terms of all suspected types of matter, even dark matter. This extra energy density is best accounted for in terms of the dark energy.

A third line of evidence comes from the observed distribution of galaxies and galaxy clusters. The effect of dark energy to cause the expansion of the universe to accelerate also causes galaxies and clusters of galaxies to be spread farther apart than we would otherwise expect – and this additional spread is exactly what is observed.

However, the idea of dark energy, especially if it is based on a cosmological constant, is fairly radical, because we have no theoretical way to explain what dark energy is or why it should exist. Therefore, the more evidence we have that it does in fact exist the better.

So it's quite welcome that a fourth line of evidence for the existence of dark energy is now much more strongly supported by data in a new study. The new evidence is based on more precise measurements of what is called the integrated Sachs-Wolfe effect. This effect is also found in observations of the CMB, but observations of a very different kind.

The effect is predicted to be manifested as microwave photons of the CMB pass through regions of the universe with densities that are higher or lower than the overall average. Consider a region of higher density, such as a supercluster of galaxies. As the photon enters the region, its energy will increase, because it is exchanging gravitational potential energy for electromagnetic energy, like a rock gains kinetic energy falling in Earth's gravitational field. The photon's energy gain is manifested in a shorter wavelength.

Galaxy superclusters are very large, from 100 to 500 million light-years in diameter. So in the time it takes a photon to cross a supercluster, the expansion of the universe will reduce the average matter density of the supercluster. The net effect is that the photon will lose less energy as it is leaving the supercluster than it gained when it entered. So the photon has a net energy gain in the process.

The universe also contains "supervoids", which are regions of size similar to superclusters where there are few galaxies, and the average matter density is less than the overall average. While a photon is passing through a supervoid, it will experience a net energy loss. On top of these energy gains and losses, a photon also gradually loses energy due to the expansion of the universe (as the photon wavelength gradually increases). There are still gains and losses after making allowance for this expansion effect. Moreover, the energy gains or losses are magnified if the expansion is accelerating.

The integrated Sachs-Wolfe effect is essentially these magnified energy gains and losses. The existence of this effect is a testable prediction of the existence of dark energy. Another way to think of the effect is as a measure of the extent that a supercluster or supervoid is expanding under the influence of dark energy, whereas there should be no expansion in the absence of dark energy. Importantly, this effect is independent of the brightness-distance relationship for Type 1a supernovae.

The new evidence for dark energy, then, is that very careful measurements of the energy of CMB photons in the directions of known superclusters and supervoids detect the existence of the integrated Sachs-Wolfe effect with very high probability, and hence another prediction based on the existence of dark energy is verified.

In the present study, about 3000 superclusters and 500 supervoids were initially selected from the Sloan Digital Sky Survey. This is out of around 10 million superclusters estimated to exist in the visible universe. Out of this sample, 50 superclusters and 50 supervoids having the largest density variation from the average were selected for closer examination.

The maximum distance of a chosen cluster was a redshift of about .5, corresponding to a distance of about 5 billion light-years. Because of the huge size of a supercluster, a typical supercluster would have an angular diameter, as seen from Earth, of about 1/25 of full circle, or 14 degrees. The researchers decided to consider circles of angular radius 4 degrees around the center of a cluster as containing the bulk of the cluster. Such circles are still about 16 times the diameter of the full Moon (1/2 angular degree).

Within each circle, the average temperature of CMB photons was measured, and compared to the overall average. The variations were very small – about 10-5K, compared to average CMB photon temperature of 2.73K – about 3 parts in a million. Nevertheless, the measurements were accurate enough that the probability of this variation being measured by chance is only about 1 in 200,000.

This is not the first research effort that has produced evidence for the integrated Sachs-Wolfe effect. However, it is based on cleaner data, and has the lowest probability of falsely showing an effect based only on chance.

News articles:

Further reading:

Supervoids and Superclusters – Web pages produced by the research team, with illustrations and background information

An Imprint of Super-Structures on the Microwave Background due to the Integrated Sachs-Wolfe Effect – short technical paper describing the research

Dark Energy Detected with Supervoids and Superclusters – longer, more leisurely presentation of the research, by the research team

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MicroRNA and stem cells II

Saturday, August 16, 2008

MicroRNA and stem cells are both pretty hot topics these days. But curiously, there haven't been a whole lot of reports that involve the two together. My last discussion of both, back in March, is here.

However, the combination of microRNA and stem cells just was back in the news, as briefly noted here.

As you recall, microRNA refers to small single-stranded RNA molecules, generally about 21 to 23 nucleotides in length. Each different microRNA (miRNA for short) is transcribed from a DNA gene like any other gene, but the resulting RNA isn't translated into a protein. Instead, the typical miRNA functions by downregulating the expression of another gene that codes for a protein.

An embryonic stem cell (ESC) has the property of pluripotency, which means that it is capable of giving rise to essentially any type of cell in the body of a multicellular organism. Whenever an ESC divides, the resulting daughter cells may also by ESCs (hence pluripotent) or they may be more specialized cells that will eventually give rise to some type of adult body cell.

In any particular ESC, the determination of remaining pluripotent or instead heading down the path to a more specialized cell type depends on what set of genes are expressed. Since miRNAs downregulate gene expression, they can keep an ESC in its pluripotent state, if they are active and suppress a gene that would make an ESC more specialized. But then if such a miRNA is blocked from being expressed, the ESC can start to become more specialized.

On the other hand, as we shall see, some miRNAs may block transcription factors that are needed to maintain a pluripotent state. Such an miRNA needs to be silent in an ESC, so some other protein needs to suppress its expression. (The miRNA called miR-21, discussed later, is an example.)

So the name of the game in studying ESCs, as far as miRNA is concerned, is to figure out what causes a miRNA gene to be expressed or not. Like other genes in an ESC, which genes are expressed is strongly controlled by a few master transcription factors.

There are four such transcription factors which seem to be especially important in ESCs: Oct4, Sox2, Nanog, and Tcf3. As discussed here, the first three of these factors have been found capable of playing a role in turning an ordinary adult cell into a pluripotent stem cell (called an "induced pluripotent stem cell").

Currently there are 336 mature mouse miRNAs known, and 441 mature human miRNAs. It is simple (given the known, complete sequences of mouse and human genomes) to locate the genes for each miRNA. However, in order to determine when a transcription factor regulates the miRNA gene, the promoter for the gene (a separate portion of DNA) must also be located. In order for a gene to be expressed, the right transcription factors have to bind to the gene's promoter.

Finding promoters is a lot harder, but there are techniques that involve searching for methylation of histone proteins that make up the nucleosomes around which cellular DNA is wrapped.

It was known, before the recent research we're discussing, that there were 14,230 sites in the genome where all four of the named master transcription factors could bind simultaneously. Most of those sites were not promoters of some miRNA, but it was straightforward to identify those that were. Of those miRNAs that appeared to be regulated by Oct4, Sox2, Nanog, and Tcf3, it was found that most are in fact preferentially expressed in ESCs. This set of miRNAs would seem to be good candidates for maintaining ESC pluripotency by downregulating other genes.

On the other hand, some of the miRNAs mediated by the transcription factors are silent in ESCs. Subsequent research found that another type of proteins (polycomb proteins) also bind to the miRNA promoters. These proteins were already known to block transcription by binding to gene promoters. But it turns out that some of these silenced miRNAs become active once the ESC loses its pluripotency and begins to differentiate.

The next step will be to figure out what each of these miRNAs regulated by Oct4, Sox2, Nanog, and Tcf3 actually does – either in the ESC or a differentiated cell. That should be very interesting, as the press release suggests:

Putting microRNAs on the stem cell map (8/7/08)
“We now have a list of what microRNAs are important in embryonic stem cells,” says Alex Marson, co-lead author on the paper and an MD/PhD student in the Young lab. “This gives us clues of which microRNAs you might want to target to direct an embryonic stem cell into another type of cell. For example, you might be able to harness a microRNA to help drive an embryonic stem cell to become a neuron, aiding with neurodegenerative disease or spinal cord injury.”

Moreover, the results give scientists a better platform for analyzing microRNA gene expression in cancer and other diseases. “We and others are finding that the overall gene circuitry for embryonic stem cells and cancer cells is very similar,” notes Marson. “Now that we have connected the circuitry to microRNAs, we can begin to compare microRNAs that are regulated in embryonic stem cells to those in cancer cells.”

Here's a somewhat more detailed description of the research: Stem Cell microRNA, Transcription Factor Interplay Uncovered (8/8/08)

Other research on miRNA and ESCs that has appeared since the previous discussion (here) gives a small taste of what may be learned about the miRNAs silenced in ESCs:

Protein Protects Embryonic Stem Cells' Versatility And Self-renewal (3/23/08)
A protein known as REST blocks the expression of a microRNA that prevents embryonic stem cells from reproducing themselves and causes them to differentiate into specific cell types, scientists at The University of Texas M. D. Anderson Cancer Center report in the journal Nature.

Researchers show RE1-silencing transcription factor (REST) plays a dual role in embryonic stem cells, said senior author Sadhan Majumder, Ph.D., professor in M. D. Anderson's Department of Cancer Genetics. "It maintains self-renewal, or the cell's ability to make more and more cells of its own type, and it maintains pluripotency, meaning that the cells have the potential to become any type of cell in the body."

The details are particularly interesting:
In studies using mouse embryonic stem cells, the researchers found that REST disarms a specific microRNA called microRNA-21 or miR-21. MicroRNAs are tiny pieces of RNA that control gene expression by binding to the gene's messenger RNA.

The team found that MiR-21 suppresses embryonic stem cell self-renewal and is associated with a corresponding loss of expression of critical self-renewal regulators, such as Oct4, Nanog, Sox2 and c-Myc. REST counters this by suppressing miR-21 to preserve the cells' self-renewal and pluripotency.

The researchers discovered the roles of REST and miR-21 in a series of experiments using cultured mouse embryonic stem cells in either a self-renewal state or a differentiating state. They found that REST expression was significantly higher in the self-renewal state. Withdrawing REST reduced the stem cells' ability to reproduce themselves and started differentiation -- even when the cells were grown under conditions conducive to self-renewal. Adding REST to differentiating cells maintained their self-renewal.

These experiments also revealed that REST is bound to the gene chromatin of a set of microRNAs with the potential to target self-renewal genes. REST controls transcription of 11 microRNAs.

Is anything special known about miR-21? Yes, in fact – it is known to play a role in cancers of the colon, liver, and thyroid. (See here.)

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Whom Do We Fear Or Trust?

Whom Do We Fear Or Trust? (8/5/08)
A pair of Princeton psychology researchers has developed a computer program that allows scientists to analyze better than ever before what it is about certain human faces that makes them look either trustworthy or fearsome.

In doing so, they have also found that the program allows them to construct computer-generated faces that display the most trustworthy or dominant faces possible.

Such work could have implications for those who care what effect their faces may have upon a beholder, from salespeople to criminal defendants, the researchers said.

There's another category of people who have a similar concern – politicians. Hmmm... salespeople, criminal defendants, politicians... lots in common there, no? What's missing from this list... preachers, TV political pundits, military officers... pretty long list.

Unfortunately, we haven't figured out how to run any large society, much less a modern one, without government and government officials, so we're stuck with politicians for some time to come, I'd guess. Well, at least that provides political scientists and researchers into aberrant psychology something to keep busy with.

The research described in the press release above isn't directly about politicians, but it's a sequel to work of the principal investigator (Alexander Todorov) that is:

Who Will Win An Election? Snap Judgments Of Face To Gauge Competence Usually Enough (10/22/07)
A split-second glance at two candidates' faces is often enough to determine which one will win an election, according to a Princeton University study.

Princeton psychologist Alexander Todorov has demonstrated that quick facial judgments can accurately predict real-world election returns. Todorov has taken some of his previous research that showed that people unconsciously judge the competence of an unfamiliar face within a tenth of a second, and he has moved it to the political arena.

His lab tests show that a rapid appraisal of the relative competence of two candidates' faces was sufficient to predict the winner in about 70 percent of the races for U.S. senator and state governor in the 2006 elections.

Other reports on this research: here, here.

Duh. At first glance all he's saying is that people tend to make snap judgments about a candidate's competence... and those candidates go on to win the election. That's not surprising, especially if one hypothesizes that voters tend not to go much beyond their snap judgment. And perhaps that is a valid conclusion, though hardly a welcome one.

In fact, Todorov had already published research showing that people make snap judgments about trustworthiness of people in general:

Snap Judgments Decide A Face's Character, Psychologist Finds (8/22/06)
We may be taught not to judge a book by its cover, but when we see a new face, our brains decide whether a person is attractive and trustworthy within a tenth of a second, according to recent Princeton research.

Princeton University psychologist Alex Todorov has found that people respond intuitively to faces so rapidly that our reasoning minds may not have time to influence the reaction -- and that our intuitions about attraction and trust are among those we form the fastest.

OK, if Todorov's research is sound, people make snap judgments about whom they will trust or fear. So it would be useful to know more precisely what factors those judgments are based on. His latest research has tried to do just that. Quoting again from the latest press release:
Based on this data, the scientists found that humans make split-second judgments on faces on two major measures -- whether the person should be approached or avoided and whether the person is weak or strong.

From there, using a commercial software program that generates composites of human faces (based on laser scans of real subjects), the scientists asked another group of test subjects to look at 300 faces and rate them for trustworthiness, dominance and threat. Common features of both trustworthiness and dominance emerged. A trustworthy face, at its most extreme, has a U-shaped mouth and eyes that form an almost surprised look.

An untrustworthy face, at its most extreme, is an angry one with the edges of the mouth curled down and eyebrows pointing down at the center. The least dominant face possible is one resembling a baby's with a larger distance between the eyes and the eyebrows than other faces. A threatening face can be obtained by averaging an untrustworthy and a dominant face.

This is all rather discouraging. What is not addressed (yet) is how accurate such snap judgments are, especially as regards trustworthiness and competence of political candidates.

It's hardly as though perspicacious people haven't been thinking about such issues for a very long time, of course. If I knew Plato better, I'm sure there'd be some choice observations in there somewhere to cite. Sort of goes along with what he said about the kind of judgments of reality made by people who can observe only shadows on the walls of a cave.

But another astute observer of human nature did have something to say about judging the intentions of people just from studying faces:

There's no art
To find the mind's construction in the face
He was a gentleman on whom I built
An absolute trust.

(Shakespeare, Macbeth, Act 1, Scene 4. This is spoken by King Duncan, regarding the Thane of Cawdor, who has just been executed for treason. Macbeth enters right after this remark, and Duncan makes him the new Thane. Slow learner, that Duncan.)

Interestingly, one of Todorov's conclusions is that the kind of face people find most trustworthy is one that features, basically, a smile. Here's Shakespeare's take on that, in words he gives to Hamlet:

O villain, villain, smiling, damn├Ęd villain!
My tables—meet it is I set it down
That one may smile, and smile, and be a villain
(Hamlet, Act 1, Scene 5)

I have addressed previous similar studies along the same lines (by other investigators) here and here.

Discouraging? Yes. Especially so if this research were to accurately describe most of the electorate. But perhaps it would be better to look at whether there are subsets of the electorate that behave quite differently. Perhaps it would work to divide the (potential) electorate into those who have at least some interest in and knowledge of politics and government, and those who don't and basically don't give a damn.

In particular, there is some evidence that "undecided" voters, those who can't make up their minds until just before voting (if they vote at all) don't simply have a difficult time making a careful judgment. Instead, many "undecideds" are actually "low-information" voters, who don't follow politics very closely, and don't especially enjoy the process. Here are some (obviously partisan) anecdotal observations on this from the 2004 election.

If this is correct, then we can write off maybe 40-50% of the potential electorate as a random factor which is basically uninformed about and uninterested in details of politics and government. If they vote at all, their votes will be based largely on impressionistic factors of appearance, charisma, or group identity – snap judgments from the physical appearance of candidates, perhaps. Although many of them won't vote, those that do might make up perhaps 10% of the total, and they are fully capable of swinging any election in one direction or another.

It is often said that a deciding factor in the 1960 presidential election was that in the first televised debate between Kennedy and Nixon, the latter was recovering from illness, looked weak, and had a decided 5 o'clock shadow. Nixon lost the popular vote by only 120,000 votes. Given how things turned out after Nixon came back to win the office in 1968, the judgments people made in 1960 may not have been so bad. But still such judgments seem like little more than a coin toss.

Further reading:

Poli Psy? – September 2000 online Scientific American article about the "shallowness" of criteria some voters use in voting decisions

The functional basis of face evaluation – June 2008 research article in PNAS about the research described in the first-mentioned press release

Inferences of Competence from Faces Predict Election Outcomes – June 2005 research article in Science by Todorov et al on the relationship between neotenous appearance and perceived competence

Appearance DOES Matter – June 2005 commentary in Science on the preceding article


Stem cell news deluge

Sunday, August 10, 2008

There's been a flood of news in the stem cell area during the past two weeks. A lot of it is important, and most of it builds on several themes related to stem cells that we've discussed before. In this post I'll just summarize the results and reference a press release. Watch for more details to follow.

Making new neurons from induced pluripotent stem cells

This is the only story here that's been reported more than a week ago (and just barely). Skin cells from an ALS (amyotrophic lateral sclerosis) patient have been reprogrammed into induced pluripotent stem cells, and then pushed towards development into motor neuron cells – containing the same defect that is manifested in ALS. These cells cannot be used to treat the disease. Instead, they will enable much more detailed research into the disease pathology.

Our most recent discussion of induced pluripotent stem cells is here.

First Neurons Created From ALS Patient's Skin Cells (7/31/08)
Harvard and Columbia scientists have for the first time used a new technique to transform an ALS ... patient's skin cells into motor neurons, a process that may be used in the future to create tailor-made cells to treat the debilitating disease.

The research – led by Kevin Eggan, Ph.D. of the Harvard Stem Cell Institute – will be published July 31 in the online version of the journal Science.

This is the first time that skin cells from a chronically-ill patient have been reprogrammed into a stem cell-like state, and then coaxed into the specific cell types that would be needed to understand and treat the disease.

Cell lines for genetic disease research

Just like the work described above, cell lines from 9 additional genetic disease have been derived from induced pluripotent stem cells, which were in turn derived from fully differentiated cells, skin cells in most cases. These cell lines will also be used for research into disease pathology. Most of the diseases in question are considered to result from mutations in more than a single gene, so that understanding the disease necessitates research into how several defective genes interact with each other or with environmental influences.

The better-known of the diseases involved are muscular dystrophy, Parkinson's disease, Huntington's disease, type 1 diabetes, and Down syndrome. There's quite a bit of news hype surrounding this announcement – although it's extremently important from a research standpoint – because the cells cannot be used as a treatment, since they carry the disease's genetic defect.

Twenty Disease-specific Stem Cell Lines Created (8/7/08)
A set of new stem cell lines will make it possible for researchers to explore ten different genetic disorders—including muscular dystrophy, juvenile diabetes, and Parkinson's disease—in a variety of cell and tissue types as they develop in laboratory cultures.

Harvard Stem Cell Institute researcher George Q. Daley, MD, PhD, also associate director of the Stem Cell Program at Children's Hospital Boston, and HSCI colleagues Konrad Hochedlinger and Chad Cowan have produced a robust new collection of disease-specific stem cell lines, all of which were developed using the new induced pluripotent stem cell (iPS) technique.

Improved technique for making induced pluripotent stem cells

You may recall from our discussion of induced pluripotent stem cells (here) that the resulting cells are vulnerable to becoming cancerous (as has been confirmed in experiments on mice), because they depend on overexpression of the gene for the c-Myc transcription factor. The new research shows that it is possible to obtain induced pluripotent stem cells by overexpressing a member of the important Wnt family of signaling proteins. (We've covered Wnt several times, most recentely here.)

Embryonic-like Stem Cells Can Be Created Without Cancer-causing Gene (8/6/08)
A drug-like molecule called Wnt can be substituted for the cancer gene c-Myc, one of four genes added to adult cells to reprogram them to an embryonic-stem-cell-like state, according to Whitehead researchers.

Researchers hope that such embryonic stem-cell-like cells, known as induced pluripotent (IPS) cells, eventually may treat diseases such as Parkinson's disease and diabetes.

Controling embryonic stem cell development

For all the future potential that may come from research into induced pluripotent stem cells, they are sufficiently different from true embryonic stem cells that we can't fully understand the latter by studing the former. In particular, true embryonic stem cells may be easier to push into any differentiated cell type, without the same cancer risk. New research illuminates development of endoderm cells from embryonic stem cells. Specific types of endoderm cells include cells of the lungs and pancreas (among many others).

Our most recent discussion of embryonic stem cells is here.

Scientists uncover the key to controlling how stem cells develop (8/8/08)
The results of a new study involving a McMaster University researcher provide insight into how scientists might control human embryonic stem cell differentiation.

In collaboration with researchers from SickKids and Mount Sinai hospitals, Dr. Jon Draper, a scientist in the McMaster Stem Cell and Cancer Research Institute, focused on producing early endoderm cells from human embryonic stem cells. ...

The researchers focused on generating stable progenitor cells capable of producing all endoderm cell types. The cells were able to maintain their distinct profiles through many stages of cell culture without losing their ability to self renew.

MicroRNA and embryonic stem cells

The last time we discussed microRNA in connection with embryonic stem cells (here) we saw that microRNA controlled genes that enabled the cells' self-renewal and differentiation properties. The latest research takes a much closer look at how microRNA and conventional transcription factors work together to regulate differentiation of embryonic stem cells, and also how they play a role in making induced pluripotent stem cells from differentiated cells.

Putting MicroRNAs On The Stem Cell Map (8/7/08)
Embryonic stem cells are always facing a choice—either to self-renew or begin morphing into another type of cell altogether.

It's a tricky choice, governed by complex gene regulatory circuitry driven by a handful of key regulators known as "master transcription factors," proteins that switch gene expression on or off.

In the past few years, scientists in the lab of Whitehead Member Richard Young and their colleagues have mapped out key parts of this regulatory circuitry, but the genes that produce the tiny snippets of RNA known as microRNAs have until now been a missing piece of the map. Since microRNAs are a second set of regulators that help to instruct stem cells whether to stay in that state, they play key roles in development.

Young and colleagues have now discovered how microRNAs fit into the map of embryonic stem cell circuitry. With this map, the scientists have moved one step closer to understanding how adult cells can be reprogrammed to an embryonic state and then to other types of cells, and to understanding the role of microRNAs in cancer and other diseases.

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Proton-electron mass ratio

Sunday, August 3, 2008

Physicists speculate a lot about whether (or to what extent) the laws of nature are exactly the same in all parts of the visible universe. This question is sometimes known as the "fundamental constants" problem.

There are a variety of such fundamental constants. The best known is the speed of light. Many theories that are part of "alternative physics" are based on the idea that the speed of light (in a vacuum) is not a constant, and may have been different early in the history of the universe. There is very little, if any, solid evidence for this, however.

A closely related constant is the fine structure constant, fondly known as alpha. It is related to the speed of light by the equation α = e2(2ℎcε0)-1, where e is the charge of an electron, ℎ is the Planck constant, c is the speed of light, and ε0 is the permittivity of free space.

There have been attempts to determine from astronomical data whether α may vary with time. This question can be investigated since α affects atomic spectra that are easily measured in a laboratory on Earth, and which can also be observed in distant astronomical objects. So far, no evidence of variability has been found. (See here, from June 2007.)

If α doesn't change with time, it is very unlikely that the speed of light does either (unless other constants also change in just the right way).

Another important fundamental constant is the ratio of the mass of a proton to the mass of an electron. (This ratio is sometimes denoted by μ, but that's confusing, as μ is used for other quantities in physics also.) In the standard model of particle physics, these masses, and their ratio, are free parameters that are not determined by the model itself. They are just there.

This ratio also affects atomic spectra, so it can also be investigated in astronomical studies. In April 2006, some evidence was reported for a difference between the laboratory value of the ratio and its value in distant quasars. The difference claimed was very small – 0.002% over a time span of 12 billion years. (See here, here.)

However, now there is more recent evidence from halfway across the universe, indicating that the ratio long ago is the same as it is now, although the time span is somewhat less (6 billion years):

Earth's laws still apply in distant Universe (6/19/08)
The laws of nature are the same in the distant Universe as they are here on Earth, according to new research conducted by an international team of astronomers, including Christian Henkel from the Max Planck Institute for Radio Astronomy (MPIfR) in Bonn. Their research, published today in Science, shows that one of the most important numbers in physics theory, the proton-electron mass ratio, is almost exactly the same in a galaxy 6 billion light years away as it is in Earth's laboratories - approximately 1836.15.

According to Michael Murphy, Swinburne astrophysicist and lead author of the study, it is an important finding, as many scientists debate whether the laws of nature may change at different times and in different places in the Universe. "We have been able to show that the laws of physics are the same in this galaxy half way across the visible Universe as they are here on Earth," he said.

The light actually comes from a quasar 7.5 billion light years away. But the spectral effect is due to ammonia molecules encountered when the light passes through a galaxy that is 6 billion light years distant.

Another account emphasizes that the latest result gives a constraint 10 times better than the 2006 result:

Changing physical constant may be constant after all (6/20/08)
There is good reason to trust the new result, Murphy says. The wavelengths at which the ammonia molecules absorb radiation depend more strongly on the proton-to-electron mass ratio than with other molecules, such as the molecular hydrogen that was used for the 2006 result. "Our constraint is 10 times better than those previously obtained," Murphy says.

Wim Ubachs, who led the 2006 analysis, agrees Murphy's result is "solid", but thinks there still might be a way to reconcile the two results. There remains the possibility that the constant varied between 6 billion and 12 billion years ago but has not varied since, he says.

Other accounts of this result:

Further reading:

Strong Limit on a Variable Proton-to-Electron Mass Ratio from Molecules in the Distant Universe – 6/20/08 research article in Science

Ammonia: Proton-electron mass ratio constant for 6 gigayears – 7/14/08 blog post on the research, and reasons why no variation in the ratio should be expected


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.


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

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