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ScienceWeek
SCIENCEWEEK
February 9, 2007
Vol. 11 - Number 6
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Nature is that lovely lady to whom we owe polio, leprosy, smallpox, syphilis, tuberculosis, and cancer.
-- Stanley Cohen
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Contents (full text below):
1. Chemistry: On the Vibrations of Atoms
2. Chemistry: On Coherence and Symmetry Breaking
3. Developmental biology: On Embryonic Polarization
4. Reproductive biology: On Sperm Alliance
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New Books Noted:
Alzheimer's Disease. Advances in Genetics, Molecular and Cellular Biology. Sangram S. Sisodia and Rudolph E. Tanzi, Eds. Springer, New York, 2007. Hardback: 296 pp., illus. ISBN 9780387351346. More information at:
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Chances Are. Adventures in Probability. Michael Kaplan and Ellen Kaplan. Penguin, New York, 2007. Paperback: 331 pp. ISBN 9780143038344.
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Chasing Hubble's Shadows. The Search for Galaxies at the Edge of Time. Jeff Kanipe. Hill and Wang (Farrar, Straus and Giroux), New York, 2007. Paperback: 217 pp., illus. ISBN 9780809034079.
http://www.amazon.com/exec/obidos/ASIN/0809034077/scienceweek
The Economics of Climate Change. The Stern Review. Nicholas Stern. Cambridge University Press, Cambridge, 2007. Paperback: 712 pp., illus. ISBN 9780521700801.
http://www.amazon.com/exec/obidos/ASIN/0521700809/scienceweek
Encyclopedia of the Solar System. 2nd ed. Lucy-Ann McFadden, Paul R. Weissman, and Torrence V. Johnson, Eds. Academic (Elsevier Science), San Diego, 2007. Hardback: 986 pp., illus. ISBN 9780120885893.
http://www.amazon.com/exec/obidos/ASIN/0120885891/scienceweek
The Evolution of Cooperation. 2nd ed. Robert Axelrod. Basic Books (Perseus), New York, 2006. Paperback: 257 pp. ISBN 9780465005642.
http://www.amazon.com/exec/obidos/ASIN/0465005640/scienceweek
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1. CHEMISTRY: ON THE VIBRATIONS OF ATOMS
The following points are made by Joel D. Brock (Science 2007 315:609):
1) For more than a century, x-ray diffraction has provided detailed information on the structure of matter on atomic length scales. The recent advent of high-energy x-ray free-electron lasers (XFELs) now provides researchers the ability to watch matter move on both atomic length and time scales. New work (1) reports the use of ultrashort x-ray pulses from an XFEL to measure the dynamics of atomic vibrations in bismuth when excited by photons. These measurements provide researchers direct tests of calculations of highly excited electronic states and provide basic insights into our fundamental understanding of condensed matter.
2) Our understanding of the static or time-averaged structure of matter on atomic length scales has been dramatically advanced by direct structural measurements with x-rays. The current technical capability of x-ray crystallography is immense. The cover of SCIENCE regularly displays the structure of biologically important macromolecules determined through x-ray crystallography, and it is not unusual for these structures (e.g., viruses) to contain millions of atoms. However, the structure of matter is not static. Developing our understanding of the fundamental behavior of matter requires structural measurements on the time scales on which matter moves.
3) There are several important physical time scales of interest. Conformational relaxations in molecular systems and electron-lattice energy transfer in crystalline solids typically occur in a few picoseconds. Faster still are atomic vibrational periods, which are typically on the order of 100 femtoseconds. The characteristic time scale for electron-electron collisions in solids is on the order of 10 femtoseconds. And, quickest of all, are correlations in the dynamics of interacting electrons, which typically decay in less than 1 femtosecond. The key feature of all these time scales is that they are all "ultrafast"; that is, a few picoseconds or shorter.
4) To date, ultrafast science has been the domain of femtosecond lasers operating at ultraviolet to infrared (IR) wavelengths. These wavelengths are not short enough for structural studies on atomic distances, and they are able to probe only those electronic states that extend over multiple atoms. However, building a suitable "hard" x-ray source (i.e., one that emits photons with wavelength in the range 1 to 2 angstroms, or an energy of about 10 keV) represents a major challenge.(2-5)
References:
1. D. M. Fritz et al., Science 315, 633 (2007).
2. R. W. Schoenlein et al., Science 287, 2237 (2000).
3. A. A. Zholents, M. S. Zolotorev, Phys. Rev. Lett. 76, 912 (1996).
4. A. Cavalieri et al., Nature 442, 664 (2006).
5. A. L. Cavalieri et al., Phys. Rev. Lett. 94, 114801 (2005).
Science http://www.sciencemag.org
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2. CHEMISTRY: ON COHERENCE AND SYMMETRY BREAKING
The following points are made by Andrei Sanov (Science 2007 315:610):
1) Coherence is the ability of waves to combine their oscillations in a defined, nonrandom fashion. It is a cornerstone of wave interference, such as when water waves join in one large swell on the ocean surface or when light waves are generated in lockstep to form a bright laser beam. In quantum mechanics, all particles behave like waves, and coherence is therefore a universal concept determining the fundamental properties of matter.
2) Coherent effects are most obvious when the interfering waves are restricted by symmetry. For example, electrons in molecules are described by coherent combinations of orbitals from different atoms. In symmetric molecules, the contributions of equivalent atoms to the bonding are limited to equal amplitudes, resulting in symmetric electron density distributions. However, in some cases, coherence can undermine symmetry, resulting in asymmetric spectral line shapes (1) or product distributions. To examine how this can happen, one may start by asking whether it is possible to distinguish two ends of a homonuclear diatomic molecule such as H2.
3) The very premise may appear absurd: It seems to violate not only molecular symmetry, but also the fundamental indistinguishability of identical nuclei. But new work (2) reports asymmetric electron emission from H2, followed by asymmetric dissociation of the remaining molecular ion to a proton and a hydrogen atom. The dissociative ionization thus breaks the inversion symmetry both of the H2 molecule and of the incident linearly polarized light.
4) The photoelectron distributions that lack inversion symmetry with respect to the molecular center of mass can be observed only because the two ends of the ionized molecules are ultimately distinguished by the different charge states of the final fragments, H and H+. Even so, the result is counterintuitive, especially if one expects the ionization merely to eject an electron from the lowest-energy orbital of H2. This orbital is symmetric with respect to inversion, that is, it is said to be of gerade (even) parity. Since quantum mechanics requires the electron parity to change upon the absorption of a single photon, the departing electron will be described by an ungerade (odd) wave function, corresponding to a perfectly symmetric photoelectron distribution.
5) This description is based on two oversimplifications. First, it assumes that the two electrons are completely independent from each other, and that the emitted and remaining electrons thus cannot exchange parity. Second, it decouples the ionization and dissociation processes by not taking into account the excited states of H2, which contribute by way of delayed autoionization. As discussed by Martín et al. (2) electron waves of both ungerade (odd) and gerade (even) parity are in fact emitted from H2 via multiple direct and indirect ionization channels. A combination of odd and even functions is, in general, neither odd nor even. Thus, interference of the gerade and ungerade waves yields an asymmetric photoelectron distribution, which generally favors one or the other end of the molecule. This implies that the two nuclei in the remaining H2+ are no longer equivalent and the probability of charge localization on either one of them may differ from 50%.(3-5)
References (abridged):
1. U. Fano, Phys. Rev. 124, 1866 (1961).
2. F. Martín et al., Science 315, 629 (2007).
3. C. Jönsson, Z. Phys. 161, 454 (1961).
4. H. D. Cohen, U. Fano, Phys. Rev. 150, 30 (1966).
5. D. Rolles et al., Nature 437, 711 (2005).
Science http://www.sciencemag.org
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3. DEVELOPMENTAL BIOLOGY: ON EMBRYONIC POLARIZATION
The following points are made by T.E. Rusten and H. Stenmark (Nature 2007 445:497):
1) Protein production can be restricted to particular areas within cells by targeting the messenger RNAs encoding them to those sites. Such localization of mRNAs can affect the function of single cells, particularly those that have a polarity such as neurons. More dramatically, it can influence the development of whole organisms. In the fruitfly Drosophila melanogaster, for instance, the bicoid mRNA is moved to the anterior of the oocyte (the developing egg). This results in a gradient of the encoded protein such that the region with the highest concentration develops into the head region in any resulting embryo (1). Mutant oocytes that lack the bicoid gene do not have such anterior organization and form embryos with two posterior ends (1). New work (2) identifies a protein complex responsible for bicoid mRNA localization, unexpectedly revealing that it is identical to a complex that helps to dictate where certain membrane proteins end up within the cell.
2) The transport and retention of bicoid mRNA in the oocyte's anterior depend on a regulatory region in its sequence called the 3' untranslated region (UTR) and on transport along the microtubule scaffolding of the cell (3). An attractive hypothesis to explain how bicoid is localized involves mRNA-binding proteins. One of these, Staufen, binds to the bicoid 3' UTR and is necessary for bicoid retention at the anterior. However, Staufen alone cannot account for specific mRNA localization because it binds to several different mRNAs, including one called oskar that localizes to the posterior of the oocyte (3). To identify the cellular factors responsible for the anterior localization of bicoid mRNA, Irion and St Johnston (2) developed a clever screen in which the transport of bicoid mRNA in oocytes mutated in various genes was followed indirectly using the Staufen protein tagged with green fluorescent protein.
3) The genetic screen showed that the correct transport did not occur when the gene encoding the Vps22 protein was mutated. This protein was already known, but in a completely different context -- the process of endosomal protein sorting (2). Cells regularly take samples of their external environment by sucking in pouches of their membrane and the local extracellular fluid. The bubble-like vesicles are transported into the cytoplasm and end up fusing with a membrane-bounded organelle called the endosome. Sorting in the endosome membrane determines the fate of the various molecules. They are wrapped into packets to send to specialized organelles so they can be digested, expelled from the cell, or recycled back to the external membrane. Together with two structurally related proteins, Vps25 and Vps36, Vps22 forms the "endosomal sorting complex required for transport" (ESCRT)-II (4,5). In conjunction with two other protein complexes, ESCRT-I and ESCRT-III, this evolutionarily conserved protein complex mediates the sorting of particular membrane proteins from endosomes to organelles called lysosomes for digestion(4,5).
4) Analysis of oocytes mutant for Vps25 and Vps36 revealed that these had a similar defect in bicoid mRNA localization to the Vps22 mutants, indicating that the entire ESCRT-II complex is required for bicoid localization (2). Irion and St Johnston also found that the Vps36 protein, and hence ESCRT-II, co-localizes with bicoid mRNA at the anterior pole of the oocyte. ESCRT-I and ESCRT-III mutants had normal localization of bicoid mRNA, suggesting that the function of ESCRT-II in bicoid localization is unrelated to its role in endosomal protein sorting.
References (abridged):
1. Driever, W. & Nusslein-Volhard, C. Cell 54, 95–104 (1988).
2. Irion, U. & St Johnston, D. Nature 445, 554–558 (2007).
3. St Johnston, D. Nature Rev. Mol. Cell Biol. 6, 363–375 (2005).
4. Hurley, J. H. & Emr, S. D. Annu. Rev. Biophys. Biomol. Struct. 35, 277–298 (2006).
5. Slagsvold, T., Pattni, K., Malerřd, L. & Stenmark, H. Trends Cell Biol. 16, 317–326 (2006).
Nature http://www.nature.com/nature
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4. Reproductive biology: On Sperm Alliance
The following points are made by Tim Lincoln (Nature 2007 445 499):
1) In 2002, biologists were presented with a vivid account of how sperm of the common wood mouse hook up together in "trains". Such trains, it was shown, form a fast vehicle in the race for the great prize -- fertilization of an egg. But only one sperm can be successful in that goal. New work (1) has now revisited the question of what prompts the selfless behaviour of the others.
2) A feature of the sperm of wood mice and many of their relatives among the murine rodents is that their heads carry a hook structure, which varies in shape and size between species. Immler et al. (1) carried out a survey of the sperm of 37 species of murine rodent. They find that hook shape and curvature are more pronounced in species in which the female is more likely to mate with different males. The principle of "together we succeed, divided we fail" makes sense in this situation. These sperm are better equipped to cooperate: so those from any one male are better able to see off the competition from another male.
3) The authors also looked at the behaviour of sperm in two of the species, the Norway rat and the house mouse. In both, the sperm formed groups. But in the house mouse, individual sperm outperformed the group in sheer speed. Immler et al. (1) speculate that maybe speed isn't everything: perhaps in this case the group can make surer progress in the journey up the female reproductive tract.
References:
1) PloS One doi: 10.1371/journal.pone.0000170; 2007)
Nature http://www.nature.com/nature
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