The researchers are working on the relationship between body cell condition and aging. Their experiments have shown that the presence of stem cells or progenitor (undifferentiated) cells can have a beneficial effect on cells afflicted with either progeria or simple old age. Merely injecting the stem cells had an impact on cells in the brain and muscles. In experiments conducted with cells in a culture dish, the proximity of stem cells – close but not touching – had a beneficial effect on unhealthy cells.

Rather obviously this research begs a question: What do the stem cells do to the aging cells? This type of research is pretty much a ‘black box’ experiment. The cells are injected and the results observed, but the chemistry or molecular-level pathways are not known. Which is why further research is required. However, it should be noted that a lot of medicine is used in which the results are accepted without knowing the underlying mechanism. These days, however, as equipment and procedures for work at the molecular level improve, it should be possible to take this kind of top-level research and successfully look for low-level linkages to the aging process.

Zircon is a very common trace mineral in many kinds of rocks and soils. It’s relatively hard, crystalline material that, among other things, often contains trace amounts of radioactive elements uranium or thorium. The radioactivity has made it possible to date zircon with considerable precision, leading to the discovery that some zircons were formed about 4.4 billion years ago, the oldest known minerals.

Scientists at the New York Center for Astrobiology at Renssalaer Polytechnic Institute reasoned that zircon might also be used to determine what kind of gasses were present in the magma that formed the zircons. That, in turn, could reveal what gasses were escaping from magma that reached the Earth’s surface and were contributing to the formation of the atmosphere. Their results, published in Nature [30 November 2011, paywalled, The oxidation state of Hadean magmas and implications for early Earth’s atmosphere] may overturn fundamental assumptions about Earth’s early atmosphere.

The heart of the research was to create zircons in the laboratory, in essence making lava with various compositions and particularly with various levels of oxygen. The key to the research was using a rare earth metal, cerium, as a component of the zircon. Cerium is found in two oxidation states (containing different quantities of oxygen molecules). The more of the cerium with higher oxygen content found in zircon, the more likely the zircon was formed in magma with higher oxygen content. Since it is a long-standing hypothesis that most of Earth’s atmosphere was formed by outgassing from magma at the surface; demonstration that magmas of higher oxygen content would produce atmosphere with more oxygen could change long held beliefs about the early Earth atmosphere.

According to the Renssalaer researchers, Dustin Trail, E. Bruce Watson and Nicholas Tailby, zircon with the higher oxygen content was prevalent during the Hadean eon (4.7 – 3.8 billion years ago), and by their calculations this indicates that Earth’s atmosphere at the time contained more oxygen than previously thought. If it holds up under further testing, this is a significant finding that could change how astrobiologists view the conditions for the formation of life. Oxygen is a key component of organic material, and in the current notion of primordial atmosphere it was in short supply. It has long been assumed that the early atmosphere was mostly methane, carbon monoxide, hydrogen sulphide and ammonia – not the best mix for life. Now with the possibility that there was far more oxygen available in the crust of the Earth and in the atmosphere, the view on the formation of water and life could be pushed much closer to the origin of the Earth. As researcher Bruce Watson put it:

“Our planet is the stage on which all of life has played out,” Watson said. “We can’t even begin to talk about life on Earth until we know what that stage is. And oxygen conditions were vitally important because of how they affect the types of organic molecules that can be formed.”

Despite being the atmosphere that life currently breathes, lives, and thrives on, our current oxidized atmosphere is not currently understood to be a great starting point for life. Methane and its oxygen-poor counterparts have much more biologic potential to jump from inorganic compounds to life-supporting amino acids and DNA. As such, Watson thinks the discovery of his group may reinvigorate theories that perhaps those building blocks for life were not created on Earth, but delivered from elsewhere in the galaxy.

[Source: EurekAlert]

This sort of hypothesis will be controversial, but as is the case with novel but plausible research, it will be tested.

This story begins with chaotic terrain on a moon of Jupiter, Europa. Ever since the space probe Galileo zipped by this part of the solar system and recorded the most detailed pictures of the surface of Europa, astroscientists have pretty much come to an agreement that Europa has a lot of water underneath the icy surface; oceans of water. The question they argued about was how thick was the surface ice? Some said, “Very thick, as in tens of kilometers”; other said, “at times and at certain places, not very thick at all – three kilometers or maybe even water on the surface.” Typically, the thick-icers had believable mathematical models to back up their story. All except for the “chaotic terrain” an area on the surface of Europa that looks exactly like it has icebergs that once floated on water. The thin-icers claimed this patch. Now we can add a third point of view, call them the middle-lakers.

In a paper published in Nature [16 November 2011, paywalled, Active formation of ‘chaos terrain’ over shallow subsurface water on Europa ] a team of scientists mostly from the University of Texas, Austin have hypothesized that enormous liquid ‘lakes’ exist in the Europa ice crust, figuratively half-way between the oceans below and the rock-like surface of ice. These lakes, some with at least the volume of the Great Lakes in the United States and Canada, may provide a means of water exchange between the truly massive oceans below (more ocean water than Earth) and the surface of the moon.

The significance of this hypothesis, beside settling the thin-icer vs thick-icer controversy by saying “both” with an intermediate layer some places, is that it increases the possibility of life on Europa. This has always been considered possible – the presence of water has long been associated with life; but on a Europa with a very thick shell of ice, the chances for energy and gasses interchange with the surface might limit the development of life. The postulated existence of the lakes means there is more dynamics in the waters of Europa, which would favor life.

Of course, this is a hypothesis. That means it needs to be tested. One of these days one or more probes will be sent from Earth to Europa and now it’s at least likely one will head for the ‘chaotic terrain’ area. Not only is that the area of most interest on the surface, but probably represents the shortest distance for drilling to the waters below. For now though, scientists in the field are quite pleased to have this alternative explanation for the chaos terrain and the behavior of Europa water. It fits the available facts, which is a good start.

[SciTechStory: On the Moon or elsewhere, follow the water]

The pituitary gland is tiny, about the size of a pea, but it has an extremely important set of roles in the body’s hormonal chemistry (which applies to almost all mammals including mice and men). As the key organ to the endocrine system, the pituitary glands secrete nine major hormones regulating growth, fertility, blood pressure, breast milk, temperature control and fluid management – among other things. When the pituitary gland is malfunctioning, a lot of bad things happen. The ability to repair and eventually replace pituitary glands with synthetic tissue is obviously a major achievement. But science is not there yet.

The big news from the Japanese researchers is that they have been able to culture the mice embryo stem cells into pituitary gland cells, which is no easy feat. It required that the cells be grown together with cells of the hypothalamus, a companion gland of the pituitary. These two glands have many symbiotic connections and it became obvious that functional pituitary cells could not be reproduced without the interaction of the hypothalamus. The researchers also pioneered new techniques for implanting the synthetic pituitary cells into living mice. This too was tricky and represents a future hurdle for applying the technique to human beings.

As is usually the case with breakthroughs accomplished with lab animals, mice in this case, there is always the caveat that a similar procedure for human beings may or may not work. Typically the biochemistry is compatible, but the scale change and complexity of the human brain sometimes make the transition from mice to men very difficult. Dr. Sasai at RIKEN believes that it will take about three years to produce human pituitary cells, but the technique for implanting them successfully might take much longer.

So far stem cells have been turned into synthetic liver, heart, muscle, eye, and other organs. The list grows. In some cases this has been done with embryonic stem cells, which has a controversial side, especially when it comes to humans. Most researchers try to do the same thing with pluripotent stem cells derived (through various techniques) from adult or differentiated stem cells, which gets around the controversy. The researchers at RIKEN would like to follow this path in the future.

November 9, 2011: It was a reminder for the neighborhood (Earth and Moon) that strangers pass in the night. Night being metaphorical in this case because the asteroid 2005 YU55 actually took about three days to orbit through the vicinity of the Earth and Moon. As asteroids go, YU55 is fairly large, about 400 meters (1300 ft) wide, what Americans would call a city block. If it collided with Earth it would make a helluva bang, on the order of many megatons of TNT, roughly a nuclear bomb that would make a crater 6.4 km (4 miles) across and 518 meters (1700 ft) deep. Of course, it didn’t this time and probably won’t collide with the Earth in the future; so it serves as a reminder that such asteroids are around and collisions can happen. In fact, because 2005 YU55 also passes close to Venus and Mars during its long orbit, it is subject to gravitational and other forces that can alter its path. Current calculations indicate that despite changes caused by Mars or Venus, the asteroid still will not be anywhere near collision course with Earth when it comes back around 2041, however, there is a margin of error.

First seen in 2005 (hence the provisional name, 2005 YU55), this particular asteroid passes between the Earth and Moon with 319,000 kilometers (198,000 miles) to spare at its closest point to the Earth. It’s too far away and too small to be seen by the naked eye, but professional and amateur astronomers will have a day in the field spotting, tracking and studying the relatively infrequent event. The next such ‘near miss’ (to put it with as much dramatic spin as possible) will be in 2028 when asteroid 2001 WN5 swings by for a passing visit.

These passing asteroids, part of a group known as the Near Earth Asteroids are also the subject of a NASA mandate for a human landing. 2005 YU55 might, in fact, be a candidate. Asteroids present an interesting opportunity to ‘hitch a ride’ through the solar system, while at the same time extracting metals and minerals too heavy to be lifted in quantity from Earth. Since asteroids have negligible gravity, it would in theory be easier to ship heavy material from them than to fight the gravity well of any planet or moon.

One of those approaches, in development by a team at the Imperial College of London (England) led by Baojan Wang and Richard Kitney, uses DNA cultivated from the common stomach bacteria Escherichia coli (E. coli). As published in Nature Communications [13 October 2011, paywalled,Engineering modular and orthogonal genetic logic gates for robust digital-like synthetic biology], their approach uses gene expression – the ability of a gene to produce proteins – as the core mechanism for a logic gate. Logic gates with names like AND, OR, NOT, NAND are key pieces of digital computers that perform many of the processing functions. Building these gates from DNA uses the combinatorial capability of genes in much the same way as “on” or “off” works for electronic circuits.

In this research, a DNA logic gate starts with a custom grown snippet of the E. coli DNA. It consists of two genes (hrpR and hrpS) that are controlled (activated) by two separate inputs (promoters). Only when the two genes are expressed, they trigger an output (hrpL promoter). In basic computer logic this is equivalent to AND (both inputs are TRUE). The output promoter can, in turn, be linked to another gate, which the researchers also tested; showing that this approach to DNA logic gates can be hooked together into more complex circuits.

This is a baby step in terms of computer processing, but behind the development of a DNA gate are the techniques for developing components from common bacteria and the ability to isolate, manipulate and link the components into more complex devices. It is, by demonstration of concept, the first step toward a biological computer. Whether it goes further down the road in a few years depends on whether the approach is inexpensive, reliable, scalable (can be done in large devices and many times), efficient and competitive with other approaches.

In that respect, this research hopes that using DNA expression will be easier to implement than some other more complex approaches. For example, a team at the California Institute of Technology (USA) built the first DNA logic gate in 2006, which uses individual molecules that attach to specific points on a DNA strand and thereby release an output molecule. The output molecule can then be counted to derive the logic (AND, OR etc.) Obviously, this is very different than using gene expression and to a certain extent is operating at a different (and more complicated) level of chemistry. There are some details of this in a previous SciTechStory post:
DNA computing: Advances in organic circuits.

These and other efforts at biological computing point to years, perhaps a decade or more, before computing devices that are truly useful become available. But at this point, it seems it will only be a matter of time. Keep in mind, the goal is not to compete with other forms of computing, but to provide a form of computing device that is compatible with living things – biologically compatible. For example, a biological computing device could be used within organs, tissues or even cells within the human body to monitor biochemistry or control various medical procedures. The applications are endless, if also typically open to both good and not so good uses.

One of the prevailing inferences, generated by computer models, is that dark matter should clump together toward the center of galaxies. This clumping allows the material in dark matter to condense into visible matter, eventually forming stars and galaxies that we see with our eyes and telescopes. This behavior is obviously fundamental to the notion of how the universe forms, its cosmology.

A good place to look for the effects of dark matter is in so called small galaxies. These are galaxies with only a few million stars; a normal galaxy has hundreds of billions of stars. With so few stars, it is estimated that small galaxies are about 99 percent dark matter, which should increase the probability of detecting the effects of dark matter. A new study of small galaxies by Matthew G. Walker and Jorge Peñarrubia at the Harvard-Smithsonian Center for Astrophysics (Cambridge, Massachusetts, USA) to be published in The Astrophysical Journal and available online [arXiv [11 August 2011 A Method for Measuring (Slopes of) the Mass Profiles of Dwarf Spheroidal Galaxies] looked at the distribution of matter in two ‘neighboring’ small galaxies of the Milky Way, Fornax and Sculptor.

What they found was surprising: the dark matter appears to be evenly distributed across several hundred million light years in each galaxy. This contradicts the prediction of dark matter being concentrated toward the center. If the finding holds, it will require major revision in many of the assumptions of astrophysics, especially on the nature of dark matter and its interaction with normal matter. Either normal matter affects dark matter more than is currently thought or dark matter is not ‘cold’ – without energy, passive and inert.

This is now a good piece of scientific ‘mystery’ with hypotheses that can be tested and validated. There is always the possibility that with such a small sample, only two galaxies, that error in measurement or analysis are at work. In short, many more small galaxies need to be studied and the distribution of dark matter refined and validated. This involves many years of work and should be done by scientists other than the original team as well. However, the finding is challenging. If it holds up, or if no satisfactory explanation is devised, it will have major impact on the theories of dark matter.

The idea behind this particular nanosensor came from study of natural biosensors within cells. All living things monitor their condition, from the largest scale of organs to the smallest nanoscale chemistry of individual cells. At the level of the cell, there are billions of specialized proteins or RNA that perform the task of a sensor by reacting to the presence of very specific molecules. For example there are many loops or cyclical chemical pathways, where a certain condition, say a need for energy, triggers a chemical and physical change in one sensor protein. It in turn signals for production of more energy. When enough energy is produced, another sensor protein accumulates to the point where it turns off energy production.

Scientists at the University of California, Santa Barbara (USA) and the University of Rome Tor Vergata wanted to emulate this natural sensor-signal process with a specific target in mind. As published in the Journal of the American Chemical Society [04 August 2011, paywalled, Transcription Factor Beacons for the Quantitative Detection of DNA Binding Activity] they developed a sensor made from DNA that becomes luminescent (glows) when it encounters a particular protein of the type called a transcription factor. These are proteins used by cells to control the production of molecules (usually other proteins). There are literally thousands of transcription factors, but when scientists ‘reprogram’ cells for example in stem cells; they often change only a handful of factors. The trick is to know whether the reprogramming has worked properly or not. That’s where the nanosensors come in.

There are many techniques for reading transcription factors; most of them require laborious separation of specific proteins and examination either under microscopes or with chemical detectors. As one of the researchers put it, “With the new sensors, we just mash the cells up, put the sensors in, and measure the level of fluorescence of the sample.”

The sensors are built by re-engineering three natural DNA sequences, each set to recognize a different transcription factor, by adding a molecular switch that becomes fluorescent when activated. Eventually this technique can be extended to thousands of transcription factors. In turn, the technique can help scientists and doctors monitor the level of drug activity, screen for certain kinds of cancer signaling proteins or any other application where transcription factors might reveal an underlying biological condition. In short, this technique could be very useful and practical.

The technique also seems relatively simple, but it will ultimately compete with many other technologies (sometimes called assay technology) that read the presence of transcription factors and other protein signaling molecules. It’s a burgeoning field of cell biology and of sensor technology-in-the-very-small.

Scientists have been trying to find ways of crossing the blood-brain barrier for at least a century – without a great deal of success. The barrier is ‘porous,’ as it must be to do the job of carrying life-sustaining substances to and from the cells of the brain; but it is very selective about the size and type of molecules it permits to cross the barrier. This selection takes place in the membrane of the blood vessels, where the chemical and physical configuration of proteins blocks or permits passage of molecules. In general there are three main approaches to getting medicine across this barrier: Piggybacking on molecules known to be able to cross the barrier, using nanoparticles small enough to ‘slip through’ the barrier and using chemical stimulators to alter the protein configuration in the barrier (something like opening a gateway). The latest effort, which counts as a success, by a research team at Cornell University (Ithaca, New York, USA) and published in the Journal of Neuroscience [14 September 2011, paywalled, Adenosine Receptor Signaling Modulates Permeability of the Blood–Brain Barrier] uses the last approach.

The research built upon the knowledge that the blood-brain barrier contains adenosine receptors, molecules of adenosine (adenine plus a sugar) that match configuration (receive) certain other molecules of adenosine. For this research, the ‘trigger’ for the receptor is NECA (an adenosine protein). When it binds (or docks) with the adenosine receptor, a path is opened in the blood-brain barrier big enough to transfer larger molecules. In this case, the researchers were successful in transporting macromolecules (e.g. big) such as antibodies (an anti-beta amyloid) and dextrans (a large glucose molecule) across the barrier. Using a similar commercial adenosine compound, Lexiscan, the same effect was achieved with a window of effectiveness of about three hours.

The anti-beta amyloid antibody is one of the medications used to treat Alzheimer’s disease, which immediately illustrates the potential benefit of being able to artificially stimulate transportation of molecules across the blood-brain barrier. The approach of this research has several very important potential benefits: It can, to a certain extent, be controlled in duration, turning the effect on an off. Unlike the piggybacking technique, this approach does not lose drug efficiency, nor does it have the problem of semi-permanent concentrations of the nanoparticle technique.

As promising as the adenosine approach may be, caveats are important: The research was conducted with mice. Although adenosine receptors are also found in human brain capillaries, there is no guarantee that they will respond in identical ways. This is indicative of the probable years of testing and clinical trials that lay ahead before this approach is ready for common applications. On the other hand, a company has already been formed, Adenios, Inc. to handle the patents and trials involved in drug testing – that is usually a solid indicator of probable success. If it works, the adenosine approach may make it finally possible to deliver the complex drugs used to fight Alzheimer’s disease, Parkinson’s disease and many other difficult to treat illnesses of the brain.

HARPS is the most successful planet hunting device to-date, with more than 150 credited to its analysis. It searches among 376 Sun-like stars, those relatively near to our own Sun, to detect as many low-mass (that is, smaller) planets as possible with the radial velocity technique. This approach uses the Doppler effect, which displaces a star’s spectral lines (color spread), to detect the presence of planets in orbit around a sun. At the moment, with relatively limited sensitivity, HARPS can only detect fairly large planets – roughly the size of Neptune in our own Solar System. Even with that limitation, HARPS has so far revealed that at least 40% of the suns it has observed have at least one Saturn-size planet. If this number holds up, it will mean yet another expansion of the estimate for planets – billions in just this galaxy alone. What is the probability that some of these planets have life?

Many probability calculations, like tossing a coin, are quite straightforward because initial conditions are known. For example, a coin has two sides and the probability of a tossed coin coming to rest standing on edge approaches zero. No such luck with exoplanets and life. The knowns, such as they are, are based solely on our own experience. As far as we know, life and water are inextricable. Life requires some kind of energy source, which is as far as we know comes from solar energy, chemical energy, or geologic energy. Pretty much every planet in a solar system has one or more of those energy sources, so that doesn’t do much for the probabilities. There is this thing about a ‘Goldilocks Planet’ – not too warm, not too cold, but just right for life. That’s probably valid, but the bandwidth of success for life could surprise us (either way). Finally there is the size of the planet, with the supposition that too big means too much gravity and no life, or conversely too small implies no atmosphere or, well we just can’t see the small planets at light-years distance anyway.

What we know about conditions for life is limited to what we know from Earth. Predictions about what kind of exoplanets will have life are, for the time being, limited to extrapolating from that knowledge. With the discovery of fifty new potential life-holding planets, the odds for the life elsewhere in the universe increase. On exactly what kind of planets – other than a correspondent to Earth – we don’t know. HARPS and its descendents will continue to refine that knowledge. One of these fine days…or years…