Hot off the presses! Apr 01 Trends Plant Sci

The Apr 01 issue of the Trends Plant Sci is now up on Pubget (About Trends Plant Sci): if you're at a subscribing institution, just click the link in the latest link at the home page. (Note you'll only be able to get all the PDFs in the issue if your institution subscribes to Pubget.)

Latest Articles Include:

• Editorial Board and Contents
  - Trends Plant Sci 14(4):i (2009)
  
• Erratum: Protein isoprenylation: the fat of the matter: Trends in Plant Science 14 (2009) 3, 163–170
  - Trends Plant Sci 14(4):181 (2009)
  
• Auxin signaling in algal lineages: fact or myth?
  - Trends Plant Sci 14(4):182-188 (2009)
  Auxin is of major importance throughout the life cycle of a plant, affecting several physiological and developmental processes, such as cell expansion and division. However, the evolutionary time point at which auxin became involved in such diverse processes is currently unclear. Despite some controversy, numerous reports demonstrate the presence of auxin in algal lineages and its effects on algal development, suggesting an early evolutionary origin of auxin-dependent mechanisms. Here, we review these reports and discuss in silico analyses of auxin signaling components. It seems that, at least in microalgae, the assumed major components of auxin signaling in land plants are absent. However, these microalgae might have alternative auxin signaling pathways that could account for their responses to auxin.
• A morphogenetic trigger: is there an emerging concept in plant developmental biology?
  - Trends Plant Sci 14(4):189-193 (2009)
  Morphogens are involved in the establishment of positional information that is essential for pattern formation. In plants, the phytohormone auxin displays some characteristics of a morphogen. Gradients of auxin distribution are required for tissue patterning within the embryo and the root apex. In some other instances, such as de novo organogenesis, auxin action can be better described in terms of a morphogenetic trigger, which is defined as a factor that induces, through local increase of its concentration, acquisition of a new developmental fate in plant cells that were originally similar to their neighbours. A morphogenetic trigger specifies the site where a new organ will be formed. In plants, formation of reiterative and modular structures might need the action of both morphogenetic triggers and morphogens.
• Nuclear regulators with a second home in organelles
  - Trends Plant Sci 14(4):194-199 (2009)
  In plants, increasing evidence points towards the existence of nuclear proteins that are also targeted to either mitochondria – a well-known phenomenon from yeast and mammalians – or to plastids. One such protein is Whirly1, which was the first protein to be identified in the nucleus and plastids of the same plant cell. Like Whirly1, most of the dual targeted (nucleus and organelle) proteins have functions in the maintenance of DNA, telomere structuring or gene expression. In some instances, proteins were even shown to be relocated from one compartment to another upon environmental or developmental clues. We hypothesize that one rationale of dual targeting is storage or sequestration of these proteins inside the organelles until specific conditions require their activity in the nucleus.
• Janus-faced charge recombinations in photosystem II photoinhibition
  - Trends Plant Sci 14(4):200-205 (2009)
  Light-induced damage of the photosynthetic apparatus in plants is an important phenomenon that primarily affects the photosystem II complex. Here, we propose a new model of photoinhibition in which charge recombination processes have a double-faced role: first, photodamage is induced by singlet oxygen, which is produced via interaction with the triplet reaction center chlorophyll (3P680) arising from the recombination of the charge-separated state between P680 and the pheophytin electron acceptor (3[P680+Phe−]). Second, photoprotection is provided by competition between 3[P680+Phe−] formation and direct recombination of the 1[P680+Phe−] and P680+QA− states. The efficiency of these two pathways is under control of the redox potential of the Phe and QA electron acceptors, which is utilized during adaptation to high light conditions.
• Thinking outside the F-box: novel ligands for novel receptors
  - Trends Plant Sci 14(4):206-213 (2009)
  The importance of regulated proteolysis in the physiology and development of plants is highlighted by the large number of genes dedicated to proteasome-dependent protein degradation. Within the SCF class of E3 ubiquitin ligases are more than 700 F-box proteins that act as recognition modules to specifically target their dedicated substrates for ubiquitylation. This review focuses on very recent studies indicating that some F-box proteins function as phytohormone or light receptors, which directly perceive signals and facilitate specific target-protein degradation to regulate downstream pathways. If this new connection between ligand-regulated proteolysis and signaling proves to be more extensive, an entirely new way of understanding the control of signal transduction is in the offing.
• The many functions of ERECTA
  - Trends Plant Sci 14(4):214-218 (2009)
  The Arabidopsis thaliana accession Landsberg erecta contains an induced mutation in the leucine-rich repeat receptor-like Ser/Thr kinase gene ERECTA. Landsberg erecta is commonly used as a genetic background in mutant screens and in natural variation studies. Therefore, the erecta mutation is present in many loss-of-function mutants and recombinant inbred lines. Information on how the absence of functional ERECTA affects the interpretation of obtained phenotypic results is scattered. In this report we inventoried ERECTA functions and highlight ERECTA as a pleiotropic regulator of developmental and physiological processes, as well as a modulator of responses to environmental stimuli.
• Singlet oxygen in plants: production, detoxification and signaling
  - Trends Plant Sci 14(4):219-228 (2009)
  Singlet oxygen (1O2) is a singular reactive oxygen species (ROS) that is produced constitutively in plant leaves in light via chlorophylls that act as photosensitizers. This 1O2 production is spatially resolved within thylakoid membranes and is enhanced under light stress conditions. 1O2 can also be produced by phytotoxins during plant–pathogen interactions. 1O2 is highly reactive, can be toxic to cells and can be involved in the signaling of programmed cell death or acclimation processes. Here, we summarize current knowledge on 1O2 management in plants and on the biological effects of this peculiar ROS. Compared with other ROS, 1O2 has received relatively little attention, but recent developments indicate that it has a crucial role in the responses of plants to light.
• Role of plant RNA-binding proteins in development, stress response and genome organization
  - Trends Plant Sci 14(4):229-236 (2009)
  RNA-binding proteins (RBPs) in eukaryotes have crucial roles in all aspects of post-transcriptional gene regulation. They are important governors of diverse developmental processes by modulating expression of specific transcripts. The Arabidopsis (Arabidopsis thaliana) genome encodes for more than 200 different RBPs, most of which are plant specific and are therefore likely to perform plant-specific functions. Indeed, recent identification and analysis of plant RBPs clearly showed that, in addition to the important role in diverse developmental processes, they are also involved in adaptation of plants to various environmental conditions. Clearly, they act by regulating pre-mRNA splicing, polyadenylation, RNA stability and RNA export, as well as by influencing chromatin modification.

Hot off the presses! Nov 01 Trends Plant Sci

The Nov 01 issue of the Trends Plant Sci is now up on Pubget (About Trends Plant Sci): if you're at a subscribing institution, just click the link in the latest link at the home page. (Note you'll only be able to get all the PDFs in the issue if your institution subscribes to Pubget.)

Latest Articles Include:

• Editorial Board
  - Trends Plant Sci 16(11):i (2011)
  
• NOX or not? Evidence for algal NADPH oxidases
  - Trends Plant Sci 16(11):579-581 (2011)
  
• Plant nanotoxicology
  - Trends Plant Sci 16(11):582-589 (2011)
  The anthropogenic release of nanoparticles (NPs) to the environment poses a potential hazard to human health and life. The interplay between NPs and biological processes is receiving increasing attention. Plants expose huge interfaces to the air and soil environment. Thus, NPs are adsorbed to the plant surfaces, taken up through nano- or micrometer-scale openings of plants and are translocated within the plant body. Persistent NPs associated with plants enter the human food chain. In this Opinion, we document the occurrence and character of NPs in the environment and evaluate the need for future research on toxicological effects. Plant nanotoxicology is introduced as a discipline that explores the effects and toxicity mechanisms of NPs in plants, including transport, surface interactions and material-specific responses.
• Mendel, 150 years on
  - Trends Plant Sci 16(11):590-596 (2011)
  Mendel's paper 'Versuche über Pflanzen-Hybriden' is the best known in a series of studies published in the late 18th and 19th centuries that built our understanding of the mechanism of inheritance. Mendel investigated the segregation of seven gene characters of pea (Pisum sativum), of which four have been identified. Here, we review what is known about the molecular nature of these genes, which encode enzymes (R and Le), a biochemical regulator (I) and a transcription factor (A). The mutations are: a transposon insertion (r), an amino acid insertion (i), a splice variant (a) and a missense mutation (le-1). The nature of the three remaining uncharacterized characters (green versus yellow pods, inflated versus constricted pods, and axial versus terminal flowers) is discussed.
• De novo shoot organogenesis: from art to science
  - Trends Plant Sci 16(11):597-606 (2011)
  In vitro shoot organogenesis and plant regeneration are crucial for both plant biotechnology and the fundamental study of plant biology. Although the importance of auxin and cytokinin has been known for more than six decades, the underlying molecular mechanisms of their function have only been revealed recently. Advances in identifying new Arabidopsis genes, implementing live-imaging tools and understanding cellular and molecular networks regulating de novo shoot organogenesis have helped to redefine the empirical models of shoot organogenesis and plant regeneration. Here, we review the functions and interactions of genes that control key steps in two distinct developmental processes: de novo shoot organogenesis and lateral root formation.
• Founder cell specification
  - Trends Plant Sci 16(11):607-613 (2011)
  Lateral organs arise from individual or groups of cells either on the flanks of meristems or within defined cellular positional contexts. The first event in organogenesis is founder cell specification. Auxin is one necessary signal in different organ specification contexts, but it is difficult to distinguish between correlative and causal signals and evidence is emerging that other signals exist and that the interplay between these signals is important for organ initiation. This review analyses the progress in understanding which signals contribute to founder cell specification and outlines the emerging complexities in the perception of positional information that are context-dependent and reliant on the establishment and coordination of different types of competencies.
• The role of mitochondrial respiration in salinity tolerance
  - Trends Plant Sci 16(11):614-623 (2011)
  NaCl is the most abundant salt in salinity-affected land. The ability of plants to sift the water table, limit NaCl uptake, compartmentalise Na+/Cl– ions and prevent negative ionic and osmotic effects on cell function, are the foundations of salinity tolerance mechanisms. In this review, we show that although the quantitative response of respiratory rate to changes in salt concentration is complex, the properties of respiratory processes are crucial for tolerance during ion exclusion and tissue tolerance. We consider whole-plant gas exchange and carbon balance analysis alongside the salt responses of mitochondrial properties and genetic studies manipulating respiratory processes. We showcase the importance of efficient ATP generation, dampened reactive oxygen species and mitochondrial osmolytes for salinity tolerance in plants.
• Molecular control and function of endoreplication in development and physiology
  - Trends Plant Sci 16(11):624-634 (2011)
  Endoreplication, also called endoreduplication, is a cell cycle variant of multicellular eukaryotes in which mitosis is skipped and cells repeatedly replicate their DNA, resulting in cellular polyploidy. In recent years, research results have shed light on the molecular mechanism of endoreplication control, but the function of this cell-cycle variant has remained elusive. However, new evidence is at last providing insight into the biological relevance of cellular polyploidy, demonstrating that endoreplication is essential for developmental processes, such as cell fate maintenance, and is a prominent response to physiological conditions, such as pathogen attack or DNA damage. Thus, endoreplication is being revealed as an important module in plant growth that contributes to the robustness of plant life.

Hot off the presses! Nov 01 Trends in Ecology & Evolution

The Nov 01 issue of the Trends in Ecology & Evolution is now up on Pubget (About Trends in Ecology & Evolution): if you're at a subscribing institution, just click the link in the latest link at the home page. (Note you'll only be able to get all the PDFs in the issue if your institution subscribes to Pubget.)

Latest Articles Include:

• Editorial Board
  - Trends in Ecology and Evolution 25(11):i (2010)
  
• Transdisciplinary research is needed to predict plant invasions in an era of global change
  - Trends in Ecology and Evolution 25(11):619-620 (2010)
  
• Biodiversity "surpluses" and "deficits" are not novel issues
  - Trends in Ecology and Evolution 25(11):620-621 (2010)
  
• Response to 'Biodiversity "surpluses" and "deficits" are not novel issues': We agree
  - Trends in Ecology and Evolution 25(11):621-622 (2010)
  
• Artifacts of the evolving mind: what tool use tells us about early human cognition
  - Trends in Ecology and Evolution 25(11):622-623 (2010)
  
• Popular ants with style and substance
  - Trends in Ecology and Evolution 25(11):623-624 (2010)
  
• Aliens, globalization, and biodiversity
  - Trends in Ecology and Evolution 25(11):624-625 (2010)
  
• Three roads diverged? Routes to phylogeographic inference
  - Trends in Ecology and Evolution 25(11):626-632 (2010)
  Phylogeographic methods facilitate inference of the geographical history of genetic lineages. Recent examples explore human migration and the origins of viral pandemics. There is longstanding disagreement over the use and validity of certain phylogeographic inference methodologies. In this paper, we highlight three distinct frameworks for phylogeographic inference to give a taste of this disagreement. Each of the three approaches presents a different viewpoint on phylogeography, most fundamentally on how we view the relationship between the inferred history of a sample and the history of the population the sample is embedded in. Satisfactory resolution of this relationship between history of the tree and history of the population remains a challenge for all but the most trivial models of phylogeographic processes. Intriguingly, we believe that some recent methods that entirely avoid inference about the history of the population will eventually help to reach a resolution .
• Rising to the challenge of sustaining coral reef resilience
  - Trends in Ecology and Evolution 25(11):633-642 (2010)
  Phase-shifts from one persistent assemblage of species to another have become increasingly commonplace on coral reefs and in many other ecosystems due to escalating human impacts. Coral reef science, monitoring and global assessments have focused mainly on producing detailed descriptions of reef decline, and continue to pay insufficient attention to the underlying processes causing degradation. A more productive way forward is to harness new theoretical insights and empirical information on why some reefs degrade and others do not. Learning how to avoid undesirable phase-shifts, and how to reverse them when they occur, requires an urgent reform of scientific approaches, policies, governance structures and coral reef management.
• Stochastic models of population extinction
  - Trends in Ecology and Evolution 25(11):643-652 (2010)
  Theoretical ecologists have long sought to understand how the persistence of populations depends on biotic and abiotic factors. Classical work showed that demographic stochasticity causes the mean time to extinction to increase exponentially with population size, whereas variation in environmental conditions can lead to a power-law scaling. Recent work has focused especially on the influence of the autocorrelation structure ('color') of environmental noise. In theoretical physics, there is a burst of research activity in analyzing large fluctuations in stochastic population dynamics. This research provides powerful tools for determining extinction times and characterizing the pathway to extinction. It yields, therefore, sharp insights into extinction processes and has great potential for further applications in theoretical biology.
• Do consistent individual differences in metabolic rate promote consistent individual differences in behavior?
  - Trends in Ecology and Evolution 25(11):653-659 (2010)
  Consistent individual differences (CIDs) in behavior are a widespread phenomenon in animals, but the proximate reasons for them are unresolved. We discuss evidence for the hypothesis that CIDs in energy metabolism, as reflected by resting metabolic rate (RMR), promote CIDs in behavior patterns that either provide net energy (e.g. foraging activity), and/or consume energy (e.g. courtship activity). In doing so, we provide a framework for linking together RMR, behavior, and life-history productivity. Empirical studies suggest that RMR is (a) related to the capacity to generate energy, (b) repeatable, and (c) correlated with behavioral output (e.g. aggressiveness) and productivity (e.g. growth). We conclude by discussing future research directions to clarify linkages between behavior and energy metabolism in this emerging research area.
• Chromosomal speciation revisited: rearranging theory with pieces of evidence
  - Trends in Ecology and Evolution 25(11):660-669 (2010)
  The suggestion that chromosomal rearrangements play a role in speciation resulted from the observation that heterokaryotypes are often infertile. However, the first chromosomal speciation models were unsatisfactory and data available to test them was scarce. Recently, large amounts of data have become available and new theoretical models have been developed explaining how rearrangements facilitate speciation in the face of gene flow. Here, we re-examine theoretical predictions and revisit different sources of data. Although rearrangements are often associated with increased levels of divergence, unequivocal demonstration that their role in suppressing recombination results in speciation is often lacking. Finally, we question some previous predictions and suggest new empirical and theoretical approaches to understanding the relevance of rearrangements in the origin of species.
• How understanding aboveground–belowground linkages can assist restoration ecology
  - Trends in Ecology and Evolution 25(11):670-679 (2010)
  The topic of aboveground–belowground linkages has seen much recent activity, resulting in several conceptual advances regarding plant–soil feedbacks, multitrophic interactions, and how organisms drive ecosystem processes. Although restoration ecology has been rapidly evolving as a scientific discipline, the principles that have developed regarding aboveground–belowground linkages have yet to be thoroughly integrated into it. In this review, we conceptually integrate the role of aboveground–belowground linkages with the principles of restoration ecology through a framework that transcends multiple levels of ecological organization, and illustrate its application through three examples: restoration of abandoned land, reversal of biological invasions, and restoration of natural disturbances. We conclude that this integration can greatly assist restoration ecology, through aiding identification of effective invention practices and prediction of ecosystem recovery.

Hot off the presses! Feb 01 Trends in Ecology & Evolution

The Feb 01 issue of the Trends in Ecology & Evolution is now up on Pubget (About Trends in Ecology & Evolution): if you're at a subscribing institution, just click the link in the latest link at the home page. (Note you'll only be able to get all the PDFs in the issue if your institution subscribes to Pubget.)

Latest Articles Include:

• Editorial Board
  - Trends in Ecology and Evolution 26(2):i (2011)
  
• Basic research in evolution and ecology enhances forensics
  - Trends in Ecology and Evolution 26(2):53-55 (2011)
  In 2009, the National Research Council recommended that the forensic sciences strengthen their grounding in basic empirical research to mitigate against criticism and improve accuracy and reliability. For DNA-based identification, this goal was achieved under the guidance of the population genetics community. This effort resulted in DNA analysis becoming the 'gold standard' of the forensic sciences. Elsewhere, we proposed a framework for streamlining research in decomposition ecology, which promotes quantitative approaches to collecting and applying data to forensic investigations involving decomposing human remains. To extend the ecological aspects of this approach, this review focuses on forensic entomology, although the framework can be extended to other areas of decomposition.
• Academic strategies in a funding crisis: research competitor, ruderal or university teacher?
  - Trends in Ecology and Evolution 26(2):56-57 (2011)
  
• Recent developments in sociobiology and the scientific method
  - Trends in Ecology and Evolution 26(2):57-58 (2011)
  
• 'Linguistic injustice' is not black and white
  - Trends in Ecology and Evolution 26(2):58-59 (2011)
  
• Conservation science must engender hope to succeed
  - Trends in Ecology and Evolution 26(2):59-60 (2011)
  
• Data archiving in ecology and evolution: best practices
  - Trends in Ecology and Evolution 26(2):61-65 (2011)
  Many ecology and evolution journals have recently adopted policies requiring that data from their papers be publicly archived. I present suggestions on how data generators, data re-users, and journals can maximize the fairness and scientific value of data archiving. Data should be archived with enough clarity and supporting information that they can be accurately interpreted by others. Re-users should respect their intellectual debt to the originators of data through citation both of the paper and of the data package. In addition, journals should consider requiring that all data for published papers be archived, just as DNA sequences must be deposited in GenBank. Data are another valuable part of the legacy of a scientific career and archiving them can lead to new scientific insights. Archiving also increases opportunities for credit to be given to the scientists who originally collected the data.
• Hypothesis testing in biogeography
  - Trends in Ecology and Evolution 26(2):66-72 (2011)
  Often, biogeography is applied only as a narrative addition to phylogenetic studies and lacks scientific rigour. However, if research questions are framed as hypotheses, biogeographical scenarios become testable. In this review, we explain some problems with narrative biogeography and show how the use of explicit hypotheses is changing understanding of how organisms came to be distributed as they are. Developing synergies between biogeography, ecology, molecular dating and palaeontology are providing novel data and hypothesis-testing opportunities. New approaches are challenging the classic 'Gondwana' paradigm and a more complicated history of the Southern Hemisphere is emerging, involving not only general drivers such as continental drift and niche conservatism, but also drowning and re-emergence of landmasses, biotic turnover and long-distance colonization.
• Vacant habitats in the Universe
  - Trends in Ecology and Evolution 26(2):73-80 (2011)
  The search for life on other planets usually makes the assumption that where there is a habitat, it will contain life. On the present-day Earth, uninhabited habitats (or vacant habitats) are rare, but might occur, for example, in subsurface oils or impact craters that have been thermally sterilized in the past. Beyond Earth, vacant habitats might similarly exist on inhabited planets or on uninhabited planets, for example on a habitable planet where life never originated. The hypothesis that vacant habitats are abundant in the Universe is testable by studying other planets. In this review, I discuss how the study of vacant habitats might ultimately inform an understanding of how life has influenced geochemical conditions on Earth.
• Animals and the invention of the Phanerozoic Earth system
  - Trends in Ecology and Evolution 26(2):81-87 (2011)
  Animals do not just occupy the modern biosphere, they permeate its structure and define how it works. Their unique combination of organ-grade multicellularity, motility and heterotrophic habit makes them powerful geobiological agents, imposing myriad feedbacks on nutrient cycling, productivity and environment. Most significantly, animals have 'engineered' the biosphere over evolutionary time, forcing the diversification of, for example, phytoplankton, land plants, trophic structure, large body size, bioturbation, biomineralization and indeed the evolutionary process itself. This review surveys how animals contribute to the modern world and provides a basis for reconstructing ancient ecosystems. Earlier, less animal-influenced biospheres worked quite differently from the one currently occupied, with the Ediacaran–Cambrian radiation of organ-grade animals marking a fundamental shift in macroecological and macroevolutionary expression.
• The evolution of the worldwide leaf economics spectrum
  - Trends in Ecology and Evolution 26(2):88-95 (2011)
  The worldwide leaf economic spectrum (WLES) is a strikingly consistent pattern of correlations among leaf traits. Although the WLES effectively summarizes variation in plant ecological strategies, little is known about its evolution. We reviewed estimates of natural selection and genetic variation for leaf traits to test whether the evolution of the WLES was limited by selection against unfit trait combinations or by genetic constraints. There was significant selection for leaf traits on both ends of the WLES spectrum, as well as significant genetic variation for these traits. In addition, genetic correlations between WLES traits were variable in strength and direction. These data suggest that genetic constraints have had a smaller role than selection in the evolution of the WLES.
• Dynamic disequilibrium of the terrestrial carbon cycle under global change
  - Trends in Ecology and Evolution 26(2):96-104 (2011)
  In this review, we propose a new framework, dynamic disequilibrium of the carbon cycles, to assess future land carbon-sink dynamics. The framework recognizes internal ecosystem processes that drive the carbon cycle toward equilibrium, such as donor pool-dominated transfer; and external forces that create disequilibrium, such as disturbances and global change. Dynamic disequilibrium within one disturbance–recovery episode causes temporal changes in the carbon source and sink at yearly and decadal scales, but has no impacts on longer-term carbon sequestration unless disturbance regimes shift. Such shifts can result in long-term regional carbon loss or gain and be quantified by stochastic statistics for use in prognostic modeling. If the regime shifts result in ecosystem state changes in regions with large carbon reserves at risk, the global carbon cycle might be destabilized.

Hot off the presses! Dec 01 Trends in Ecology & Evolution

The Dec 01 issue of the Trends in Ecology & Evolution is now up on Pubget (About Trends in Ecology & Evolution): if you're at a subscribing institution, just click the link in the latest link at the home page. (Note you'll only be able to get all the PDFs in the issue if your institution subscribes to Pubget.)

Latest Articles Include:

• Editorial Board
  - Trends in Ecology and Evolution 25(12):i (2010)
  
• Light pollution as a biodiversity threat
  - Trends in Ecology and Evolution 25(12):681-682 (2010)
  
• Swarm intelligence in plant roots
  - Trends in Ecology and Evolution 25(12):682-683 (2010)
  
• Astrobiology in Antarctica
  - Trends in Ecology and Evolution 25(12):683-684 (2010)
  
• Community ecology: stasis, evolution or revolution?
  - Trends in Ecology and Evolution 25(12):684-685 (2010)
  
• Names are key to the big new biology
  - Trends in Ecology and Evolution 25(12):686-691 (2010)
  Those who seek answers to big, broad questions about biology, especially questions emphasizing the organism (taxonomy, evolution and ecology), will soon benefit from an emerging names-based infrastructure. It will draw on the almost universal association of organism names with biological information to index and interconnect information distributed across the Internet. The result will be a virtual data commons, expanding as further data are shared, allowing biology to become more of a 'big science'. Informatics devices will exploit this 'big new biology', revitalizing comparative biology with a broad perspective to reveal previously inaccessible trends and discontinuities, so helping us to reveal unfamiliar biological truths. Here, we review the first components of this freely available, participatory and semantic Global Names Architecture.
• Assessing rapid evolution in a changing environment
  - Trends in Ecology and Evolution 25(12):692-698 (2010)
  Climate change poses a serious threat to species persistence. Effective modelling of evolutionary responses to rapid climate change is therefore essential. In this review we examine recent advances in phylogenetic comparative methods, techniques normally used to study adaptation over long periods, which allow them to be applied to the study of adaptation over shorter time scales. This increased applicability is largely due to the emergence of more flexible models of character evolution and the parallel development of molecular technologies that can be used to assess adaptive variation at loci scattered across the genome. The merging of phylogenetic and population genetic approaches to the study of adaptation has significant potential to advance our understanding of rapid responses to environmental change.
• Making statistics biologically relevant in fragmented landscapes
  - Trends in Ecology and Evolution 25(12):699-704 (2010)
  The biological impacts of habitat fragmentation are routinely assessed using standard statistical modelling techniques that are used across many ecological disciplines. However, to assess the biological relevance of fragmentation impacts, we must consider an extra, spatial dimension to the standard statistical model: the biological importance of a significant and well supported model with large effect sizes crucially depends on the configuration of habitat within the study area. We argue that mapping the outputs from statistical models across a study area generates biologically meaningful estimates of fragmentation impacts. Integrating traditional statistical approaches with geographic information systems will facilitate rigorous comparisons of fragmentation impacts between taxa, studies and ecosystems.
• Adaptation genomics: the next generation
  - Trends in Ecology and Evolution 25(12):705-712 (2010)
  Understanding the genetics of how organisms adapt to changing environments is a fundamental topic in modern evolutionary ecology. The field is currently progressing rapidly because of advances in genomics technologies, especially DNA sequencing. The aim of this review is to first briefly summarise how next generation sequencing (NGS) has transformed our ability to identify the genes underpinning adaptation. We then demonstrate how the application of these genomic tools to ecological model species means that we can start addressing some of the questions that have puzzled ecological geneticists for decades such as: How many genes are involved in adaptation? What types of genetic variation are responsible for adaptation? Does adaptation utilise pre-existing genetic variation or does it require new mutations to arise following an environmental change?
• Species differences in responses to captivity: stress, welfare and the comparative method
  - Trends in Ecology and Evolution 25(12):713-721 (2010)
  Approximately 26 billion animals, spanning over 10 000 species, are kept on farms and in zoos, conservation breeding centers, research laboratories and households. Captive animals are often healthier, longer-lived and more fecund than free-living conspecifics, but for some species the opposite is true. Captivity is a very long way from the ideal 'common garden' often assumed by evolutionary and ecological researchers using data for captive animals. The use of comparative methods to investigate the fundamental biological causes of these species differences would help to improve husbandry and enclosure design, and might even reveal relationships between susceptibilities to poor captive welfare and susceptibilities to anthropogenic threat in the wild. Studies of these species differences could also inspire and facilitate 'evo-mecho' research into the functions of behavioral control mechanisms.

Hot off the presses! May 01 Trends Pl Sci

The May 01 issue of the Trends Pl Sci is now up on Pubget (About Trends Pl Sci): if you're at a subscribing institution, just click the link in the latest link at the home page. (Note you'll only be able to get all the PDFs in the issue if your institution subscribes to Pubget.)

Latest Articles Include:

• Editorial Board
  - Trends Pl Sci 16(5):i (2011)
  
• Combining phenotypic data from ordinal rating scales in multiple plant experiments
  - Trends Pl Sci 16(5):235-237 (2011)
  
• Self-incompatibility: Smi silences through a novel sRNA pathway
  - Trends Pl Sci 16(5):238-241 (2011)
  Self-incompatibility in Brassicaceae is determined by the interaction between S-Locus Protein 11 (SP11) on the pollen and S-receptor kinase (SRK) in the stigma. Pollen from heterozygotes generally displays products of both SP11 alleles, but in some heterozygotes SP11 expression is monoallelic, with one allele (SP11R) being silenced by promoter methylation. An exciting development in understanding the mechanism behind monoallelic silencing came recently when Y. Tarutani et al. [Nature 2010;466:983–986] identified a 24-nucleotide sRNA (termed Smi) derived from a non-coding gene within the dominant S-haplotype, and suggested that Smi directs promoter methylation. We propose that rather than having a direct effect on DNA methylation, Smi is the first step in a novel cis-acting siRNA pathway that directs widespread monoallelic SP11R promoter methylation.
• MicroRNA misregulation: an overlooked factor generating somaclonal variation?
  - Trends Pl Sci 16(5):242-248 (2011)
  Somaclonal variation is an important phenomenon that can be observed at high levels in plant tissue culture. Although known to science since plant cell culture techniques were first developed, its origins remain mysterious. Here, we propose that misregulation of microRNAs and small RNA pathways can make a significant contribution to the phenomenon. For many reasons, microRNAs and related small RNAs appear ideal candidates. Their mode of action gives them disproportionate influence over the transcriptome, proteome and epigenome. They regulate important developmental and physiological events such as meristem formation, phase changes and hormone responses. However, the genomic locations of microRNA genes and their unique biogenesis might make them unusually susceptible to aberrant regulation in vitro.
• Jasmonate-induced defenses: a tale of intelligence, collaborators and rascals
  - Trends Pl Sci 16(5):249-257 (2011)
  Plants have sophisticated defense systems to protect their tissues against the attack of herbivorous organisms. Many of these defenses are orchestrated by the oxylipin jasmonate. A growing body of evidence indicates that the expression of jasmonate-induced responses is tightly regulated by the ecological context of the plant. Ecological information is provided by molecular signals that indicate the nature of the attacker, the value of the attacked organs, phytochrome status and thereby proximity of competing plants, association with beneficial organisms and history of plant interactions with pathogens and herbivores. This review discusses recent advances in this field and highlights the need to map the activities of informational modulators to specific control points within our emerging model of jasmonate signaling.
• MicroRNA networks and developmental plasticity in plants
  - Trends Pl Sci 16(5):258-264 (2011)
  Plant microRNAs (miRNAs) are embedded in regulatory networks that coordinate different gene expression programs in support of developmental plasticity. Modification of miRNA-target nodes during evolution might in turn underlie morphological and physiological diversity. A survey of the literature indicates that miRNA-target nodes themselves are organized in networks, and here we discuss some of the developmental traits they control along with possible interactions between miRNA and their targets. Because miRNAs and their interactions are not only at the heart of regulating many aspects of developmental plasticity, but because they also have an inherently quantitative mode of action, they present important targets for biotechnology applications.
• Viral suppressors of RNA silencing
  - Trends Pl Sci 16(5):265-272 (2011)
  The infection and replication of viruses in the host induce diverse mechanisms for combating viral infection. One of the best-studied antiviral defence mechanisms is based on RNA silencing. Consistently, several viral suppressors of RNA silencing (VSRs) have been identified from almost all plant virus genera, which are surprisingly diverse within and across kingdoms, exhibiting no obvious sequence similarities. VSRs efficiently inhibit host antiviral responses by interacting with the key components of cellular silencing machinery, often mimicking their normal cellular functions. Recent findings have revealed that the impact of VSRs on endogenous pathways is more complex and profound than had been estimated thus far. This review highlights the current understanding of and new insights into the mechanisms and functions of plant VSRs.
• Organization and dynamics of plant interphase chromosomes
  - Trends Pl Sci 16(5):273-281 (2011)
  Eukaryotic chromosomes occupy distinct territories within interphase nuclei. The arrangement of chromosome territories (CTs) is important for replication, transcription, repair and recombination processes. Our knowledge about interphase chromatin arrangement is mainly based on results from in situ labeling approaches. The phylogenetic affiliation of a species, cell cycle, differentiation status and environmental factors are all likely to influence interphase nuclear architecture. In this review we survey current data about relative positioning of CTs, somatic pairing of homologs, and sister chromatid alignment in meristematic and differentiated tissues, using data derived mainly from Arabidopsis thaliana, wheat (Triticum aestivum) and their relatives. We discuss morphological constraints and epigenetic impacts on nuclear architecture, the evolutionary stability of CT arrangements, and alterations of nuclear architecture during transcription and repair.
• Fast-forward genetics enabled by new sequencing technologies
  - Trends Pl Sci 16(5):282-288 (2011)
  New sequencing technologies are dramatically accelerating progress in forward genetics, and the use of such methods for the rapid identification of mutant alleles will be soon routine in many laboratories. A straightforward extension will be the cloning of major-effect genetic variants in crop species. In the near future, it can be expected that mapping by sequencing will become a centerpiece in efforts to discover the genes responsible for quantitative trait loci. The largest impact, however, might come from the use of these strategies to extract genes from non-model, non-crop plants that exhibit heritable variation in important traits. Deployment of such genes to improve crops or engineer microbes that produce valuable compounds heralds a potential paradigm shift for plant biology.

Hot off the presses! Aug 01 Trends Ecol Evol

The Aug 01 issue of the Trends Ecol Evol is now up on Pubget (About Trends Ecol Evol): if you're at a subscribing institution, just click the link in the latest link at the home page. (Note you'll only be able to get all the PDFs in the issue if your institution subscribes to Pubget.)

Latest Articles Include:

• Editorial Board
  - Trends Ecol Evol 26(8):i (2011)
  
• Biodiversity databases should gain support from journals
  - Trends Ecol Evol 26(8):377-378 (2011)
  
• The need for jumpstarting amphibian genome projects
  - Trends Ecol Evol 26(8):378-379 (2011)
  
• Active scepticism must drive biodiversity conservation science
  - Trends Ecol Evol 26(8):379-380 (2011)
  
• Avoiding the fate of Troy: response to Arlettaz et al
  - Trends Ecol Evol 26(8):380 (2011)
  We agree entirely with Arlettaz et al. [1] that we face an environmental crisis of extraordinary proportions. However, their analysis of how to respond perfectly illustrates our point. In particular, we would transpose their statement 'Although we agree that communication strategies must accommodate human psychology to succeed, we believe that neglecting or euphemizing the dramatic impact that humans have on the biosphere, just through fear of the Cassandra syndrome when addressing an inconvenient truth, is not an acceptable alternative discourse.' to 'Although acknowledging the dramatic impact humans exert on the biosphere, there is no acceptable alternative discourse; to adopting communication strategies that accommodate human psychology.'
• Toward an integrated concept of the phenotype
  - Trends Ecol Evol 26(8):381-382 (2011)
  
• Importance versus intensity of ecological effects: why context matters
  - Trends Ecol Evol 26(8):383-388 (2011)
  In any ecological study, target organisms are usually impacted by multiple environmental drivers. In plant interaction research, recent debate has focussed on the importance of competition; that is, its role in regulating plant success relative to other environmental drivers. Despite being clearly and specifically defined, the apparently simple concept of the importance of competition has been commonly overlooked, and its recognition has helped reconcile long-running debates about the dependence of competition on environmental severity. In this review, we argue that extending this formalised concept of importance to other aspects of ecology would be beneficial. We discuss approaches for measuring importance, and provide examples where explicit acknowledgement of this simple concept might promote understanding and resolve debate.
• Magic traits in speciation: 'magic' but not rare?
  - Trends Ecol Evol 26(8):389-397 (2011)
  Speciation with gene flow is greatly facilitated when traits subject to divergent selection also contribute to non-random mating. Such traits have been called 'magic traits', which could be interpreted to imply that they are rare, special, or unrealistic. Here, we question this assumption by illustrating that magic traits can be produced by a variety of mechanisms, including ones in which reproductive isolation arises as an automatic by-product of adaptive divergence. We also draw upon the theoretical literature to explore whether magic traits have a unique role in speciation or can be mimicked in their effects by physically linked trait-complexes. We conclude that magic traits are more frequent than previously perceived, but further work is needed to clarify their importance.
• Decision-making under great uncertainty: environmental management in an era of global change
  - Trends Ecol Evol 26(8):398-404 (2011)
  Global change issues are complex and the consequences of decisions are often highly uncertain. The large spatial and temporal scales and stakes involved make it important to take account of present and potential consequences in decision-making. Standard approaches to decision-making under uncertainty require information about the likelihood of alternative states, how states and actions combine to form outcomes and the net benefits of different outcomes. For global change issues, however, the set of potential states is often unknown, much less the probabilities, effect of actions or their net benefits. Decision theory, thresholds, scenarios and resilience thinking can expand awareness of the potential states and outcomes, as well as of the probabilities and consequences of outcomes under alternative decisions.
• Faunal histories from Holocene ancient DNA
  - Trends Ecol Evol 26(8):405-413 (2011)
  Recent studies using ancient DNA have been instrumental in advancing understanding of the impact of Holocene climate change on biodiversity. Ancient DNA has been used to track demography, migration and diversity, and is providing new insights into the long-term dynamics of species and population distributions. The Holocene is key to understanding how the past has impacted on the present, as it bridges the gap between contemporary phylogeographic studies and those with inference on Pleistocene patterns, based on ancient DNA studies. Here, we examine the major patterns of Holocene faunal population dynamics and connectivity; highlighting the dynamic nature of species and population responses to Holocene climatic change, thereby providing an 'analogue' for understanding potential impacts of future change.
• Using new tools to solve an old problem: the evolution of endothermy in vertebrates
  - Trends Ecol Evol 26(8):414-423 (2011)
  During the past 30 years, the evolution of endothermy has been a topic of keen interest to palaeontologists and evolutionary physiologists. While palaeontologists have found abundant Permian and Triassic fossils, suggesting important clues regarding the timing of origin of endothermy, physiologists have proposed several plausible hypotheses of how the metabolic elevation leading to endothermy could have occurred. More recently, molecular biologists have developed powerful tools to infer past adaptive processes, and gene expression mechanisms that describe the organization of genomes into phenotypes. Here, we argue that the evolution of endothermy could now be elucidated based on a joint, and perhaps unprecedented, effort of researchers from the fields of genomics, physiology and evolution.
• The contribution of statistical physics to evolutionary biology
  - Trends Ecol Evol 26(8):424-432 (2011)
  Evolutionary biology shares many concepts with statistical physics: both deal with populations, whether of molecules or organisms, and both seek to simplify evolution in very many dimensions. Often, methodologies have undergone parallel and independent development, as with stochastic methods in population genetics. Here, we discuss aspects of population genetics that have embraced methods from physics: non-equilibrium statistical mechanics, travelling waves and Monte-Carlo methods, among others, have been used to study polygenic evolution, rates of adaptation and range expansions. These applications indicate that evolutionary biology can further benefit from interactions with other areas of statistical physics; for example, by following the distribution of paths taken by a population through time.

Hot off the presses! Jun 25 Nature

The Jun 25 issue of the Nature is now up on Pubget (About Nature): if you're at a subscribing institution, just click the link in the latest link at the home page. (Note you'll only be able to get all the PDFs in the issue if your institution subscribes to Pubget.)

Latest Articles Include:

• Cheerleader or watchdog?
  - Nature 459(7250):1033 (2009)
  Science journalism is under threat. What can scientists do to help?
• Raising the standards
  - Nature 459(7250):1033-1034 (2009)
  A fledgling effort in China will show people what is happening on the environmental front.
• Orphan giant
  - Nature 459(7250):1034 (2009)
  Strong advocacy is needed if progress is to be made against tuberculosis.
• Animal biology: Birds of a feather
  - Nature 459(7250):1036 (2009)
  
• Astronomy: Honing the Hubble constant
  - Nature 459(7250):1036 (2009)
  
• Neurobiology: Sweet memories
  - Nature 459(7250):1036 (2009)
  
• Chemistry: The tiniest acid drop
  - Nature 459(7250):1036 (2009)
  
• Nanotechnology: Mass spec goes mechanical
  - Nature 459(7250):1036 (2009)
  
• Atmospheric science: Rain on physics
  - Nature 459(7250):1036-1037 (2009)
  
• Biology: A light touch
  - Nature 459(7250):1037 (2009)
  
• Organic chemistry: Give and take
  - Nature 459(7250):1037 (2009)
  
• Genetics: Depression link revoked
  - Nature 459(7250):1037 (2009)
  
• Cognitive science: The tool becomes him
  - Nature 459(7250):1037 (2009)
  
• Journal club
  Fuhrer MS - Nature 459(7250):1037 (2009)
  
• US human spacefaring questioned
  Hand E - Nature 459(7250):1038-1039 (2009)
  When it comes to how NASA should spend its money putting people in space, just about everyone has an opinion — some of them strident. But at the moment, the opinions that matter most are those in a ten-person committee that listened quietly as key players pleaded their case at a meeting on 17 June in Washington DC.
• New protein structures replace the old
  Sanderson K - Nature 459(7250):1038-1039 (2009)
  Protein structures are getting regular makeovers with the help of 're-refinement' software developed by Dutch structural biologists. The Protein Data Bank (PDB) holds nearly 53,000 three-dimensional structures of protein molecules and nucleic acids that have mainly been deciphered through X-ray crystallography.
• Climate burden of refrigerants rockets
  - Nature 459(7250):1040 (2009)
  Modern refrigerants designed to protect the ozone layer are poised to become a major contributor to global warming because of their future explosive growth in the developing world, scientists report this week. Hydrofluorocarbon chemicals (HFCs) were developed to phase out ozone-depleting gases, in response to the Montreal Protocol.
• Deficit dooms Swedish gene institute
  Dalton R - Nature 459(7250):1040-1041 (2009)
  Cost overruns have sliced into the historically important biology programme of Sweden's Lund University, culminating in a departmental reorganization that has some scientists fuming. The Institute of Genetics, where in the winter of 1955–56 the correct number of human chromosomes was established (J.
• G8 cancels science parley
  Abbott A - Nature 459(7250):1041 (2009)
  The Italian government has caught scientists off guard by cancelling the G8 science and technology meeting that was to have begun on 25 June. The meeting would have brought together science ministers of the G8 nations to discuss issues such as how to monitor climate change and maintain environment-friendly energy supplies.
• Florida universities hit by funding crisis
  Schrope M - Nature 459(7250):1042-1043 (2009)
  This March, Michael Perfit, chair of the geology department at the University of Florida in Gainesville, learned that budget cuts might slash 11 of the 24 faculty and staff positions in his group. "It was like someone saying your whole family was killed in a car accident," he says.
• Biology society narrows Chinese rifts
  Cyranoski D - Nature 459(7250):1044 (2009)
  Scientific relations warm between mainland China and Taiwan. Warming scientific relations between Taiwan and mainland China were on view last week at a meeting in Taipei of the Society of Chinese Bioscientists in America (SCBA). Historically a Taiwanese-dominated academic networking group, the society last week announced its first president-elect born and raised in mainland China: Xiao-Fan Wang, a cancer biologist at Duke University in Durham, North Carolina. And a bill introduced in the Taiwanese legislature in January could mean that many more mainland Chinese scientists will be soon be living and working in Taiwan. The legislation would permit Taiwanese universities to recognize university degrees from mainland institutions such as Peking University and Tsinghua University. "It's ridiculous that we don't," says Ji-Wang Chern, dean of research and development at the National Taiwan University in Taipei. Carmay Lim, a computational biophysicist at the Academia Sinica in Taipei, says she has not been able to offer PhD positions to mainland students whom she wanted to stay on in her lab. "Because of the politics between Taiwan and [mainland] China, scientists like myself lose good students to universities in other parts of the world," she says. Few details of the bill are publicly available, but Chern says it is likely to be adopted. The proposal aligns with generally better relations between mainland China and Taiwan, especially since Ma Ying-jeou became president of Taiwan in May 2008. The easing of tensions could be seen in the relaxed atmosphere of the SCBA meeting. Society scientists recall past episodes in which a senior education ministry official from Beijing stormed out after not being allowed to move her talk ahead of a Taiwanese scientist, and a 2001 meeting where Nobel laureate Yuan Tseh Lee suggested that China was hurting chances for diplomacy and scientific collaboration by building up missiles aimed at Taiwan. His counterpart from the Chinese Academy of Sciences defended China's actions as a valid protection against imperialism. "There has been nothing like that here," says Chung S. Yang, a cancer researcher at Rutgers University in Piscataway, New Jersey, and former SCBA president. ADVERTISEMENT New society president Kuan-Teh Jeang, a virologist at the US National Institutes of Health in Bethesda, Maryland, says the SCBA will be changing dramatically in ways that could help to unite Chinese scientists. He hopes to turn it into an organization with more lobbying power, an enhanced role in advising government and academic institutions on interactions with Chinese institutions overseas and, possibly within a year, its own online open-access journal. "We need to be ready to extend beyond niche special interests," he says. "We should participate in the mainstream." Add your own comment You can be as critical or controversial as you like, but please don't get personal or offensive, and do keep it brief. Remember this is for feedback and discussion - not for publishing papers, press releases or advertisements, for example. If you ramble on in an annoying way too often, we may remove your posting privileges. You need to be registered with Nature to leave a comment. Please log in or register as a new user. You will be re-directed back to this page. * Log in / register
• Chemistry publisher in move from print journals
  - Nature 459(7250):1045 (2009)
  
• Researchers urge action on medical-isotope shortage
  - Nature 459(7250):1045 (2009)
  
• Climate projections taken to finest detail
  - Nature 459(7250):1045 (2009)
  
• EU legislation increases clinical-trial workloads
  - Nature 459(7250):1045 (2009)
  A review of the effects of the legislation governing clinical trials in the European Union has backed up some researchers' complaints about the regulations. The 2001 European Clinical Trials Directive, which came into force from 2004, was intended to harmonize the rules governing clinical trials. But it has faced criticism from researchers who think it is overly complex and bureaucratic (see Nature doi:10.1038/news.2009.163; 2009). Last week, the final report from the European Commission-funded project assessing the directive concluded that the measures increase workloads on trial sponsors and ethics committees, and delay the start of trials. The number of commercially-sponsored clinical trials in Europe increased by about 30% between 2003 and 2007, the report adds, whereas the number of non-commercially sponsored clinical trials remained constant. Add your own comment You can be as critical or controversial as you like, but please don't get personal or offensive, and do keep it brief. Remember this is for feedback and discussion - not for publishing papers, press releases or advertisements, for example. If you ramble on in an annoying way too often, we may remove your posting privileges. You need to be registered with Nature to leave a comment. Please log in or register as a new user. You will be re-directed back to this page. * Log in / register
• More financial woes for climate satellites
  - Nature 459(7250):1045 (2009)
  NOAA Ineffective management and cost overruns are plaguing an already troubled satellite system for tracking weather and climate, the US Government Accountability Office (GAO) reported to Congress on 17 June. The National Polar-orbiting Operational Environmental Satellite System (NPOESS; illustrated above) was conceived in 1994 as a three-way project between the Department of Defense, the National Oceanic and Atmospheric Administration (NOAA) and NASA. "This tri-agency experiment has been an epic failure," says the GAO's David Powner. In 2002, NPOESS was supposed to cost $7 billion for six satellites, with the first to launch in 2009 (Nature 782–785; 2007). Auditors now think that the current estimate — $14 billion for four satellites beginning in 2014 — is at least $1 billion off the mark. A separate report, conducted by an independent review team for NPOESS management, recommends that the White House appoint a top-level decision-maker, and suggests that NOAA should be made lead agency on the system. Add your own comment You can be as critical or controversial as you like, but please don't get personal or offensive, and do keep it brief. Remember this is for feedback and discussion - not for publishing papers, press releases or advertisements, for example. If you ramble on in an annoying way too often, we may remove your posting privileges. You need to be registered with Nature to leave a comment. Please log in or register as a new user. You will be re-directed back to this page. * Log in / register
• Journal of the century
  - Nature 459(7250):1045 (2009)
  With a new impact factor of 31.434, up from 28.103 last year, Nature maintains its position as the leading weekly science journal, according to the 2008 Journal Citation Report. Also, Nature was last week named 'journal of the century' by the BioMedical & Life Sciences Division (DBIO) of the Special Libraries Association (SLA). Voted for by DBIO's 686 members, the award was given to celebrate the SLA's centenary and recognizes the most influential journal of the past 100 years. Add your own comment You can be as critical or controversial as you like, but please don't get personal or offensive, and do keep it brief. Remember this is for feedback and discussion - not for publishing papers, press releases or advertisements, for example. If you ramble on in an annoying way too often, we may remove your posting privileges. You need to be registered with Nature to leave a comment. Please log in or register as a new user. You will be re-directed back to this page. * Log in / register
• Cyberinfrastructure: Feed me data
  Ledford H - Nature 459(7250):1047-1049 (2009)
  In April 2008, Richard Jorgensen found himself in front of a group of expectant researchers gathered in Cold Spring Harbor Laboratory, New York. The pressure was on: Jorgensen had recently been placed in charge of iPlant, a US$50-million, five-year programme funded by the National Science Foundation (NSF).
• Science journalism: Breaking the convention?
  Brumfiel G - Nature 459(7250):1050-1051 (2009)
  Blogs and Twitter are opening up meetings to those not actually there. Does that mean too much access to science in the raw, asks Geoff Brumfiel. Download a PDF of this story. Last July, Lars Jensen carried a small shoulder bag of equipment into the atrium of the glass-and-steel conference centre in Toronto, Ontario. Jensen, a bioinformatician at the University of Copenhagen, was one of about 1,400 researchers at the annual Intelligent Systems for Molecular Biology meeting. With him he had the tools of any modern conference attendee: a laptop, a handheld PDA and a digital camera to snap a few photos of his trip. Jensen immediately did what most researchers do: he logged on to the wireless network. He used his PDA to check FriendFeed — an online social network similar to Facebook that is popular among biologists. "Anyone else signed up for the 'orienteering' event today?" Shirley Wu, a graduate student at Stanford University, California, had written on a page that members had already devoted to the conference. "Nah," Jensen typed, "bloggers don't need icebreaker events ;-)" Jensen's joke about face-to-face contact proved prescient. Over the next few days, he and nearly 30 other researchers met mostly via their screens in the FriendFeed conference group. During sessions, many group members posted brief comments sent from their laptops or mobile phones to the popular website Twitter, and automatically cross-posted to FriendFeed. Some of these communiqués described a comment from a talk or the flavour of a session. Other posts were links to relevant papers, or photos from around the conference centre. At one point the group even served as a public address system: "HL33: Session Chair MIA — if anyone sees Yanay Ofran they may want to point him to the session," wrote Shannon McWeeney, a bioinformatics researcher at the Oregon Health & Science University in Portland. The virtual coverage "was not something that we had arranged beforehand", Jensen says. But by the time he and others were finished, hundreds of comments had been posted to the group. The information was so complete that Jensen, Wu and the other ring leaders were able to use it to write an authoritative conference summary that was later published (N. Saunders et al. PLoS Comp. Biol. e1000263; 2009). For technophiles and advocates of scientific openness, this is the way of the future. Online groups allow meeting attendees to post and discuss research as it is presented, and follow parallel sessions. They also provide an opportunity for researchers not at the meeting, as well as a far wider community, to actively participate in it. "I think it is extremely efficient," says Jean-Claude Bradley, a chemist at Drexel University in Philadelphia, Pennsylvania. Jonathan Eisen, an evolutionary biologist at the University of California, Davis, adds that 'twittering' about a presentation he is listening to helps him to focus. "I don't want to screw up and say something that's technically wrong or conceptually wrong," he says. But some worry that these tools will undermine meetings. By disseminating scientific results far beyond the lecture hall, blogging and social networking blurs the line between journalists and researchers. Scientists in competitive fields may be more reluctant to discuss new findings if they can be posted on the Internet within seconds. And at a time when many conference attendees are already surfing the web rather than paying attention to the presenter, messaging is yet another annoyance. "Frankly, it can be a distraction if people are typing on their keyboards in the meeting," says David Stewart, the director of meetings and courses at Cold Spring Harbor Laboratory in New York. "I could take pictures of every slide and it would be on the Internet within seconds." Lars Jensen Blogging without leave Last month, Stewart unwittingly found himself at the centre of the debate about such technologies at Cold Spring Harbor's annual Biology of Genomes meeting. The meeting was oversubscribed, and many researchers were interested in following the proceedings on the web. Cold Spring Harbor streamed video of the talks online for those who had registered and paid a fee, but an informal group of bloggers also began following events. Among them was Daniel MacArthur, a geneticist and author of the blog Genetic Future. MacArthur says that he decided to blog from the conference at the request of a number of people who couldn't attend. "They asked whether it would be possible to communicate interesting things during the sessions." MacArthur's comprehensive postings were read by many scientists but they irked journalists attending the meeting. The meeting rules stated that reporters had to seek permission from speakers before publishing material on their work, rules that Cold Spring Harbor instituted in part because some journals, such as Nature, discourage scientists from talking to the press before their work is published. But those rules didn't apply to scientist-bloggers like MacArthur and, after he posted details from a few talks, reporters contacted Stewart for clarification on the policies. The complaint was a wake-up call: "For the first time, I became aware that people were blogging about the data at the meeting," Stewart says. Blogging can create much thornier issues for researchers. Many presenters are already cautious about revealing unpublished results at meetings for fear that rivals in the audience might note them down. Now that the note-taking is taking place live and on the web, the speed and distance that information spreads has jumped to a new level. "With the set-up I have now, I would be able to sit in a conference, take pictures of every slide that is being shown, and it would be on the Internet within seconds, while the talk is still going on," says Jensen. This kind of direct-to-web exposure creates problems for many industrial and applied researchers. In the United States, patent applications must be filed within a year of any information becoming available to the public. The exact date of that 'public disclosure' used to be difficult to nail down, but no more, says Michael Natan, chief executive officer of Oxonica Materials, a nanotechnology company in Mountain View, California. In the Internet age, time-stamped photographs of a talk can let competitors know the exact minute a researcher presented a patentable result. Consequently, "people in industry will be much more circumspect about what they present in public", he says. Even basic researchers have reason to fret. Last year, a group of theoretical physicists photographed slides from a meeting presentation, extracted the data, and used them in their own analysis, which they published online (see Nature 7; 2008). In that case, the theorists were given permission by a presenter, and the photographs were properly cited, but the situation illustrates how easily data can find their way into the public sphere. In many fields, competition is so intense that you must conceal to survive, says Natan. "Frankly, it can be a distraction if people are typing on their keyboards in the meeting." David Stewart For denizens of the blogosphere, these sorts of concerns seem a little out of date. "I think scientific conferences are about your sharing with the world what you're doing," says Francis Ouellette, a researcher at the Ontario Institute for Cancer Research in Toronto, who twittered at the Cold Spring Harbor Meeting. "Whether or not the participant you're sharing with is in the room is somewhat inconsequential." Ouellette and many other active bloggers are also members of the 'open science' movement, which encourages researchers to make their data public as quickly as possible. Bradley sees this openness as a powerful deterrent to anyone hoping to scoop him at a conference because anything cribbed from his talk is already out on the Internet for everyone else to view. "If someone actually does copy something, I think it would be pretty embarrassing," he says, "it's already there, and it's indexed to Google." The rights of scientists Prompted by his recent experience, Stewart has come up with a pragmatic solution. At future meetings, anyone communicating information to third parties, whether by news story, blog or 'tweet', will now be required to ask presenters beforehand. "What we really want to do is to protect the rights of individual scientists to present their data in a pre-published form," he says. "I'm not saying don't blog, I'm saying blog by all means, but get permission." MacArthur says that the new policies seem like a fairly good compromise, but, he adds: "I'm hopeful that other conferences will tend to adopt more open policies." Conference organizers contacted by Nature had a wide range of policies on social networking. Many societies have banned digital photography in talks and poster sessions and some consider bloggers to be members of the media and subject them to certain reporting restrictions. However, almost nobody has developed a policy on when twittering is fair play. "This has not come up in the past but it may be something we consider in the future," says Kevin Wilson, a spokesman for the American Society for Cell Biology in Bethesda, Maryland. Journals are also pondering how best to handle social networking at meetings. Nature generally supports social media tools, says Philip Campbell, Nature's editor-in-chief. And as long as it's not a deliberate attempt to hype a new finding, he says that researchers should feel free to talk to colleagues who blog or twitter. Ginger Pinholster, the director of public programmes for the American Association for the Advancement of Science, the publisher of Science, agrees. As long as the scientist wasn't trying to promote his or her work to the public, it wouldn't be a problem. She adds that blogging unpublished results is a problem that "we just haven't run into yet". ADVERTISEMENT Although Cold Spring Harbor has opted for control, the organizers of the Intelligent Systems for Molecular Biology meeting are choosing total openness. When this year's meeting opens in Stockholm later this week, they are planning to fully embrace social networking tools. FriendFeed entries will be created for each talk at the meeting, and the entries for the keynote sessions will be posted directly to the meeting's main website. That means some people could get the buzz of the meeting without travelling to Stockholm at all. But that's not why Lars Jensen is staying at home this year. The main papers being presented have already been published, he says, so there won't be much new. He might follow the sessions online, but then again, he might catch up the old-fashioned way. "I have colleagues who are going," he says. "I can always ask them afterwards whether anything interesting happened." Add your own comment You can be as critical or controversial as you like, but please don't get personal or offensive, and do keep it brief. Remember this is for feedback and discussion - not for publishing papers, press releases or advertisements, for example. If you ramble on in an annoying way too often, we may remove your posting privileges. You need to be registered with Nature to leave a comment. Please log in or register as a new user. You will be re-directed back to this page. * Log in / register
• Interrogation: hard for psychologists to act as whistleblowers
  Jackson MR - Nature 459(7250):1052 (2009)
  I was disappointed in your Editorial 'Responsible interrogation' (Nature 459, 300; 2009). You accept the role of psychologists in secret interrogations because they can supposedly act as whistleblowers against inhumane treatment.
• Interrogation: our professional body forbids involvement
  Wagner LB - Nature 459(7250):1052 (2009)
  Your Editorial 'Responsible interrogation' (Nature 459, 300; 2009) takes a remarkably unscientific approach to the topic of psychologists' participation in national-security interrogations, in that it omits important current facts. The scale of this omission is comparable to failing to mention Helicobacter pylori in a discussion of peptic ulcers, the treatment of which was revolutionized by the discovery that most are caused by H. pylori
• Free will: it's a normal biological property, not a gift or a mystery
  Doyle RO - Nature 459(7250):1052 (2009)
  In his Essay 'Is free will an illusion?' (Nature 459, 164–165; 2009), Martin Heisenberg argues that humans must have free will because freedom of action has been demonstrated in other animals — including those as small as fruitflies and bacteria.
• Free will: emotions and consciousness could contribute
  Vermeersch E - Nature 459(7250):1052-1053 (2009)
  In his Essay 'Is free will an illusion?' (Nature 459, 164–165; 2009), Martin Heisenberg suggests that belief in free will is supported by quantum events.
• How air capture could help to promote a Copenhagen solution
  Chichilnisky G Eisenberger P - Nature 459(7250):1053 (2009)
  Your News Feature 'Sucking it up' (Nature 458, 1094–1097; 2009) reports on the issue of the capture of carbon dioxide from air. This is timely, as in February this year, President Obama and the Canadian Prime Minister, Stephen Harper, agreed to work together on carbon capture and sequestration as part of an effort to build a North American environmental and energy accord.
• Planck's power lies in its unique instrument combination
  Mandolesi N Planck LFI co-investigators - Nature 459(7250):1053 (2009)
  Your News Feature 'The test of inflation' (Nature 458, 820–824; 2009) highlights some of the exciting scientific data to be collected by the European Space Agency's Planck spacecraft, and the theoretical issues underlying its objectives to study the moments after the Big Bang.You discuss the new high-frequency 52-bolometer detector, but do not mention the 22-radiometer low-frequency instrument (LFI).
• Science journalism: Toppling the priesthood
  Murcott T - Nature 459(7250):1054-1055 (2009)
  In the first of three essays, Toby Murcott argues that the process of science needs to be opened up if journalists are to provide proper critique.
• Science journalism: Too close for comfort
  Rensberger B - Nature 459(7250):1055-1056 (2009)
  In the second of three essays, Boyce Rensberger tracks the progression of scientific correspondents from cheerleaders to watchdogs.
• Science journalism: The Arab boom
  El-Awady N - Nature 459(7250):1057 (2009)
  As research increases in Arab countries, the media is stepping up to report on it. In the third of three essays, Nadia El-Awady says the local journalism has much room for improvement.
• From rubber ducks to ocean gyres
  - Nature 459(7250):1058-1059 (2009)
  The tale of Curtis Ebbesmeyer's use of beachcombing to reveal patterns of ocean circulation conveys the romance of early marine science, but his lessons for today are serious, finds Simon Boxall.
• Cooking debate goes off the boil
  - Nature 459(7250):1059-1060 (2009)
  
• Our changing body image
  - Nature 459(7250):1060-1061 (2009)
  
• Science journalism: From the newsroom
  - Nature 459(7250):1061 (2009)
  The Washington Post's national environmental reporter Juliet Eilperin and its executive editor Marcus Brauchli discuss the future of science coverage in their newspaper.
• Structural biology: Protein dynamics from disorder
  Tolman JR - Nature 459(7250):1063-1064 (2009)
  The functions of proteins are often crucially dependent on how they move, but measuring the absolute magnitudes of protein motions hasn't been possible. A spectroscopic method looks set to change all that.
• Granular media: Structures in sand streams
  Lohse D van der Meer D - Nature 459(7250):1064-1065 (2009)
  An ingenious experiment that involves dropping a costly, high-speed video camera from a height of several metres reveals how free-falling streams of granular matter, such as sand, break up into grain clusters.
• Cell biology: A score for membrane fusion
  Collins RN Zimmerberg J - Nature 459(7250):1065-1066 (2009)
  Intracellular membrane fusion has been mimicked in vitro using a mix of 17 purified proteins and lipid bilayers. This technical tour de force allows the study of how cells orchestrate and perform such fusion events.
• 50 & 100 years ago
  - Nature 459(7250):1067 (2009)
  In 1956, as an experiment, an agency was started in the London area to put women graduates in touch with any suitable part-time work ... Many potential employers are prejudiced against part-time workers; it was felt that they might have more confidence if they could interview not one but a number of suitable candidates for each vacancy ... It also seemed clear that much of this work could be done at home and that it would be greatly welcomed, especially by mothers of young children ... Many employers were sympathetic to the idea and more jobs gradually became available ... Fewer permanent than temporary jobs are filled. This seems to reflect a general reluctance on the part of married women to commit themselves to permanent work.
• Planetary science: Enceladus with a grain of salt
  Spencer J - Nature 459(7250):1067-1068 (2009)
  The observation that water plumes erupt from cracks on Saturn's moon Enceladus has fired speculation about a possible subsurface ocean. The latest searches for sodium salts point to the existence of such an ocean.
• Stem cells: The stress of forming blood cells
  Pardanaud L Eichmann A - Nature 459(7250):1068-1069 (2009)
  The first heartbeat is an important moment in an embryo's life. The biomechanical forces created by pulsatile flow promote the formation of haematopoietic stem cells that equip the body with its mature blood cells.
• Nuclear physics: Unexpected doubly magic nucleus
  Janssens RV - Nature 459(7250):1069-1070 (2009)
  Nuclei with a 'magic' number of both protons and neutrons, dubbed doubly magic, are particularly stable. The oxygen isotope 24O has been found to be one such nucleus — yet it lies just at the limit of stability.
• Recent advances and emerging trends in plant hormone signalling
  Santner A Estelle M - Nature 459(7250):1071-1078 (2009)
  Plant growth and development is regulated by a structurally unrelated collection of small molecules called plant hormones. During the last 15 years the number of known plant hormones has grown from five to at least ten. Furthermore, many of the proteins involved in plant hormone signalling pathways have been identified, including receptors for many of the major hormones. Strikingly, the ubiquitin–proteasome pathway plays a central part in most hormone-signalling pathways. In addition, recent studies confirm that hormone signalling is integrated at several levels during plant growth and development.
• A soma-to-germline transformation in long-lived Caenorhabditis elegans mutants
  Curran SP Wu X Riedel CG Ruvkun G - Nature 459(7250):1079-1084 (2009)
  Unlike the soma, which ages during the lifespan of multicellular organisms, the germ line traces an essentially immortal lineage. Genomic instability in somatic cells increases with age, and this decline in somatic maintenance might be regulated to facilitate resource reallocation towards reproduction at the expense of cellular senescence. Here we show that Caenorhabditis elegans mutants with increased longevity exhibit a soma-to-germline transformation of gene expression programs normally limited to the germ line. Decreased insulin-like signalling causes the somatic misexpression of the germline-limited pie-1 and pgl family of genes in intestinal and ectodermal tissues. The forkhead boxO1A (FOXO) transcription factor DAF-16, the major transcriptional effector of insulin-like signalling, regulates pie-1 expression by directly binding to the pie-1 promoter. The somatic tissues of insulin-like mutants are more germline-like and protected from genotoxic stress. Gene inact! ivation of components of the cytosolic chaperonin complex that induce increased longevity also causes somatic misexpression of PGL-1. These results indicate that the acquisition of germline characteristics by the somatic cells of C. elegans mutants with increased longevity contributes to their increased health and survival.
• GOLPH3 modulates mTOR signalling and rapamycin sensitivity in cancer
  Scott KL Kabbarah O Liang MC Ivanova E Anagnostou V Wu J Dhakal S Wu M Chen S Feinberg T Huang J Saci A Widlund HR Fisher DE Xiao Y Rimm DL Protopopov A Wong KK Chin L - Nature 459(7250):1085-1090 (2009)
  Genome-wide copy number analyses of human cancers identified a frequent 5p13 amplification in several solid tumour types, including lung (56%), ovarian (38%), breast (32%), prostate (37%) and melanoma (32%). Here, using integrative analysis of a genomic profile of the region, we identify a Golgi protein, GOLPH3, as a candidate targeted for amplification. Gain- and loss-of-function studies in vitro and in vivo validated GOLPH3 as a potent oncogene. Physically, GOLPH3 localizes to the trans-Golgi network and interacts with components of the retromer complex, which in yeast has been linked to target of rapamycin (TOR) signalling. Mechanistically, GOLPH3 regulates cell size, enhances growth-factor-induced mTOR (also known as FRAP1) signalling in human cancer cells, and alters the response to an mTOR inhibitor in vivo. Thus, genomic and genetic, biological, functional and biochemical data in yeast and humans establishes GOLPH3 as a new oncogene that is commonly targeted for! amplification in human cancer, and is capable of modulating the response to rapamycin, a cancer drug in clinical use.
• Reconstitution of Rab- and SNARE-dependent membrane fusion by synthetic endosomes
  Ohya T Miaczynska M Coskun U Lommer B Runge A Drechsel D Kalaidzidis Y Zerial M - Nature 459(7250):1091-1097 (2009)
  Rab GTPases and SNAREs (soluble N-ethylmaleimide-sensitive factor attachment protein receptors) are evolutionarily conserved essential components of the eukaryotic intracellular transport system. Although pairing of cognate SNAREs is sufficient to fuse membranes in vitro, a complete reconstitution of the Rab–SNARE machinery has never been achieved. Here we report the reconstitution of the early endosomal canine Rab5 GTPase, its key regulators and effectors together with SNAREs into proteoliposomes using a set of 17 recombinant human proteins. These vesicles behave like minimal 'synthetic' endosomes, fusing with purified early endosomes or with each other in vitro. Membrane fusion measured by content-mixing and morphological assays requires the cooperativity between Rab5 effectors and cognate SNAREs which, together, form a more efficient 'core machinery' than SNAREs alone. In reconstituting a fusion mechanism dependent on both a Rab GTPase and SNAREs, our work shows t! hat the two machineries act coordinately to increase the specificity and efficiency of the membrane tethering and fusion process.
• Sodium salts in E-ring ice grains from an ocean below the surface of Enceladus
  Postberg F Kempf S Schmidt J Brilliantov N Beinsen A Abel B Buck U Srama R - Nature 459(7250):1098-1101 (2009)
  Saturn's moon Enceladus emits plumes of water vapour and ice particles from fractures near its south pole1, 2, 3, 4, 5, suggesting the possibility of a subsurface ocean5, 6, 7. These plume particles are the dominant source of Saturn's E ring7, 8. A previous in situ analysis9 of these particles concluded that the minor organic or siliceous components, identified in many ice grains, could be evidence for interaction between Enceladus' rocky core and liquid water9, 10. It was not clear, however, whether the liquid is still present today or whether it has frozen. Here we report the identification of a population of E-ring grains that are rich in sodium salts (0.5–2% by mass), which can arise only if the plumes originate from liquid water. The abundance of various salt components in these particles, as well as the inferred basic pH, exhibit a compelling similarity to the predicted composition of a subsurface Enceladus ocean in contact with its rock core11. The plume vapou! r is expected to be free of atomic sodium. Thus, the absence of sodium from optical spectra12 is in good agreement with our results. In the E ring the upper limit for spectroscopy12 is insufficiently sensitive to detect the concentrations we found.
• No sodium in the vapour plumes of Enceladus
  Schneider NM Burger MH Schaller EL Brown ME Johnson RE Kargel JS Dougherty MK Achilleos NA - Nature 459(7250):1102-1104 (2009)
  The discovery of water vapour and ice particles erupting from Saturn's moon Enceladus fuelled speculation that an internal ocean was the source1, 2, 3. Alternatively, the source might be ice warmed, melted or crushed by tectonic motions4. Sodium chloride (that is, salt) is expected to be present in a long-lived ocean in contact with a rocky core. Here we report a ground-based spectroscopic search for atomic sodium near Enceladus that places an upper limit on the mixing ratio in the vapour plumes orders of magnitude below the expected ocean salinity5. The low sodium content of escaping vapour, together with the small fraction of salt-bearing particles6, argues against a situation in which a near-surface geyser is fuelled by a salty ocean through cracks in the crust1. The lack of observable sodium in the vapour is consistent with a wide variety of alternative eruption sources, including a deep ocean6, a freshwater reservoir, or ice. The existing data may be insufficient ! to distinguish between these hypotheses.
• Optically controlled locking of the nuclear field via coherent dark-state spectroscopy
  Xu X Yao W Sun B Steel DG Bracker AS Gammon D Sham LJ - Nature 459(7250):1105-1109 (2009)
  A single electron or hole spin trapped inside a semiconductor quantum dot forms the foundation for many proposed quantum logic devices1, 2, 3, 4, 5, 6. In group III–V materials, the resonance and coherence between two ground states of the single spin are inevitably affected by the lattice nuclear spins through the hyperfine interaction7, 8, 9, while the dynamics of the single spin also influence the nuclear environment10, 11, 12, 13, 14, 15. Recent efforts12, 16 have been made to protect the coherence of spins in quantum dots by suppressing the nuclear spin fluctuations. However, coherent control of a single spin in a single dot with simultaneous suppression of the nuclear fluctuations has yet to be achieved. Here we report the suppression of nuclear field fluctuations in a singly charged quantum dot to well below the thermal value, as shown by an enhancement of the single electron spin dephasing time T 2*, which we measure using coherent dark-state spectroscopy. The! suppression of nuclear fluctuations is found to result from a hole-spin assisted dynamic nuclear spin polarization feedback process, where the stable value of the nuclear field is determined only by the laser frequencies at fixed laser powers. This nuclear field locking is further demonstrated in a three-laser measurement, indicating a possible enhancement of the electron spin T 2* by a factor of several hundred. This is a simple and powerful method of enhancing the electron spin coherence time without use of 'spin echo'-type techniques8, 12. We expect that our results will enable the reproducible preparation of the nuclear spin environment for repetitive control and measurement of a single spin with minimal statistical broadening.
• High-speed tracking of rupture and clustering in freely falling granular streams
  Royer JR Evans DJ Oyarte L Guo Q Kapit E Möbius ME Waitukaitis SR Jaeger HM - Nature 459(7250):1110-1113 (2009)
  Thin streams of liquid commonly break up into characteristic droplet patterns owing to the surface-tension-driven Plateau–Rayleigh instability1, 2, 3. Very similar patterns are observed when initially uniform streams of dry granular material break up into clusters of grains4, 5, 6, even though flows of macroscopic particles are considered to lack surface tension7, 8. Recent studies on freely falling granular streams tracked fluctuations in the stream profile9, but the clustering mechanism remained unresolved because the full evolution of the instability could not be observed. Here we demonstrate that the cluster formation is driven by minute, nanoNewton cohesive forces that arise from a combination of van der Waals interactions and capillary bridges between nanometre-scale surface asperities. Our experiments involve high-speed video imaging of the granular stream in the co-moving frame, control over the properties of the grain surfaces and the use of atomic force mic! roscopy to measure grain–grain interactions. The cohesive forces that we measure correspond to an equivalent surface tension five orders of magnitude below that of ordinary liquids. We find that the shapes of these weakly cohesive, non-thermal clusters of macroscopic particles closely resemble droplets resulting from thermally induced rupture of liquid nanojets10, 11, 12.
• Enhanced carbon pump inferred from relaxation of nutrient limitation in the glacial ocean
  Pichevin LE Reynolds BC Ganeshram RS Cacho I Pena L Keefe K Ellam RM - Nature 459(7250):1114-1117 (2009)
  The modern Eastern Equatorial Pacific (EEP) Ocean is a large oceanic source of carbon to the atmosphere1. Primary productivity over large areas of the EEP is limited by silicic acid and iron availability, and because of this constraint the organic carbon export to the deep ocean is unable to compensate for the outgassing of carbon dioxide that occurs through upwelling of deep waters. It has been suggested that the delivery of dust-borne iron to the glacial ocean2, 3 could have increased primary productivity and enhanced deep-sea carbon export in this region, lowering atmospheric carbon dioxide concentrations during glacial periods. Such a role for the EEP is supported by higher organic carbon burial rates documented in underlying glacial sediments4, 5, but lower opal accumulation rates cast doubts on the importance of the EEP as an oceanic region for significant glacial carbon dioxide drawdown6, 7. Here we present a new silicon isotope record that suggests the paradoxi! cal decline in opal accumulation rate in the glacial EEP results from a decrease in the silicon to carbon uptake ratio of diatoms under conditions of increased iron availability from enhanced dust input. Consequently, our study supports the idea of an invigorated biological pump in this region during the last glacial period that could have contributed to glacial carbon dioxide drawdown. Additionally, using evidence from silicon and nitrogen isotope changes, we infer that, in contrast to the modern situation, the biological productivity in this region is not constrained by the availability of iron, silicon and nitrogen during the glacial period. We hypothesize that an invigorated biological carbon dioxide pump constrained perhaps only by phosphorus limitation was a more common occurrence in low-latitude areas of the glacial ocean.
• 142Nd evidence for an enriched Hadean reservoir in cratonic roots
  Upadhyay D Scherer EE Mezger K - Nature 459(7250):1118-1121 (2009)
  The isotope 146Sm undergoes -decay to 142Nd, with a half-life of 103 million years. Measurable variations in the 142Nd/144Nd values of rocks resulting from Sm–Nd fractionation could therefore only have been produced within about 400 million years of the Solar System's formation (that is, when 146Sm was extant). The 142Nd/144Nd compositions of terrestrial rocks1, 2, 3, 4, 5, 6, 7 are accordingly a sensitive monitor of the main silicate differentiation events that took place in the early Earth. High 142Nd/144Nd values measured in some Archaean rocks from Greenland1, 2, 3, 4, 5 hint at the existence of an early incompatible-element-depleted mantle. Here we present measurements of low 142Nd/144Nd values in 1.48-gigayear-(Gyr)-old lithospheric mantle-derived alkaline rocks from the Khariar nepheline syenite complex in southeastern India8. These data suggest that a reservoir that was relatively enriched in incompatible elements formed at least 4.2 Gyr ago and traces of its! isotopic signature persisted within the lithospheric root of the Bastar craton until at least 1.48 Gyr ago. These low 142Nd/144Nd compositions may represent a diluted signature of a Hadean (4 to 4.57 Gyr ago) enriched reservoir that is characterized by even lower values. That no evidence of the early depleted mantle has been observed in rocks younger than 3.6 Gyr (refs 3, 4, 7) implies that such domains had effectively mixed back into the convecting mantle by then. In contrast, some early enriched components apparently escaped this fate. Thus, the mantle sampled by magmatism since 3.6 Gyr ago may be biased towards a depleted composition that would be balanced by relatively more enriched reservoirs that are 'hidden' in Hadean crust6, the D'' layer9, 10, 11 of the lowermost mantle or, as we propose here, also within the roots of old cratons.
• Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic
  Smith GJ Vijaykrishna D Bahl J Lycett SJ Worobey M Pybus OG Ma SK Cheung CL Raghwani J Bhatt S Peiris JS Guan Y Rambaut A - Nature 459(7250):1122-1125 (2009)
  In March and early April 2009, a new swine-origin influenza A (H1N1) virus (S-OIV) emerged in Mexico and the United States1. During the first few weeks of surveillance, the virus spread worldwide to 30 countries (as of May 11) by human-to-human transmission, causing the World Health Organization to raise its pandemic alert to level 5 of 6. This virus has the potential to develop into the first influenza pandemic of the twenty-first century. Here we use evolutionary analysis to estimate the timescale of the origins and the early development of the S-OIV epidemic. We show that it was derived from several viruses circulating in swine, and that the initial transmission to humans occurred several months before recognition of the outbreak. A phylogenetic estimate of the gaps in genetic surveillance indicates a long period of unsampled ancestry before the S-OIV outbreak, suggesting that the reassortment of swine lineages may have occurred years before emergence in humans, and! that the multiple genetic ancestry of S-OIV is not indicative of an artificial origin. Furthermore, the unsampled history of the epidemic means that the nature and location of the genetically closest swine viruses reveal little about the immediate origin of the epidemic, despite the fact that we included a panel of closely related and previously unpublished swine influenza isolates. Our results highlight the need for systematic surveillance of influenza in swine, and provide evidence that the mixing of new genetic elements in swine can result in the emergence of viruses with pandemic potential in humans2.
• Down's syndrome suppression of tumour growth and the role of the calcineurin inhibitor DSCR1
  Baek KH Zaslavsky A Lynch RC Britt C Okada Y Siarey RJ Lensch MW Park IH Yoon SS Minami T Korenberg JR Folkman J Daley GQ Aird WC Galdzicki Z Ryeom S - Nature 459(7250):1126-1130 (2009)
  The incidence of many cancer types is significantly reduced in individuals with Down's syndrome1, 2, 3, 4, and it is thought that this broad cancer protection is conferred by the increased expression of one or more of the 231 supernumerary genes on the extra copy of chromosome 21. One such gene is Down's syndrome candidate region-1 (DSCR1, also known as RCAN1), which encodes a protein that suppresses vascular endothelial growth factor (VEGF)-mediated angiogenic signalling by the calcineurin pathway5, 6, 7, 8, 9, 10. Here we show that DSCR1 is increased in Down's syndrome tissues and in a mouse model of Down's syndrome. Furthermore, we show that the modest increase in expression afforded by a single extra transgenic copy of Dscr1 is sufficient to confer significant suppression of tumour growth in mice, and that such resistance is a consequence of a deficit in tumour angiogenesis arising from suppression of the calcineurin pathway. We also provide evidence that attenuati! on of calcineurin activity by DSCR1, together with another chromosome 21 gene Dyrk1a, may be sufficient to markedly diminish angiogenesis. These data provide a mechanism for the reduced cancer incidence in Down's syndrome and identify the calcineurin signalling pathway, and its regulators DSCR1 and DYRK1A, as potential therapeutic targets in cancers arising in all individuals.
• Biomechanical forces promote embryonic haematopoiesis
  Adamo L Naveiras O Wenzel PL McKinney-Freeman S Mack PJ Gracia-Sancho J Suchy-Dicey A Yoshimoto M Lensch MW Yoder MC García-Cardeña G Daley GQ - Nature 459(7250):1131-1135 (2009)
  Biomechanical forces are emerging as critical regulators of embryogenesis, particularly in the developing cardiovascular system1, 2. After initiation of the heartbeat in vertebrates, cells lining the ventral aspect of the dorsal aorta, the placental vessels, and the umbilical and vitelline arteries initiate expression of the transcription factor Runx1 (refs 3–5), a master regulator of haematopoiesis, and give rise to haematopoietic cells4. It remains unknown whether the biomechanical forces imposed on the vascular wall at this developmental stage act as a determinant of haematopoietic potential6. Here, using mouse embryonic stem cells differentiated in vitro, we show that fluid shear stress increases the expression of Runx1 in CD41+c-Kit+ haematopoietic progenitor cells7, concomitantly augmenting their haematopoietic colony-forming potential. Moreover, we find that shear stress increases haematopoietic colony-forming potential and expression of haematopoietic markers! in the para-aortic splanchnopleura/aorta–gonads–mesonephros of mouse embryos and that abrogation of nitric oxide, a mediator of shear-stress-induced signalling8, compromises haematopoietic potential in vitro and in vivo. Collectively, these data reveal a critical role for biomechanical forces in haematopoietic development.
• Subcellular homeostasis of phytohormone auxin is mediated by the ER-localized PIN5 transporter
  Mravec J Skůpa P Bailly A Hoyerová K Krecek P Bielach A Petrásek J Zhang J Gaykova V Stierhof YD Dobrev PI Schwarzerová K Rolcík J Seifertová D Luschnig C Benková E Zazímalová E Geisler M Friml J - Nature 459(7250):1136-1140 (2009)
  The plant signalling molecule auxin provides positional information in a variety of developmental processes by means of its differential distribution (gradients) within plant tissues1. Thus, cellular auxin levels often determine the developmental output of auxin signalling. Conceptually, transmembrane transport and metabolic processes regulate the steady-state levels of auxin in any given cell2, 3. In particular, PIN auxin-efflux-carrier-mediated, directional transport between cells is crucial for generating auxin gradients2, 4, 5. Here we show that Arabidopsis thaliana PIN5, an atypical member of the PIN gene family, encodes a functional auxin transporter that is required for auxin-mediated development. PIN5 does not have a direct role in cell-to-cell transport but regulates intracellular auxin homeostasis and metabolism. PIN5 localizes, unlike other characterized plasma membrane PIN proteins, to endoplasmic reticulum (ER), presumably mediating auxin flow from the cyt! osol to the lumen of the ER. The ER localization of other PIN5-like transporters (including the moss PIN) indicates that the diversification of PIN protein functions in mediating auxin homeostasis at the ER, and cell-to-cell auxin transport at the plasma membrane, represent an ancient event during the evolution of land plants.
• Yurt, Coracle, Neurexin IV and the Na+,K+-ATPase form a novel group of epithelial polarity proteins
  - Nature 459(7250):1141-1145 (2009)
  The integrity of polarized epithelia is critical for development and human health. Many questions remain concerning the full complement and the function of the proteins that regulate cell polarity1. Here we report that the Drosophila FERM proteins Yurt (Yrt)2 and Coracle (Cora)3 and the membrane proteins Neurexin IV (Nrx-IV)4 and Na+,K+-ATPase5 are a new group of functionally cooperating epithelial polarity proteins. This 'Yrt/Cora group' promotes basolateral membrane stability and shows negative regulatory interactions with the apical determinant Crumbs (Crb). Genetic analyses indicate that Nrx-IV and Na+,K+-ATPase act together with Cora in one pathway, whereas Yrt acts in a second redundant pathway. Moreover, we show that the Yrt/Cora group is essential for epithelial polarity during organogenesis but not when epithelial polarity is first established or during terminal differentiation. This property of Yrt/Cora group proteins explains the recovery of polarity in embr! yos lacking the function of the Lethal giant larvae (Lgl) group of basolateral polarity proteins6, 7. We also find that the mammalian Yrt orthologue EPB41L5 (also known as YMO1 and Limulus)8, 9, 10 is required for lateral membrane formation, indicating a conserved function of Yrt proteins in epithelial polarity.
• Structural insight into the autoinhibition mechanism of AMP-activated protein kinase
  Chen L Jiao ZH Zheng LS Zhang YY Xie ST Wang ZX Wu JW - Nature 459(7250):1146-1149 (2009)
  The AMP-activated protein kinase (AMPK) is characterized by its ability to bind to AMP, which enables it to adjust enzymatic activity by sensing the cellular energy status and maintain the balance between ATP production and consumption in eukaryotic cells1, 2. It also has important roles in the regulation of cell growth and proliferation, and in the establishment and maintenance of cell polarity3. These important functions have rendered AMPK an important drug target for obesity, type 2 diabetes and cancer treatments4. However, the regulatory mechanism of AMPK activity by AMP binding remains unsolved. Here we report the crystal structures of an unphosphorylated fragment of the AMPK -subunit (KD-AID) from Schizosaccharomyces pombe that contains both the catalytic kinase domain and an autoinhibitory domain (AID), and of a phosphorylated kinase domain from Saccharomyces cerevisiae (Snf1-pKD). The AID binds, from the 'backside', to the hinge region of its kinase domain, for! ming contacts with both amino-terminal and carboxy-terminal lobes. Structural analyses indicate that AID binding might constrain the mobility of helix C, hence resulting in an autoinhibited KD-AID with much lower kinase activity than that of the kinase domain alone. AMP activates AMPK both allosterically and by inhibiting dephosphorylation5, 6. Further in vitro kinetic studies demonstrate that disruption of the KD-AID interface reverses the autoinhibition and these AMPK heterotrimeric mutants no longer respond to the change in AMP concentration. The structural and biochemical data have shown the primary mechanism of AMPK autoinhibition and suggest a conformational switch model for AMPK activation by AMP.
• dUTP incorporation into genomic DNA is linked to transcription in yeast
  Kim N Jinks-Robertson S - Nature 459(7250):1150-1153 (2009)
  Highly activated transcription is associated with eukaryotic genome instability, resulting in increased rates of mitotic recombination and mutagenesis. The association between high transcription and genome stability is probably due to a variety of factors including an enhanced accumulation of DNA damage, transcription-associated supercoiling, collision between replication forks and the transcription machinery, and the persistence of RNA–DNA hybrids1. In the case of transcription-associated mutagenesis, we previously showed that there is a direct proportionality between the level of transcription and the mutation rate in the yeast Saccharomyces cerevisiae 2, and that the molecular nature of the mutations is affected by highly activated transcription2, 3. Here we show that the accumulation of apurinic/apyrimidinic sites is greatly enhanced in highly transcribed yeast DNA. We further demonstrate that most apurinic/apyrimidinic sites in highly transcribed DNA are derived! from the removal of uracil, the presence of which is linked to direct incorporation of dUTP in place of dTTP. These results show an unexpected relationship between transcription and the fidelity of DNA synthesis, and raise intriguing cell biological issues with regard to nucleotide pool compartmentalization.
• Self-assembly of DNA into nanoscale three-dimensional shapes
  Douglas SM Dietz H Liedl T Högberg B Graf F Shih WM - Nature 459(7250):1154 (2009)
  Nature 459, 414–418 (2009) In this Letter, Figure 3 was printed incorrectly. The corrected figure is presented below.
• The missing memristor found
  Strukov DB Snider GS Stewart DR Williams RS - Nature 459(7250):1154 (2009)
  Nature 453, 80–83 (2008) In Fig. 2a of this Letter, the resistance for the right-hand element of the bottom circuit should be ROFF(1 - w/D), instead of the shown value ROFFw/D. Also, the correct value of window function should be w(D - W)/D2, rather than w(1 - W)/D2. All simulation results presented in the paper use the correct formulae.
• Codename: Phoenix
  Tang J - Nature 459(7250):1160 (2009)
  Here comes the rain.