ScienceWeek

SCIENCEWEEK

October 6, 2006

Vol. 10 - Number 40

-------------------------------

Visit and join the new SCIENCE AND POLITICS newsgroup (open to everyone for news and discussion). You can read and participate by Web or by Email. Post commentary, queries, announcements, job openings, etc. This new discussion group is moderated and sponsored by ScienceWeek. Join the group at: http://groups.google.com/group/scipol

--------------------------------

Imagine a survivor of a failed civilization with only a tattered book on aromatherapy for guidance in arresting a cholera epidemic. Yet, such a book would more likely be found amid the debris than a comprehensible medical text.

-- James Lovelock

--------------------------------

Contents (full reports below):

1. Genomics: Genomes and the Tree of Life. Only a decade has elapsed since the first prokaryote and eukaryote genomes were decoded. More than 400 genomes have been completed, some 1600 additional genomes are currently in progress, and genome-scale data sets (e.g., expressed sequence tags) are being generated at an unprecedented rate. Among the many fields feeling the impact of this...

2. Chemistry: On Cell Membrane Domains. Cell membranes consist of a richly heterogeneous fluid mosaic of lipids and proteins. Molecular complexes, from tens to hundreds of nanometers in size, dynamically assemble and dissolve while performing the biochemical functions of life. But the spatial organization of the cell membrane and its role in the regulation of biochemical processes remain...

3. Evolution: On Phenotype Conservation With Genotype Divergence. From penguins to mushrooms and baobabs, the world around us harbors a bewildering diversity of life forms. Much of the evolution of this diversity is due to changes in the underlying genetic regulatory architecture. But what happens to such architecture when organisms that diverged long ago retain the same traits (or "phenotypes")? Can this regulatory...

4. Climate Change: On Global Methane Emissions. Methane is a potent greenhouse gas -- per molecule, more than 20 times as powerful as carbon dioxide. Moreover, when methane emissions rise, so too does the concentration of the pollutant ozone in the troposphere, the lowest layer of Earth's atmosphere. Methane also consumes hydroxyl radicals, whose oxidative effects are essential to...

--------------------------------

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. Publication date: October 3, 2006.

Review: "JUNK SCIENCE is a passionate, minutely-informed and scrupulously fair analysis of all the abuses and misuses of science that are rampant today -- a clarion call to action which concerns us all. One might wish that such a book were not needed, but it is, more now than ever before." -- Oliver Sacks, M.D., author of AWAKENINGS and THE MAN WHO MISTOOK HIS WIFE FOR A HAT.

More information about JUNK SCIENCE at: http://www.amazon.com/exec/obidos/ASIN/0312352417/scienceweek

--------------------------------

Also Noted:

Contemporary Poetry and Contemporary Science. Robert Crawford. Oxford University Press, Oxford, 2006. Hardback: 250 pp. £19.99. ISBN 0199258120. More information at: http://www.amazon.com/exec/obidos/ASIN/0199258120/scienceweek

The Cosmos. A Historical Perspective. Craig G. Fraser. Greenwood, New York, 2006. Hardback: 193 pp., illus. $65, £36.99. ISBN 0313332185. More information at: http://www.amazon.com/exec/obidos/ASIN/0313332185/scienceweek

The Artists and the Mathematician. The Story of Nicolas Bourbaki, the Genius Mathematician Who Never Existed. Amir D. Aczel. Thunder's Mouth (Avalon Publishing Group), New York, 2006. Hardback: 251 pp. $23.95. ISBN 1560259310. More information at: http://www.amazon.com/exec/obidos/ASIN/1560259310/scienceweek

Better But Not Well. Mental Health Policy in the United States since 1950. Richard G. Frank and Sherry A. Glied. Johns Hopkins University Press, Baltimore, 2006. Paperback: 204 pp., illus. $21.95. ISBN 0801884438. More information at: http://www.amazon.com/exec/obidos/ASIN/0801884438/scienceweek

=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

1. GENOMICS: GENOMES AND THE TREE OF LIFE

The following points are made by Antonis Rokas (Science 2006 313:1897):

1) Only a decade has elapsed since the first prokaryote and eukaryote genomes were decoded. More than 400 genomes have been completed, some 1600 additional genomes are currently in progress, and genome-scale data sets (e.g., expressed sequence tags) are being generated at an unprecedented rate. Among the many fields feeling the impact of this genomic avalanche is phylogenetics, the discipline concerned with discovering the evolutionary interrelationships among all living organisms, an effort frequently visualized in the form of the "Tree of Life" (1). The wealth of genomic data has allowed the discovery of new molecular markers for phylogenetic reconstruction, such as rare genomic changes, but it has also presented new challenges for theoretical phylogenetic research.

2) The dramatic increase in data set sizes has led, in many cases, to increased confidence in the inference of evolutionary relationships (2,3). Data sets with small gene numbers can generate inaccurate phylogenies because of sampling error or simply the lack of sufficient amounts of data (3). Although typical genome-scale phylogenetic studies have been rich in sequence data and thin in species number (3), as the number of sequenced genomes increases, genome-scale phylogenetic analyses are beginning to feature much larger numbers of species (4).

3) But further increases in data set sizes present challenges as well. Analyzing many thousands of nucleotides for hundreds or thousands of species requires substantial computational power to efficiently search among all possible trees (5). More sophisticated statistical algorithms are also needed for discovering the trees best supported by the data. Several clades of the Tree of Life, including the one of Metazoa, are proving difficult to resolve too. Most parameters of sequence evolution vary across lineages. Slight biases -- amplified by the sheer volume of data -- can potentially mislead phylogenetic algorithms and provide high support for the wrong trees.

4) Whereas the linear information in genome sequences may not always suffice, other rare features in the genomes' contents, such as sequence rearrangements or integrations of mobile genetic elements, offer some powerful alternative markers for addressing such challenging phylogenetic riddles. The use of such rare genomic changes is feasible only in a genomic context and can frequently yield remarkably precise evolutionary trees. In the mammalian lineage, this approach has led to the discovery of several new clades such as the Pegasoferae, which unexpectedly combines bats with horses, cats, dogs, and pangolins. Even though the use of rare genomic changes is still in its infancy, the first steps toward placing rare genomic changes-based phylogenetic reconstruction in a robust statistical framework have already been taken, thus allowing a better evaluation of their usefulness in phylogenetic reconstruction.

References (abridged):

1. J. Cracraft, M. J. Donoghue, Eds., Assembling the Tree of Life (Oxford Univ. Press, Oxford, 2004)

2. M. D. Katinka et al., Nature 414, 450 (2001)

3. A. Rokas, B. L. Williams, N. King, S. B. Carroll, Nature 425, 798 (2003)

4. F. D. Ciccarelli et al., Science 311, [1283] (2006)

5. U. W. Roshan, B. M. Moret, T. Warnow, T. L. Williams, Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference, 98 (IEEE Press, Piscataway, NJ, 2004)

Science http://www.sciencemag.org

ScienceWeek http://scienceweek.com

=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

2. CHEMISTRY: ON CELL MEMBRANE DOMAINS

The following points are made by Jay T. Groves (Science 2006 313:1901):

1) Cell membranes consist of a richly heterogeneous fluid mosaic of lipids and proteins. Molecular complexes, from tens to hundreds of nanometers in size, dynamically assemble and dissolve while performing the biochemical functions of life. But the spatial organization of the cell membrane and its role in the regulation of biochemical processes remain little understood, because current imaging technologies cannot resolve the most important features. New work (1) takes the next step in biomembrane imaging by using a form of secondary ion mass spectrometry (NanoSIMS) to map the chemical composition of a lipid membrane with 70 to 100 nm resolution.

2) Present knowledge of the organization of living cells comes mostly from fluorescence and electron microscopy. Over the past 20 years, fluorescence microscopy has flourished, due in part to the introduction of an extensive array of fluorescent probe molecules. By synthetically or genetically -- such as with green fluorescent protein -- coupling a fluorescent probe to the protein of interest, the ambiguity of what is being observed is broken. The ability to track a specific protein in living cells has revealed a tremendous wealth of information about the inner workings of biological systems. However, the spatial resolution of optical imaging techniques is generally restricted to a few hundred nanometers. Electron microscopy can be used to view cellular structures down to molecular length scales, allowing the bilayer structure of lipid membranes to be directly imaged. However, the lateral organization within the membrane has been more difficult to resolve. The need for imaging biomembrane organization at length scales of 10 to 300 nm thus remains largely unmet.

3) Imaging mass spectrometry has the potential to step into this resolution gap. In recent years, this technique, which offers unparalleled chemical specificity, has been increasingly used to study biological systems (2,3). There are several ways in which mass spectrometry may be performed in a spatially resolved manner. In matrix-assisted laser desorption ionization (MALDI), a focused laser spot is scanned over a sample that has been prepared in a chemical matrix. The method produces relatively large molecular ions and enables direct identification of peptides and proteins without the need for specific labeling. Imaging MALDI has been successfully applied to biological tissue samples and has been used as a bioanalytical tool in array-based protein assays (4,5). However, the spatial resolution is typically limited by the laser spot size (about 1 micron).

4) Secondary ion mass spectrometry (SIMS) provides an alternative strategy. In this method, the sample is bombarded with an incident ion or molecular beam. The beam locally vaporizes the sample into secondary molecular and atomic ions. In time-of-flight SIMS, the incident ion beam is pulsed, and the secondary ion mass-to-charge ratio (m/z), and hence its identity, is determined by the time it takes these secondary ions to reach the ion detector. Imaging time-of-flight SIMS can be used to map the chemical composition of cell membranes. For example, using an ion beam with a diameter of 200 nm, researchers were able to resolve the heterogeneous distribution of lipids at highly curved intercellular fusion pores with a spatial resolution of about 250 nm. An acyl chain fragment (C5H9), which is a secondary ion produced from most membrane lipids, served as a general membrane marker. The specific identity of the lipids was determined from molecular fragments of their chemically distinct phosphate head groups.

References (abridged):

1. M. L. Kraft, P. K. Weber, M. L. Longo, I. D. Hutcheon, S. G. Boxer, Science 313, 1948 (2006)

2. P. Chaurand et al., Toxicol. Pathol. 33, 92 (2005)

3. N. Winograd, Anal. Chem. 77, 142A (2005)

4. R. L. Caldwell, R. M. Caprioli, Mol. Cell. Proteomics 4, 394 (2005)

5. R. M. A. Heeren, Proteomics 5, 4316 (2005)

Science http://www.sciencemag.org

ScienceWeek http://scienceweek.com

=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

3. EVOLUTION: ON PHENOTYPE CONSERVATION WITH GENOTYPE DIVERGENCE

The following points are made by Antonis Rokas (Nature 2006 443:401):

1) From penguins to mushrooms and baobabs, the world around us harbors a bewildering diversity of life forms. Much of the evolution of this diversity is due to changes in the underlying genetic regulatory architecture (1). But what happens to such architecture when organisms that diverged long ago retain the same traits (or "phenotypes")? Can this regulatory architecture diverge while the overlying phenotypes remain similar? New work (2) examines the gene-regulatory circuit that governs mating type in several yeast species, and the work identifies a remarkable example of divergence at the genotypic level (the DNA sequence) despite conservation at the phenotypic level.

2) The yeast species Saccharomyces cerevisiae and Candida albicans are seemingly very different: S. cerevisiae is the cornerstone of the baking and brewing industries, whereas C. albicans is the most commonly encountered fungal pathogen in humans. Both yeasts have one thing in common, however -- sex. Although yeasts do not have different sexes per se, both species have two molecularly distinct mating types. Mating type in yeasts is controlled by the MAT genetic region (locus), which exists in two versions, MATa and MATalpha. A cell's mating type is determined by which version it expresses. Thus, cells expressing the a protein become a cells by expressing a-specific genes (asgs), and are specialized for mating with yeasts of the opposite mating type -- alpha. Likewise, alpha-expressing cells become alpha cells, express alpha-specific genes (asgs), and can mate only with yeasts of the a type.

3) Underlying this apparent similarity in mating phenotype in the two species (a-expressing cells become a cells, and alpha-expressing cells become alpha cells), the detailed genetic mechanisms by which mating-type identity is achieved seem to diverge considerably. In the a cells of C. albicans, the asgs are only expressed once they have been activated by the a2 protein, whereas in S. cerevisiae the MATa2 gene (encoding the a2 protein) is absent and the asgs are expressed by default in its a cells. In the case of alpha cells, the alpha1 protein activates alphasgs in both yeasts, but in S. cerevisiae alpha2 is also required to repress the asgs (otherwise they are always "on").

4) Tsong et al (2) find that in three distantly related yeasts the regulatory architectures are remarkably divergent. This is despite the conservation of the regulatory logic: specifically, in all three yeasts, a-specific genes (asgs) are turned on in a cells and turned off in a cells. The Mcm1 protein is equally expressed in both cell types and is required for both asg and asg regulation, sometimes in concert with the a2 and alpha2 proteins. Major transitions in the regulatory architecture are indicated by red arrows. As the regulatory architecture in C. albicans also occurs in an evolutionarily diverse set of other yeasts, it is most probably closer to the ancestral one. If so, two key modifications must have occurred in the regulatory architecture of a direct ancestor of S. cerevisiae, namely the loss of the MATa2 gene and the gain of asg repression by the alpha2 protein.

References (abridged):

1. Carroll, S. B. PLoS Biol. 3, e245 (2005)

2. Tsong, A. E. , Tuch, B. B. , Li, H. & Johnson, A. D. Nature 443, 415-420 (2006)

3. Acton, T. B. , Mead, J. , Steiner, A. M. & Vershon, A. K. Mol. Cell. Biol. 20, 1-11 (2000)

4. True, J. R. & Haag, E. S. Evol. Dev. 3, 109-119 (2001)

5. Weiss, K. M. & Fullerton, S. M. Theor. Popul. Biol. 57, 187-195 (2000)

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

ScienceWeek http://scienceweek.com

=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

4. CLIMATE CHANGE: ON GLOBAL METHANE EMISSIONS

The following points are made by Jos Lelieveld (Nature 2006 443:405):

1) Methane is a potent greenhouse gas -- per molecule, more than 20 times as powerful as carbon dioxide (1). Moreover, when methane emissions rise, so too does the concentration of the pollutant ozone in the troposphere, the lowest layer of Earth's atmosphere (2). Methane also consumes hydroxyl radicals, whose oxidative effects are essential to atmospheric cleansing. New work (3) recounts the results of an international effort to measure atmospheric methane concentrations and combine these data with a computer model of atmospheric chemistry and transport. The bad news is that the slowdown in global methane emissions in the past few decades was only temporary: reports of the emissions' control have been exaggerated.

2) At present, about two-thirds of global methane comes from anthropogenic sources, and most emissions occur in the Northern Hemisphere. Of naturally produced methane, the largest proportion stems from bacteria in wetlands that produce the gas when decomposing organic material. The growth rate of atmospheric methane was more than 10% per decade before 1980, but by the 1990s it had dropped to nearly zero (4). Bousquet et al (3) compute the global methane source distribution, especially its variability over recent decades. This is a rather controversial issue, as it is difficult to determine whether this variability should be attributed to fluctuations in the sources or in the sinks; the sink mechanisms are dominated by the good offices of the atmospheric hydroxyl radicals (5).

3) The authors used a so-called inversion modelling technique, which starts from observed concentrations at Earth's surface and back-calculates using models of transport and loss processes to optimize source estimates. The measurements stem from a global network of monitoring stations, and include isotope data (in particular, the relative proportion of carbon-13) that provide an additional clue as to what methane came from where. Methane from biomass burning, fossil-fuel-related sources, and bacterial processes have distinct isotopic signatures; methane emissions from wetlands, for example, are substantially depleted in carbon-13.

4) The approach is novel because the model computations optimized both methane emissions and methane loss through hydroxyl oxidation. The crux of the findings is that fluctuations of natural emissions, in particular by wetlands in the tropics, are a dominant factor in the variability of methane from year to year. These emissions are in turn sensitive to meteorological parameters: during dry periods, methane flux from wetlands is depressed. Thus, during the most recent part of the analysis period -- from 1999 onward -- extended droughts have reduced natural methane emissions. This has concealed the fact that anthropogenic emissions have resumed their increase, an increase perhaps associated with the accelerating use of fossil fuels by booming Asian economies. Continued monitoring of atmospheric methane, and especially its relation to wetland inundation and drying, will be needed to substantiate this prediction.

References (abridged):

1. Ramaswamy, V. et al. in Climate Change 2001: The Third Assessment Report of the Intergovernmental Panel on Climate Change (eds Houghton, J. T. et al.) 349-416 (Cambridge Univ. Press, 2001)

2. Lelieveld, J. , Crutzen, P. J. & Dentener, F. J. Tellus 50B, 128-150 (1998)

3. Bousquet, P. et al. Nature 443, 439-443 (2006)

4. Dlugokencky, E. J. et al. Geophys. Res. Lett. 30, 1992 (2003)

5. Houweling, S. et al. J. Geophys. Res. 104, 26137-26160 (1999)

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

ScienceWeek http://scienceweek.com

=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=