Science Roundup

This month in Science Roundup:
Sponsor: Cold Spring Harbor Laboratory Press Publications
AAAS members can now receive a special 15% discount on eight exceptional books for lab scientists and educators from Cold Spring Harbor Laboratory Press Publications. Go to http://www.cshlpress.com/affiliates/aaas.htm . Click on "Enter CSHL Store" and browse "Special Offers for Affiliates."


Building the Body From Genes
http://www.sciencemag.org/sciext/genomicevolution/

Through comparative genomics, scientists are learning about the forces that have promoted diversity or imposed constraints on our biological machinery. In a special section of the 29 Sep 2006 issue, Science offered insights in the genetic infrastructure needed to build our bodies. News and Review articles discussed genes that have helped differentiate our brain from those of our primate cousins, the complex evolution of eyes and the gene family that underlies much of life’s morphological diversity, and the gene regulatory networks involved in heart development. And three Perspectives in the Signal Transduction Knowledge Environment (STKE) looked at complex regulatory networks that allow genes to specify cell fate, tissue formation, and organ development. In addition to illuminating human physiology and giving us a view of our evolutionary history, comparative genomics has inspired new approaches to diagnosing and treating diseases. A collection of articles on ScienceCareers.org highlighted new career opportunities in human genetics and health fields that have opened up as an outgrowth of these insights and recent technological advances. Several stories from the issue were featured on the 29 Sep Science Podcast ( http://www.sciencemag.org/about/podcast.dtl#20060929 ).


Ribozyme Insights

Catalytic RNAs, or ribozymes, are sometimes viewed as descendents of an early, perhaps pre-protein era of life because they are made of genetic material but also possess enzyme-like properties. Two studies reported in the 22 Sep 2006 Science expand our knowledge of the evolution and mechanism of action of so-called self-cleaving ribozymes ( see the related Perspective by M. D. Been; http://www.sciencemag.org/cgi/content/short/313/5794/1745 ).

--Few self-cleaving ribozymes have been detected in humans, and mammals in general, leading to speculation that they have been lost over evolution. Now Salehi-Ashtiani et al. ( http://www.sciencemag.org/cgi/content/short/313/5794/1788 ) report the discovery of four self-cleaving ribozyme sequences in the human genome, one of which shares biochemical and structural properties with ribozymes in hepatitis delta virus -- a human pathogen. Genomic analysis revealed that this particular ribozyme is present in all mammals, but not in other vertebrates, which suggests that it may have evolved as recently as 200 million years ago.

--Klein and Ferré-D’Amaré ( http://www.sciencemag.org/cgi/content/short/313/5794/1752 ) described the crystal structures of the bacterial self-cleaving ribozyme glmS , which regulates the synthesis of glucosamine-6-phosphate (GlcN6P) -- a key metabolic precursor of bacterial cell walls. Interestingly, the ribozyme requires binding of this metabolite to activate self-cleavage. The new structures capture the ribozyme in the precleavage state, bound and unbound to a GlcN6P, and in the postcleavage state. Unlike other riboswitches, where metabolite binding regulates activity by inducing a conformational change, the conformation of glmS is similar in all three states. Instead, GlcN6P appears to participate in catalysis by binding to a preformed site.


Aromatic Communication

The aromas emitted by plants serve to attract insect pollinators and can convey complex information regarding plant location, identity, and physical condition. Some studies have suggested that these volatile compounds also enable plants to communicate with each other, but this notion has been hotly debated. Now, a Report by Runyon et al. ( http://www.sciencemag.org/cgi/content/short/313/5795/1964 ) in the 29 Sep 2006 Science shows that a parasitic weed called dodder -- which can only survive by attaching to the stems or leaves of other plants and sapping their nutrients -- can respond to volatile emissions from other plants and effectively sniff out an appropriate host. The team showed that dodder seedlings exhibit direct growth toward host tomato plants rather than artificial plants; and toward a vial of extracted tomato-plant volatiles rather than a vial of only solvent. Moreover, the team found that seedlings could distinguish between tomato and wheat volatiles; one compound from wheat seems to be a repellant, which may explain why the weed preferentially grew toward aromas. The results offer compelling evidence that chemical cues can indeed mediate important ecological interactions among plant species, and were highlighted in an accompanying News story by E. Pennisi ( http://www.sciencemag.org/cgi/content/short/313/5795/1867a ).


In Search of Cancer Genes

Scientists have long known that the sparks that kindle cancer are mutations in a cell’s genes, and the elucidation of the human genome sequence has made it possible to identify these genetic alterations in unprecedented detail. In a Research Article published online on Science Express on 7 Sep 2006, Sjoblom et al. ( http://www.sciencemag.org/cgi/content/abstract/1133427 ) described their systematic analysis of the so-called cancer genomes of two common tumor types, breast and colorectal cancers, which together account for ~940,000 cancer deaths each year (14% of the total). Examination of more than 13,000 genes in 11 breast and 11 colon cancer samples uncovered a much larger and richer set of cancer genes than expected. The team found that the average tumor has about 90 mutated genes, about 11 of which are thought to be cancer-promoting. They identified a total of 189 "candidate" cancer genes, some of which are known offenders, but many of which have not been linked to cancer before and are predicted to affect a wide range of cellular functions, including transcription and cellular adhesion. The genetic landscape of these cancers turned even more complex when the researchers discovered that the panel of cancer genes differed between colon and breast cancers, and that individual tumors derived from the same tissue type show different patterns of mutations. An accompanying News story by J. Kaiser in the 8 Sept issue highlighted the study ( http://www.sciencemag.org/cgi/content/short/313/5792/1370 ).


Social Experience and Sleep

Sleep is crucial for survival across the animal kingdom, but its function remains a mystery. Studies in humans, rats, and other animals have suggested that sleep plays a role in learning and memory, but no direct molecular link has been demonstrated…until now. In a study reported in the 22 Sep 2006 Science , Ganguly-Fitzgerald et al. ( http://www.sciencemag.org/cgi/content/short/313/5794/1775 ) took advantage of the behavioral and physiological similarities between fruit fly and mammalian sleep to investigate the molecular connection between experience, sleep, and memory. The team first compared the sleep habits of flies housed in groups of 30 or more to those of flies kept in isolation and found that the socialized flies slept significantly more during the day than their isolated counterparts. The researchers theorized that the extra stimulation of social interactions necessitated extra "down time" to process. Indeed, they found that socialized flies that couldn’t see or smell -- and therefore received less sensory input than they would otherwise -- didn’t need any more sleep than the isolated flies. Further experiments revealed that experience-dependent changes in sleep need required dopamine and cyclic adenosine monophosphate (cAMP) signaling pathways, which are involved in learning and memory, and subset of 17 long-term memory genes. A Science NOW story by G. Vogel ( http://sciencenow.sciencemag.org/cgi/content/full/2006/921/4 ) published on 21 Sep highlighted the study.


Race, Stereotypes, and Achievement

U.S. schools have long struggled with a racial achievement gap -- a pattern of race-related disparity in student performance. Teaching quality and the availability of education opportunities may in part account for this disparity, but social-psychological factors also play a role. For example, the risk of confirming a negative stereotype aimed at one’s group can undermine academic performance in minority students by elevating their level of psychological threat. Now, in a Report in the 1 Sep 2006 Science , Cohen et al. ( http://www.sciencemag.org/cgi/content/short/313/5791/1307 ) show that reducing stereotype threat by way a brief intervention in a classroom setting, can have a positive, long-lasting effect on the achievement of minority students. At the beginning of the school year, African American and European American seventh graders in a suburban middle school were given a "self-affirmation" exercise in which they were asked to spend 15 minutes writing about why certain values, such as creativity or personal relationships, were most important to them. Students in a control group were asked to write about values that were not important to them. Subsequent analysis of end-of the-semester grades revealed that the self-affirmation assignment significantly improved the grades of African American students and reduced the racial achievement gap by 40%. The authors suggest that the exercise was effective in part because it interrupted the negative cycle in which stereotype threat and poor performance feed off one another. An accompanying Perspective by T. D. Wilson ( http://www.sciencemag.org/cgi/content/short/313/5791/1251 ), and a segment of the 1 September podcast ( http://www.sciencemag.org/about/podcast.dtl#20060901 ) highlighted the findings.


Genome Firsts

This month in Science , researchers reported the genome sequences of two widely destructive plant pathogens and a common North American tree. The sequences reveal important insights into the evolution and survival of these organisms.

--Tyler et al. ( 1 Sep 2006; http://www.sciencemag.org/cgi/content/short/313/5791/1261 ) described the first two genome sequences of the genus Phytophthora -- a group distantly related to diatoms and kelp that includes the pathogens behind root rot in soybeans, sudden oak death, and potato blight. The genomes each contain some 350 infection-associated genes, whose striking diversity suggests that the pathogens and their host plants are locked in a coevolutionary battle for survival. Sequence analysis also revealed the signature of a photosynthetic ancestor. An accompanying News story by E. Stokstad ( http://www.sciencemag.org/cgi/content/short/313/5791/1217a ) highlighted the Research Article.

--Tuskan et al. ( 15 Sep 2006 ; http://www.sciencemag.org/cgi/content/short/313/5793/1596 ) presented the draft genome of the black cottonwood, Populus trichocarpa , the first tree to be sequenced (see the related News story by E. Stokstad; http://www.sciencemag.org/cgi/content/short/313/5793/1556a ). The tree has undergone two whole-genome duplication events, one of which occurred at the same time as in Arabidopsis , an annual flowering plant. The Populus genome appears to have evolved more slowly than Arabidopsis , with reduced rates of nucleotide substitution, tandem gene duplication, and chromosomal rearrangement, but has an expanded repertoire of genes for traits important for trees including disease resistance, root and shoot development, metabolite transport and cell wall biosynthesis. Dr. Tuskan talked about the work in a segment of the 15 Sep Science podcast ( http://www.sciencemag.org/about/podcast.dtl#20060915 ).


Alien Earths

Previous hypotheses of planetary formation have suggested that few solar systems elsewhere in the galactic neighborhood contain water-rich, Earth-like worlds. Part of the explanation for this involves so-called "hot Jupiters" -- giant gas planets that orbit closer to their parent stars than Mercury does to the sun. Because these planets are believed to form in the cold, outer regions of protoplanetary disks, astronomers have assumed that the turbulent inward migration of hot Jupiters would disrupt any other planets in that system and/or vacuum up or eject out much of the dust and rock that might otherwise come together to form terrestrial planets. But results of new simulations reported in the 8 Sep 2006 Science now suggest that more than a third of the known giant planet systems outside our solar system may harbor Earth-like planets. Raymond et al. ( http://www.sciencemag.org/cgi/content/short/313/5792/1413 ) simulated the growth, over about 200 millions years, of terrestrial planets in systems where a gas giant migrates inward. The researchers found that Earth-mass planets can still form interior to the migrating giants, and that outside the giant planet’s orbit, rocky debris flung into the habitable zone -- where liquid water can exist on a planet’s surface -- can also coalesce to form very water-rich earth-mass planets. A Science NOW story by P. Berardelli ( http://sciencenow.sciencemag.org/cgi/content/full/2006/908/1 ) highlighted the Report.


Oldest New World Writing

The Olmec civilization flourished along the Gulf Coast of Mexico about 1200 to 400 years before the common era (BCE), and may have laid the foundation for the complex societies of the Maya and Aztec. Researchers have unearthed evidence of a rich Olmec culture including jewelry, pottery, and colossal stone head statues, but unambiguous evidence of an early Olmec writing system has been lacking. Now, in a Research Article in the 15 Sep 2006 Science , Rodríguez Martínez et al. ( http://www.sciencemag.org/cgi/content/short/313/5793/1610 ) report the discovery of a stone block from a rock quarry in Veracruz , Mexico -- a center of the Olmec civilization -- inscribed with a series of unknown symbols. The block has been dated to early in the first millennium CE, making it the oldest evidence of writing in the New World . Although still undeciphered, the glyphs in the blocks 62-sign inscription bear similarity to other Olmec imagery. They also have a distinct orientation, are sometimes repeated, and form a pattern of linear sequences of variable length that is consistent with a system of writing. An accompanying News story by A. Lawler ( http://www.sciencemag.org/cgi/content/short/313/5793/1551 ) highlighted the exciting find, and Dr. Stephen Houston, a co-author on the study, offered additional historical context to the discovery in a segment of the 15 Sep podcast ( http://www.sciencemag.org/about/podcast.dtl#20060915 ).


Krill Cause a Stir

Turbulence near the surface of the ocean helps transport nutrients to deeper waters and exchange gases with the atmosphere. Physical factors such as wind and tides are assumed to drive this ocean mixing, but a new study in the 22 Sep 2006 Science suggests that marine life may also play a significant role. Kunze et al. ( http://www.sciencemag.org/cgi/content/short/313/5794/1768 ) report that krill -- small shrimp-like crustaceans upon which baleen whales are notably famed to feed -- can increase near-surface mixing by several orders of magnitude. Prompted by theoretical claims that living creatures can cause substantial ocean turbulence on a global scale, the team investigated "biomixing" around the Sannich Inlet on the coast of British Columbia , Canada , where turbulence is typically as low as in the deep, open ocean. The inlet is home to a dense population of krill, which typically hide from predators at a depth of 100 meters during the day, but rise to the surface to feed by night. The researchers lowered an instrument suite into the path of the migrating krill and found that turbulence shot up three to four orders of magnitude for 10 to 15 minutes as the krill passed. An accompanying News story by R. A. Kerr ( http://www.sciencemag.org/cgi/content/short/313/5794/1717a ) highlighted the results and other evidence supporting the notion that marine creatures may be an important source of mixing in the upper ocean.


Dating the Hawaiian-Emperor Bend

The Hawaiian Islands sit within a long chain of seamounts that comprises more than 120 volcanoes and stretches for more than 6000 kilometers across the Pacific Ocean . The islands and seamounts in this so-called Hawaiian-Emperor chain get progressively younger from north to south, and this age progression has been attributed to the relative motion of the Pacific plate over a southward drifting "hot spot" deep in the mantle. However, one of the chain’s most distinctive features -- a sharp bend that occurs about 3500 kilometers west of Kilauea -- has been difficult to explain, because its previously accepted age of 43 million years does not correspond to a known shift in the motion of the Pacific plate. In a Report in the 1 Sep 2006 Science , Sharp and Clague ( http://www.sciencemag.org/cgi/content/short/313/5791/1281 ) presented a new timeline for the formation of the Hawaiian-Emperor chain based on argon isotope ages of eight of the chain’s volcanoes. The results imply that the Pacific plate changed speed and direction several millions years earlier than had been thought, and that the bend started forming ~50 million years ago and took more than 8 million years to complete. As noted in an accompanying Perspective by J. M. Stock ( http://www.sciencemag.org/cgi/content/short/313/5791/1250 ), the new ages "help to clarify the connections among mantle dynamics, Pacific plate motion, and major reorganizations of plate boundaries in the western Pacific Ocean ."


Ethane Clouds on Titan

Like Earth’s atmosphere, the atmosphere of Titan -- Saturn’s largest moon -- consists mostly of nitrogen. But its second most abundant constituent is methane, not oxygen. Because solar ultraviolet light breaks down methane, and ethane is the largest byproduct of this breakdown, scientists theorized that Titan’s surface would be covered in seas of liquid ethane. But they were puzzled to find that the moon’s surface is instead mostly covered by moist dunes. Now, in a study in the 15 Sep 2006 Science , Griffith et al. ( http://www.sciencemag.org/cgi/content/short/313/5793/1620 ) explain that a vast cloud hovering near Titan’s north pole may contain much of the mysterious missing ethane. The Cassini spacecraft’s Visual and Infrared Mapping Spectrometer detected the cloud at altitudes of 30 to 50 kilometers, at the edge of Titan’s arctic circle. The cloud’s spectral properties indicate that it is composed of ethane and forms by condensation as cold air downwells near the winter pole. Although most of the northern polar region is hidden in winter’s shadow, the researchers surmise that if it is cold enough, ethane snow may be falling and perhaps contributing to polar ethane ice caps. As noted in an accompanying Perspective by F. M. Flasar ( http://www.sciencemag.org/cgi/content/short/313/5793/1582 ) the discovery of ethane clouds on Titan offers new insight into complex planetary atmospheres.


Imaging Membrane Lipids

Cell membranes consist of a fluid mix 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. Fluorescence and electron microscopy have been used to view membrane structures and movements and the molecular level, but the spatial organization of membranes has been more difficult to resolve. In a Report in the 29 Sep 2006 Science , Kraft et al. ( http://www.sciencemag.org/cgi/content/short/313/5795/1948 ) described a new method for determining a membrane’s chemical composition with a resolution of less than 100 nanometers. The technique involves nanoscale secondary ion mass spectrometry (NanoSIMS), in which a tightly focused beam of cesium ions locally vaporizes a membrane sample into secondary molecular and atomic ions that can be identified using a conventional high-resolution mass spectrometer. By selectively incorporating a distinctive stable isotope into each of two lipids in a membrane, the team was able to image and quantify the lipid composition within small specified regions of the bilayer with a spatial resolution of 70 to 100 nm. As noted in an accompanying Perspective by J. T. Groves ( http://www.sciencemag.org/cgi/content/short/313/5795/1901 ) "[t]his observation sits squarely in the current blind spot with respect to biomembrane structure imaging."


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In Science’s STKE


p53 and Tumor Angiogenesis

The tumor suppressor protein, p53, transcriptionally activates genes that control cell cycle arrest, apoptosis, and other cellular processes that help to prevent tumor development. In a Perspective published 26 Sep 2006 in Science ’s Signal Transduction Knowledge Environment (STKE), J. Folkman ( http://stke.sciencemag.org/cgi/content/abstract/sigtrans;2006/354/pe35 ) highlighted recent work showing that that p53 appears to keep tumors in check by activating the gene encoding alpha(II) collagen prolyl-4-hydroxylase ( see Report by Teodoro et al. in the 18 Aug issue of Science ; http://www.sciencemag.org/cgi/content/abstract/313/5789/968 ) . This enzyme is required for the extracellular release of the collagen-derived peptides endostatin and tumstatin, which are potent inhibitors of tumor angiogenesis. As Folkman discusses, these findings " make it clear that p53 guards the genome from cancer, not only by suppressing abnormal cell proliferation, but also by preventing continuous expansion of tumor mass through suppression of angiogenesis."


Also in STKE this month:

--Karlova and de Vries discussed advances in our understanding of brassinosteroids -- plant signaling molecules that are involved in a variety of processes, including stem elongation, leaf development, stress resistance ( 26 Sep 2006; http://stke.sciencemag.org/cgi/content/abstract/2006/354/pe36 )
--Harbeck et al. presented a real-time imaging method that allows investigation of the interactions between Ca 2+ and cAMP signaling ( 19 Sep 2006 ; http://stke.sciencemag.org/cgi/content/abstract/sigtrans;2006/353/pl6 )
--Iisma et al. highlighted the mechanisms by which enzymes called transglutaminases regulate G protein-coupled receptors (19 Sep 2006; http://stke.sciencemag.org/cgi/content/abstract/sigtrans;2006/353/pe34 )


Sponsor: Cold Spring Harbor Laboratory Press Publications
AAAS members can now receive a special 15% discount on eight exceptional books for lab scientists and educators from Cold Spring Harbor Laboratory Press Publications. Go to http://www.cshlpress.com/affiliates/aaas.htm . Click on "Enter CSHL Store" and browse "Special Offers for Affiliates."