ScienceWeek

SCIENCEWEEK

August 11, 2006

Vol. 10 - Number 32

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Back issues of ScienceWeek can be searched for subjects, names, terms, etc. at: http://scienceweek.com/swfr.htm

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Our biology has made us into creatures who are constantly recreating our psychic and material environments, and whose individual lives are the outcomes of an extraordinary multiplicity of intersecting causal pathways. Thus, it is our biology that makes us free.

-- Richard Lewontin

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Contents:

1. Atmosphere: On the Ice Age Cycle

The exposure of Earth's surface to the Sun's rays (or insolation) varies on time scales of thousands of years as a result of regular changes in Earth's orbit around the Sun (eccentricity), in the tilt of Earth's axis (obliquity), and in the direction of Earth's axis of rotation (precession). According to the Milankovitch theory, these insolation changes drive the glacial cycles that have dominated Earth's climate for the past 3 million years.

2. Planetary Science: On Puzzling Neptune Trojans

"Trojan" asteroids are small bodies that revolve about the Sun at the same distance as their host planet and share the planet's orbital path. They are locked at the two gravitationally stable locations, called triangular Lagrangian points, in distinct clouds that lead or trail the planet by about 60°. Jupiter has the most of these Trojans, which are small rocky-icy bodies...

3. Biochemistry: Protein Folding and Chaperone Cages

Proteins are the action molecules of life, but cells face a problem in making them. Proteins consist of amino acids joined into linear polypeptide chains by intracellular structures called ribosomes. Each chain folds into a compact shape whose surface properties determine the biological function unique to that protein.

4. Developmental biology: On Tube Formation

In simple organisms, only one or a few cells thick, diffusion brings nutrients and oxygen to individual cells and removes their waste. But in larger animals, this process is no longer sufficient, so transport tubes evolved to allow materials to move quickly throughout the organism. Such transport systems include blood vessels and the tubes that make up the...

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Also Noted:

Ages in Chaos: James Hutton and the Discovery of Deep Time. Stephen Baxter. Tom Doherty Assoc., 2006, 246 pp. $13.95. ISBN 0765312689. More information at: http://www.amazon.com/exec/obidos/ASIN/0765312689/scienceweek

Not Even Wrong: The Failure of String Theory and the Search for Unity in Physical Law. Peter Woit. Basic Books, 2006 (September), 304 pp. $26.00. ISBN 0465092756. More information at: http://www.amazon.com/exec/obidos/ASIN/0465092756/scienceweek

Global Warming in the 21st Century: Vol. 1, Our Evolving Climate Crisis. Vol. 2, Melting Ice and Warming Seas. Vol. 3, Plants and Animals in Peril. Bruce E. Johnson. Praeger, Westport, CT, 2006 Hardback: 3 vols. 911 pp., illus. $275, £155. ISBN 0275985857. More information at: http://www.amazon.com/exec/obidos/ASIN/0275985857/scienceweek

Health and Human Flourishing: Religion, Medicine, and Moral Anthropology. Carol R. Taylor and Roberto Dell'Oro, Eds. Georgetown University Press, Washington, DC, 2006 Hardback: 292 pp. $44.95. ISBN 1589010787. More information at: http://www.amazon.com/exec/obidos/ASIN/1589010787/scienceweek

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1. ATMOSPHERE: ON THE ICE AGE CYCLE

The following points are made by Didier Paillard (Science 2006 313:455):

1) The exposure of Earth's surface to the Sun's rays (or insolation) varies on time scales of thousands of years as a result of regular changes in Earth's orbit around the Sun (eccentricity), in the tilt of Earth's axis (obliquity), and in the direction of Earth's axis of rotation (precession). According to the Milankovitch theory, these insolation changes drive the glacial cycles that have dominated Earth's climate for the past 3 million years.

2) For example, between 3 million and 1 million years before the present (late Pliocene to early Pleistocene, hereafter LP-EP), the glacial oscillations followed a 41,000-year cycle. These oscillations correspond to insolation changes driven by obliquity changes. But during this time, precession-driven changes in insolation on a 23,000-year cycle were much stronger than the obliquity-driven changes. Why is the glacial record for the LP-EP dominated by obliquity, rather than by the stronger precessional forcing? How should the Milankovitch theory be adapted to account for this "41,000-year paradox"?

3) Two different solutions are available. The first involves a rethinking of how the insolation forcing should be defined (1), whereas the second suggests that the Antarctic ice sheet may play an important role (2). The two solutions question some basic principles that are often accepted without debate. Huybers (1) argues that the summer insolation traditionally used in ice age models may not be the best parameter. Because ice mass balance depends on whether the temperature is above or below the freezing point, a physically more relevant parameter should be the insolation integrated over a given threshold that allows for ice melting. This new parameter more closely follows a 41,000-year periodicity, thus providing a possible explanation for the LP-EP record. Raymo et al (2) question another pillar of ice age research by suggesting that the East Antarctic ice sheet could have contributed substantially to sea-level changes during the LP-EP. The East Antarctic ice sheet is land-based and should therefore be sensitive mostly to insolation forcing, whereas the West Antarctic ice sheet is marine-based and thus influenced largely by sea-level changes. Because the obliquity forcing is symmetrical with respect to the hemispheres, whereas the precessional forcing is antisymmetrical, the contributions of the northern and southern ice sheets to the global ice volume record will add up for the 41,000-year cycle, but cancel each other out for the 23,000-year cycle, thus explaining the 41,000-year paradox.

4) Both hypotheses could be part of the solution. Huybers's idea is based on a sound and simple physical premise and is certainly valid to some extent. The hypothesis of Raymo et al provides a scenario for an increasing contribution of the 23,000-year cycles under a colder climate, through a transition from a land-based to a marine-based East Antarctic ice sheet around 1 million years ago. Indeed, though not dominant, the precessional cycles are present in the climate record of the past 1 million years (the late Pleistocene). Still, neither hypothesis can account for the beginning of Northern Hemisphere glaciations around 3 million years ago. Furthermore, during the past 1 million years, glacial-interglacial oscillations have largely been dominated by a 100,000-year periodicity, yet there is no notable associated 100,000-year insolation forcing. There is currently no consensus on what drives these late Pleistocene 100,000-year cycles.(3-5)

References (abridged):

1. P. Huybers, Science 313, 508 (2006)

2. M. E. Raymo, L. E. Lisiecki, K. H. Nisancioglu, Science 313, 492 (2006)

3. E. Bard, C. R. Geosci. 336, 603 (2004)

4. U. Siegenthaler et al., Science 310, [1313] (2005)

5. D. Paillard, F. Parrenin, Earth Planet. Sci. Lett. 227, 263 (2004)

Science http://www.sciencemag.org

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2. PLANETARY SCIENCE: ON PUZZLING NEPTUNE TROJANS

The following points are made by Francesco Marzari (Science 2006 313:451):

1) "Trojan" asteroids are small bodies that revolve about the Sun at the same distance as their host planet and share the planet's orbital path. They are locked at the two gravitationally stable locations, called triangular Lagrangian points, in distinct clouds that lead or trail the planet by about 60°. Jupiter has the most of these Trojans, which are small rocky-icy bodies with diameters less than 300 km and are similar in composition to other minor bodies such as short-period comets, Kuiper Belt objects (KBOs), and Centaurs, small bodies that orbit between Jupiter and Neptune. About 2000 Jupiter Trojans are known today, but astronomers believe there may be as many of these asteroids in the kilometer-size range as there are main-belt asteroids (1). Four asteroids are also known to orbit in the Lagrangian points for Mars; these might possibly be rare remnants of planetesimals that formed in the terrestrial planet region. Moreover, Trojans are now known to gather near Neptune, and new work (2) reports the discovery of the fourth such object, with important implications for theories of solar system formation.

2) Astronomers theorize that Trojans are pristine bodies that originated very early in the history of the solar system and were captured in the final phase of planet formation. Different theories, not necessarily mutually exclusive, have been proposed to explain how planetesimals passing close to a planet fall into the force traps around the Lagrangian points. Among these are broadening of the tadpole-shaped regions of stable Trojan motion around the triangular Lagrangian points because of the growth of the planet's mass, direct collisional placement, drag-driven capture in the presence of the gaseous nebula, and chaotic trapping during giant planet migration. There is as yet no general consensus on the source region of putative Trojans in the planetesimal disk. Some capture mechanisms demand that they formed near the planet's orbit, thus reflecting the physical and chemical composition of the planetary building blocks. The recent theory of chaotic capture, suggesting that planetesimals in temporary Trojan trajectories can be frozen into stable orbits as soon as planetary migration drives the host planet far away from a dynamically perturbed region (3), opens the possibility that Trojans might have formed in more distant regions of the planetesimal disk of the early solar system, sharing the same environment as KBOs.

3) In the course of the Deep Ecliptic Survey, a NASA-funded survey of the outer solar system, astronomers announced in 2001 the discovery of the first known member of a long-sought population of bodies: the Neptune Trojans. Sheppard and Trujillo (2) report the discovery of the fourth object in this group, which is noteworthy in that it exhibits a high inclined orbit (about 25 deg). This finding strongly supports the idea that Neptune Trojans fill a thick disk with a population comparable to, or even larger than, that of Jupiter Trojans. At the same time, the discovery puts constraints on the mechanism by which they were captured.

4) What makes the Neptune Trojans so special for astronomers? According to recent theories, the outer solar system might have been a tumultuous environment. During the last stage of planetary formation, the giant planets may have migrated away from their formation sites by exchanging angular momentum with the residual planetesimal disk. Jupiter drifted inward, although only slightly, whereas Saturn, Uranus, and Neptune migrated outward by larger amounts. This past planetary migration explains many of the observable characteristics of KBOs, in particular of the resonant ones called Plutinos. However, the migration process may not have been so smooth as initially thought, and numerical simulations performed by Tsiganis et al (4) show that the passage of Jupiter and Saturn through a 2:1 resonance may have ignited a period of strong chaotic evolution of Uranus and Neptune. In this scenario, the two planets had frequent close encounters and may even have exchanged orbits before their eccentricities finally settled down, allowing a more quiet migration to the present orbits. (3-5)

References:

1. D. C. Jewitt, C. A. Trujillo, J. X. Luu, Astron. J. 120, 1140 (2000)

2. S. S. Sheppard, C. A. Trujillo, Science 313, 511 (2006)

3. A. Morbidelli, H. F. Levison, K. Tsiganis, R. Gomes, Nature 435, 462 (2005)

4. K. Tsiganis, R. Gomes, A. Morbidelli, H. F. Levison, Nature 435, 459 (2005)

5. E. I. Chiang, Y. Lithwick, Astrophys. J. 628, L520 (2005)

Science http://www.sciencemag.org

ScienceWeek http://scienceweek.com

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3. BIOCHEMISTRY: PROTEIN FOLDING AND CHAPERONE CAGES

The following points are made by R. John Ellis (Nature 2006 442:360):

1) Proteins are the action molecules of life, but cells face a problem in making them. Proteins consist of amino acids joined into linear polypeptide chains by intracellular structures called ribosomes. Each chain folds into a compact shape whose surface properties determine the biological function unique to that protein. The information required to fold correctly resides in the sequence of amino acids, and this is determined by the ribosomes, which translate a messenger RNA copy of the gene for each chain. But to synthesize proteins rapidly enough, each mRNA molecule is translated by more than one ribosome at the same time. The result is that partly folded identical chains accumulate within touching distance of one another, raising the possibility that they will bind together to form non-functional aggregates.

2) This universal problem is combated by proteins called "molecular chaperones", of which more than 50 families are known (1). One family is the chaperonins, the best-studied member being GroEL–GroES, found in bacteria. GroEL–GroES prevents aggregation by encapsulating each partly folded chain inside its cage structure, where the chain can continue to fold in isolation from similar chains (2,3). In earlier work, the laboratory of Ulrich Hartl found (4) that a particular protein -- bacterial Rubisco --folds three to four times faster inside the cage than it does in free solution under conditions where aggregation is minimized. This laboratory now reports (5) that both the size and surface charge of the cage are optimized to speed up the folding of several different types of chain.

3) GroEL and GroES bind to one another in the presence of the nucleotides ATP or ADP to create a large complex containing a cavity, termed a cage (or nanocage), at one end. GroES acts as a removable lid to keep the protein chain inside the cage while it is folding. Inside this cage, the chain continues to fold until its hydrophobic amino acids, which cause aggregation, are buried within the correctly folded compact protein. This cage was initially termed an "Anfinsen cage" to indicate the assumption that the chain folds inside the cavity in a manner determined by its amino-acid sequence, just as a denatured protein refolds in the classical experiment of Christian Anfinsen. The new experiments (5) show that this model is incomplete, because the folding rate of some proteins depends on the relative sizes of the folding chain and the cage, and on the inside surface properties of the cage. Thus, GroEL–GroES is more than an anti-aggregation device -- it also enables some proteins to fold faster than they do outside the cage.

4) About 85 different proteins of the bacterium Escherichia coli are thought to require encapsulation inside GroEL–GroES to fold correctly. Of these, 60% are 30–50 kilodaltons in size, and only 14% are greater than 50 kDa in size. The cage of GroEL–GroES measures 80 times 85 angstroms, sufficient in principle to house proteins up to 70 kDa. However, the available volume is somewhat less, owing to the presence of 23 amino acids at the end of each GroEL subunit. Removal of these "tails" does not affect the basic mechanism, so they provide a way of changing the size of the cage. By removing the tail or extending it stepwise, Tang et al (5) altered the volume of the cage in increments from +4% to -13%, and measured the effects of these changes on the rate of folding of four different proteins in the size range 33–50 kDa.

References (abridged):

1. Ellis, R. J. in Molecular Chaperones and Cell Signalling (eds Henderson, B. & Pockley, G.) 3–21 (Cambridge Univ. Press, 2005)

2. Saibil, H. R. & Ranson, N. A. Trends Biochem. Sci. 27, 627–632 (2002)

3. Fenton, W. A. & Horwich, A. L. Q. Rev. Biophys. 36, 229–256 (2003)

4. Brinker, A. et al. Cell 107, 223–233 (2001)

5. Tang, Y. -C. et al. Cell 125, 903–914 (2006)

Nature http://www.nature.com/nature

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4. DEVELOPMENTAL BIOLOGY: ON TUBE FORMATION

The following points are made by K. Mostov and F. Martin-Belmonte (Nature 2006 442:363):

1) In simple organisms, only one or a few cells thick, diffusion brings nutrients and oxygen to individual cells and removes their waste. But in larger animals, this process is no longer sufficient, so transport tubes evolved to allow materials to move quickly throughout the organism. Such transport systems include blood vessels and the tubes that make up the digestive, respiratory and other organ systems. Generally these tubes are lined by a single layer of cells known as epithelial cells, but the inner surface of blood vessels are coated with modified epithelial cells called endothelial cells. Tubes must have a continuous hollow space, or lumen, in the center to allow free passage of materials. A century-old question is how lumina form in tubes during development. Kamei et al (1) have watched living embryos to discover how lumina are made during the development of fish.

2) Lumen formation has been examined previously using static images of endothelial and epithelial cells in culture. A commonly observed feature in these pictures is the formation of large (2) vacuoles -- membrane-bounded compartments -- in the cell. These are thought to be formed by a process called endocytosis, in which cells suck in a small portion of their outer plasma membrane to form a pocket and then pinch it off to create an internal "bubble" containing some of the extracellular fluid. It had been imagined that these vacuoles fuse together and with the plasma membrane to produce lumina between cells, although the evidence, based on static images, was not definitive.

3) Now Kamei et al (1) have filmed this process, first in an endothelial culture system and then in the developing blood vessels of fish embryos -- which fortunately are transparent. In both cases the movies show actual fusion of the vacuoles with the plasma membrane to create lumina between cells. In essence, the cells first create tiny intracellular lumina by sipping up extracellular fluid into endocytic vacuoles. These then fuse with the plasma membrane, thereby combining many small intracellular lumina into a single extracellular lumen between the cells that will line the nascent tube.

4) These movies of lumen creation are astounding: if a picture is worth a thousand words, the power of these films to answer a long-standing question is certainly worth a million. Kamei et al (1) exploit this power to show how developing lumina extend from one cell to another to lengthen the tube. To do so, they injected nanometer-sized fluorescent beads (quantum dots) into the blood circulation of the fish embryo. The quantum dots appeared first in a large blood vessel, the dorsal aorta. Then, as a new, smaller vessel began to bud off, the quantum dots emerged in the lumen of a previously unlabelled vacuole in an endothelial cell adjoining the aorta. Quantum dots showed up successively in a second and then a third neighboring cell, as each cell's intracellular vacuole fused with its plasma membrane to extend the lumen of the nascent endothelial tube. (3-5)

References (abridged):

1. Kamei, M. et al. Nature 442, 453–456 (2006)

2. Davis, G. E. & Bayless, K. J. Microcirculation 10, 27–44 (2003)

3. Lubarsky, B. & Krasnow, M. A. Cell 112, 19–28 (2003)

4. Hogan, B. L. & Kolodziej, P. A. Nature Rev. Genet. 3, 513–523 (2002)

5. Debnath, J. & Brugge, J. S. Nature Rev. Cancer 5, 675–688 (2005)

Nature http://www.nature.com/nature

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