Science Roundup


Sponsored by:

Canadian Science Policy Conference


In advance of the 2012 AAAS Annual Meeting in Vancouver, AAAS staff will take part in the 2011 Canadian Science Policy Conference (CSPC 2011), November 16-18 in Ottawa. Billed as the most comprehensive, multi-sector, multi-disciplinary science policy forum in Canada, with more than 400 participants, the event will feature a special keynote address by Hon. Gary Goodyear, Minister of State (Science and Technology). Other keynote sessions will feature chief scientists, a university president, three MPs, two provincial legislators, and other high-level speakers. Topics to be addressed will include innovation policy, science and politics in Canada, and much more, encompassing 17 panels, five themes and more than 70 speakers. Register now. Log onto http://www.cspc2011.ca or contact info@cspc2011.ca.



PERSPECTIVE: The Genomic Basis of Local Climatic Adaptation

Summary: Many plant populations are locally adapted and genetically differentiated for traits related to fitness, but the genetic basis of this adaptation remains poorly known. The best genomic resources for plants are available either for model species such as Arabidopsis thaliana, or for crop plants such as maize. In contrast, studies of fitness variation in natural conditions are spread over a large number of species with poorly understood genomes. Two reports in the 7 October 2011 issue of Science, by Fournier-Level et al. on page 86 and Hancock et al. on page 83, report a major advance toward finding the genomic sites related to climatic adaptation in A. thaliana by combining genome-wide analysis of single-nucleotide polymorphism (SNP) and fitness estimates. Such information may eventually be used to better predict and manage climate change responses.


REPORT: Detection of Pulsed Gamma Rays Above 100 GeV from the Crab Pulsar

Abstract: We report the detection of pulsed gamma rays from the Crab pulsar at energies above 100 giga–electron volts (GeV) with the Very Energetic Radiation Imaging Telescope Array System (VERITAS) array of atmospheric Cherenkov telescopes. The detection cannot be explained on the basis of current pulsar models. The photon spectrum of pulsed emission between 100 mega–electron volts and 400 GeV is described by a broken power law that is statistically preferred over a power law with an exponential cutoff. It is unlikely that the observation can be explained by invoking curvature radiation as the origin of the observed gamma rays above 100 GeV. Our findings require that these gamma rays be produced more than 10 stellar radii from the neutron star.
Supporting online material


EDITORIAL: Genomics Is Not Enough

Summary: Next week, the international congress of human genetics convenes in Montreal, where genomic science, its technologies, genetic disease, and personalized medicine will be discussed. Translating current knowledge into medical practice is an important goal for the public who support medical research, and for the scientists and clinicians who articulate the critical research needs of our time. However, despite innumerable successful gene discoveries through genomics, a major impediment is our lack of knowledge of how these genes affect the fundamental biological mechanisms that are dysregulated in disease. If genomic medicine is to prosper, we need to turn our attention to this gaping hole.


REPORT: A 100,000-Year-Old Ochre-Processing Workshop at Blombos Cave, South Africa

Abstract: The conceptual ability to source, combine, and store substances that enhance technology or social practices represents a benchmark in the evolution of complex human cognition. Excavations in 2008 at Blombos Cave, South Africa, revealed a processing workshop where a liquefied ochre-rich mixture was produced and stored in two Haliotis midae (abalone) shells 100,000 years ago. Ochre, bone, charcoal, grindstones, and hammerstones form a composite part of this production toolkit. The application of the mixture is unknown, but possibilities include decoration and skin protection.
Supporting online material


NEWS FOCUS: Vital Details of Global Warming Are Eluding Forecasters

Summary: Climate researchers are quite comfortable with their projections for the world under a strengthening greenhouse, at least on the broadest scales. But ask researchers what's in store for the Seattle area, the Pacific Northwest, or even the western half of the United States, and they'll often demur. Switching from global models to models focusing on a single region creates a more detailed forecast, although it also creates more uncertainty. But help is on the way. Regional modelers are well into their first extensive comparison of global-regional model combinations to sort out the uncertainties.


PERSPECTIVE: Keeping Bacteria at a Distance

Summary: The human intestine harbors enormous amounts of bacteria that have an essential role in host metabolism, but how this mutualistic balance is maintained is unclear. The current understanding has focused on the concept that bacteria continuously interact with the intestinal immune system in a balanced proinflammatory and tolerogenic way. The discovery of a protective inner mucus layer in the colon that separates bacteria from the epithelium has broadened this view. On page 255 of the 14 October 2011 issue, Vaishnava et al. show that the antibacterial protein RegIIIγ secreted by specialized epithelial cells is involved in limiting the epithelial contact with bacteria in the small intestine. This observation further substantiates the role of intestinal epithelial cells and the mucus that covers them as important parts of the innate immune defense.


NEWS & ANALYSIS: Pre-Clovis Mastodon Hunters Make a Point

Summary: On page 351 of the 21 October 2011 issue of Science, researchers report new analyses of the remains of a mastodon found in the 1970s with a bone spear point in its rib. Scientists used DNA and radiocarbon dating to demonstrate that the point came from a mastodon bone shaped into a weapon by humans and used a startling 13,800 years ago. That's nearly 1000 years before the Clovis culture, long considered to be the first culture in the New World. The find adds to the wave of recent compelling evidence demonstrating an earlier, pre-Clovis settling of the Americas. Although a few Clovis-first holdouts remain unconvinced, the early bone point also suggests that the extinction of large mammals such as mastodons and mammoths may have begun long before the Clovis people came on the scene.


REPORT: Pre-Clovis Mastodon Hunting 13,800 Years Ago at the Manis Site, Washington

Abstract: The tip of a projectile point made of mastodon bone is embedded in a rib of a single disarticulated mastodon at the Manis site in the state of Washington. Radiocarbon dating and DNA analysis show that the rib is associated with the other remains and dates to 13,800 years ago. Thus, osseous projectile points, common to the Beringian Upper Paleolithic and Clovis, were made and used during pre-Clovis times in North America. The Manis site, combined with evidence of mammoth hunting at sites in Wisconsin, provides evidence that people were hunting proboscideans at least two millennia before Clovis.
Supporting online material


NEWS FOCUS: The Sterile Neutrino: Fertile Concept or Dead End?

Summary: For 15 years, researchers have accumulated hints that the "sterile neutrino"—a more-elusive cousin of the nearly undetectable neutrinos—might be out there. But most physicists have found the evidence unconvincing, as most of the results pointing toward sterile neutrinos are of marginal statistical significance. Recently, however, the case for sterile neutrinos has grown stronger, bolstered by a new analysis of data from nuclear reactors. So last month 60 physicists from around the world gathered to hash out the arguments for and against the existence of sterile neutrinos and to try to decide whether it's worth staging a dedicated experiment to settle the matter. Performing such an experiment won't be easy. The hypothetical neutrinos are called sterile because they do not interact at all with known particles. Still, physicists say, it's time to figure out what it will take to discover or rule out sterile neutrinos once and for all.
Podcast Interview


REPORT: Fatty Acids Identified in the Burmese Python Promote Beneficial Cardiac Growth

Abstract: Burmese pythons display a marked increase in heart mass after a large meal. We investigated the molecular mechanisms of this physiological heart growth with the goal of applying this knowledge to the mammalian heart. We found that heart growth in pythons is characterized by myocyte hypertrophy in the absence of cell proliferation and by activation of physiological signal transduction pathways. Despite high levels of circulating lipids, the postprandial python heart does not accumulate triglycerides or fatty acids. Instead, there is robust activation of pathways of fatty acid transport and oxidation combined with increased expression and activity of superoxide dismutase, a cardioprotective enzyme. We also identified a combination of fatty acids in python plasma that promotes physiological heart growth when injected into either pythons or mice.
Supporting online material


NEWS & ANALYSIS: Dispute Over Tumor Suppressor Gene Runx3 Boils Over

Summary: A key, decade-old finding by a prominent Japanese cancer researcher based at the National University of Singapore (NUS) is under fire from a group in Israel that calls it "irreproducible." If the challenge overturns the original work, which identified a gene called Runx3 as a tumor suppressor, hundreds of scientific papers might be affected. The dispute began with a scientific disagreement almost a decade ago and escalated sharply after the group in Israel filed a formal complaint earlier this fall with NUS, which recently launched an investigation.


NEWS & ANALYSIS: Dismay, Confusion Greet Human Stem Cell Patent Ban

Summary: Has the environmental group Greenpeace dealt a major blow to the medical use of human embryonic stem (hES) cells in Europe? That's what biologists, patent specialists, and lawyers are furiously debating after the European Union's Court of Justice ruled last week that processes and products that involve such cells are not patentable. Patents on hES cells are forbidden by a 1998 E.U. Directive on biopatents that bans the "use of human embryos for industrial or commercial purposes," the court concluded in a case that Greenpeace had initiated.



In Science Signaling

RESEARCH ARTICLE: Phosphorylation of Mad Controls Competition Between Wingless and BMP Signaling

Abstract: Bone morphogenetic proteins (BMPs) and Wnts are growth factors that provide essential patterning signals for cell proliferation and differentiation. Here, we describe a molecular mechanism by which the phosphorylation state of the Drosophila transcription factor Mad determines its ability to transduce either BMP or Wingless (Wg) signals. Previously, Mad was thought to function in gene transcription only when phosphorylated by BMP receptors. We found that the unphosphorylated form of Mad was required for canonical Wg signaling by interacting with the Pangolin-Armadillo transcriptional complex. Phosphorylation of the carboxyl terminus of Mad by BMP receptor directed Mad toward BMP signaling, thereby preventing Mad from functioning in the Wg pathway. The results show that Mad has distinct signal transduction roles in the BMP and Wnt pathways depending on its phosphorylation state.
Supplementary Materials


RESEARCH ARTICLE: Agrobacterium Counteracts Host-Induced Degradation of Its Effector F-Box Protein

Abstract: The SCF (Skp1–Cul1–F-box protein) ubiquitin ligase complex plays a pivotal role in various biological processes, including host-pathogen interactions. Many pathogens exploit the host SCF machinery to promote efficient infection by translocating pathogen-encoded F-box proteins into the host cell. How pathogens ensure sufficient amounts of the F-box effectors in the host cell despite the intrinsically unstable nature of F-box proteins, however, remains unclear. We found that the Agrobacterium F-box protein VirF, an important virulence factor, undergoes rapid degradation through the host proteasome pathway. This destabilization of VirF was counteracted by VirD5, another bacterial effector that physically associated with VirF. These observations reveal a previously unknown counterdefense strategy used by pathogens against potential host antimicrobial responses.
Supplementary Materials


REVIEW: Working Without Kinase Activity: Phosphotransfer-Independent Functions of Extracellular Signal–Regulated Kinases

Abstract: The mitogen-activated protein kinases (MAPKs) extracellular signal–regulated kinase 1 (ERK1) and ERK2 play well-characterized roles in the regulation of key cellular processes, such as proliferation, differentiation, and survival, by acting as serine and threonine kinases in the phosphorylation of ∼200 substrates that are distributed in different subcellular localizations. However, over the past few years, evidence has mounted that indicates that the mechanism of action of ERK1 and ERK2 may extend beyond their role as canonical kinases. For example, proteins such as poly(ADP-ribose) polymerase 1, topoisomerase II, and MAPK phosphatase 3 (MKP-3) are activated by a direct interaction with ERK2 that does not involve any phosphotransfer activity. In addition, ERK2 binds to DNA and acts as a transcriptional regulator independently of its function as a kinase. Moreover, other studies demonstrate that ERK1 and ERK2 can regulate cell cycle entry by disrupting the interaction between the retinoblastoma pocket protein and lamin A in a kinase-independent fashion. These findings strongly support the notion that ERK1 and ERK2 can play functionally important roles independently of their regular catalytic activities and provide the basis for a new perspective from which to view these hitherto archetypical signaling kinases.



In Science Translational Medicine

RESEARCH ARTICLE: Increased Gene Dosage of Ube3a Results in Autism Traits and Decreased Glutamate Synaptic Transmission in Mice

Abstract: People with autism spectrum disorder are characterized by impaired social interaction, reduced communication, and increased repetitive behaviors. The disorder has a substantial genetic component, and recent studies have revealed frequent genome copy number variations (CNVs) in some individuals. A common CNV that occurs in 1 to 3% of those with autism—maternal 15q11-13 duplication (dup15) and triplication (isodicentric extranumerary chromosome, idic15)—affects several genes that have been suggested to underlie autism behavioral traits. To test this, we tripled the dosage of one of these genes, the ubiquitin protein ligase Ube3a, which is expressed solely from the maternal allele in mature neurons, and reconstituted the three core autism traits in mice: defective social interaction, impaired communication, and increased repetitive stereotypic behavior. The penetrance of these autism traits depended on Ube3a gene copy number. In animals with increased Ube3a gene dosage, glutamatergic, but not GABAergic, synaptic transmission was suppressed as a result of reduced presynaptic release probability, synaptic glutamate concentration, and postsynaptic action potential coupling. These results suggest that Ube3a gene dosage may contribute to the autism traits of individuals with maternal 15q11-13 duplication and support the idea that increased E3A ubiquitin ligase gene dosage results in reduced excitatory synaptic transmission.
Supplementary material


RESEARCH ARTICLE: Vitamin D Is Required for IFN-γ–Mediated Antimicrobial Activity of Human Macrophages

Abstract: Control of tuberculosis worldwide depends on our understanding of human immune mechanisms, which combat the infection. Acquired T cell responses are critical for host defense against microbial pathogens, yet the mechanisms by which they act in humans remain unclear. We report that T cells, by the release of interferon-γ (IFN-γ), induce autophagy, phagosomal maturation, the production of antimicrobial peptides such as cathelicidin, and antimicrobial activity against Mycobacterium tuberculosis in human macrophages via a vitamin D–dependent pathway. IFN-γ induced the antimicrobial pathway in human macrophages cultured in vitamin D–sufficient sera, but not in sera from African-Americans that have lower amounts of vitamin D and who are more susceptible to tuberculosis. In vitro supplementation of vitamin D–deficient serum with 25-hydroxyvitamin D3 restored IFN-γ–induced antimicrobial peptide expression, autophagy, phagosome-lysosome fusion, and antimicrobial activity. These results suggest a mechanism in which vitamin D is required for acquired immunity to overcome the ability of intracellular pathogens to evade macrophage-mediated antimicrobial responses. The present findings underscore the importance of adequate amounts of vitamin D in all human populations for sustaining both innate and acquired immunity against infection.
Supplementary material


RESEARCH ARTICLE: A Neutralizing Human Monoclonal Antibody Protects African Green Monkeys from Hendra Virus Challenge

Abstract: Hendra virus (HeV) is a recently emerged zoonotic paramyxovirus that can cause a severe and often fatal disease in horses and humans. HeV is categorized as a biosafety level 4 agent, which has made the development of animal models and testing of potential therapeutics and vaccines challenging. Infection of African green monkeys (AGMs) with HeV was recently demonstrated, and disease mirrored fatal HeV infection in humans, manifesting as a multisystemic vasculitis with widespread virus replication in vascular tissues and severe pathologic manifestations in the lung, spleen, and brain. Here, we demonstrate that m102.4, a potent HeV-neutralizing human monoclonal antibody (hmAb), can protect AGMs from disease after infection with HeV. Fourteen AGMs were challenged intratracheally with a lethal dose of HeV, and 12 subjects were infused twice with a 100-mg dose of m102.4 beginning at either 10, 24, or 72 hours after infection and again about 48 hours later. The presence of viral RNA, infectious virus, and HeV-specific immune responses demonstrated that all subjects were infected after challenge. All 12 AGMs that received m102.4 survived infection, whereas the untreated control subjects succumbed to disease on day 8 after infection. Animals in the 72-hour treatment group exhibited neurological signs of disease, but all animals started to recover by day 16 after infection. These results represent successful postexposure in vivo efficacy by an investigational drug against HeV and highlight the potential impact a hmAb can have on human disease.
Supplementary material


RESEARCH ARTICLE: The Impact of a Consortium of Fermented Milk Strains on the Gut Microbiome of Gnotobiotic Mice and Monozygotic Twins

Abstract: Understanding how the human gut microbiota and host are affected by probiotic bacterial strains requires carefully controlled studies in humans and in mouse models of the gut ecosystem where potentially confounding variables that are difficult to control in humans can be constrained. Therefore, we characterized the fecal microbiomes and metatranscriptomes of adult female monozygotic twin pairs through repeated sampling 4 weeks before, 7 weeks during, and 4 weeks after consumption of a commercially available fermented milk product (FMP) containing a consortium of Bifidobacterium animalis subsp. lactis, two strains of Lactobacillus delbrueckii subsp. bulgaricus, Lactococcus lactis subsp. cremoris, and Streptococcus thermophilus. In addition, gnotobiotic mice harboring a 15-species model human gut microbiota whose genomes contain 58,399 known or predicted protein-coding genes were studied before and after gavage with all five sequenced FMP strains. No significant changes in bacterial species composition or in the proportional representation of genes encoding known enzymes were observed in the feces of humans consuming the FMP. Only minimal changes in microbiota configuration were noted in mice after single or repeated gavage with the FMP consortium. However, RNA-Seq analysis of fecal samples and follow-up mass spectrometry of urinary metabolites disclosed that introducing the FMP strains into mice results in significant changes in expression of microbiome-encoded enzymes involved in numerous metabolic pathways, most prominently those related to carbohydrate metabolism. B. animalis subsp. lactis, the dominant persistent member of the FMP consortium in gnotobiotic mice, up-regulates a locus in vivo that is involved in the catabolism of xylooligosaccharides, a class of glycans widely distributed in fruits, vegetables, and other foods, underscoring the importance of these sugars to this bacterial species. The human fecal metatranscriptome exhibited significant changes, confined to the period of FMP consumption, that mirror changes in gnotobiotic mice, including those related to plant polysaccharide metabolism. These experiments illustrate a translational research pipeline for characterizing the effects of FMPs on the human gut microbiome.
Supplementary material

IMAGE CREDITS (In order of appearance): NORWAY SPRUCE, MICHAEL HIEBER/ISTOCKPHOTO.COM; A. THALIANA, ALBERTO SALGUERO/WIKIMEDIA COMMONS, TEK IMAGE/SCIENCE PHOTO LIBRARY, B. STRAUCH/SCIENCE, CENTER FOR THE STUDY OF THE FIRST AMERICANS, TEXAS A&M UNIVERSITY, LOS ALAMOS NATIONAL LABORATORY,


Sponsored by:

Canadian Science Policy Conference


In advance of the 2012 AAAS Annual Meeting in Vancouver, AAAS staff will take part in the 2011 Canadian Science Policy Conference (CSPC 2011), November 16-18 in Ottawa. Billed as the most comprehensive, multi-sector, multi-disciplinary science policy forum in Canada, with more than 400 participants, the event will feature a special keynote address by Hon. Gary Goodyear, Minister of State (Science and Technology). Other keynote sessions will feature chief scientists, a university president, three MPs, two provincial legislators, and other high-level speakers. Topics to be addressed will include innovation policy, science and politics in Canada, and much more, encompassing 17 panels, five themes and more than 70 speakers. Register now. Log onto http://www.cspc2011.ca or contact info@cspc2011.ca.