Dealing with Data
Special Online Collection
Scientific innovation has been called on to spur economic recovery; science and technology are essential to improving public health and welfare and to inform sustainability; and the scientific community has been criticized for not being sufficiently accountable and transparent. Data collection, curation, and access are central to all of these issues. In the 11 Feb 2011 issue, Science joined with colleagues from its sister publications to provide a broad look at the issues surrounding the growing influx of research data. Articles in Science highlighted both the challenges posed by the data deluge -- in fields from neuroscience to particle physics -- and the opportunities that can be realized if we can better organize and access the data. In the 9 Feb issue of Science Translational Medicine, two Commentaries examined the ownership of clinical trial results and patient privacy. In its 15 Feb issue, Science Signaling tackled some of the key issues related to the data deluge faced by cell signaling researchers. And rounding out the special collection, articles in Science Careers highlighted the informatics and computational skills required to deal with research data, the challenges associated with sharing clinical data, and the new opportunities afforded by biomedical ontologies.
Earthquake Warning Signal?
To improve warning systems and minimize damage, it is important to understand the moments leading up to large earthquakes. In a Research Article in the 18 Feb 2011 Science, Bouchon et al. reported on a persistent and repeating low-frequency seismic signal observed in the hour before the 1999 magnitude 7.6 Izmit earthquake in Turkey that may have been the beginning stages of the major slip along the fault. Using new techniques for extracting information from seismic recordings that look like mostly noise, as well as other methods, the team found some 22 foreshocks in addition to the 18 obvious ones, all of them imperceptible at the surface. Seismogram traces indicate that these events originated from the base of the brittle crust near the hypocenter, suggesting that slip accumulated leading up to the earthquake. The increase of seismic noise over this time frame indicates possible movement along the fault before the main quake. It is not yet clear whether similar patterns are likely to have occurred before other large earthquakes, or whether such patterns occur in the absence of any subsequent rupture. A News story by R. A. Kerr highlighted the study.
Human Genome Anniversary
Special Online Collection
In February 2001, Science and Nature published two papers that provided the first detailed look at the human genome: a string of some 3 billion nucleotides whose unique sequence forms the genetic blueprint for each individual. This February, a special month-long series celebrated the 10th anniversary of that momentous achievement (see the related Editorial by B. Alberts in the 4 Feb 2011 issue). News features explored the impacts of the genomics revolution on medicine, the challenges of dealing with genomic data, the emerging field of forensic genetics, and the broad applications of genomics technologies. In addition, a collection of insightful individuals representing many different viewpoints offered brief essays about what the availability of human genome sequences has meant to them or their communities. Among the contributors were Desmond Tutu, Archbishop Emeritus of Cape Town, South Africa; Francis Collins, director of the U.S. National Institutes of Health; and dance artist Liz Lerman.
Fighting Malaria with Fungi
Fungi that infect mosquitoes are potential tools for supporting malaria control efforts. Such biocontrol agents can be genetically engineered to make them more effective, to counter resistance as it evolves, or to express a range of foreign proteins into their hosts. In a study described in the 25 Feb 2011 Science, Fang et al. engineered the mosquito-infecting fungus Metarhizium anisopliae to deliver molecules that selectively block development of the malaria-causing parasite Plasmodium falciparum within its mosquito host--namely a peptide that blocks attachment of sporozoites (infective parasitic cells) to mosquito salivary glands, an antibody that causes sporozoites to clump, or an antimicrobial toxin called scorpine. Treatment of infected mosquitoes with these engineered fungi reduced sporozoite counts by 71%, 85%, and 90%, respectively. The combination of scorpine and the peptide reduced sporozoite counts by 98%. These findings -- combined with that fact that fungi lend themselves to strategies currently used for delivery of chemical insecticides, such as sprays and bed nets -- suggest that fungus-mediated inhibition of malaria parasites could become a valuable weapon for combating the disease. Senior author Raymond St. Leger discussed the promise of the approach in a related podcast segment.
Mars Dunes in Springtime
Sand dunes are found all over the surface of Mars, but whether the dunes are active or represent relic deposits from the ancient past has been unclear. In the 4 Feb 2011 Science, Hansen et al. reported satellite images that document extensive modification of northern polar dunes within a Mars year. The new data come from the High-Resolution Imaging Science Experiment onboard the Mars Reconnaissance Orbiter, which has been capturing seasonal activity on the planet for two Mars years. The observed changes in the dunes, including the formation of new alcoves and gullies, followed by deposition of fresh sediment by the wind, are seasonal and are caused by sand and ice avalanching down the dunes. The patterns and timing of the changes indicate that martian dunes are subject to a modification process not found on Earth: springtime sublimation of Mars' seasonal polar caps of carbon dioxide frost. According to the team's model, heat from the sun in spring causes the frozen caps to crack and rupture, thus triggering sand and ice to cascade down the slipfaces of the dunes.
A Telling Arch
In early human evolution, walking upright required several evolutionary changes and adaptations. A key change was the development of longitudinal and transverse arches of the foot to provide critical shock absorption during the stance phase of the gait, as well as a rigid lever that would permit flexibility during locomotion at different speeds and across irregular terrain. Australopithecus is the first human that is thought to have been a fully terrestrial biped, but this has been debated owing to a lack of key foot bones from this species and other hominins. Now, a 3.2-million-year-old foot bone from a member of Lucy's species, A. afarensis, reveals that this hominin was no flat foot (see the related ScienceNOW story by A. Gibbons). In a Report in the the 11 Feb. 2011 Science, Ward et al. described a key element of the foot of A. afarensis discovered in Hadar, Ethiopia -- a complete fourth metatarsal, one of the long bones that connects the toe to the base of the foot. The bone's morphology indicates that this early human's foot was stiff and had a well-formed longitudinal arch, features which the team concludes "show that the A. afarensis foot was functionally like that of modern humans and support the hypothesis that his species was a committed terrestrial biped."
The Art of Science
Special Online Collection
Researchers are generating mind-boggling volumes of data at exponentially increasing rates. The ability to process that information and display it in ways that enhance understanding is an increasingly important aspect of the way scientists communicate with each other -- and especially with students and the general public. That is why, for the past 8 years, Science and the U.S. National Science Foundation have co-sponsored annual challenges to promote cutting-edge efforts to visualize scientific data, principles, and ideas. A special section of the 18 Feb 2011 issue presented the winners and honorable mentions in the 2010 International Science & Engineering Visualization Challenge, which drew 111 entries from 63 countries. The winners -- in categories including illustration, informational graphics, photography, and multimedia -- captured an "ocean" composed of a single layer of molecules, an HIV particle as a study in orange and gray, a phantasmagoria of fungi, and the long-distance travels of items dumped in the trash in Seattle. An online slide presentation showcased the awardees, and a podcast feature included conversations with one of this year's winners as well as one of the competition's judges.
Preparing for Implantation
Reproduction in mammals is coordinated by an intricate sequence of events and signals that culminate in implantation of the embryo in the uterus. These signals must be produced at the correct time, in the proper place, and in the amounts needed; perturbation of any of these factors can prevent establishment of pregnancy, resulting in infertility. In the 18 Feb 2011 Science, Li et al. reported that the transcription factor Hand2 regulates signals that establish conditions in the mammalian uterus to support pregnancy (also see the related Perspective by Hewitt and Korach). Just before ovulation, a surge of estrogen drives the proliferation of the epithelial cells that line the uterus. Progesterone, which increases after ovulation, further prepares the uterus for pregnancy in part by putting the brakes on this tissue growth. Using targeted genetic mutation in mice, Li et al. showed that Hand2 is a target of progesterone regulation in the stromal cells of the uterus and that it controls estrogen-induced epithelial proliferation via a mechanism involving fibroblast growth factors, thereby creating an epithelium that is receptive to embryo implantation. The findings suggest that Hand2 is an important factor to be considered for hormone therapy to block the proliferative actions of estrogen in the endometrium.
An Ecoresponsive Genome
Water fleas of the genus Daphnia, small planktonic crustaceans found all over the world, have the ability to alter their phenotypes in response to environmental cues and are among the oldest model systems in biological research. In a Research Article in the 4 Feb 2011 Science, Colbourne et al. reported on the genome of Daphnia pulex -- a keystone species of freshwater ecosystems and also the first crustacean genome to be sequenced ( listen to the related podcast interview with lead authors John Colbourne and Michael Pfrender). The genome is relatively modest in size, measuring about 200 megabases, but its 30,000 genes exceed the number found in many other genomes, including the human genome. Many genes are duplicates, and more than a third of the genes appear to be unique to the Daphnia lineage. Using expressed sequence tag libraries and genome-wide tiling microarray experiments, the team further demonstrated that genes responsive to ecological conditions are overrepresented in duplicated genes and in genes without known homologs. An accompanying Perspective by D. Ebert noted that the Daphnia model is currently being used in such fields as ecotoxicology, population genetics, and phenotypic plasticity, and that the publication of the D. pulex genome "will allow this list to expand to embrace the emerging field of environmental genomics."
Spin Filtering with DNA
Spintronics devices, which exploit both the charge of electrons and their spin, hold great promise for creating circuits that are faster and more energy efficient than standard electronics. The most efficient way to manipulate spins, which exist in "up" or "down" states, has been by means of a magnetic field, which can be applied to create an excess of one electron spin population over another. In the 18 Feb 2011 Science, Göhler et al. reported on a new way of filtering electron spins, using a thin layer of ordered double-stranded DNA molecules adsorbed to a gold surface, that is considerably more efficient than magnet-based filters (see the related Perspective by Rikken). The team shone laser light on the gold, which liberates unpolarized electrons, and then measured the spin of the electrons after their passage through the DNA layer. They found that one spin type passes through much more easily, meaning that this layer acts as a spin filter, strongly hindering the passage of the other spin type. This filter effect is observed only if the DNA is assembled on the gold surface as a closely packed ordered array of helices, and is stronger if the helices are longer, reaching selectivities of 60%. Beyond the applications for spintronic devices, the discovery that DNA has a strong effect on electron spin suggests that spin interactions could also play a role in some biological processes.
In Science Signaling
Antiviral Mitochondrial Action
Mitochondria are the energy generators of the cell, but they also act as platforms upon which complexes of proteins respond to RNA-containing viruses within the cytosol. In a Research Article in the 1 Feb issue of Science Signaling, Koshiba et al. presented evidence that suggests that the contribution of mitochondria to these antiviral responses is not as passive as originally thought. Indeed, their data suggest that maintenance of the internal physiological functions of mitochondria coupled with the functions of the external protein complexes is needed to fight viral infections.
Also in Science Signaling this month:
-- Ross highlighted research that illuminates reciprocal regulation between a G protein and its effector (8 Feb 2011)
-- Ahmad et al. reported that an inflammatory response of epithelial cells may be co-opted to promote survival of cancer cells (15 Feb 2011)
-- Chen et al. determined how mTORC2 and Akt signaling can be attenuated by cellular stress (22 Feb 2011)
In Science Translational Medicine
A Micro-NMR Smart Phone for Spotting Cancer
Smart phones have provided millions with hours of mindless entertainment, but their true value may lie in the hands of clinicians at the patient's bedside. Accurate diagnosis and staging of tumors through analysis of core biopsies are essential for ensuring that patients receive rapid treatment with the most appropriate cancer drugs available. However, current techniques for analyzing tumor biopsies such as immunohistochemistry and flow cytometry are costly, time consuming, and can require more tissue than is typically available from a single biopsy. In the 23 Feb 2011 issue of Science Translational Medicine, Weissleder and colleagues unveiled a new portable micro-NMR device, operated by smart phone technology, that enables accurate diagnosis of malignant tumors from the scarce cancer cells present in fine needle aspirate biopsies (see the related ScienceNOW story by J. Kaiser). The micro-NMR system uses nanoparticle-based magnetic affinity ligands to detect the expression of protein markers known to be associated with cancer and delivers a diagnosis with 96% accuracy in under 60 minutes. In contrast, immunohistochemistry, a gold standard of cancer diagnostics, sports an accuracy of 84% and yields results within three days.
Also in Science Transational Medicine this month:
-- Bingel et al. revealed that an individual's expectation that a pain treatment will or will not work can alter both its subjective effectiveness and the pain-related activity in the brain. (See also the accompanying Perspective by Gollub and Kong) (16 Feb 2011)
-- Dahl et al. showed that tissue-engineered vascular grafts survive long-term storage and perform well after transplant in large-animal models. (2 Feb 2011)
-- Terry and Terry argued that the time has come to crowd-source data for diagnostic and therapeutics development. (9 Feb 2011)
-- Guevara-Aguirre et al. showed that Ecuadorians who have a genetic mutation in the growth hormone receptor almost never die of cancer or diabetes complications, possibly because of high resistance to oxidative damage and low circulating insulin. (16 Feb 2011)
Image credits (in order of appearance): Yael Fitzpatrick, Science; Mark M. Miller, www.millermedart.com; NASA/JPL/University of Arizona; Seth B. Darling, Argonne National Laboratory/Steven J. Sibener, University of Chicago; Jan Michels, Functional Morphology and Biomechanics, Christian-Albrechts-Universitat zu Kiel
