Plant Genomes
Special Online Collection

Plants play an integral role in human life and in the environment: In addition to providing food and oxygen, plants mitigate the impacts of greenhouse gases, enrich soils that nurture other living things, and provide valuable fuels, fibers, and medicines. In a special section of the 25 April 2008 issue, Science explored how current knowledge of plant genomes is lending insights to investigations from plant biochemistry to ecosystems. Perspectives discussed a range of topics including plant genome structure and organization, the effects of natural variation on phenotype, and plant metabolism, while articles in the News section highlighted some of the successes and challenges facing genetically modified plants. On Science Online, an interactive presentation featuring video commentary, informational graphics, and an animation highlighted how plant genome research is contributing to our understanding of plant biology and evolution and leading to tangible benefits for society. Science Careers looked and the breadth of research experiences and career opportunities afforded by plant genomics, and News writer E. Youngsteadt spoke with several scientists at the recent 50th Annual Maize Genetics Conference in a related podcast segment.


Antibiotic-Consuming Bacteria

Although antibiotics remain a crucial line of defense against bacterial infections, the spread of multiple-antibiotic resistance in human pathogens has been alarming. New results reported in the 4 Apr 2008 Science add to concerns about the dwindling power of our main weapons against infection. In a survey of soil microbes isolated from 11 diverse sites, Dantas et al. discovered hundreds of bacteria that were able to subsist on 18 different antibiotics -- including natural and synthetic compounds -- as their sole carbon source. Phylogenetic profiling of these bacteria revealed species from several different phyla, including many that are closely related to human pathogens. Furthermore, each antibiotic-consuming isolate was resistant to multiple antibiotics at clinically relevant concentrations. The phenomenon suggests that this previously unrecognized source of antibiotic-consuming bacteria represents a potential reservoir of antibiotic resistance genes for pathogenic bacteria. An News story by M. Leslie and a podcast interview with senior author Dr. George Church highlighted the findings.


Cooperative Neuron Guidance

Coordinating motor and sensory pathways in the nervous system ensures efficient execution of bodily movements. Motor neurons in the spinal cord extend axons that drive peripheral muscle contraction, while sensory neurons send feedback to motor neurons about muscle position, touch, and pain. How do these pathways remain coordinated but not entangled? In a Report in the 11 Apr 2008 Science, Gallarda et al. explained that cell contact-dependent communication between adjacent motor and sensory neurons prevents miswiring of developing neural circuits. The team showed that in mice, axons carrying signals from spinal cord to muscle are kept separate from those going in the opposite direction by ephrin/Eph receptor signaling. In general, these protein families guide axons to their targets by enabling growth cones to communicate with surrounding cells. The researchers found that ephrin signaling controls the repulsion of motor neurons from neighboring sensory neurons and that this repulsive signaling not only inhibits the intermingling of sensory and motor axons, but also blocks motor axons from projecting in the wrong direction and infiltrating sensory pathways. An accompanying Perspective by K. K. Murai and E. B. Pasquale noted that findings such as these "will continue to guide our understanding of developing and remodeling events that control neural circuit assembly and function."


Tracking Seasonal Influenza

Influenza viruses infect 5 to 15% of the global population on average, resulting in ~500,000 deaths annually. Despite substantial progress in many areas of influenza research, questions such as when and to what extent the virus will evolve and spread remain unanswered. In a Research Article in the 18 Apr 2008 Science, Russell et al. used antigenic and genetic analyses of hemagglutinin (a viral surface protein targeted by the immune system) as a marker to investigate the global evolution and epidemiology of influenza A (H3N2) viruses from 2002 to 2007. Their analysis shows that influenza epidemics were seeded each year by viruses that originated in East and Southeast Asia. Moreover, the researchers found evidence that temporally overlapping epidemics in the region create a circulation network in which the viruses continually circulate by passing from epidemic to epidemic. Travel and trade connections explain the global dissemination of influenza strains on a one-way route out of Asia, taking about 6 to 9 months to reach Europe and North America. Several months later, these strains arrive at their evolutionary graveyard in South America. The results suggest that the antigenic characteristics of currently circulating viruses in east and Southeast Asia may be useful for forecasting global vaccine needs. A related News story by M. Enserink profiled senior author of the study Derek Smith, and Smith, along with first author Colin Russell, discussed the work in a podcast segment.


Phosphatidylserine Insights

Lipids are increasingly recognized as essential for cells to transduce signals. The membrane lipid phosphatidylserine (PS), for example, is important for initiating blood coagulation and for the clearance of dead cell remnants (apoptotic bodies). Two Reports in the 25 Apr 2008 Science provided further insights into the biology of phosphatidylserine. Darland-Ransom identified an enzyme in Caenorhabditis elegans, aminophospholipid translocase 1 (TAT-1), which appears to restrict PS to the inner side of the plasma membrane in normal cells. Without this enzyme, PS is abnormally exposed on the cell surface, a situation that leads otherwise healthy cells to be randomly engulfed by neighboring phagocytes via a process dependent on a PS receptor. Meanwhile, Mercer and Helenius revealed a role of phosphatidylserine in viral infection. Using live-cell imaging of a vaccinia virus infecting cultured cells, the team found that exposed PS in the viral membrane is required for viral entry. In the late stage of vaccinia virus infection, a host cell undergoes apoptosis and externalizes PS in its plasma membrane. A virus budding from this cell thereby acquires a membrane envelope that exposes PS on its outer surface, thus stimulating noninfected cells to uptake the virus in a process similar to the engulfment of apoptotic cell debris. An accompanying Perspective by G. D. Fairn and S. Grinstein highlighted the studies.


Mercury on the Move

Mercury is a persistent contaminant in river ecosystems worldwide and can cause mortality, reproductive failure, and other health effects in predatory wildlife and humans. According to a Brevium in the 18 Apr 2008 Science, aquatic mercury can also affect animals in adjacent terrestrial habitats. Scientists have long focused on bioaccumulation of mercury in aquatic birds, but in the new study, Cristol et al. document contamination of birds and insects in the woods around a mercury-contaminated river. Specifically, the team found potentially harmful mercury levels in the blood and feathers of 12 terrestrial bird species that live near the Shenandoah River in the eastern United States, which has been tainted by industrial mercury. Diet analysis revealed that insects and arachnids -- particularly predatory spiders -- delivered much of the dietary mercury to these birds. In a related podcast interview, Dr. Cristol noted that the next steps will be to determine the mechanism(s) by which the spiders are accumulating mercury and to examine how widespread the movement of aquatic mercury into terrestrial food webs is.


Breaking the Clovis Barrier

A decade ago, most archaeologists believed that the first people in America were the so-called Clovis people, who left distinctive stone tools across the United States and Central America beginning about 13,000 years ago. But evidence for an earlier peopling of the Americas has been steadily growing. In a Report published online in Science Express on 3 Apr 2008, Gilbert et al. reported the identification of ancient DNA from fossilized human feces (coprolites) from an Oregon cave that predates the Clovis culture by about 1000 years (see the related News story by M. Balter in the 4 Apr issue). Using accelerator mass spectrometry, the team dated the coprolites to about 14,000 years ago. In addition, mitochondrial DNA (mtDNA) with genetic signatures typical of Native Americans -- and not shared by any other population groups -- was extracted from six of the 14 coprolites that were examined. Based on analyses of mtDNA isolated from the excavation team members as well as researchers back in the lab, the researchers believe that modern contamination is unlikely to explain their findings. The team also performed experiments to exclude the possibility that they had sampled DNA that had leached from younger to older stratigraphic layers in the cave. Senior author Dr. Eske Willerslev discussed the work in a podcast interview.


Ocean Acid Test

One of the worrying consequences of increasing atmospheric carbon dioxide is ocean acidification. As the oceans absorb carbon dioxide, the pH will drop, making it more difficult for calcifying organisms such as corals to produce and maintain their skeletons. Now, in a study in the 18 Apr 2008 Science, Iglesias-Rodriguez et al. report that the response of calcifying organisms to ocean acidification may be much more complex than previously thought. The team presented laboratory evidence that, contrary to expectation, high atmospheric carbon dioxide levels actually increase calcification and net primary production in the coccolithophore species Emiliania huxleyi (a type of marine phytoplankton). These results appear to be consistent with evidence from the deep ocean, which indicate that there has been a 40% increase in average coccolith mass over the past 220 years (see the ScienceNOW story by P. Berardelli). As noted in an accompanying Perspective by V. J. Fabry, published online 17 Apr, differential responses of marine calcifiers to elevated carbon dioxide levels could result in "competitive advantages that could drive the reorganization of many planktonic and benthic ecosystems, which in turn could have significant ecological and biogeochemical implications."


Racetrack Memory

Today, there are two main means of storing digital information: solid-state random access memories, which are fast but expensive, and hard disk drives, which are cheap but slow. Recent developments in the controlled movement of domain walls (interfaces between regions of different magnetization direction) in magnetic nanowires, by short pulses of spin-polarized current, hold promise for a new type of memory device with the high performance and reliability of conventional solid-state memory at the low cost of hard disk storage. In a Review in the 11 Apr 2008 Science, Parkin et al. explained the basic concept of these so-called "racetrack memory" systems, in which bits of information consist of magnetized "domains" pushed along metal nanowires by flowing electrons. Researchers read the data bits by measuring the wire's resistance, which is affected by the "walls" between oppositely magnetized domains. Theoretically, arrays of racetracks can be built on a chip to enable high-density data storage. In a related Report, Hayashi et al. provided proof of the racetrack memory concept, showing that it is possible to shift multiple domain walls to and fro along a magnetic wire repeatedly at high speed using nanosecond current pulses without any external magnetic fields. As noted in an accompanying News story by A. Cho only time will tell whether racetrack memory will emerge as a commercially viable technology.


Synchronizing Rock Clocks

Precise measurement of geological time is a prerequisite for understanding Earth's history. Numerical calibration of the geological time scale is currently based on independent radioisotopic (argon-argon) dating and astronomical dating of cyclic sedimentary layers that reflect precisely timed variations in Earth's orbit. However, these techniques yield discrepancies of ~1.0%, or 1 million years in a 100-million-year-old age, with the astronomical method providing more precise ages for the younger part of the time scale, and the argon method providing better dates for older intervals. As reported in the 25 April 2008 Science, Kuiper et al. have now improved the accuracy of the calibration by an order of magnitude. The researchers compared astronomical and argon-argon ages of layered marine deposits in Morocco to calibrate the age of Colorado's Fish Canyon Tuff, which is the most widely used standard in argon-argon geochronology. By their recalibration, the Fish Canyon standard is 0.65% older than previously thought. The researchers also recalculated some key dates in geologic history and push back the Cretaceous/Tertiary boundary and the accompanying mass extinction from 65.5 million years ago to about 66 million years ago. A News story by R. A. Kerr highlighted the study.


Graphite Whiskers in Meteorites

Meteorites retain a record of the earliest period of our solar system's history, before the planets were born. As such, they hold clues to the variety of local stellar sources that contributed to our protoplanetary disk and the physical and chemical processes that occurred within it. In a Report in the 4 Apr 2008 Science, Fries and Steele (published online 28 Feb) reported the discovery of needle-like carbon structures called graphite whiskers in grains of several primitive meteorites. These whiskers have been postulated to be responsible for affecting the brightness of type 1a supernovae (used as a distance measure in astronomy) and the cosmic microwave background. The researchers identified the whiskers using Raman imaging and electron microscopy and suggest that they likely condensed from the early hot solar nebula and may be present in other stellar systems. As noted in an accompanying Perspective by P. A. Bland, the next step will be to extend the search to the most primitive meteorites, cosmic dust, and cometary samples to identify whiskers that exhibit isotopic signatures characteristic of formation in the atmosphere of stars other than the Sun.



--------------
In Science Signaling

SRC-3 in the Balance

Overexpression of nuclear receptor coactivators is a frequent event in breast cancer cells, and is key to their proliferation. Foremost among these coactivators is SRC-3, which becomes overexpressed in more than 50% of breast cancers. Because of its oncogenic potential, normal cells must carefully control its cellular concentration. In a Perspective in the 1 Apr 2008 issue, D. M. Lonard and B. W. O'Malley proposed a model for how cellular concentration of SRC-3 influences the estrogen-regulated growth of normal and cancerous breast cells. In normal cells, a limiting concentration of SRC-3 leads to competition among transcription factors for SRC-3 binding, and incomplete interaction with estrogen receptor (ER) bound to the promoters of estrogen-regulated genes, thus leading to lower level activation of these growth-promoting genes. In breast cancer cells, overexpression of SRC-3 leads to saturation of the coactivator at the promoters growth related genes and supports a maximum rate of replication for these cancer cells. Transcription-coupled degradation of SRC-3 may function as a safety mechanism to curtail the activity of this potentially dangerous oncogene.

Also in Science Signaling this month:
-- E. Canalis highlighted recent evidence establishing a role for Notch signaling in bone remodeling (29 Apr 2008)
-- M. Lackmann and A. W. Boyd looked at developments in our understanding of Eph receptors, which are involved in guiding organ development and patterning of the vascular, skeletal, and nervous systems (15 Apr 2008)
-- Liu et al. discussed the role of calpains -- a family of cystein proteases -- in synaptic function, memory formation, and neurotoxicity (8 Apr 2008).