Science Roundup

This month in Science Roundup:



Modeling the Mind
http://www.sciencemag.org/sciext/compneuro/

In areas ranging from molecules to the highest brain functions, scientists are using mathematical models and computer simulations to study and predict the behavior of the nervous system. In a special section of the 6 Oct 2006 issue, Science highlighted some recent advances in the field of computational neuroscience.  Three Review articles examined single-neuron dynamics and computations, the role of neuronal network states in sensory responsiveness, and models of high-level cognition, while two News stories profiled enterprising researchers who are developing new technologies inspired by theories of brain function and the mathematical principles underlying human vision.  Science’s Signal Transduction Knowledge Environment cast an eye on excitatory signaling in the brain with Review and Perspective articles that emphasized the central role of glutamate receptors in brain function and pathology. And a collection of articles on ScienceCareers.org explored career and funding opportunities for scientists eager to forge connections between neuroscience, informatics, and engineering.


The Smallest Genomes

Many endosymbiotic bacteria -- bacteria that live with the body or cells of another organism -- undergo genome reduction as they adapt to intracellular life within their hosts. Now two studies reported in the 13 Oct 2006 Science defy previous notions of how small these genomes can become. Both genomes -- the smallest sequenced to date -- derive from insect symbionts and have lost important genes functions that threaten the very existence of these microbes.  Pérez-Brocal et al. ( http://www.sciencemag.org/cgi/content/short/314/5797/312 ) reported on the ~422-kilobase-pair genome of the aphid symbiont Buchnera aphidicola.  This bacterium has lost most metabolic functions, including the ability to synthesize riboflavin and the essential amino acid tryptophan.  The researchers suggest that these losses are being complemented, and might eventually be replaced by, a coexisting secondary symbiont.  Nakabachi et al. ( http://www.sciencemag.org/cgi/content/short/314/5797/267 ) described the even smaller genome of Carsonella ruddii -- a symbiont of phloem-sap-feeding insects. Its ~160-kb chromosome encodes no more than 182 proteins and is missing numerous genes considered essential for life, including those for transport and membrane synthesis.  Rather than being replaced by a secondary symbiont, the team surmises that as in the case of organelles, the lost genes may have been transferred to the host nuclear genome.  As noted in an accompanying Perspective by S.G.E. Andersson ( http://www.sciencemag.org/cgi/content/short/314/5797/259 ), future studies of these and other tiny bacterial genomes will provide clues about organelle evolution and the various routes taken to minimal gene-sets in nature.


The Buzz on Honey Bees

The honey bee lives in societies that rival our own in complexity, and has therefore become a model system for studying the roots of social behavior.  It has also contributed to our understanding of human health issues from immunity to longevity, and is valued by farmers for its ability to produce honey and pollinate crops.  The recent sequencing of the genome of the Western honey bee Apis mellifera has therefore inspired a variety of studies aimed at elucidating aspects of honey bee biology and evolution, three of which are described in the 27 Oct 2006 Science.  Whitfield et al. ( http://www.sciencemag.org/cgi/content/short/314/5799/642 ) performed a global population genetic analysis, which suggests that the honey bee originated in Africa and expanded into Eurasia at least twice, and that African "killer" bees are a mix of three genetically distinct lineages ( listen to the an interview with Dr. Whitfield in the 27 Oct podcast; http://www.sciencemag.org/about/podcast.dtl#20061027 ). Wang et al. ( http://www.sciencemag.org/cgi/content/full/314/5799/645 ) reported that unlike other insects studied, the honey bee has a vertebrate-like set of enzymes needed to methylate genes, implying that methylation may be important in silencing genes in bees as well as in vertebrates.  Hummon et al. ( http://www.sciencemag.org/cgi/content/short/314/5799/647 ) identified nearly 200 candidate neuropeptides in the honey bee genome, which may be important in regulating this insect’s social behavior.  In a related study Poiner and Danforth ( http://www.sciencemag.org/cgi/content/short/314/5799/614 ) described a 100-million-year-old fossil bee, preserved in amber, that provides insights into the morphology of the earliest bees.  An accompanying News story by E. Pennisi ( http://www.sciencemag.org/cgi/content/short/314/5799/578 ) highlighted the studies.


Life-or-Death Decisions

To remain healthy, cells with damaged DNA must either delay progression of the cell cycle for a repair job or commit cellular suicide (apoptosis).  A new study reported in the 13 Oct 2006 Science, now provides a mechanism through which cells with genomic damage may switch between these alternative fates.  Cyclin-dependent kinases (CDKs) phosphorylate (add phosphate to) a number of cellular proteins and are the major driving force of the cell cycle engine.  CDK2 regulates the most vulnerable period of the cell cycle during which the genome must be faithfully replicated, and its function is often abolished after DNA damage.  This inhibition plays a central role in DNA damage-induced cell cycle arrest and DNA repair.  Huang et al. ( http://www.sciencemag.org/cgi/content/short/314/5797/294 ) now show that CDK2 also influences cell survival -- by altering the localization of the transcription factor FOXO1.  FOXO1 induces apoptosis by activating a number of cell death genes.  Under normal conditions, it is phosphorylated by CDK2, a modification that sequesters the transcription factor in the cytoplasm (away from its target genes in the nucleus) thereby preventing unwanted cell death.  In cells with extensive DNA damage, however, reduced phosphorylation of FOXO1 allows the factor to move into the nucleus, where it can enhance expression of apoptosis-inducing genes.  As noted in an accompanying Perspective by J. Bartek and J. Lukas ( http://www.sciencemag.org/cgi/content/short/314/5797/261 ), understanding how cells balance life-and-death decisions has important implications for understanding cancer pathogenesis and disease management.


Math, Science, and Gender

The role of gender in math and science performance has fueled considerable debate on issues ranging from education practices to career choices and advancement. In an Education Forum in the 27 Oct 2006 Science, J. S. Hyde and M. C. Linn ( http://www.sciencemag.org/cgi/content/short/314/5799/599 ) offered a review of meta-analyses of research on gender differences, which suggests that girls and boys are more similar than different in their psychological traits and cognitive abilities.  The authors argue that too often, small differences in performance -- reflected in studies such as the National Assessment of Educational Progress Report Card -- are exaggerated and end up reinforcing subtle, persistent, biases, e.g., that girls lack mathematical and scientific aptitude.  Efforts to improve math and science performance in schools, they suggest, should focus more on factors such as differences in students’ aggression and activity levels than on gender ( listen to the an interview with Dr. Hyde in the 27 Oct podcast; http://www.sciencemag.org/about/podcast.dtl#20061027 ).

In another study, published in the 20 Oct 2006 Science, Dar-Nimrod-and Heine ( http://www.sciencemag.org/cgi/content/short/314/5798/435 ) took a closer look at how stereotypes influence women’s performance in math.  The team showed that women who read an essay ascribing gender differences in math performance to genetics (implying that the differences are inescapable) performed worse on subsequent math tests than women who read an essay attributing the differences to life experience.  Their results show that merely considering the role of genes in math performance can have adverse effects.


Tracking Marine Sulfur

Marine phytoplankton produce large amounts of a compound called dimethylsulfoniopropionate (DMSP) for use as an osmolyte, predator deterrent, and antioxidant.  A major breakdown product of DMSP is the gas dimethylsulfide (DMS), which contributes to atmospheric aerosol formation at levels that could influence climate.  However, the processes that influence how much DMS is emitted to the air have been unclear.  Now two Reports in the 27 Oct 2006 Science have provided new pieces to the marine sulfur cycle puzzle.  Howard et al. ( http://www.sciencemag.org/cgi/content/short/314/5799/649 ) surveyed genome samples collected from seawater, looking for genes involved in demethylation -- the first step of the DMSP degradation pathway that competes with DMS production by turning the precursor into other sulfur compounds that remain in the ocean.  The team estimates that one-third of surface ocean bacteria harbor a DMSP demethylase homolog and thereby route a substantial fraction of global marine primary production away from DMS formation and into the marine microbial food web.

In the open ocean, microbes known as SAR11 bacteria are the most important demethylators, but in coastal waters, a different group called the Roseobacter takes over this role. Vila-Costa et al. ( http://www.sciencemag.org/cgi/content/short/314/5799/652 ) reported that cyanobacteria and diatoms also act to retain sulfur in the planktonic food web by assimilitating DMSP produced by other plankton. An accompanying Perspective by G. Malin ( http://www.sciencemag.org/cgi/content/short/314/5799/607 ) highlighted the studies.


Diversity Gradient Explained

Organisms ranging from plants to vertebrates, across habitats from grasslands to oceans, show a pronounced decrease in biodiversity from the tropics to the poles.  Although the existence of the so-called latitudinal diversity gradient (LDG) has been known for more than a century, researchers have long debated the evolutionary dynamics underlying it.  Do more species originate in the tropics or do they have a greater tendency to persist there?  According to a new Research Article in the 6 Oct 2006 Science, the answer is: both.  Jablonski et al. ( http://www.sciencemag.org/cgi/content/short/314/5796/102 ) performed a large-scale survey of the fossil record to document the patterns of origination, extinction, and migration of marine bivalves over the past 11 million years.  They found that the tropics are the source of most of the world’s bivalve biodiversity. More than two-thirds made their first appearance there and later extended their geographic ranges poleward.  The results thus support the notion of the tropics as both a cradle and a museum of biodiversity.  An accompanying Perspective by C. R. Marshall ( http://www.sciencemag.org/cgi/content/short/314/5796/66 ) highlighted the Report.


Golden Insights

Many of the world’s valuable metals -- including zinc, copper, and gold -- are mined from hydrothermal ore deposits, formed as hot, mineral-laden fluids circulate through Earth’s crust.  For years, geologists have debated where these fluids come from, how much is required to form a major deposit, and how long this process takes.  In a Report in the 13 Oct 2006 Science, Simmons and Brown ( http://www.sciencemag.org/cgi/content/short/314/5797/288 ) shed new light on the origins of one of the world’s largest hydrothermal gold ores: the Ladolam deposit on Lihir Island, Papua New Guinea. Several geothermal wells, drilled more than a kilometer deep to facilitate mining, provided the team with access to the ultra-hot (>275 degrees Celsius) magmatic fluids upstream of the ore deposit. Extracted samples were found to contain ~15 parts per billion of dissolved gold -- a higher concentration than observed in other active geothermal systems.  Given the geothermal heat flow caused by the ascending fluids and their initial gold content, the researchers calculate that the entire Ladolam deposit -- some 1300 tons of gold -- formed within ~55,000 years.  Their results indicate that the combination of sustained metal flux and efficient precipitation were critical to forming the deposit in a compact volume of rock in a relatively short period of time.  An accompanying Perspective by C. A. Heinrich ( http://www.sciencemag.org/cgi/content/short/314/5797/263 ) considered whether the deposit could have formed even more quickly.


Geoengineering Climate

Increasing concentrations of atmospheric carbon dioxide and other greenhouse gases present a two-pronged threat: global warming and acidification of the oceans.  Reducing anthropogenic emissions poses both economic and technical challenges, and it is unclear whether it can be done quickly enough to avoid potentially damaging consequences.  One alternative approach that has been proposed is to mitigate the effects of greenhouse gases by geoengineering.  In a Report in the 20 Oct 2006 Science (published online 14 Sep), Wigley ( http://www.sciencemag.org/cgi/content/short/314/5798/452 ) looked at one method that involves injecting sulfate aerosol precursors into the stratosphere, which would increase cloud cover.  The net effect would be to reflect more sunlight back into space, thus reducing global warming.  Wigley used the extended cloud cover following the eruption of Mount Pinatubo in 1991 as a starting point for calculations of different scenarios.  That volcanic eruption released some 10 million tons of sulfur into the stratosphere, causing detectable short-term cooling without seriously disrupting the climate system. According to Wigley’s analysis, an annual flux of half that amount would have a substantial influence on climate.  A related News story by R. A. Kerr ( http://www.sciencemag.org/cgi/content/short/314/5798/401a ) highlighted the growing scientific and ethical debate over so-called stratospheric shading.


Magnetic Loops in the Galaxy

In addition to a massive black hole, the center of the Milky Way harbors a number of unusual features including oddly shaped gas filaments and regions of hot molecular gas that exhibit violent motions.  In a study reported in the 6 Oct 2006 Science, Fukui et al. ( http://www.sciencemag.org/cgi/content/short/314/5796/106 ) used carbon monoxide emission spectra to map previously unexplored regions of this curious inner-galactic realm.  Their results revealed the presence of giant loops of dense molecular gas located a few thousand light-years from the galactic center and extending almost a thousand light-years above the galactic plane.  The team suggests that the loops are the product of magnetic buoyancy effects.  These magnetic field disturbances are known to cause arches and loops to flare up from the sun’s surface, but have not been definitely observed on galactic scales (some 12 orders of magnitude larger than the solar phenomena).  Although evidence of a magnetic field in the giant loops has yet to be documented, model simulations show that the magnetic scenario can explain the heat and high velocity of these gaseous regions.  An accompanying Perspective by M. Morris ( http://www.sciencemag.org/cgi/content/short/314/5796/70 ) highlighted the Report.


Molecular Imaging with Xenon

Magnetic resonance imaging (MRI) relies on strong magnets and radio waves to detect hydrogen atoms in water and fat and has proven extremely valuable for imaging tissues and organs within living organisms. However, its application to biological imaging at the cellular and molecular level has been limited because of inherently low sensitivity.  In a Report in the 20 Oct 2006 Science, Schröder et al. ( http://www.sciencemag.org/cgi/content/short/314/5798/446 ) describe a new MRI technique based on xenon rather than hydrogen, that allows detection of signals from molecules present at 10,000 times lower concentrations than those detectable by conventional MRI techniques.  The technique involves xenon biosensors, which trap hyperpolarized Xe atoms in molecular cages that have been linked to an antibody or ligand to enable binding to a specific biological target.  These biosensors generate highly selective contrast at sites where they are bound, boosting the strength of the MRI signal and resulting in spatial images of the chosen molecular or cellular target. A sophisticated detection scheme involving the exchange of free hyperpolarized xenon with bound xenon dramatically amplifies the sensor signal.  An accompanying Perspective by B. Driehuys  ( http://www.sciencemag.org/cgi/content/short/314/5798/432 ) explained how the new technique could become a valuable tool for medical diagnosis, simultaneously providing information at the molecular, functional, and anatomical levels.


Plutonium’s Travels

Previous studies have suggested that hazardous radioactive chemicals in nuclear waste, which don’t dissolve easily in water, could still be transported in groundwater while bound to small particles called colloids.  But researchers have been uncertain about the nature of these colloids and about how fast and how far the particles can travel.  In a Report in the 27 Oct 2006 Science, Novikov et al. ( http://www.sciencemag.org/cgi/content/short/314/5799/638 ) discussed new insights gained from one of the most contaminated nuclear sites in the world.  The team investigated plutonium migration in Mayak, Russia, where plutonium salts, uranium, and other radionuclides from a nuclear waste reprocessing plant have contaminated a lake connected to a groundwater system.  They found that over the course of about 55 years, plutonium has traveled a distance of roughly 4 kilometers bound to iron-oxide colloids.  The researchers note that because potential nuclear waste repository sites each have different physical and chemical conditions, specific studies of how radioactive particles travel will be necessary for each site.



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In Science’s STKE

Understanding IKK Kinases

Members of the nuclear factor kappa B (NF-kappaB) family of transcription factors regulate expression of a large number of genes involved in immune responses, inflammation, cell survival, and cancer. These transcription factors are rapidly activated in response to various stimuli, including cytokines, infectious agents, and radiation-induced DNA double-strand breaks. In nonstimulated cells, they are bound to inhibitory kappa B (IkappaB) proteins and thereby sequestered in the cytoplasm. Cell stimulation leads to IkappaB phosphorylation, which marks these proteins for degradation and ultimately frees NF-kappaB to translocate to the nucleus and activate transcription of target genes. Two protein kinases, IKKalpha and IKKbeta, mediate phosphorylation of IkappaB proteins and represent a point of convergence for most signal transduction pathways leading to NK-kappaB activation. In a Review article published 17 Oct 2006 in Science’s Signal Transduction Knowledge Environment (STKE), H. Häcker and M. Karin ( http://stke.sciencemag.org/cgi/content/abstract/sigtrans;2006/357/re13 ) discussed the molecular mechanisms that regulate IKKs and IKK-related kinases and their host defense–related functions.  The full characterization of the biochemical events that lead to the activation of these kinases should lead to new insight into inflammatory diseases and the mechanisms of innate immunity.


Also in STKE this month:

--Mulligan and MacVicar looked at the influence of astrocyte swelling–induced glutamate release on neuronal activity ( 17 Oct 2006; http://stke.sciencemag.org/cgi/content/abstract/sigtrans;2006/357/pe42 )
--Zamoyska highlighted the activation by superantigens of an alternative signaling pathway during T cell activation ( 24 Oct 2006; http://stke.sciencemag.org/cgi/content/abstract/sigtrans;2006/358/pe45 )
--Vandenabeele et al. discussed the role of caspase inhibitors in promoting alternative cell death pathways ( 24 Oct 2006; http://stke.sciencemag.org/cgi/content/abstract/sigtrans;2006/358/pe44 )