 This month in Science Roundup:
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Spatial Cell BiologySpecial Issue Introduction The location of a cell within an organism and the location within the cell of its constituent parts affect everything it does, including the functions it is capable of performing, its signaling partners, and whether and how it grows and divides. A special section of the 27 Nov 2009 Science explored a variety of topics that contribute to our understanding of spatial cell biology. A Perspective described how position within the body affects a cell’s differentiation and functional characteristics and how cells use specific gene expression programs to encode location. Four Review articles focused on eukaryotic cells, discussing the central role of actin in cell shape and movement, how the intracellular localization of messenger RNAs leads to localized translation of their encoded proteins, the influence of the extracellular matrix and its constituent proteins on cell physiology, and cell signaling in space in time. The final Review in the section highlighted the intricate internal organization of bacteria, explaining that the dynamic subcellular localization of protein complexes is an integral feature of regulatory processes of these single-celled organisms. Amazing Maize Maize is one of the most important crop species worldwide. It is a vital source of food and fuel and a valuable model organism for genetic research. In the 20 November 2009 Science, Schnable et al. presented the genome sequence of the B73 maize line, 85% of which is composed of hundreds of families of transposable elements. The genome contains over 32,000 genes and shows that uneven gene losses were involved in returning an ancient allotetraploid maize genome (four sets of chromosomes) to a genetically diploid state. Vielle-Calzada et al. sequenced the genome of the Mexican popcorn variety Palomero Toluqueño, which, when compared to the B73 sequence reveals multiple loci impacted by domestication. Swanson-Wagner et al. analyzed gene expression patterns in maize hybrids and found that differential gene expression is driven primarily by the paternally inherited allele of trans-eQTL (DNA elements located on chromosomes that control the differential expression of genes located on other chromosomes). And Gore et al. presented a first-generation haplotype map of maize that provides a foundation for uniting breeding efforts across the world and for dissecting complex traits through genome-wide association studies. An accompanying Perspective by C. Feuillet and K. Eversole noted that "[y]ears of hard work by the maize community to accumulate resources, populations, phenotypic data, and agronomic knowledge can now be integrated with sequence information to accelerate crop improvement." 
IBEX and the HeliosphereThe Sun moves through the local interstellar medium, continuously emitting ionized, supersonic solar wind plasma and carving out a cavity in interstellar space called the heliosphere. Since early 2009, NASA's Interstellar Boundary Explorer (IBEX) has been building all-sky maps of the emissions of energetic neutral atoms produced at the boundary between the heliosphere and the interstellar medium. As described by McComas et al., Fuselier et al., Funsten et al., and Möbius et al. in the 13 Nov 2009 Science (all published online 15 Oct), these data provide new information about the interaction of the heliosphere with the local interstellar medium and about the interstellar environment itself (see the related News story by R.A. Kerr in the 16 Oct issue). The maps reveal a ribbon of unexpectedly intense emissions -- with energies ranging from 0.2 to 6 kiloelectron volts -- that covers a broad swath of sky. Emissions from the band are two- to threefold brighter than outside the band, in contrast to current models that predict much smaller variations across the sky. Schwadron et al. (published online 15 Oct) compared the IBEX observations with models of the heliosphere and determined that to date no model fully explains the observations. In a related Report, Krimigis et al. presented an all-sky image of energetic neutral atoms obtained with the Ion and Neutral Camera onboard the Cassini spacecraft orbiting Saturn. Taken together, the data indicate that the shape of the heliosphere is not consistent with that of a comet, as was previously thought. Compact but Complex The genome of Mycoplasma pneumoniae -- one of the causative agents of "walking pneumonia" -- is among the smallest found in self-replicating organisms. As such, it represents an excellent model organism in which to attempt a systems-level understanding of its biological organization. Three papers in the 27 Nov 2009 Science described comprehensive and quantitative analyses of the proteome, metabolic network, and transcriptome of M. pneumoniae that reveal levels of complexity and control previously assumed to be restricted to eukaryotes (see the Perspective by H. Ochman and R. Raghavan). Kühner et al. combined analysis of protein interactions by mass spectrometry with extensive structural information on M. pneumoniae proteins and single-particle electron microscopy to elucidate how proteins are organized within the cell and work together in some 200 molecular machines. Yus et al. integrated biochemical, structural, and computational information to reconstruct the metabolic network of M. pneumoniae. Compared to the metabolic pathways of bacteria with larger genomes, the M. pneumoniae network contains few branches and redundancies, but includes numerous enzymes that perform multiple functions. Finally, Güell et al. analyzed the expression patterns of the complete set of RNAs encoded in the M. pneumoniae genome and found that the bacterium makes extensive use of noncoding RNAs and has exon- and intron-like structure within transcriptional operons that allows complex gene regulation resembling that of eukaryotes. Measuring Greenland's Ice Loss Recent measurements of the rate of mass loss from the Greenland ice sheet vary approximately by a factor of three. Resolving these discrepancies is essential for determining the current mass balance of the ice sheet and for projecting future sea level rise. Now, in a Report in the 13 Nov 2009 Science, van den Broeke et al. present consistent estimates of the rates of mass loss produced by two fully independent methods -- one based on observations of ice movement combined with model calculations, and the other on remote gravity measurements made by the GRACE (Gravity Recovery and Climate Experiment) satellites. The team determined that between 2000 and 2008, the ice sheet has lost ~1500 gigatons of mass, equivalent to 0.46 millimeters per year of global sea level rise. Since 2006, however, high summer melt rates have increased Greenland ice sheet mass loss to 273 gigatons per year (0.75 millimeters per year of equivalent sea level rise). The combination of approaches also enabled the researchers to resolve the separate contributions of surface processes (runoff and precipitation) and of ice dynamics, the two major routes of ice mass loss.  Gene Therapy SuccessAfter years of setbacks and skepticism and neglect by the pharmaceutical industry, the promise of gene therapy in gaining some ground. In a Research Article in the 6 Nov 2009 Science, Cartier et al. reported the first successful use of gene therapy to treat X-linked adrenoleukodystrophy (ALD) -- a fatal hereditary brain disease -- in two young boys (see the ScienceNOW story by J. Kaiser). ALD is caused by a defect in the gene ABCD1, which encodes a transporter protein needed to break down certain fats; without the protein, the fats build up and damage the myelin sheathing that protects nerves. ALD is typically treated by a bone marrow transplant, but serious complications can result and sometimes no appropriate donors are available. In the new gene therapy-based approach, the researchers removed the blood cells from each boy and treated the cells with a so-called lentiviral vector, a modified HIV virus carrying the gene for a functional ALD protein. The treated cells where then infused back into the patients. Expression of the transferred gene was still detectable in the patient's blood cells two years later, and both patients showed neurological improvement and a delay in disease progression comparable to that seen with bone marrow transplants. An accompanying Perspective by L. Naldini noted that the study supports further testing of this therapeutic strategy in ALD and other genetic diseases and represents a long-sought rewarding achievement in the field of gene therapy. When Molecules Meet Surfaces Models and theories have become quite successful at predicting the outcomes of reactions between small molecules in the gas phase, but getting theoretical calculations to agree with experimental data from scattering molecules on metal surfaces -- which is of interest for understanding reactions in industrial catalysis -- has been more challenging. This is because the pathways of atomic motions during a chemical reaction on a metal surface do not follow the same rules that govern gas-phase (or liquid-phase) chemical reactions. In the 6 Nov 2009 Science, two Reports shed new light on the ways in which molecules interact with metal surfaces. Shenvi et al. applied a recently developed theoretical framework to examine how energy is dissipated as a molecule approaches a metal surface. They presented a comprehensive picture of how vibrations and rotations of nitric oxide molecules affect scattering from a gold surface that successfully accounts for recent experimental observations. Díaz et al. described a method to calculate the reactive scattering of molecular hydrogen on a copper surface that results in excellent agreement with extensive experimental results for that system at the level of individual quantum states. An accompanying Perspective by E. Hasselbrink highlighted the studies.  Megafaunal DeclineOne of the most dramatic environmental changes in recent Earth history was the disappearance of very big animals -- mammoths, mastodons, moa, and hundreds of others -- from most of the land area of the globe by about 10,000 years ago. What caused these extinctions and how did they affect the world's ecosystems? A Report in the 20 Nov 2009 Science shed new light on these questions. Gill et al. analyzed pollen, charcoal, and Sporormiella fungus -- which produces spores in the dung of large herbivorous vertebrates -- from the sediments of Appleman Lake, Indiana and several New York sites. Because the spores accumulate in sediments along with pollen and charcoal, changes in biomass of large herbivores can be matched to sediment records of vegetation and fire, which can in turn be dated and aligned with other archaeological and environmental records. The researchers found that megafaunal decline began ~14,800 years ago and took more than a thousand years, and that this decline preceded both the formation of late-glacial plant communities and an increase in wildfires. All this happened long before a proposed extraterrestrial impact, thus ruling out vegetation change, fire, and cosmic disaster as primary causes of megafaunal extinction. An accompanying Perspective by C. Johnson highlighted the study, and considered the role that early human communities may have had in the demise of the megafauna and the ecological changes that followed. Visualizing Calcite Crystallization For single crystals to remain intact, there is typically a limit to the size and number of defects that can be included before the underlying lattice is destroyed. Biological crystals, however, such as the calcite crystals that make up sea urchin spines or the prismatic layer if mollusk shells, incorporate macromolecules such as proteins and polysaccharides that enhance the mechanical properties of these structures. In a Report in the 27 Nov 2009 Science, Li et al. sought to better understand how large molecules can be distributed in a crystal without substantially disrupting the crystalline lattice. The team used electron tomography to study the crystallization of calcite (calcium carbonate) in an agarose gel and found that the crystals physically entrapped the agarose macromolecules. Random, three-dimensional networks of agarose nanofibers were incorporated into calcite crystals by allowing both high- and low-energy fiber/crystal interface facets to accommodate the curvatures of the agarose polymer chains. The results suggest that physical interactions alone may be sufficient for the incorporation of macromolecules inside inorganic single crystals (as opposed to specific chemical interaction between the organic component and the growing crystal). An accompanying Perspective by M. D. Hollingsworth highlighted the Report.  Pollination Before Flowering Plants
The rise of angiosperms (flowering plants) in the Early Cretaceous (~140 million years ago) was accompanied by coevolution of a variety of insects, including flies, bees, and wasps required for pollination. In the 6 Nov 2009 Science, Ren et al. made a case for insect pollination as early as the Middle Jurassic (~170 million years ago), before flowering plants even evolved. Based on comparative morphology of fossil insect mouthparts as well as elemental analysis of the fossils and their surrounding matrix, the team reported that three families of scorpionflies had long, tubular mouth parts that enabled them to feed on a nectarlike fluid produced by a group of now-extinct non-angiosperm seed plants. Although the team found no pollen associated with the fossils, the diversity and specialization of the insects and related plant structures suggest that they engaged in pollination mutualisms. All three scorpionfly families became extinct during the later Early Cretaceous, as angiosperms began to dominate. An accompanying Perspective by J. Ollerton and E. Coulthard noted that the findings may represent the earliest known example of coevolution between plants and pollinators and, if correct, "will change our understanding of the early ecology and evolution of pollination by insects." Worm Survival Strategies From bacteria to vertebrates, organisms can respond to changing environmental conditions by arresting their development. Studies in the nematode worm Caenorhabditis elegans are beginning to show not only the diversity of strategies used, but also the molecular mechanisms mediating them. Two studies in the 13 Nov Science revealed how members of two multigene families -- nuclear hormone receptors and G protein–coupled receptors -- perceive and translate environmental cues to regulate diapause stages (reversible states of dormancy) in C. elegans. Developing worms secrete a complex mixture of chemicals, collectively termed dauer pheromone, the concentration of which determines whether the worm will proceed through the reproductive cycle or enter into a developmentally arrested dauer phase. Kim et al. (published online 1 Oct) found that subsets of dauer pheromone components act via distinct G protein–coupled receptors either to initiate long-term effects on development and physiology by modulating the neuroendocrine axis, or to trigger short-term acute effects on behavior by altering neuronal responses. Angelo and Van Gilst (published online 27 Aug) showed that in starved worms, the germline component of the reproductive system is actively killed, with the exception of a small set of preserved stem cells. When the worms are able to feed again, these cells regenerate into an entirely new and functional germline. The nuclear receptor NHR-49 is required for entry and recovery from this starvation-induced diapause. A related Perspective by A. Ogawa and R.J. Sommer noted that "[t]hese two studies further establish nematodes as a unique model for studying animal survival strategies and the environmental regulation of life histories." Protecting Chromosome Ends The ends of eukaryotic chromosomes have the potential to be mistaken for damaged or broken DNA and must therefore be protected from cellular DNA damage response pathways. In the 13 Nov 2009 Science, a special Viewpoint article by T. de Lange discussed how protein-DNA complexes called telomeres -- featured in the 2009 Nobel prize for physiology or medicine -- solve this so-called end-protection problem. In mammals, a six-subunit protein complex called shelterin binds with high selectivity to telomeric DNA. Different components of this complex stabilize the chromosome ends and avoid cell death. The damage response pathways in some unicellular eukaryotes, such as yeast, differ from those in mammals and their telomeres are tailored to respond to these differences. An interactive figure illustrated how telomeres address the unique problem facing the ends of linear chromosomes, and Science senior editor G. Riddihough discussed the details with de Lange in an accompanying audio interview.
Sponsored by:
CTSciNet, Science Careers in Translation
Build new scientific relationships and explore the best way to conduct a clinical and translational science career at CTSciNet, the new online community from Science, Science Careers, and AAAS made possible from the Burroughs Welcome Fund.
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