ScienceWeek

SCIENCEWEEK

October 20, 2006

Vol. 10 - Number 42

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We are a scientific civilization. That means a civilization in which knowledge and its integrity are crucial. Science is only a Latin word for knowledge... Knowledge is our destiny.

-- Jacob Bronowski (1908-1974)

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Contents (full reports below):

1. Genetics: On the Smallest Microbial Genome. The race to find the smallest microbial genome has taken a new and unexpected turn. New work reports the ~422-kb genome of an aphid endosymbiont, Buchnera aphidicola. Even smaller is the ~160-kb genome of a psyllid endosymbiont, Carsonella ruddii, reported by Nakabachi et al. These two bacterial genomes are the smallest sequenced to date...

2. Chemistry: On the Quantum Chemistry of Complex Systems. In 1926, Erwin Schroedinger first derived the analytical solutions for the electronic states of the hydrogen atom (1). Not long after this, Paul Dirac said: "The underlying physical laws necessary for the mathematical treatment of a large part of physics and the whole of chemistry are thus completely known, and the difficulty is only that the exact...

3. Particle physics: On the Big Bang and Phase Transitions. The idea of phase transitions -- abrupt changes in the state of matter -- is familiar from such common sights as the bubbling water in a boiling kettle. Phase transitions on a grand scale may have taken place in the early Universe, both enriching and complicating Big Bang cosmology. For example, the early Universe's gas of quasi-free quarks and gluons must...

4. Neuroscience: On Controlled Brain Capillaries. The control of brain blood flow poses an intriguing "plumbing" problem. On the one hand, high overall flows are required to maintain healthy brain function, because in humans the brain accounts for 20% of the body's energy consumption even though it forms only 5% of the total weight. On the other hand, there is a need to precisely regulate increases and...

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Also Noted:

Stem Cells in Reproduction and in the Brain. J. Morser, S.-I. Nishikawa, and H. R. Schueler, Eds. Springer, Berlin, 2006. Hardback: 258 pp., illus. $89.95. ISBN 3540314369. More information at: http://www.amazon.com/exec/obidos/ASIN/3540314369/scienceweek

Understanding Carbon Nanotubes. From Basics to Applications. A. Loiseau et al., Eds. Springer, Berlin, 2006. Hardback: 566 pp., illus. $129. ISBN 3540269223. More information at: http://www.amazon.com/exec/obidos/ASIN/3540269223/scienceweek

Cats of Africa. Behavior, Ecology, and Conservation. Luke Hunter. Photography by Gerald Hinde. Johns Hopkins University Press, Baltimore, 2006. Hardback: 176 pp., illus. $39.95. ISBN 0801884829. More information at: http://www.amazon.com/exec/obidos/ASIN/0801884829/scienceweek

College Students in Distress. A Resource Guide for Faculty, Staff, and Campus Community. Bruce S. Sharkin. Haworth, Binghamton, NY, 2006. Paperback: 150 pp. $19.95. ISBN 0789025256. More information at: http://www.amazon.com/exec/obidos/ASIN/0789025256/scienceweek

Special Note: A New Book by the Editor of ScienceWeek: ------------------------------------------------------

JUNK SCIENCE. How Politicians, Corporations, and Other Hucksters Betray Us. Dan Agin. Thomas Dunne Books/St. Martin's Press, New York, 2006. Hardback: 336 pp., $24.95. ISBN 0312352417. More information at: http://www.amazon.com/exec/obidos/ASIN/0312352417/scienceweek

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1. GENETICS: ON THE SMALLEST MICROBIAL GENOME

The following points are made by Siv G. Andersson (Science 2006 314:259):

1) The race to find the smallest microbial genome has taken a new and unexpected turn. New work (1) reports the ~422-kb genome of an aphid endosymbiont, Buchnera aphidicola. Even smaller is the ~160-kb genome of a psyllid endosymbiont, Carsonella ruddii, reported by Nakabachi et al (2). These two bacterial genomes are the smallest sequenced to date. In addition to satisfying our desire to crown world-record holders, these genomes are approaching the sizes of terrestrial plant mitochondrial (<600 kb) and chloroplast (less than 220 kb) genomes.

2) Symbiotic relationships are widespread among invertebrates, including relationships involving medically and agriculturally important pests. An estimated 10% of insect species house "farms" of bacterial endosymbionts that provide nutrients such as cofactors, amino acids, or other essential compounds that the host insects cannot obtain from their diet (3). The best-studied example is B. aphidicola. This bacterium, which produces all the essential amino acids except tryptophan, resides within a specialized group of aphid cells. B. aphidicola has been directly inherited from insect mother to offspring for a few hundred million years. During the evolution of this host-symbiont relationship, approximately 75% of the ancestral B. aphidicola genome has been eliminated, resulting in genomes that are currently 600 to 700 kb in size (4,5). This small genome size is indicative of a closed ecosystem in which a bacterial genome encodes the near-minimal set of genes required for bacterial growth. Indeed, ~88% of the endosymbiont enzymes can be predicted by computer network analysis of minimal reaction sets stimulated under endosymbiont growth conditions.

3) Not only are these two bacterial genomes among the smallest, they are also among the most stable, with no acquisition of external DNA, no repeated sequences greater than 25 bp, and no chromosome rearrangements over the past 50 to 100 million years (5). This would represent a biological system of supreme stability, were it not for the slow erosion of endosymbiont genomes. This deterioration accounts for an estimated loss of about one gene per 5 to 10 million years (5). This is as expected from Muller's ratchet, which proposes that deleterious mutations accumulate in small asexual populations with no incorporation of new genes. In effect, such organisms may decrease in fitness over time until they become extinct. It is debated whether sequence erosion will eventually come to a halt, or whether endosymbiont genomes will continue to deteriorate, causing the demise of these microbes and the collapse of their hosts.

4) The two genomes now presented have surpassed the previous lower limit for sequenced genomes of B. aphidicola, which range in size from 615 to 641 kb. The genome of B. aphidicola from the aphid Cinara cedri (the B. aphidicola strain BCc) consists of a ~416-kb chromosome with 362 protein-coding genes and a 6-kb circular plasmid (1). The ~160 kb chromosome of C. ruddii encodes no more than 182 proteins (2). Absent from both organisms are genes encoding most membrane and transport functions, a finding indicative of freely diffusible systems with a passive exchange of metabolites. No genes for the biosynthesis of tryptophan were identified in the BCc genome, although it has been shown experimentally that the aphid host is dependent on the bacterial provision of tryptophan (10). Intuitively, we would expect such extensive gene loss in an endosymbiont genome to be lethal for the insect. Pérez-Brocal et al (1) suggest a possible way out of this conundrum -- replacement of the BCc strain with a secondary endosymbiont to supply tryptophan.

References (abridged):

1. V. Pérez-Brocal et al., Science 314, 312 (2006).

2. A. Nakabachi et al. Science 314, 267 (2006).

3. C. Dale, N. A. Moran, Cell 126, 453 (2006). [CrossRef]

4. S. Shigenobu et al., Nature 407, 81 (2000). [CrossRef]

5. I. Tamas et al. Science 296, [2376] (2002).

Science http://www.sciencemag.org

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2. CHEMISTRY: ON THE QUANTUM CHEMISTRY OF COMPLEX SYSTEMS

The following points are made by David C. Clary (Science 2006 314:265):

1) In 1926, Erwin Schroedinger first derived the analytical solutions for the electronic states of the hydrogen atom (1). Not long after this, Paul Dirac said: "The underlying physical laws necessary for the mathematical treatment of a large part of physics and the whole of chemistry are thus completely known, and the difficulty is only that the exact application of these laws leads to equations much too complicated to be soluble. It therefore becomes desirable that approximate practical methods of applying quantum mechanics should be developed, which can lead to an explanation of the main features of complex atomic systems without too much computation" (2).

2) What progress has been achieved, some 80 years later, in applying quantum mechanics to complex atomic systems? A symposium at the first European Chemistry Congress in Budapest in August of 2006 (3) provided a snapshot of the progress in this field. Invited talks by Hans-Joachim Werner, Michael A. Robb, and Evert J. Baerends illustrated the current capabilities of quantum chemistry.

3) It is only for one-electron systems, such as the hydrogen atom, that Schroedinger's equation has an exact analytical solution. Even for two-electron molecules such as H2, numerical solutions are needed. Progress in the applicability of quantum chemistry has therefore depended on advances in computer power. It is now possible, using readily available computer packages, to calculate the energies and properties of many small molecules to an accuracy that can rival that obtained experimentally. This advance has been achieved through the development of theories and computational techniques that provide a rigorous description of electron motion (orbitals) and correlated interactions of electrons. The challenge is to extend these methods and computer programs to solving the Schroedinger equation for systems such as the very large molecules and nanostructures of interest in biology and materials science.

4) Werner clearly defined the main bottleneck that has prevented accurate electronic structure calculations from being applied to large molecules: the prohibitive scaling of computational cost with the number of electrons (N) in a molecule. This scaling is N^(7) for conventional methods, which allow for the correlation of all pairs of electrons in a molecule. Werner and co-workers are one of the groups that have developed powerful methods that allow only electrons close to each other to be correlated; this allows for "linear scaling," that is, a dependence in computational cost on N (4). The accurate description of electron orbitals in molecules also presents difficulties, with the computer time depending on (NA)^(4) in conventional methods, where NA is the number of basis functions used to describe an electron. A recently developed "density fitting" procedure has reduced this dependence to NA (5). Another advance that improves the accuracy of the calculations is the explicit inclusion of the interelectronic distance in the wave functions used in these approaches. These computational developments allow accurate quantum chemistry to be extended to molecular systems with many more atoms than was possible previously.

References (abridged):

1. E. Schroedinger, Ann. Phys. 79, 361 (1926)

2. P. A. M. Dirac, Proc. R. Soc. London Ser. A 123, 714 (1929)

3. New Developments in Theoretical and Computational Chemistry, symposium at the first European Chemistry Congress, Budapest, Hungary, 27 to 31 August 2006.

4. T. Hrenar, G. Rauhut, H.-J. Werner, J. Phys. Chem. A 110, 2060 (2006)

5. M. Schütz et al., J. Chem. Phys. 121, 737 (2004)

Science http://www.sciencemag.org

ScienceWeek http://scienceweek.com

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3. PARTICLE PHYSICS: ON THE BIG BANG AND PHASE TRANSITIONS

The following points are made by Frank Wilczek (Nature 2006 443:637):

1) The idea of phase transitions -- abrupt changes in the state of matter -- is familiar from such common sights as the bubbling water in a boiling kettle. Phase transitions on a grand scale may have taken place in the early Universe, both enriching and complicating Big Bang cosmology. For example, the early Universe's gas of quasi-free quarks and gluons must at some point have condensed into composite particles bound together by the nuclear strong force. These particles, made up of quarks stuck together by gluons, which act as the mediator particles of the strong force, are the baryons -- the class of particle that includes protons and neutrons -- and the mesons of today's normal "hadronic" matter.

2) It had once seemed plausible that this phase change was marked by a true, abrupt thermodynamic phase transition, such as that seen in the kettle, at a temperature of around 10^(13) kelvin. Through a difficult and fundamental calculation, new work (1) has demonstrated that this change, although drastic, actually sets in smoothly as the temperature falls. The methods could be used to illuminate several other open questions.

3) According to conventional Big Bang cosmology, the early Universe contained matter in thermal equilibrium at extremely high temperatures. As the Universe expanded and cooled, neutrinos and eventually photons ceased to interact significantly, and fell out of equilibrium. These freeze-outs occurred at temperatures of 10^(10) K and 10^(3) K, respectively. (The relic photons, redshifted down to a temperature of just around 3 K, owing to the Universe's subsequent expansion, constitute the present-day cosmic microwave background radiation.) But at the earliest times, before neutrinos and photons decoupled from the rest of matter, densities and energies were so high, and reaction rates therefore so fast, that any local deviations from equilibrium were quickly repaired. That might seem to be a recipe for dullness. But as anyone who's seen the agitation in a boiling kettle will know, phase transitions can spice up the action.

4) The most dramatic consequences come by way of first-order phase transitions, which involve discontinuous changes in the organization of matter. Suppose phase A has a lower free energy above some critical temperature T*, and that below T* phase B has a lower free energy. The phase with the lower free energy is always the natural choice, so as we start from phase A at high temperature and cool through T*, bubbles of B may appear. At temperatures below T*, a sufficiently large bubble of phase B can grow, as gains in volume free energy within the bubble overcome surface tension at the interface. Eventually, then, we will have only B. It may, however, take a very long time to nucleate a sufficiently large bubble. In the meantime, A persists below T*: this is the phenomenon of supercooling. In a cosmological context, the unusual equation of state associated with supercooling can induce a period of faster-than-light expansion -- the phenomenon known as inflation. Alternatively, the bubbles might suddenly appear in many different places, then grow and collide. Those violent events can leave their imprint on the gravitational field, leading to seed fluctuations from which galaxies or black holes might eventually evolve. Gravitational waves might be yet another result, awaiting detection today as a relic background. Different processing of matter within the regions of A and B might also lead to deviations from standard predictions for the abundances of the light elements, or even package matter into unusual forms, such as superdense quark matter.

References:

1. Aoki, Y. , Endro 2acutedi, G. , Fodor, Z. , Katz, S. D. & Szabó, K. K. Nature 443, 675-678 (2006)

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

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4. NEUROSCIENCE: ON CONTROLLED BRAIN CAPILLARIES

The following points are made by B. A. MacVicar and M. W. Salter (Nature 2006 443:642):

1) The control of brain blood flow poses an intriguing "plumbing" problem. On the one hand, high overall flows are required to maintain healthy brain function, because in humans the brain accounts for 20% of the body's energy consumption even though it forms only 5% of the total weight. On the other hand, there is a need to precisely regulate increases and decreases in flow to match the changing metabolic needs of specific brain regions. It has been known for more than 100 years (1) that the brain regulates its own blood supply. It can increase blood flow specifically to discrete regions to follow increases in neuronal activity. This principle has been exploited in functional magnetic resonance imaging and positron emission tomography, which have been extensively used to map the brain regions that are associated with different tasks (2). However, the cellular mechanisms by which specific brain regions regulate blood flow, and therefore their own nutrient intake and waste removal, are not fully understood. New work (3) implicates new players in regulating blood flow at the smallest level in the brain -- cells known as pericytes.

2) The large blood vessels supplying the brain are the carotid and vertebral arteries, which then branch to form the network of pial arteries covering the surface of the brain. In the cerebral cortex, the pial vessels branch into smaller arteries, which enter the brain tissue itself and are called the penetrating arterioles. These arterioles branch into secondary and tertiary arterioles, until they reach the smallest vessel supplying the brain tissue, the capillary, which is only wide enough for one red blood cell to pass through it at a time. The capillaries then feed into the venuoles and veins, which carry the blood away.

3) By virtue of the smooth muscle that surrounds them, arteries and arterioles can regulate blood flow. Various processes, including the release of mediators from the endothelial cells that line these vessels, cause contraction or relaxation of the smooth muscle cells, thereby decreasing or increasing the diameter of the artery or arteriole -- as a consequence, as we know from Poiseuille's law of fluid dynamics, blood flow can be controlled.

4) It had been suspected that blood flow through capillaries is also regulated, even though there are no surrounding smooth muscle cells to constrict them. The suspicions were based on the observation that capillaries are enwrapped at intervals by a little-studied cell type with contractile capabilities, the pericyte. Peppiatt et al (3) now show definitively that pericytes in living tissue of the central nervous system can constrict and relax, correspondingly changing capillary diameter, and that they do this in response to changes in neuronal activity. Pericytes were identified by staining with a specific marker. The cells are spaced at intervals along capillaries, and also occur at capillary junctions. Their cell bodies abut the capillaries, with their processes enwrapping them.(4,5)

References (abridged):

1. Roy, C. S. & Sherrington, C. S. J. Physiol. (Lond.) 11, 85-108 (1890)

2. Lauritzen, M. & Gold, L. J. Neurosci. 23, 3972-3980 (2003)

3. Peppiatt, C. M. , Howarth, C. , Mobbs, P. & Attwell, D. Nature 443, 700-704 (2006)

4. Chaigneau, E. , Oheim, M. , Audinat, E. & Charpak, S. Proc. Natl Acad. Sci. USA 100, 13081-13086 (2003)

5. Kleinfeld, D. , Mitra, P. P. , Helmchen, F. & Denk, W. Proc. Natl Acad. Sci. USA 95, 15741-15746 (1998)

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

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