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This month in Science Roundup:
The Tree of LifeHow many species exist on Earth, and where does each one fit in the grand scheme of evolution? Efforts to answer these daunting but compelling questions were the subject of a special section of the 13 Jun 2003 Science. Biologists worldwide are committed to the massive undertaking of cataloging all organisms, living and extinct, and charting their relationships in space and time. As noted in a News story by E. Pennisi, systematists are turning to the tactics of big science -- large-scale, collaborative projects that simultaneously draw from molecular and morphological data and taxonomic information -- to aid their efforts. Science illustrated the complexity of the task at hand with a draft Tree of Life that represents the 80,000 living organisms now classified. (A special web-enhanced version of the tree included descriptions of some of the major branch points and links to web pages of known taxa from blue-green algae to grasshoppers; http://www.sciencemag.org/feature/data/tol/). A series of Viewpoint articles examined efforts to reconcile molecular and paleontological dates of the major branch points in the tree of life; evolution of the protein repertoire through gene duplication, divergence, and recombination; the complex origins of eukaryotic organisms; the emerging field of phylogenomics; and the value of phylogenies in assessing conservation priorities. Finally, an Editorial by J. A. M. Graves (http://www.sciencemag.org/cgi/content/short/300/5626/1621) emphasized the importance understanding the fundamentals of molecular evolution and the forces that drive genomic change as we seek to find the unifying principles that have built the tree of life.
Eukaryotic organisms generally carry some amount of genetic baggage -- "selfish" DNA sequences like transposons that proliferate but serve no obvious function. Not surprisingly, organisms have evolved various mechanisms to rid their genomes of these potentially overbearing sequences, including targeted mutagenesis and gene silencing by DNA methylation. In a report in the 6 Jun 2003 Science Yao et al. (http://www.sciencemag.org/cgi/content/short/300/5625/1581) reported new evidence that the single-celled protozoan Tetrahymena thermophila uses an RNA-based recognition system to guide deletion of unnecessary DNA. Tetrahymena contain two nuclei: A micronucleus that is transcriptionally inactive and serves as a "storehouse" for the cell's genome, and a macronucleus that is responsible for all gene expression in the organism. During reproduction, the micronucleus divides and differentiates to form the new macro- and micronucleus of the daughter cell, and the old macronucleus is destroyed. Formation of the new macronucleus involves substantial genome-wide DNA rearrangement and deletion of nearly 15% of the genome deemed extraneous or repetitive. Yao et al. have shown that injection of double-stranded RNA triggers the specific deletion of homologous DNA regions. Foreign DNA sequences introduced into the micronucleus were also efficiently deleted from daughter macronuclei. These results suggest an unusual genome surveillance and defense system that prevents superfluous genetic material from being amplified and protects the genome from invading DNA. An accompanying Perspective by E. U. Selker (http://www.sciencemag.org/cgi/content/short/300/5625/1517) highlighted the report and its potential evolutionary implications.
Myosins are a diverse protein family comprising 18 different classes. They act as ATP-powered molecular motors that move along actin filaments and drive a diversity of functions from muscle contraction to trafficking of cellular vesicles. Mysosin V is responsible for carrying cargo throughout the cell, but exactly how this movement occurs has remained a controversial question in biophysics. The protein is composed of two head structures held together by a coiled-coil stalk, and two theories have been put forth to describe its mode of action: An "inchworm" mechanism, and a "hand-over-hand" walking mechanism. In a research article in the 27 Jun 2002 Science, Yildiz et al. (http://www.sciencemag.org/cgi/content/short/300/5628/2061) provided convincing evidence that the hand-over-hand mechanism is more likely. The researchers used a fluorescent imaging technique to measure the step size of single molecules to within 1.5 nanometers, and showed that myosin V moves by successively flopping the rear of the molecule over the stationary head. As noted in an accompanying Perspective by J. E. Molloy and C. Veigel (http://www.sciencemag.org/cgi/content/short/300/5628/2045), details of how myosins motor will be of particular interest to nanotechnologists looking to construct synthetic nanometer-sized motors.
The HIV/AIDS epidemic continues to ravage humanity at a worrying pace. Recent studies showing the molecular trickery HIV has mastered to dodge our immune systems only reinforces the importance of understanding how this deadly virus evolves and thrives, if we are to have any hope of conquering it. In the 13 Jun 2003 Science, Bailes et al. (http://www.sciencemag.org/cgi/content/full/300/5626/1713) provided interesting insight into the origins of HIV. They showed that the simian immunodeficiency virus (SIV) of chimpanzees -- considered to be the source of human HIV-1 -- is a result of successive recombination events between SIV viruses carried by two species of monkey preyed upon by chimps. The report has important public health implications, raising questions of whether other chimp-adapted SIVs might infect humans, and whether current HIV strains are likely to recombine unpredictably.
These possibilities further illuminate the challenges facing current treatment and vaccine efforts. In a Policy Forum in the 27 Jun 2003 Science, R. D. Klausner et al. (http://www.sciencemag.org/cgi/content/short/300/5628/2036) called for establishment of a global HIV vaccine enterprise to meet those challenges. Their proposal calls for a new collaborative model of research that would increase resources and prioritize the R&D agenda of the major public and private stakeholders -- with the ultimate goal of increasing the probability of, and shortening the time to, development of effective HIV vaccines for global use. A related Editorial in the same issue by V. McGovern and Q. Bond (http://www.sciencemag.org/cgi/content/short/300/5628/2003) more broadly pleaded for strong government commitment to basic biomedical research in the form of a global health research fund.
As we learn more about cellular regulation, a complex network of signaling pathways is beginning to emerge. A special section of the 6 Jun 2003 Science highlighted recent developments in our understanding of several of the cascades that comprise this intricate signal-transduction landscape. Seven Viewpoint articles described signaling pathways involved in immune responses to allergens and microbial pathogens; cardiac function; circadian rhythms; neuron survival; movement of the amoeba Dictyostelium in response to chemical signals (chemotaxis); and Wnt-mediated responses, which specify a number of aspects of early development including cell fate, migration, and polarity. To provide a more comprehensive view of how these biochemical circuits work, the articles were coupled with new additions to the Connections Maps database at Science's Signal Transduction Knowledge Environment (http://stke.sciencemag.org/cm/). Equipped with user-friendly navigational tools described in an accompanying STKE Editorial Guide, these interactive diagrams allow users to explore how diverse pathways and their components relate to each other, and to begin to uncover the signaling "hubs" and network properties of the cellular signaling world.
Adding to the innumerable lessons we have learned from the bacterial world about molecular evolution, ecology, and physiology, two studies published in Science this month described unexpected microbial feats that may shed light on aspects of aging and fighting infection.
Most economic theories minimize or ignore the influence of human emotions and instead assume that people make choices based on rational principles. In a revealing report in the 13 Jun 2003 Science, Sanfey et al. (http://www.sciencemag.org/cgi/content/short/300/5626/1755) showed that emotional influences actually play an important role in human decision-making. The researchers used functional magnetic resonance imaging (fMRI) to image the brains of players of an "ultimatum game." In this game, two players split a sum of money; one player proposes a split and the other can accept it or reject it. Accepting the sum ends the game, as does rejecting (but in the latter case, neither player receives any money). Considerable research has shown that low or unfair offers are typically rejected 50% of the time, demonstrating that in certain situations, people are motivated to actively turn down rewards -- whether out of pride, spite, or some other factor. The new fMRI results bolstered this idea, and showed that offers perceived as unfair elicited activity in the brain areas related to both emotion (anterior insula) and cognition (dorsolateral prefrontal cortex). Interestingly, the anterior insula is well known for its involvement in negative emotional states, lending further support to the notion that emotional processes contribute to decision-making. An accompanying Perspective by C. F. Camerer (http://www.sciencemag.org/cgi/content/short/300/5626/1673) discussed how neuroeconomic studies likes these are influencing game theory and methods for predicting the behavior of people, markets, and even countries, in matters of choice.
Kin selection -- the cooperative behavior shown between genetically-related animals -- has been the subject of intense debate among scientists studying the evolution of social behavior. Do animals actively choose to "stick to their own", or is their altruism merely a side effect of some other factor like living in close proximity? Two reports in the 20 Jun 2003 Science illustrated some of the complexities of this issue.
As noted in an accompanying Perspective by J. L. Dickinson and W. D. Koenig (http://www.sciencemag.org/cgi/content/short/300/5627/1887), "progress in understanding social evolution will involve teasing apart the importance of kinship from other forms of selection based on genetic similarity as distinct and potentially important pathways to social behavior."
Two reports in Science this June described achievements in spectroscopy that will help scientists understand the dynamics of atomic interactions and biological and chemical processes.
Since February 2002, the Thermal Emission Imaging System (THEMIS) aboard the Mars Odyssey spacecraft has been capturing thermal and visible images of the rocky martian surface. In a research article in the 27 Jun 2003 Science, Christensen et al. (http://www.sciencemag.org/cgi/content/short/300/5628/2056) summarized these images to create a more comprehensive view of the planet's surface dynamics over time. Because temperatures are related to material properties such as composition, topography, and structural integrity, thermal images provide a unique window on erosion and other geologic processes that have helped shape Mars. The team's analysis revealed distinct rock layers of variable thickness, implying temporal changes in the processes or environments during or after their formation; kilometer-scale outcrops of exposed bedrock; large dust-covered expanses; and compositional variations at 100-meter scales including a thick buried layer of olivine-rich basalt. Polar observations further identified temporal patches of water frost in the north polar cap. As noted in an accompanying Perspective by M. P. Golombek (http://www.sciencemag.org/cgi/content/short/300/5628/2043), the combination of visible and thermal images acquired by THEMIS will enable planetary geologists to "map the entire surface with unprecedented insight into the geologic history and evolution of Mars."
In another Mars-related report in the 27 Jun 2003 issue, Mitrofanov et al. (http://www.sciencemag.org/cgi/content/short/300/5628/2081) determined that the planet's northern polar permafrost contains more water than the southern polar latitudes. Their results are consistent with the seasonal cycling of carbon dioxide and water between the Mars surface and atmosphere and may have implications for understanding climate change and other meteorological processes.
Ninety-six percent of the universe consists of mass and energy we can't see. A special section of the 20 Jun 2003 Science was dedicated to the dark stars, dark matter, and dark energy that collectively embody this dark side of the cosmos. The foremost challenge posed by the dark side is finding ways to learn about and understand the vast expanse that is invisible to conventional optical telescopes. A News story by R. Irion described how researchers plan to map the distribution of dark matter throughout the universe by analyzing its subtle effects on light from distant galaxies -- a technique called weak gravitational lensing. A related review article reviewed efforts to discern the nature of dark matter, which is six times more abundant than ordinary matter but remains poorly understood. Meanwhile, C. Seife reported that physicists are trying to crack "dark energy" -- the mysterious "antigravity" force that suffuses the universe. As noted in a companion review article, the negative pressure of dark energy produces cosmic acceleration, which many believe could explain the rapid expansion of the universe over the past seven billion years. Other reviews discussed black holes, the best-understood component of the dark side, and the "dark age of the universe" -- the period between dispersal of cosmic microwave background radiation (following the big bang) and formation of the first stars.
Science Online shed further light on darkness with links to missions, experiments, models, and previous Science papers bearing on various topics in cosmology (http://www.sciencemag.org/feature/data/darkside/).
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