Nature AOP Nature is a weekly international journal publishing the finest peer-reviewed research in all fields of science and technology on the basis of its originality, importance, interdisciplinary interest, timeliness, accessibility, elegance and surprising conclusions. Nature also provides rapid, authoritative, insightful and arresting news and interpretation of topical and coming trends affecting science, scientists and the wider public. http://www.nature.com/nature/current_issue/ Nature Publishing Group en © Nature Publishing Group Nature 0028-0836 1476-4679 © Nature Publishing Group permissions@nature.com Nature AOP http://www.nature.com/includes/rj_globnavimages/nature_logo.gif http://www.nature.com/nature/ The dynein regulatory complex is required for ciliary motility and otolith biogenesis in the inner ear http://dx.doi.org/10.1038/nature07520 In teleosts, proper balance and hearing depend on mechanical sensors in the inner ear. These sensors include actin-based microvilli and microtubule-based cilia that extend from the surface of sensory hair cells and attach to biomineralized ‘ear stones’ (or otoliths). Otolith number, size and placement are under strict developmental control, but the mechanisms that ensure otolith assembly atop specific cells of the sensory epithelium are unclear. Here we demonstrate that cilia motility is required for normal otolith assembly and localization. Using in vivo video microscopy, we show that motile tether cilia at opposite poles of the otic vesicle create fluid vortices that attract otolith precursor particles, thereby biasing an otherwise random distribution to direct localized otolith seeding on tether cilia. Independent knockdown of subunits for the dynein regulatory complex and outer-arm dynein disrupt cilia motility, leading to defective otolith biogenesis. These results demonstrate a requirement for the dynein regulatory complex in vertebrates and show that cilia-driven flow is a key epigenetic factor in controlling otolith biomineralization. The dynein regulatory complex is required for ciliary motility and otolith biogenesis in the inner ear

Nature advance online publication 30 November 2008. doi:10.1038/nature07520

Authors: Jessica R. Colantonio, Julien Vermot, David Wu, Adam D. Langenbacher, Scott Fraser, Jau-Nian Chen & Kent L. Hill

In teleosts, proper balance and hearing depend on mechanical sensors in the inner ear. These sensors include actin-based microvilli and microtubule-based cilia that extend from the surface of sensory hair cells and attach to biomineralized ‘ear stones’ (or otoliths). Otolith number, size and placement are under strict developmental control, but the mechanisms that ensure otolith assembly atop specific cells of the sensory epithelium are unclear. Here we demonstrate that cilia motility is required for normal otolith assembly and localization. Using in vivo video microscopy, we show that motile tether cilia at opposite poles of the otic vesicle create fluid vortices that attract otolith precursor particles, thereby biasing an otherwise random distribution to direct localized otolith seeding on tether cilia. Independent knockdown of subunits for the dynein regulatory complex and outer-arm dynein disrupt cilia motility, leading to defective otolith biogenesis. These results demonstrate a requirement for the dynein regulatory complex in vertebrates and show that cilia-driven flow is a key epigenetic factor in controlling otolith biomineralization.

]]> The dynein regulatory complex is required for ciliary motility and otolith biogenesis in the inner ear Jessica R. Colantonio Julien Vermot David Wu Adam D. Langenbacher Scott Fraser Jau-Nian Chen Kent L. Hill doi:10.1038/nature07520 Nature 2008-11-30 Nature 2008-11-30 Letter Protein kinase R reveals an evolutionary model for defeating viral mimicry http://dx.doi.org/10.1038/nature07529 Distinguishing self from non-self is a fundamental biological challenge. Many pathogens exploit the challenge of self discrimination by employing mimicry to subvert key cellular processes including the cell cycle, apoptosis and cytoskeletal dynamics. Other mimics interfere with immunity. Poxviruses encode K3L, a mimic of eIF2α, which is the substrate of protein kinase R (PKR), an important component of innate immunity in vertebrates. The PKR–K3L interaction exemplifies the conundrum imposed by viral mimicry. To be effective, PKR must recognize a conserved substrate (eIF2α) while avoiding rapidly evolving substrate mimics such as K3L. Using the PKR–K3L system and a combination of phylogenetic and functional analyses, we uncover evolutionary strategies by which host proteins can overcome mimicry. We find that PKR has evolved under intense episodes of positive selection in primates. The ability of PKR to evade viral mimics is partly due to positive selection at sites most intimately involved in eIF2α recognition. We also find that adaptive changes on multiple surfaces of PKR produce combinations of substitutions that increase the odds of defeating mimicry. Thus, although it can seem that pathogens gain insurmountable advantages by mimicking cellular components, host factors such as PKR can compete in molecular ‘arms races’ with mimics because of evolutionary flexibility at protein interaction interfaces challenged by mimicry. Protein kinase R reveals an evolutionary model for defeating viral mimicry

Nature advance online publication 30 November 2008. doi:10.1038/nature07529

Authors: Nels C. Elde, Stephanie J. Child, Adam P. Geballe & Harmit S. Malik

Distinguishing self from non-self is a fundamental biological challenge. Many pathogens exploit the challenge of self discrimination by employing mimicry to subvert key cellular processes including the cell cycle, apoptosis and cytoskeletal dynamics. Other mimics interfere with immunity. Poxviruses encode K3L, a mimic of eIF2α, which is the substrate of protein kinase R (PKR), an important component of innate immunity in vertebrates. The PKR–K3L interaction exemplifies the conundrum imposed by viral mimicry. To be effective, PKR must recognize a conserved substrate (eIF2α) while avoiding rapidly evolving substrate mimics such as K3L. Using the PKR–K3L system and a combination of phylogenetic and functional analyses, we uncover evolutionary strategies by which host proteins can overcome mimicry. We find that PKR has evolved under intense episodes of positive selection in primates. The ability of PKR to evade viral mimics is partly due to positive selection at sites most intimately involved in eIF2α recognition. We also find that adaptive changes on multiple surfaces of PKR produce combinations of substitutions that increase the odds of defeating mimicry. Thus, although it can seem that pathogens gain insurmountable advantages by mimicking cellular components, host factors such as PKR can compete in molecular ‘arms races’ with mimics because of evolutionary flexibility at protein interaction interfaces challenged by mimicry.

]]> Protein kinase R reveals an evolutionary model for defeating viral mimicry Nels C. Elde Stephanie J. Child Adam P. Geballe Harmit S. Malik doi:10.1038/nature07529 Nature 2008-11-30 Nature 2008-11-30 Letter Discovery of a sexual cycle in the opportunistic fungal pathogen Aspergillus fumigatus http://dx.doi.org/10.1038/nature07528 Aspergillus fumigatus is a saprotrophic fungus whose spores are ubiquitous in the atmosphere. It is also an opportunistic human pathogen in immunocompromised individuals, causing potentially lethal invasive infections, and is associated with severe asthma and sinusitis. The species is only known to reproduce by asexual means, but there has been accumulating evidence for recombination and gene flow from population genetic studies, genome analysis, the presence of mating-type genes and expression of sex-related genes in the fungus. Here we show that A. fumigatus possesses a fully functional sexual reproductive cycle that leads to the production of cleistothecia and ascospores, and the teleomorph Neosartorya fumigata is described. The species has a heterothallic breeding system; isolates of complementary mating types are required for sex to occur. We demonstrate increased genotypic variation resulting from recombination between mating type and DNA fingerprint markers in ascospore progeny from an Irish environmental subpopulation. The ability of A. fumigatus to engage in sexual reproduction is highly significant in understanding the biology and evolution of the species. The presence of a sexual cycle provides an invaluable tool for classical genetic analyses and will facilitate research into the genetic basis of pathogenicity and fungicide resistance in A. fumigatus, with the aim of improving methods for the control of aspergillosis. These results also yield insights into the potential for sexual reproduction in other supposedly ‘asexual’ fungi. Discovery of a sexual cycle in the opportunistic fungal pathogen Aspergillus fumigatus

Nature advance online publication 30 November 2008. doi:10.1038/nature07528

Authors: Céline M. O’Gorman, Hubert T. Fuller & Paul S. Dyer

Aspergillus fumigatus is a saprotrophic fungus whose spores are ubiquitous in the atmosphere. It is also an opportunistic human pathogen in immunocompromised individuals, causing potentially lethal invasive infections, and is associated with severe asthma and sinusitis. The species is only known to reproduce by asexual means, but there has been accumulating evidence for recombination and gene flow from population genetic studies, genome analysis, the presence of mating-type genes and expression of sex-related genes in the fungus. Here we show that A. fumigatus possesses a fully functional sexual reproductive cycle that leads to the production of cleistothecia and ascospores, and the teleomorph Neosartorya fumigata is described. The species has a heterothallic breeding system; isolates of complementary mating types are required for sex to occur. We demonstrate increased genotypic variation resulting from recombination between mating type and DNA fingerprint markers in ascospore progeny from an Irish environmental subpopulation. The ability of A. fumigatus to engage in sexual reproduction is highly significant in understanding the biology and evolution of the species. The presence of a sexual cycle provides an invaluable tool for classical genetic analyses and will facilitate research into the genetic basis of pathogenicity and fungicide resistance in A. fumigatus, with the aim of improving methods for the control of aspergillosis. These results also yield insights into the potential for sexual reproduction in other supposedly ‘asexual’ fungi.

]]> Discovery of a sexual cycle in the opportunistic fungal pathogen Aspergillus fumigatus Céline M. O’Gorman Hubert T. Fuller Paul S. Dyer doi:10.1038/nature07528 Nature 2008-11-30 Nature 2008-11-30 Letter MicroRNA-21 contributes to myocardial disease by stimulating MAP kinase signalling in fibroblasts http://dx.doi.org/10.1038/nature07511 MicroRNAs comprise a broad class of small non-coding RNAs that control expression of complementary target messenger RNAs. Dysregulation of microRNAs by several mechanisms has been described in various disease states including cardiac disease. Whereas previous studies of cardiac disease have focused on microRNAs that are primarily expressed in cardiomyocytes, the role of microRNAs expressed in other cell types of the heart is unclear. Here we show that microRNA-21 (miR-21, also known as Mirn21) regulates the ERK–MAP kinase signalling pathway in cardiac fibroblasts, which has impacts on global cardiac structure and function. miR-21 levels are increased selectively in fibroblasts of the failing heart, augmenting ERK–MAP kinase activity through inhibition of sprouty homologue 1 (Spry1). This mechanism regulates fibroblast survival and growth factor secretion, apparently controlling the extent of interstitial fibrosis and cardiac hypertrophy. In vivo silencing of miR-21 by a specific antagomir in a mouse pressure-overload-induced disease model reduces cardiac ERK–MAP kinase activity, inhibits interstitial fibrosis and attenuates cardiac dysfunction. These findings reveal that microRNAs can contribute to myocardial disease by an effect in cardiac fibroblasts. Our results validate miR-21 as a disease target in heart failure and establish the therapeutic efficacy of microRNA therapeutic intervention in a cardiovascular disease setting. MicroRNA-21 contributes to myocardial disease by stimulating MAP kinase signalling in fibroblasts

Nature advance online publication 30 November 2008. doi:10.1038/nature07511

Authors: Thomas Thum, Carina Gross, Jan Fiedler, Thomas Fischer, Stephan Kissler, Markus Bussen, Paolo Galuppo, Steffen Just, Wolfgang Rottbauer, Stefan Frantz, Mirco Castoldi, Jürgen Soutschek, Victor Koteliansky, Andreas Rosenwald, M. Albert Basson, Jonathan D. Licht, John T. R. Pena, Sara H. Rouhanifard, Martina U. Muckenthaler, Thomas Tuschl, Gail R. Martin, Johann Bauersachs & Stefan Engelhardt

MicroRNAs comprise a broad class of small non-coding RNAs that control expression of complementary target messenger RNAs. Dysregulation of microRNAs by several mechanisms has been described in various disease states including cardiac disease. Whereas previous studies of cardiac disease have focused on microRNAs that are primarily expressed in cardiomyocytes, the role of microRNAs expressed in other cell types of the heart is unclear. Here we show that microRNA-21 (miR-21, also known as Mirn21) regulates the ERK–MAP kinase signalling pathway in cardiac fibroblasts, which has impacts on global cardiac structure and function. miR-21 levels are increased selectively in fibroblasts of the failing heart, augmenting ERK–MAP kinase activity through inhibition of sprouty homologue 1 (Spry1). This mechanism regulates fibroblast survival and growth factor secretion, apparently controlling the extent of interstitial fibrosis and cardiac hypertrophy. In vivo silencing of miR-21 by a specific antagomir in a mouse pressure-overload-induced disease model reduces cardiac ERK–MAP kinase activity, inhibits interstitial fibrosis and attenuates cardiac dysfunction. These findings reveal that microRNAs can contribute to myocardial disease by an effect in cardiac fibroblasts. Our results validate miR-21 as a disease target in heart failure and establish the therapeutic efficacy of microRNA therapeutic intervention in a cardiovascular disease setting.

]]> MicroRNA-21 contributes to myocardial disease by stimulating MAP kinase signalling in fibroblasts Thomas Thum Carina Gross Jan Fiedler Thomas Fischer Stephan Kissler Markus Bussen Paolo Galuppo Steffen Just Wolfgang Rottbauer Stefan Frantz Mirco Castoldi Jürgen Soutschek Victor Koteliansky Andreas Rosenwald M. Albert Basson Jonathan D. Licht John T. R. Pena Sara H. Rouhanifard Martina U. Muckenthaler Thomas Tuschl Gail R. Martin Johann Bauersachs Stefan Engelhardt doi:10.1038/nature07511 Nature 2008-11-30 Nature 2008-11-30 Letter A core gut microbiome in obese and lean twins http://dx.doi.org/10.1038/nature07540 The human distal gut harbours a vast ensemble of microbes (the microbiota) that provide important metabolic capabilities, including the ability to extract energy from otherwise indigestible dietary polysaccharides. Studies of a few unrelated, healthy adults have revealed substantial diversity in their gut communities, as measured by sequencing 16S rRNA genes, yet how this diversity relates to function and to the rest of the genes in the collective genomes of the microbiota (the gut microbiome) remains obscure. Studies of lean and obese mice suggest that the gut microbiota affects energy balance by influencing the efficiency of calorie harvest from the diet, and how this harvested energy is used and stored. Here we characterize the faecal microbial communities of adult female monozygotic and dizygotic twin pairs concordant for leanness or obesity, and their mothers, to address how host genotype, environmental exposure and host adiposity influence the gut microbiome. Analysis of 154 individuals yielded 9,920 near full-length and 1,937,461 partial bacterial 16S rRNA sequences, plus 2.14 gigabases from their microbiomes. The results reveal that the human gut microbiome is shared among family members, but that each person’s gut microbial community varies in the specific bacterial lineages present, with a comparable degree of co-variation between adult monozygotic and dizygotic twin pairs. However, there was a wide array of shared microbial genes among sampled individuals, comprising an extensive, identifiable ‘core microbiome’ at the gene, rather than at the organismal lineage, level. Obesity is associated with phylum-level changes in the microbiota, reduced bacterial diversity and altered representation of bacterial genes and metabolic pathways. These results demonstrate that a diversity of organismal assemblages can nonetheless yield a core microbiome at a functional level, and that deviations from this core are associated with different physiological states (obese compared with lean). A core gut microbiome in obese and lean twins

Nature advance online publication 30 November 2008. doi:10.1038/nature07540

Authors: Peter J. Turnbaugh, Micah Hamady, Tanya Yatsunenko, Brandi L. Cantarel, Alexis Duncan, Ruth E. Ley, Mitchell L. Sogin, William J. Jones, Bruce A. Roe, Jason P. Affourtit, Michael Egholm, Bernard Henrissat, Andrew C. Heath, Rob Knight & Jeffrey I. Gordon

The human distal gut harbours a vast ensemble of microbes (the microbiota) that provide important metabolic capabilities, including the ability to extract energy from otherwise indigestible dietary polysaccharides. Studies of a few unrelated, healthy adults have revealed substantial diversity in their gut communities, as measured by sequencing 16S rRNA genes, yet how this diversity relates to function and to the rest of the genes in the collective genomes of the microbiota (the gut microbiome) remains obscure. Studies of lean and obese mice suggest that the gut microbiota affects energy balance by influencing the efficiency of calorie harvest from the diet, and how this harvested energy is used and stored. Here we characterize the faecal microbial communities of adult female monozygotic and dizygotic twin pairs concordant for leanness or obesity, and their mothers, to address how host genotype, environmental exposure and host adiposity influence the gut microbiome. Analysis of 154 individuals yielded 9,920 near full-length and 1,937,461 partial bacterial 16S rRNA sequences, plus 2.14 gigabases from their microbiomes. The results reveal that the human gut microbiome is shared among family members, but that each person’s gut microbial community varies in the specific bacterial lineages present, with a comparable degree of co-variation between adult monozygotic and dizygotic twin pairs. However, there was a wide array of shared microbial genes among sampled individuals, comprising an extensive, identifiable ‘core microbiome’ at the gene, rather than at the organismal lineage, level. Obesity is associated with phylum-level changes in the microbiota, reduced bacterial diversity and altered representation of bacterial genes and metabolic pathways. These results demonstrate that a diversity of organismal assemblages can nonetheless yield a core microbiome at a functional level, and that deviations from this core are associated with different physiological states (obese compared with lean).

]]> A core gut microbiome in obese and lean twins Peter J. Turnbaugh Micah Hamady Tanya Yatsunenko Brandi L. Cantarel Alexis Duncan Ruth E. Ley Mitchell L. Sogin William J. Jones Bruce A. Roe Jason P. Affourtit Michael Egholm Bernard Henrissat Andrew C. Heath Rob Knight Jeffrey I. Gordon doi:10.1038/nature07540 Nature 2008-11-30 Nature 2008-11-30 Letter Major gradients in putatively nitrifying and non-nitrifying Archaea in the deep North Atlantic http://dx.doi.org/10.1038/nature07535 Aerobic nitrification of ammonia to nitrite and nitrate is a key process in the oceanic nitrogen cycling mediated by prokaryotes. Apart from Bacteria belonging to the β- and γ-Proteobacteria involved in the first nitrification step, Crenarchaeota have recently been recognized as main drivers of the oxidation of ammonia to nitrite in soil as well as in the ocean, as indicated by the dominance of archaeal ammonia monooxygenase (amoA) genes over bacterial amoA. Evidence is accumulating that archaeal amoA genes are common in a wide range of marine systems. Essentially, all these reports focused on surface and mesopelagic (200–1,000 m depth) waters, where ammonia concentrations are higher than in waters below 1,000 m depth. However, Crenarchaeota are also abundant in the water column below 1,000 m, where ammonia concentrations are extremely low. Here we show that, throughout the North Atlantic Ocean, the abundance of archaeal amoA genes decreases markedly from subsurface waters to 4,000 m depth, and from subpolar to equatorial deep waters, leading to pronounced vertical and latitudinal gradients in the ratio of archaeal amoA to crenarchaeal 16S ribosomal RNA (rRNA) genes. The lack of significant copy numbers of amoA genes and the very low fixation rates of dark carbon dioxide in the bathypelagic North Atlantic suggest that most bathypelagic Crenarchaeota are not autotrophic ammonia oxidizers: most likely, they utilize organic matter and hence live heterotrophically. Major gradients in putatively nitrifying and non-nitrifying Archaea in the deep North Atlantic

Nature advance online publication 26 November 2008. doi:10.1038/nature07535

Authors: Hélène Agogué, Maaike Brink, Julie Dinasquet & Gerhard J. Herndl

Aerobic nitrification of ammonia to nitrite and nitrate is a key process in the oceanic nitrogen cycling mediated by prokaryotes. Apart from Bacteria belonging to the β- and γ-Proteobacteria involved in the first nitrification step, Crenarchaeota have recently been recognized as main drivers of the oxidation of ammonia to nitrite in soil as well as in the ocean, as indicated by the dominance of archaeal ammonia monooxygenase (amoA) genes over bacterial amoA. Evidence is accumulating that archaeal amoA genes are common in a wide range of marine systems. Essentially, all these reports focused on surface and mesopelagic (200–1,000 m depth) waters, where ammonia concentrations are higher than in waters below 1,000 m depth. However, Crenarchaeota are also abundant in the water column below 1,000 m, where ammonia concentrations are extremely low. Here we show that, throughout the North Atlantic Ocean, the abundance of archaeal amoA genes decreases markedly from subsurface waters to 4,000 m depth, and from subpolar to equatorial deep waters, leading to pronounced vertical and latitudinal gradients in the ratio of archaeal amoA to crenarchaeal 16S ribosomal RNA (rRNA) genes. The lack of significant copy numbers of amoA genes and the very low fixation rates of dark carbon dioxide in the bathypelagic North Atlantic suggest that most bathypelagic Crenarchaeota are not autotrophic ammonia oxidizers: most likely, they utilize organic matter and hence live heterotrophically.

]]> Major gradients in putatively nitrifying and non-nitrifying Archaea in the deep North Atlantic Hélène Agogué Maaike Brink Julie Dinasquet Gerhard J. Herndl doi:10.1038/nature07535 Nature 2008-11-26 Nature 2008-11-26 Letter Nuclear receptor corepressor and histone deacetylase 3 govern circadian metabolic physiology http://dx.doi.org/10.1038/nature07541 Rhythmic changes in histone acetylation at circadian clock genes suggest that temporal modulation of gene expression is regulated by chromatin modifications. Furthermore, recent studies demonstrate a critical relationship between circadian and metabolic physiology. The nuclear receptor corepressor 1 (Ncor1) functions as an activating subunit for the chromatin modifying enzyme histone deacetylase 3 (Hdac3). Lack of Ncor1 is incompatible with life, and hence it is unknown whether Ncor1, and particularly its regulation of Hdac3, is critical for adult mammalian physiology. Here we show that specific, genetic disruption of the Ncor1–Hdac3 interaction in mice causes aberrant regulation of clock genes and results in abnormal circadian behaviour. These mice are also leaner and more insulin-sensitive owing to increased energy expenditure. Unexpectedly, loss of a functional Ncor1–Hdac3 complex in vivo does not lead to sustained increases in known catabolic genes, but instead significantly alters the oscillatory patterns of several metabolic genes, demonstrating that circadian regulation of metabolism is critical for normal energy balance. These findings indicate that activation of Hdac3 by Ncor1 is a nodal point in the epigenetic regulation of circadian and metabolic physiology. Nuclear receptor corepressor and histone deacetylase 3 govern circadian metabolic physiology

Nature advance online publication 26 November 2008. doi:10.1038/nature07541

Authors: Theresa Alenghat, Katherine Meyers, Shannon E. Mullican, Kirstin Leitner, Adetoun Adeniji-Adele, Jacqueline Avila, Maja Bućan, Rexford S. Ahima, Klaus H. Kaestner & Mitchell A. Lazar

Rhythmic changes in histone acetylation at circadian clock genes suggest that temporal modulation of gene expression is regulated by chromatin modifications. Furthermore, recent studies demonstrate a critical relationship between circadian and metabolic physiology. The nuclear receptor corepressor 1 (Ncor1) functions as an activating subunit for the chromatin modifying enzyme histone deacetylase 3 (Hdac3). Lack of Ncor1 is incompatible with life, and hence it is unknown whether Ncor1, and particularly its regulation of Hdac3, is critical for adult mammalian physiology. Here we show that specific, genetic disruption of the Ncor1–Hdac3 interaction in mice causes aberrant regulation of clock genes and results in abnormal circadian behaviour. These mice are also leaner and more insulin-sensitive owing to increased energy expenditure. Unexpectedly, loss of a functional Ncor1–Hdac3 complex in vivo does not lead to sustained increases in known catabolic genes, but instead significantly alters the oscillatory patterns of several metabolic genes, demonstrating that circadian regulation of metabolism is critical for normal energy balance. These findings indicate that activation of Hdac3 by Ncor1 is a nodal point in the epigenetic regulation of circadian and metabolic physiology.

]]> Nuclear receptor corepressor and histone deacetylase 3 govern circadian metabolic physiology Theresa Alenghat Katherine Meyers Shannon E. Mullican Kirstin Leitner Adetoun Adeniji-Adele Jacqueline Avila Maja Bućan Rexford S. Ahima Klaus H. Kaestner Mitchell A. Lazar doi:10.1038/nature07541 Nature 2008-11-26 Nature 2008-11-26 Letter Parallel adaptations to high temperatures in the Archaean eon http://dx.doi.org/10.1038/nature07393 Fossils of organisms dating from the origin and diversification of cellular life are scant and difficult to interpret, for this reason alternative means to investigate the ecology of the last universal common ancestor (LUCA) and of the ancestors of the three domains of life are of great scientific value. It was recently recognized that the effects of temperature on ancestral organisms left ‘genetic footprints’ that could be uncovered in extant genomes. Accordingly, analyses of resurrected proteins predicted that the bacterial ancestor was thermophilic and that Bacteria subsequently adapted to lower temperatures. As the archaeal ancestor is also thought to have been thermophilic, the LUCA was parsimoniously inferred as thermophilic too. However, an analysis of ribosomal RNAs supported the hypothesis of a non-hyperthermophilic LUCA. Here we show that both rRNA and protein sequences analysed with advanced, realistic models of molecular evolution provide independent support for two environmental-temperature-related phases during the evolutionary history of the tree of life. In the first period, thermotolerance increased from a mesophilic LUCA to thermophilic ancestors of Bacteria and of Archaea–Eukaryota; in the second period, it decreased. Therefore, the two lineages descending from the LUCA and leading to the ancestors of Bacteria and Archaea–Eukaryota convergently adapted to high temperatures, possibly in response to a climate change of the early Earth, and/or aided by the transition from an RNA genome in the LUCA to organisms with more thermostable DNA genomes. This analysis unifies apparently contradictory results into a coherent depiction of the evolution of an ecological trait over the entire tree of life. Parallel adaptations to high temperatures in the Archaean eon

Nature advance online publication 26 November 2008. doi:10.1038/nature07393

Authors: Bastien Boussau, Samuel Blanquart, Anamaria Necsulea, Nicolas Lartillot & Manolo Gouy

Fossils of organisms dating from the origin and diversification of cellular life are scant and difficult to interpret, for this reason alternative means to investigate the ecology of the last universal common ancestor (LUCA) and of the ancestors of the three domains of life are of great scientific value. It was recently recognized that the effects of temperature on ancestral organisms left ‘genetic footprints’ that could be uncovered in extant genomes. Accordingly, analyses of resurrected proteins predicted that the bacterial ancestor was thermophilic and that Bacteria subsequently adapted to lower temperatures. As the archaeal ancestor is also thought to have been thermophilic, the LUCA was parsimoniously inferred as thermophilic too. However, an analysis of ribosomal RNAs supported the hypothesis of a non-hyperthermophilic LUCA. Here we show that both rRNA and protein sequences analysed with advanced, realistic models of molecular evolution provide independent support for two environmental-temperature-related phases during the evolutionary history of the tree of life. In the first period, thermotolerance increased from a mesophilic LUCA to thermophilic ancestors of Bacteria and of Archaea–Eukaryota; in the second period, it decreased. Therefore, the two lineages descending from the LUCA and leading to the ancestors of Bacteria and Archaea–Eukaryota convergently adapted to high temperatures, possibly in response to a climate change of the early Earth, and/or aided by the transition from an RNA genome in the LUCA to organisms with more thermostable DNA genomes. This analysis unifies apparently contradictory results into a coherent depiction of the evolution of an ecological trait over the entire tree of life.

]]> Parallel adaptations to high temperatures in the Archaean eon Bastien Boussau Samuel Blanquart Anamaria Necsulea Nicolas Lartillot Manolo Gouy doi:10.1038/nature07393 Nature 2008-11-26 Nature 2008-11-26 Letter Role for Spi-C in the development of red pulp macrophages and splenic iron homeostasis http://dx.doi.org/10.1038/nature07472 Tissue macrophages comprise a heterogeneous group of cell types differing in location, surface markers and function. Red pulp macrophages are a distinct splenic subset involved in removing senescent red blood cells. Transcription factors such as PU.1 (also known as Sfpi1) and C/EBPα (Cebpa) have general roles in myelomonocytic development, but the transcriptional basis for producing tissue macrophage subsets remains unknown. Here we show that Spi-C (encoded by Spic), a PU.1-related transcription factor, selectively controls the development of red pulp macrophages. Spi-C is highly expressed in red pulp macrophages, but not monocytes, dendritic cells or other tissue macrophages. Spic-/- mice have a cell-autonomous defect in the development of red pulp macrophages that is corrected by retroviral Spi-C expression in bone marrow cells, but have normal monocyte and other macrophage subsets. Red pulp macrophages highly express genes involved in capturing circulating haemoglobin and in iron regulation. Spic-/- mice show normal trapping of red blood cells in the spleen, but fail to phagocytose these red blood cells efficiently, and develop an iron overload localized selectively to splenic red pulp. Thus, Spi-C controls development of red pulp macrophages required for red blood cell recycling and iron homeostasis. Role for Spi-C in the development of red pulp macrophages and splenic iron homeostasis

Nature advance online publication 26 November 2008. doi:10.1038/nature07472

Authors: Masako Kohyama, Wataru Ise, Brian T. Edelson, Peter R. Wilker, Kai Hildner, Carlo Mejia, William A. Frazier, Theresa L. Murphy & Kenneth M. Murphy

Tissue macrophages comprise a heterogeneous group of cell types differing in location, surface markers and function. Red pulp macrophages are a distinct splenic subset involved in removing senescent red blood cells. Transcription factors such as PU.1 (also known as Sfpi1) and C/EBPα (Cebpa) have general roles in myelomonocytic development, but the transcriptional basis for producing tissue macrophage subsets remains unknown. Here we show that Spi-C (encoded by Spic), a PU.1-related transcription factor, selectively controls the development of red pulp macrophages. Spi-C is highly expressed in red pulp macrophages, but not monocytes, dendritic cells or other tissue macrophages. Spic-/- mice have a cell-autonomous defect in the development of red pulp macrophages that is corrected by retroviral Spi-C expression in bone marrow cells, but have normal monocyte and other macrophage subsets. Red pulp macrophages highly express genes involved in capturing circulating haemoglobin and in iron regulation. Spic-/- mice show normal trapping of red blood cells in the spleen, but fail to phagocytose these red blood cells efficiently, and develop an iron overload localized selectively to splenic red pulp. Thus, Spi-C controls development of red pulp macrophages required for red blood cell recycling and iron homeostasis.

]]> Role for Spi-C in the development of red pulp macrophages and splenic iron homeostasis Masako Kohyama Wataru Ise Brian T. Edelson Peter R. Wilker Kai Hildner Carlo Mejia William A. Frazier Theresa L. Murphy Kenneth M. Murphy doi:10.1038/nature07472 Nature 2008-11-26 Nature 2008-11-26 Letter Ferritin is used for iron storage in bloom-forming marine pennate diatoms http://dx.doi.org/10.1038/nature07539 Primary productivity in 30–40% of the world’s oceans is limited by availability of the micronutrient iron. Regions with chronically low iron concentrations are sporadically pulsed with new iron inputs by way of dust or lateral advection from continental margins. Addition of iron to surface waters in these areas induces massive phytoplankton blooms dominated primarily by pennate diatoms. Here we provide evidence that the bloom-forming pennate diatoms Pseudo-nitzschia and Fragilariopsis use the iron-concentrating protein, ferritin, to safely store iron. Ferritin has not been reported previously in any member of the Stramenopiles, a diverse eukaryotic lineage that includes unicellular algae, macroalgae and plant parasites. Phylogenetic analyses suggest that ferritin may have arisen in this small subset of diatoms through a lateral gene transfer. The crystal structure and functional assays of recombinant ferritin derived from Pseudo-nitzschia multiseries reveal a maxi-ferritin that exhibits ferroxidase activity and binds iron. The protein is predicted to be targeted to the chloroplast to control the distribution and storage of iron for proper functioning of the photosynthetic machinery. Abundance of Pseudo-nitzschia ferritin transcripts is regulated by iron nutritional status, and is closely tied to the loss and recovery of photosynthetic competence. Enhanced iron storage with ferritin allows the oceanic diatom Pseudo-nitzschia granii to undergo several more cell divisions in the absence of iron than the comparably sized, oceanic centric diatom Thalassiosira oceanica. Ferritin in pennate diatoms probably contributes to their success in chronically low-iron regions that receive intermittent iron inputs, and provides an explanation for the importance of these organisms in regulating oceanic CO2 over geological timescales. Ferritin is used for iron storage in bloom-forming marine pennate diatoms

Nature advance online publication 26 November 2008. doi:10.1038/nature07539

Authors: Adrian Marchetti, Micaela S. Parker, Lauren P. Moccia, Ellen O. Lin, Angele L. Arrieta, Francois Ribalet, Michael E. P. Murphy, Maria T. Maldonado & E. Virginia Armbrust

Primary productivity in 30–40% of the world’s oceans is limited by availability of the micronutrient iron. Regions with chronically low iron concentrations are sporadically pulsed with new iron inputs by way of dust or lateral advection from continental margins. Addition of iron to surface waters in these areas induces massive phytoplankton blooms dominated primarily by pennate diatoms. Here we provide evidence that the bloom-forming pennate diatoms Pseudo-nitzschia and Fragilariopsis use the iron-concentrating protein, ferritin, to safely store iron. Ferritin has not been reported previously in any member of the Stramenopiles, a diverse eukaryotic lineage that includes unicellular algae, macroalgae and plant parasites. Phylogenetic analyses suggest that ferritin may have arisen in this small subset of diatoms through a lateral gene transfer. The crystal structure and functional assays of recombinant ferritin derived from Pseudo-nitzschia multiseries reveal a maxi-ferritin that exhibits ferroxidase activity and binds iron. The protein is predicted to be targeted to the chloroplast to control the distribution and storage of iron for proper functioning of the photosynthetic machinery. Abundance of Pseudo-nitzschia ferritin transcripts is regulated by iron nutritional status, and is closely tied to the loss and recovery of photosynthetic competence. Enhanced iron storage with ferritin allows the oceanic diatom Pseudo-nitzschia granii to undergo several more cell divisions in the absence of iron than the comparably sized, oceanic centric diatom Thalassiosira oceanica. Ferritin in pennate diatoms probably contributes to their success in chronically low-iron regions that receive intermittent iron inputs, and provides an explanation for the importance of these organisms in regulating oceanic CO2 over geological timescales.

]]> Ferritin is used for iron storage in bloom-forming marine pennate diatoms Adrian Marchetti Micaela S. Parker Lauren P. Moccia Ellen O. Lin Angele L. Arrieta Francois Ribalet Michael E. P. Murphy Maria T. Maldonado E. Virginia Armbrust doi:10.1038/nature07539 Nature 2008-11-26 Nature 2008-11-26 Letter Analysis of combinatorial cis-regulation in synthetic and genomic promoters http://dx.doi.org/10.1038/nature07521 Transcription factor binding sites are being discovered at a rapid pace. It is now necessary to turn attention towards understanding how these sites work in combination to influence gene expression. Quantitative models that accurately predict gene expression from promoter sequence will be a crucial part of solving this problem. Here we present such a model, based on the analysis of synthetic promoter libraries in yeast (Saccharomyces cerevisiae). Thermodynamic models based only on the equilibrium binding of transcription factors to DNA and to each other captured a large fraction of the variation in expression in every library. Thermodynamic analysis of these libraries uncovered several phenomena in our system, including cooperativity and the effects of weak binding sites. When applied to the S. cerevisiae genome, a model of repression by Mig1 (which was trained on synthetic promoters) predicts a number of Mig1-regulated genes that lack significant Mig1-binding sites in their promoters. The success of the thermodynamic approach suggests that the information encoded by combinations of cis-regulatory sites is interpreted primarily through simple protein–DNA and protein–protein interactions, with complicated biochemical reactions—such as nucleosome modifications—being downstream events. Quantitative analyses of synthetic promoter libraries will be an important tool in unravelling the rules underlying combinatorial cis-regulation. Analysis of combinatorial cis-regulation in synthetic and genomic promoters

Nature advance online publication 23 November 2008. doi:10.1038/nature07521

Authors: Jason Gertz, Eric D. Siggia & Barak A. Cohen

Transcription factor binding sites are being discovered at a rapid pace. It is now necessary to turn attention towards understanding how these sites work in combination to influence gene expression. Quantitative models that accurately predict gene expression from promoter sequence will be a crucial part of solving this problem. Here we present such a model, based on the analysis of synthetic promoter libraries in yeast (Saccharomyces cerevisiae). Thermodynamic models based only on the equilibrium binding of transcription factors to DNA and to each other captured a large fraction of the variation in expression in every library. Thermodynamic analysis of these libraries uncovered several phenomena in our system, including cooperativity and the effects of weak binding sites. When applied to the S. cerevisiae genome, a model of repression by Mig1 (which was trained on synthetic promoters) predicts a number of Mig1-regulated genes that lack significant Mig1-binding sites in their promoters. The success of the thermodynamic approach suggests that the information encoded by combinations of cis-regulatory sites is interpreted primarily through simple protein–DNA and protein–protein interactions, with complicated biochemical reactions—such as nucleosome modifications—being downstream events. Quantitative analyses of synthetic promoter libraries will be an important tool in unravelling the rules underlying combinatorial cis-regulation.

]]> Analysis of combinatorial cis-regulation in synthetic and genomic promoters Jason Gertz Eric D. Siggia Barak A. Cohen doi:10.1038/nature07521 Nature 2008-11-23 Nature 2008-11-23 Letter Dynamics of DNA replication loops reveal temporal control of lagging-strand synthesis http://dx.doi.org/10.1038/nature07512 In all organisms, the protein machinery responsible for the replication of DNA, the replisome, is faced with a directionality problem. The antiparallel nature of duplex DNA permits the leading-strand polymerase to advance in a continuous fashion, but forces the lagging-strand polymerase to synthesize in the opposite direction. By extending RNA primers, the lagging-strand polymerase restarts at short intervals and produces Okazaki fragments. At least in prokaryotic systems, this directionality problem is solved by the formation of a loop in the lagging strand of the replication fork to reorient the lagging-strand DNA polymerase so that it advances in parallel with the leading-strand polymerase. The replication loop grows and shrinks during each cycle of Okazaki fragment synthesis. Here we use single-molecule techniques to visualize, in real time, the formation and release of replication loops by individual replisomes of bacteriophage T7 supporting coordinated DNA replication. Analysis of the distributions of loop sizes and lag times between loops reveals that initiation of primer synthesis and the completion of an Okazaki fragment each serve as a trigger for loop release. The presence of two triggers may represent a fail-safe mechanism ensuring the timely reset of the replisome after the synthesis of every Okazaki fragment. Dynamics of DNA replication loops reveal temporal control of lagging-strand synthesis

Nature advance online publication 23 November 2008. doi:10.1038/nature07512

Authors: Samir M. Hamdan, Joseph J. Loparo, Masateru Takahashi, Charles C. Richardson & Antoine M. van Oijen

In all organisms, the protein machinery responsible for the replication of DNA, the replisome, is faced with a directionality problem. The antiparallel nature of duplex DNA permits the leading-strand polymerase to advance in a continuous fashion, but forces the lagging-strand polymerase to synthesize in the opposite direction. By extending RNA primers, the lagging-strand polymerase restarts at short intervals and produces Okazaki fragments. At least in prokaryotic systems, this directionality problem is solved by the formation of a loop in the lagging strand of the replication fork to reorient the lagging-strand DNA polymerase so that it advances in parallel with the leading-strand polymerase. The replication loop grows and shrinks during each cycle of Okazaki fragment synthesis. Here we use single-molecule techniques to visualize, in real time, the formation and release of replication loops by individual replisomes of bacteriophage T7 supporting coordinated DNA replication. Analysis of the distributions of loop sizes and lag times between loops reveals that initiation of primer synthesis and the completion of an Okazaki fragment each serve as a trigger for loop release. The presence of two triggers may represent a fail-safe mechanism ensuring the timely reset of the replisome after the synthesis of every Okazaki fragment.

]]> Dynamics of DNA replication loops reveal temporal control of lagging-strand synthesis Samir M. Hamdan Joseph J. Loparo Masateru Takahashi Charles C. Richardson Antoine M. van Oijen doi:10.1038/nature07512 Nature 2008-11-23 Nature 2008-11-23 Letter Pulsed contractions of an actin–myosin network drive apical constriction http://dx.doi.org/10.1038/nature07522 Apical constriction facilitates epithelial sheet bending and invagination during morphogenesis. Apical constriction is conventionally thought to be driven by the continuous purse-string-like contraction of a circumferential actin and non-muscle myosin-II (myosin) belt underlying adherens junctions. However, it is unclear whether other force-generating mechanisms can drive this process. Here we show, with the use of real-time imaging and quantitative image analysis of Drosophila gastrulation, that the apical constriction of ventral furrow cells is pulsed. Repeated constrictions, which are asynchronous between neighbouring cells, are interrupted by pauses in which the constricted state of the cell apex is maintained. In contrast to the purse-string model, constriction pulses are powered by actin–myosin network contractions that occur at the medial apical cortex and pull discrete adherens junction sites inwards. The transcription factors Twist and Snail differentially regulate pulsed constriction. Expression of snail initiates actin–myosin network contractions, whereas expression of twist stabilizes the constricted state of the cell apex. Our results suggest a new model for apical constriction in which a cortical actin–myosin cytoskeleton functions as a developmentally controlled subcellular ratchet to reduce apical area incrementally. Pulsed contractions of an actin–myosin network drive apical constriction

Nature advance online publication 23 November 2008. doi:10.1038/nature07522

Authors: Adam C. Martin, Matthias Kaschube & Eric F. Wieschaus

Apical constriction facilitates epithelial sheet bending and invagination during morphogenesis. Apical constriction is conventionally thought to be driven by the continuous purse-string-like contraction of a circumferential actin and non-muscle myosin-II (myosin) belt underlying adherens junctions. However, it is unclear whether other force-generating mechanisms can drive this process. Here we show, with the use of real-time imaging and quantitative image analysis of Drosophila gastrulation, that the apical constriction of ventral furrow cells is pulsed. Repeated constrictions, which are asynchronous between neighbouring cells, are interrupted by pauses in which the constricted state of the cell apex is maintained. In contrast to the purse-string model, constriction pulses are powered by actin–myosin network contractions that occur at the medial apical cortex and pull discrete adherens junction sites inwards. The transcription factors Twist and Snail differentially regulate pulsed constriction. Expression of snail initiates actin–myosin network contractions, whereas expression of twist stabilizes the constricted state of the cell apex. Our results suggest a new model for apical constriction in which a cortical actin–myosin cytoskeleton functions as a developmentally controlled subcellular ratchet to reduce apical area incrementally.

]]> Pulsed contractions of an actin–myosin network drive apical constriction Adam C. Martin Matthias Kaschube Eric F. Wieschaus doi:10.1038/nature07522 Nature 2008-11-23 Nature 2008-11-23 Letter Altered circadian rhythms regulate growth vigour in hybrids and allopolyploids http://dx.doi.org/10.1038/nature07523 Segregating hybrids and stable allopolyploids display morphological vigour, and Arabidopsis allotetraploids are larger than the parents Arabidopsis thaliana and Arabidopsis arenosa—the mechanisms for this are unknown. Circadian clocks mediate metabolic pathways and increase fitness in animals and plants. Here we report that epigenetic modifications of the circadian clock genes CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) and LATE ELONGATED HYPOCOTYL (LHY) and their reciprocal regulators TIMING OF CAB EXPRESSION 1 (TOC1) and GIGANTEA (GI) mediate expression changes in downstream genes and pathways. During the day, epigenetic repression of CCA1 and LHY induced the expression of TOC1, GI and downstream genes containing evening elements in chlorophyll and starch metabolic pathways in allotetraploids and F1 hybrids, which produced more chlorophyll and starch than the parents in the same environment. Mutations in cca1 and cca1 lhy and the daily repression of cca1 by RNA interference (RNAi) in TOC1::cca1(RNAi) transgenic plants increased the expression of downstream genes and increased chlorophyll and starch content, whereas constitutively expressing CCA1 or ectopically expressing TOC1::CCA1 had the opposite effect. The causal effects of CCA1 on output traits suggest that hybrids and allopolyploids gain advantages from the control of circadian-mediated physiological and metabolic pathways, leading to growth vigour and increased biomass. Altered circadian rhythms regulate growth vigour in hybrids and allopolyploids

Nature advance online publication 23 November 2008. doi:10.1038/nature07523

Authors: Zhongfu Ni, Eun-Deok Kim, Misook Ha, Erika Lackey, Jianxin Liu, Yirong Zhang, Qixin Sun & Z. Jeffrey Chen

Segregating hybrids and stable allopolyploids display morphological vigour, and Arabidopsis allotetraploids are larger than the parents Arabidopsis thaliana and Arabidopsis arenosa—the mechanisms for this are unknown. Circadian clocks mediate metabolic pathways and increase fitness in animals and plants. Here we report that epigenetic modifications of the circadian clock genes CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) and LATE ELONGATED HYPOCOTYL (LHY) and their reciprocal regulators TIMING OF CAB EXPRESSION 1 (TOC1) and GIGANTEA (GI) mediate expression changes in downstream genes and pathways. During the day, epigenetic repression of CCA1 and LHY induced the expression of TOC1, GI and downstream genes containing evening elements in chlorophyll and starch metabolic pathways in allotetraploids and F1 hybrids, which produced more chlorophyll and starch than the parents in the same environment. Mutations in cca1 and cca1 lhy and the daily repression of cca1 by RNA interference (RNAi) in TOC1::cca1(RNAi) transgenic plants increased the expression of downstream genes and increased chlorophyll and starch content, whereas constitutively expressing CCA1 or ectopically expressing TOC1::CCA1 had the opposite effect. The causal effects of CCA1 on output traits suggest that hybrids and allopolyploids gain advantages from the control of circadian-mediated physiological and metabolic pathways, leading to growth vigour and increased biomass.

]]> Altered circadian rhythms regulate growth vigour in hybrids and allopolyploids Zhongfu Ni Eun-Deok Kim Misook Ha Erika Lackey Jianxin Liu Yirong Zhang Qixin Sun Z. Jeffrey Chen doi:10.1038/nature07523 Nature 2008-11-23 Nature 2008-11-23 Letter The replisome uses mRNA as a primer after colliding with RNA polymerase http://dx.doi.org/10.1038/nature07527 The replisome uses mRNA as a primer after colliding with RNA polymerase

Nature advance online publication 19 November 2008. doi:10.1038/nature07527

Authors: Richard T. Pomerantz & Mike O’Donnell

]]> The replisome uses mRNA as a primer after colliding with RNA polymerase Richard T. Pomerantz Mike O’Donnell doi:10.1038/nature07527 Nature 2008-11-19 Nature 2008-11-19 Article Successful range-expanding plants experience less above-ground and below-ground enemy impact http://dx.doi.org/10.1038/nature07474 Many species are currently moving to higher latitudes and altitudes. However, little is known about the factors that influence the future performance of range-expanding species in their new habitats. Here we show that range-expanding plant species from a riverine area were better defended against shoot and root enemies than were related native plant species growing in the same area. We grew fifteen plant species with and without non-coevolved polyphagous locusts and cosmopolitan, polyphagous aphids. Contrary to our expectations, the locusts performed more poorly on the range-expanding plant species than on the congeneric native plant species, whereas the aphids showed no difference. The shoot herbivores reduced the biomass of the native plants more than they did that of the congeneric range expanders. Also, the range-expanding plants developed fewer pathogenic effects in their root-zone soil than did the related native species. Current predictions forecast biodiversity loss due to limitations in the ability of species to adjust to climate warming conditions in their range. Our results strongly suggest that the plants that shift ranges towards higher latitudes and altitudes may include potential invaders, as the successful range expanders may experience less control by above-ground or below-ground enemies than the natives. Successful range-expanding plants experience less above-ground and below-ground enemy impact

Nature advance online publication 19 November 2008. doi:10.1038/nature07474

Authors: Tim Engelkes, Elly Morriën, Koen J. F. Verhoeven, T. Martijn Bezemer, Arjen Biere, Jeffrey A. Harvey, Lauren M. McIntyre, Wil L. M. Tamis & Wim H. van der Putten

Many species are currently moving to higher latitudes and altitudes. However, little is known about the factors that influence the future performance of range-expanding species in their new habitats. Here we show that range-expanding plant species from a riverine area were better defended against shoot and root enemies than were related native plant species growing in the same area. We grew fifteen plant species with and without non-coevolved polyphagous locusts and cosmopolitan, polyphagous aphids. Contrary to our expectations, the locusts performed more poorly on the range-expanding plant species than on the congeneric native plant species, whereas the aphids showed no difference. The shoot herbivores reduced the biomass of the native plants more than they did that of the congeneric range expanders. Also, the range-expanding plants developed fewer pathogenic effects in their root-zone soil than did the related native species. Current predictions forecast biodiversity loss due to limitations in the ability of species to adjust to climate warming conditions in their range. Our results strongly suggest that the plants that shift ranges towards higher latitudes and altitudes may include potential invaders, as the successful range expanders may experience less control by above-ground or below-ground enemies than the natives.

]]> Successful range-expanding plants experience less above-ground and below-ground enemy impact Tim Engelkes Elly Morriën Koen J. F. Verhoeven T. Martijn Bezemer Arjen Biere Jeffrey A. Harvey Lauren M. McIntyre Wil L. M. Tamis Wim H. van der Putten doi:10.1038/nature07474 Nature 2008-11-19 Nature 2008-11-19 Letter Detecting influenza epidemics using search engine query data http://dx.doi.org/10.1038/nature07634 Seasonal influenza epidemics are a major public health concern, causing tens of millions of respiratory illnesses and 250,000 to 500,000 deaths worldwide each year. In addition to seasonal influenza, a new strain of influenza virus against which no previous immunity exists and that demonstrates human-to-human transmission could result in a pandemic with millions of fatalities. Early detection of disease activity, when followed by a rapid response, can reduce the impact of both seasonal and pandemic influenza. One way to improve early detection is to monitor health-seeking behaviour in the form of queries to online search engines, which are submitted by millions of users around the world each day. Here we present a method of analysing large numbers of Google search queries to track influenza-like illness in a population. Because the relative frequency of certain queries is highly correlated with the percentage of physician visits in which a patient presents with influenza-like symptoms, we can accurately estimate the current level of weekly influenza activity in each region of the United States, with a reporting lag of about one day. This approach may make it possible to use search queries to detect influenza epidemics in areas with a large population of web search users. Detecting influenza epidemics using search engine query data

Nature advance online publication 19 November 2008. doi:10.1038/nature07634

Authors: Jeremy Ginsberg, Matthew H. Mohebbi, Rajan S. Patel, Lynnette Brammer, Mark S. Smolinski & Larry Brilliant

Seasonal influenza epidemics are a major public health concern, causing tens of millions of respiratory illnesses and 250,000 to 500,000 deaths worldwide each year. In addition to seasonal influenza, a new strain of influenza virus against which no previous immunity exists and that demonstrates human-to-human transmission could result in a pandemic with millions of fatalities. Early detection of disease activity, when followed by a rapid response, can reduce the impact of both seasonal and pandemic influenza. One way to improve early detection is to monitor health-seeking behaviour in the form of queries to online search engines, which are submitted by millions of users around the world each day. Here we present a method of analysing large numbers of Google search queries to track influenza-like illness in a population. Because the relative frequency of certain queries is highly correlated with the percentage of physician visits in which a patient presents with influenza-like symptoms, we can accurately estimate the current level of weekly influenza activity in each region of the United States, with a reporting lag of about one day. This approach may make it possible to use search queries to detect influenza epidemics in areas with a large population of web search users.

]]> Detecting influenza epidemics using search engine query data Jeremy Ginsberg Matthew H. Mohebbi Rajan S. Patel Lynnette Brammer Mark S. Smolinski Larry Brilliant doi:10.1038/nature07634 Nature 2008-11-19 Nature 2008-11-19 Letter Emergence of complex cell properties by learning to generalize in natural scenes http://dx.doi.org/10.1038/nature07481 A fundamental function of the visual system is to encode the building blocks of natural scenes—edges, textures and shapes—that subserve visual tasks such as object recognition and scene understanding. Essential to this process is the formation of abstract representations that generalize from specific instances of visual input. A common view holds that neurons in the early visual system signal conjunctions of image features, but how these produce invariant representations is poorly understood. Here we propose that to generalize over similar images, higher-level visual neurons encode statistical variations that characterize local image regions. We present a model in which neural activity encodes the probability distribution most consistent with a given image. Trained on natural images, the model generalizes by learning a compact set of dictionary elements for image distributions typically encountered in natural scenes. Model neurons show a diverse range of properties observed in cortical cells. These results provide a new functional explanation for nonlinear effects in complex cells and offer insight into coding strategies in primary visual cortex (V1) and higher visual areas. Emergence of complex cell properties by learning to generalize in natural scenes

Nature advance online publication 19 November 2008. doi:10.1038/nature07481

Authors: Yan Karklin & Michael S. Lewicki

A fundamental function of the visual system is to encode the building blocks of natural scenes—edges, textures and shapes—that subserve visual tasks such as object recognition and scene understanding. Essential to this process is the formation of abstract representations that generalize from specific instances of visual input. A common view holds that neurons in the early visual system signal conjunctions of image features, but how these produce invariant representations is poorly understood. Here we propose that to generalize over similar images, higher-level visual neurons encode statistical variations that characterize local image regions. We present a model in which neural activity encodes the probability distribution most consistent with a given image. Trained on natural images, the model generalizes by learning a compact set of dictionary elements for image distributions typically encountered in natural scenes. Model neurons show a diverse range of properties observed in cortical cells. These results provide a new functional explanation for nonlinear effects in complex cells and offer insight into coding strategies in primary visual cortex (V1) and higher visual areas.

]]> Emergence of complex cell properties by learning to generalize in natural scenes Yan Karklin Michael S. Lewicki doi:10.1038/nature07481 Nature 2008-11-19 Nature 2008-11-19 Letter Frequent in-frame somatic deletions activate gp130 in inflammatory hepatocellular tumours http://dx.doi.org/10.1038/nature07475 Inflammatory hepatocellular adenomas are benign liver tumours defined by the presence of inflammatory infiltrates and by the increased expression of inflammatory proteins in tumour hepatocytes. Here we show a marked activation of the interleukin (IL)-6 signalling pathway in this tumour type; sequencing candidate genes pinpointed this response to somatic gain-of-function mutations in the IL6ST gene, which encodes the signalling co-receptor gp130. Indeed, 60% of inflammatory hepatocellular adenomas harbour small in-frame deletions that target the binding site of gp130 for IL-6, and expression of four different gp130 mutants in hepatocellular cells activates signal transducer and activator of transcription 3 (STAT3) in the absence of ligand. Furthermore, analysis of hepatocellular carcinomas revealed that rare gp130 alterations are always accompanied by β-catenin-activating mutations, suggesting a cooperative effect of these signalling pathways in the malignant conversion of hepatocytes. The recurrent gain-of-function gp130 mutations in these human hepatocellular adenomas fully explains activation of the acute inflammatory phase observed in tumourous hepatocytes, and suggests that similar alterations may occur in other inflammatory epithelial tumours with STAT3 activation. Frequent in-frame somatic deletions activate gp130 in inflammatory hepatocellular tumours

Nature advance online publication 19 November 2008. doi:10.1038/nature07475

Authors: Sandra Rebouissou, Mohamed Amessou, Gabrielle Couchy, Karine Poussin, Sandrine Imbeaud, Camilla Pilati, Tina Izard, Charles Balabaud, Paulette Bioulac-Sage & Jessica Zucman-Rossi

Inflammatory hepatocellular adenomas are benign liver tumours defined by the presence of inflammatory infiltrates and by the increased expression of inflammatory proteins in tumour hepatocytes. Here we show a marked activation of the interleukin (IL)-6 signalling pathway in this tumour type; sequencing candidate genes pinpointed this response to somatic gain-of-function mutations in the IL6ST gene, which encodes the signalling co-receptor gp130. Indeed, 60% of inflammatory hepatocellular adenomas harbour small in-frame deletions that target the binding site of gp130 for IL-6, and expression of four different gp130 mutants in hepatocellular cells activates signal transducer and activator of transcription 3 (STAT3) in the absence of ligand. Furthermore, analysis of hepatocellular carcinomas revealed that rare gp130 alterations are always accompanied by β-catenin-activating mutations, suggesting a cooperative effect of these signalling pathways in the malignant conversion of hepatocytes. The recurrent gain-of-function gp130 mutations in these human hepatocellular adenomas fully explains activation of the acute inflammatory phase observed in tumourous hepatocytes, and suggests that similar alterations may occur in other inflammatory epithelial tumours with STAT3 activation.

]]> Frequent in-frame somatic deletions activate gp130 in inflammatory hepatocellular tumours Sandra Rebouissou Mohamed Amessou Gabrielle Couchy Karine Poussin Sandrine Imbeaud Camilla Pilati Tina Izard Charles Balabaud Paulette Bioulac-Sage Jessica Zucman-Rossi doi:10.1038/nature07475 Nature 2008-11-19 Nature 2008-11-19 Letter Suppression of Myc oncogenic activity by ribosomal protein haploinsufficiency http://dx.doi.org/10.1038/nature07449 The Myc oncogene regulates the expression of several components of the protein synthetic machinery, including ribosomal proteins, initiation factors of translation, RNA polymerase III and ribosomal DNA. Whether and how increasing the cellular protein synthesis capacity affects the multistep process leading to cancer remains to be addressed. Here we use ribosomal protein heterozygote mice as a genetic tool to restore increased protein synthesis in Eμ-Myc/+ transgenic mice to normal levels, and show that the oncogenic potential of Myc in this context is suppressed. Our findings demonstrate that the ability of Myc to increase protein synthesis directly augments cell size and is sufficient to accelerate cell cycle progression independently of known cell cycle targets transcriptionally regulated by Myc. In addition, when protein synthesis is restored to normal levels, Myc-overexpressing precancerous cells are more efficiently eliminated by programmed cell death. Our findings reveal a new mechanism that links increases in general protein synthesis rates downstream of an oncogenic signal to a specific molecular impairment in the modality of translation initiation used to regulate the expression of selective messenger RNAs. We show that an aberrant increase in cap-dependent translation downstream of Myc hyperactivation specifically impairs the translational switch to internal ribosomal entry site (IRES)-dependent translation that is required for accurate mitotic progression. Failure of this translational switch results in reduced mitotic-specific expression of the endogenous IRES-dependent form of Cdk11 (also known as Cdc2l and PITSLRE), which leads to cytokinesis defects and is associated with increased centrosome numbers and genome instability in Eμ-Myc/+ mice. When accurate translational control is re-established in Eμ-Myc/+ mice, genome instability is suppressed. Our findings demonstrate how perturbations in translational control provide a highly specific outcome for gene expression, genome stability and cancer initiation that have important implications for understanding the molecular mechanism of cancer formation at the post-genomic level. Suppression of Myc oncogenic activity by ribosomal protein haploinsufficiency

Nature advance online publication 16 November 2008. doi:10.1038/nature07449

Authors: Maria Barna, Aya Pusic, Ornella Zollo, Maria Costa, Nadya Kondrashov, Eduardo Rego, Pulivarthi H. Rao & Davide Ruggero

The Myc oncogene regulates the expression of several components of the protein synthetic machinery, including ribosomal proteins, initiation factors of translation, RNA polymerase III and ribosomal DNA. Whether and how increasing the cellular protein synthesis capacity affects the multistep process leading to cancer remains to be addressed. Here we use ribosomal protein heterozygote mice as a genetic tool to restore increased protein synthesis in Eμ-Myc/+ transgenic mice to normal levels, and show that the oncogenic potential of Myc in this context is suppressed. Our findings demonstrate that the ability of Myc to increase protein synthesis directly augments cell size and is sufficient to accelerate cell cycle progression independently of known cell cycle targets transcriptionally regulated by Myc. In addition, when protein synthesis is restored to normal levels, Myc-overexpressing precancerous cells are more efficiently eliminated by programmed cell death. Our findings reveal a new mechanism that links increases in general protein synthesis rates downstream of an oncogenic signal to a specific molecular impairment in the modality of translation initiation used to regulate the expression of selective messenger RNAs. We show that an aberrant increase in cap-dependent translation downstream of Myc hyperactivation specifically impairs the translational switch to internal ribosomal entry site (IRES)-dependent translation that is required for accurate mitotic progression. Failure of this translational switch results in reduced mitotic-specific expression of the endogenous IRES-dependent form of Cdk11 (also known as Cdc2l and PITSLRE), which leads to cytokinesis defects and is associated with increased centrosome numbers and genome instability in Eμ-Myc/+ mice. When accurate translational control is re-established in Eμ-Myc/+ mice, genome instability is suppressed. Our findings demonstrate how perturbations in translational control provide a highly specific outcome for gene expression, genome stability and cancer initiation that have important implications for understanding the molecular mechanism of cancer formation at the post-genomic level.

]]> Suppression of Myc oncogenic activity by ribosomal protein haploinsufficiency Maria Barna Aya Pusic Ornella Zollo Maria Costa Nadya Kondrashov Eduardo Rego Pulivarthi H. Rao Davide Ruggero doi:10.1038/nature07449 Nature 2008-11-16 Nature 2008-11-16 Letter Myelomonocytic cell recruitment causes fatal CNS vascular injury during acute viral meningitis http://dx.doi.org/10.1038/nature07591 Lymphocytic choriomeningitis virus infection of the mouse central nervous system (CNS) elicits fatal immunopathology through blood–brain barrier breakdown and convulsive seizures. Although lymphocytic-choriomeningitis-virus-specific cytotoxic T lymphocytes (CTLs) are essential for disease, their mechanism of action is not known. To gain insights into disease pathogenesis, we observed the dynamics of immune cells in the meninges by two-photon microscopy. Here we report visualization of motile CTLs and massive secondary recruitment of pathogenic monocytes and neutrophils that were required for vascular leakage and acute lethality. CTLs expressed multiple chemoattractants capable of recruiting myelomonocytic cells. We conclude that a CD8+ T-cell-dependent disorder can proceed in the absence of direct T-cell effector mechanisms and rely instead on CTL-recruited myelomonocytic cells. Myelomonocytic cell recruitment causes fatal CNS vascular injury during acute viral meningitis

Nature advance online publication 16 November 2008. doi:10.1038/nature07591

Authors: Jiyun V. Kim, Silvia S. Kang, Michael L. Dustin & Dorian B. McGavern

Lymphocytic choriomeningitis virus infection of the mouse central nervous system (CNS) elicits fatal immunopathology through blood–brain barrier breakdown and convulsive seizures. Although lymphocytic-choriomeningitis-virus-specific cytotoxic T lymphocytes (CTLs) are essential for disease, their mechanism of action is not known. To gain insights into disease pathogenesis, we observed the dynamics of immune cells in the meninges by two-photon microscopy. Here we report visualization of motile CTLs and massive secondary recruitment of pathogenic monocytes and neutrophils that were required for vascular leakage and acute lethality. CTLs expressed multiple chemoattractants capable of recruiting myelomonocytic cells. We conclude that a CD8+ T-cell-dependent disorder can proceed in the absence of direct T-cell effector mechanisms and rely instead on CTL-recruited myelomonocytic cells.

]]> Myelomonocytic cell recruitment causes fatal CNS vascular injury during acute viral meningitis Jiyun V. Kim Silvia S. Kang Michael L. Dustin Dorian B. McGavern doi:10.1038/nature07591 Nature 2008-11-16 Nature 2008-11-16 Letter Low conservation of gene content in the Drosophila Y chromosome http://dx.doi.org/10.1038/nature07463 Chromosomal organization is sufficiently evolutionarily stable that large syntenic blocks of genes can be recognized even between species as distantly related as mammals and puffer fish (450 million years (Myr) of divergence). In Diptera, the gene content of the X chromosome and the autosomes is well conserved: in Drosophila more than 95% of the genes have remained on the same chromosome arm in the 12 sequenced species (63 Myr of divergence, traversing 400 Myr of evolution), and the same linkage groups are clearly recognizable in mosquito genomes (260 Myr of divergence). Here we investigate the conservation of Y-linked gene content among the 12 sequenced Drosophila species. We found that only a quarter of the Drosophila melanogaster Y-linked genes (3 out of 12) are Y-linked in all sequenced species, and that most of them (7 out of 12) were acquired less than 63 Myr ago. Hence, whereas the organization of other Drosophila chromosomes traces back to the common ancestor with mosquitoes, the gene content of the D. melanogaster Y chromosome is much younger. Gene losses are known to have an important role in the evolution of Y chromosomes, and we indeed found two such cases. However, the rate of gene gain in the Drosophila Y chromosomes investigated is 10.9 times higher than the rate of gene loss (95% confidence interval: 2.3–52.5), indicating a clear tendency of the Y chromosomes to increase in gene content. In contrast with the mammalian Y chromosome, gene gains have a prominent role in the evolution of the Drosophila Y chromosome. Low conservation of gene content in the Drosophila Y chromosome

Nature advance online publication 16 November 2008. doi:10.1038/nature07463

Authors: Leonardo B. Koerich, Xiaoyun Wang, Andrew G. Clark & Antonio Bernardo Carvalho

Chromosomal organization is sufficiently evolutionarily stable that large syntenic blocks of genes can be recognized even between species as distantly related as mammals and puffer fish (450 million years (Myr) of divergence). In Diptera, the gene content of the X chromosome and the autosomes is well conserved: in Drosophila more than 95% of the genes have remained on the same chromosome arm in the 12 sequenced species (63 Myr of divergence, traversing 400 Myr of evolution), and the same linkage groups are clearly recognizable in mosquito genomes (260 Myr of divergence). Here we investigate the conservation of Y-linked gene content among the 12 sequenced Drosophila species. We found that only a quarter of the Drosophila melanogaster Y-linked genes (3 out of 12) are Y-linked in all sequenced species, and that most of them (7 out of 12) were acquired less than 63 Myr ago. Hence, whereas the organization of other Drosophila chromosomes traces back to the common ancestor with mosquitoes, the gene content of the D. melanogaster Y chromosome is much younger. Gene losses are known to have an important role in the evolution of Y chromosomes, and we indeed found two such cases. However, the rate of gene gain in the Drosophila Y chromosomes investigated is 10.9 times higher than the rate of gene loss (95% confidence interval: 2.3–52.5), indicating a clear tendency of the Y chromosomes to increase in gene content. In contrast with the mammalian Y chromosome, gene gains have a prominent role in the evolution of the Drosophila Y chromosome.

]]> Low conservation of gene content in the Drosophila Y chromosome Leonardo B. Koerich Xiaoyun Wang Andrew G. Clark Antonio Bernardo Carvalho doi:10.1038/nature07463 Nature 2008-11-16 Nature 2008-11-16 Letter Structural recognition and functional activation of FcγR by innate pentraxins http://dx.doi.org/10.1038/nature07468 Pentraxins are a family of ancient innate immune mediators conserved throughout evolution. The classical pentraxins include serum amyloid P component (SAP) and C-reactive protein, which are two of the acute-phase proteins synthesized in response to infection. Both recognize microbial pathogens and activate the classical complement pathway through C1q (refs 3 and 4). More recently, members of the pentraxin family were found to interact with cell-surface Fcγ receptors (FcγR) and activate leukocyte-mediated phagocytosis. Here we describe the structural mechanism for pentraxin’s binding to FcγR and its functional activation of FcγR-mediated phagocytosis and cytokine secretion. The complex structure between human SAP and FcγRIIa reveals a diagonally bound receptor on each SAP pentamer with both D1 and D2 domains of the receptor contacting the ridge helices from two SAP subunits. The 1:1 stoichiometry between SAP and FcγRIIa infers the requirement for multivalent pathogen binding for receptor aggregation. Mutational and binding studies show that pentraxins are diverse in their binding specificity for FcγR isoforms but conserved in their recognition structure. The shared binding site for SAP and IgG results in competition for FcγR binding and the inhibition of immune-complex-mediated phagocytosis by soluble pentraxins. These results establish antibody-like functions for pentraxins in the FcγR pathway, suggest an evolutionary overlap between the innate and adaptive immune systems, and have new therapeutic implications for autoimmune diseases. Structural recognition and functional activation of FcγR by innate pentraxins

Nature advance online publication 16 November 2008. doi:10.1038/nature07468

Authors: Jinghua Lu, Lorraine L. Marnell, Kristopher D. Marjon, Carolyn Mold, Terry W. Du Clos & Peter D. Sun

Pentraxins are a family of ancient innate immune mediators conserved throughout evolution. The classical pentraxins include serum amyloid P component (SAP) and C-reactive protein, which are two of the acute-phase proteins synthesized in response to infection. Both recognize microbial pathogens and activate the classical complement pathway through C1q (refs 3 and 4). More recently, members of the pentraxin family were found to interact with cell-surface Fcγ receptors (FcγR) and activate leukocyte-mediated phagocytosis. Here we describe the structural mechanism for pentraxin’s binding to FcγR and its functional activation of FcγR-mediated phagocytosis and cytokine secretion. The complex structure between human SAP and FcγRIIa reveals a diagonally bound receptor on each SAP pentamer with both D1 and D2 domains of the receptor contacting the ridge helices from two SAP subunits. The 1:1 stoichiometry between SAP and FcγRIIa infers the requirement for multivalent pathogen binding for receptor aggregation. Mutational and binding studies show that pentraxins are diverse in their binding specificity for FcγR isoforms but conserved in their recognition structure. The shared binding site for SAP and IgG results in competition for FcγR binding and the inhibition of immune-complex-mediated phagocytosis by soluble pentraxins. These results establish antibody-like functions for pentraxins in the FcγR pathway, suggest an evolutionary overlap between the innate and adaptive immune systems, and have new therapeutic implications for autoimmune diseases.

]]> Structural recognition and functional activation of FcγR by innate pentraxins Jinghua Lu Lorraine L. Marnell Kristopher D. Marjon Carolyn Mold Terry W. Du Clos Peter D. Sun doi:10.1038/nature07468 Nature 2008-11-16 Nature 2008-11-16 Letter Highly efficient molybdenum-based catalysts for enantioselective alkene metathesis http://dx.doi.org/10.1038/nature07594 Discovery of efficient catalysts is one of the most compelling objectives of modern chemistry. Chiral catalysts are in particularly high demand, as they facilitate synthesis of enantiomerically enriched small molecules that are critical to developments in medicine, biology and materials science. Especially noteworthy are catalysts that promote—with otherwise inaccessible efficiency and selectivity levels—reactions demonstrated to be of great utility in chemical synthesis. Here we report a class of chiral catalysts that initiate alkene metathesis with very high efficiency and enantioselectivity. Such attributes arise from structural fluxionality of the chiral catalysts and the central role that enhanced electronic factors have in the catalytic cycle. The new catalysts have a stereogenic metal centre and carry only monodentate ligands; the molybdenum-based complexes are prepared stereoselectively by a ligand exchange process involving an enantiomerically pure aryloxide, a class of ligands scarcely used in enantioselective catalysis. We demonstrate the application of the new catalysts in an enantioselective synthesis of the Aspidosperma alkaloid, quebrachamine, through an alkene metathesis reaction that cannot be promoted by any of the previously reported chiral catalysts. Highly efficient molybdenum-based catalysts for enantioselective alkene metathesis

Nature advance online publication 16 November 2008. doi:10.1038/nature07594

Authors: Steven J. Malcolmson, Simon J. Meek, Elizabeth S. Sattely, Richard R. Schrock & Amir H. Hoveyda

Discovery of efficient catalysts is one of the most compelling objectives of modern chemistry. Chiral catalysts are in particularly high demand, as they facilitate synthesis of enantiomerically enriched small molecules that are critical to developments in medicine, biology and materials science. Especially noteworthy are catalysts that promote—with otherwise inaccessible efficiency and selectivity levels—reactions demonstrated to be of great utility in chemical synthesis. Here we report a class of chiral catalysts that initiate alkene metathesis with very high efficiency and enantioselectivity. Such attributes arise from structural fluxionality of the chiral catalysts and the central role that enhanced electronic factors have in the catalytic cycle. The new catalysts have a stereogenic metal centre and carry only monodentate ligands; the molybdenum-based complexes are prepared stereoselectively by a ligand exchange process involving an enantiomerically pure aryloxide, a class of ligands scarcely used in enantioselective catalysis. We demonstrate the application of the new catalysts in an enantioselective synthesis of the Aspidosperma alkaloid, quebrachamine, through an alkene metathesis reaction that cannot be promoted by any of the previously reported chiral catalysts.

]]> Highly efficient molybdenum-based catalysts for enantioselective alkene metathesis Steven J. Malcolmson Simon J. Meek Elizabeth S. Sattely Richard R. Schrock Amir H. Hoveyda doi:10.1038/nature07594 Nature 2008-11-16 Nature 2008-11-16 Letter Experience leaves a lasting structural trace in cortical circuits http://dx.doi.org/10.1038/nature07487 Sensory experiences exert a powerful influence on the function and future performance of neuronal circuits in the mammalian neocortex. Restructuring of synaptic connections is believed to be one mechanism by which cortical circuits store information about the sensory world. Excitatory synaptic structures, such as dendritic spines, are dynamic entities that remain sensitive to alteration of sensory input throughout life. It remains unclear, however, whether structural changes at the level of dendritic spines can outlast the original experience and thereby provide a morphological basis for long-term information storage. Here we follow spine dynamics on apical dendrites of pyramidal neurons in functionally defined regions of adult mouse visual cortex during plasticity of eye-specific responses induced by repeated closure of one eye (monocular deprivation). The first monocular deprivation episode doubled the rate of spine formation, thereby increasing spine density. This effect was specific to layer-5 cells located in binocular cortex, where most neurons increase their responsiveness to the non-deprived eye. Restoring binocular vision returned spine dynamics to baseline levels, but absolute spine density remained elevated and many monocular deprivation-induced spines persisted during this period of functional recovery. However, spine addition did not increase again when the same eye was closed for a second time. This absence of structural plasticity stands out against the robust changes of eye-specific responses that occur even faster after repeated deprivation. Thus, spines added during the first monocular deprivation experience may provide a structural basis for subsequent functional shifts. These results provide a strong link between functional plasticity and specific synaptic rearrangements, revealing a mechanism of how prior experiences could be stored in cortical circuits. Experience leaves a lasting structural trace in cortical circuits

Nature advance online publication 12 November 2008. doi:10.1038/nature07487

Authors: Sonja B. Hofer, Thomas D. Mrsic-Flogel, Tobias Bonhoeffer & Mark Hübener

Sensory experiences exert a powerful influence on the function and future performance of neuronal circuits in the mammalian neocortex. Restructuring of synaptic connections is believed to be one mechanism by which cortical circuits store information about the sensory world. Excitatory synaptic structures, such as dendritic spines, are dynamic entities that remain sensitive to alteration of sensory input throughout life. It remains unclear, however, whether structural changes at the level of dendritic spines can outlast the original experience and thereby provide a morphological basis for long-term information storage. Here we follow spine dynamics on apical dendrites of pyramidal neurons in functionally defined regions of adult mouse visual cortex during plasticity of eye-specific responses induced by repeated closure of one eye (monocular deprivation). The first monocular deprivation episode doubled the rate of spine formation, thereby increasing spine density. This effect was specific to layer-5 cells located in binocular cortex, where most neurons increase their responsiveness to the non-deprived eye. Restoring binocular vision returned spine dynamics to baseline levels, but absolute spine density remained elevated and many monocular deprivation-induced spines persisted during this period of functional recovery. However, spine addition did not increase again when the same eye was closed for a second time. This absence of structural plasticity stands out against the robust changes of eye-specific responses that occur even faster after repeated deprivation. Thus, spines added during the first monocular deprivation experience may provide a structural basis for subsequent functional shifts. These results provide a strong link between functional plasticity and specific synaptic rearrangements, revealing a mechanism of how prior experiences could be stored in cortical circuits.

]]> Experience leaves a lasting structural trace in cortical circuits Sonja B. Hofer Thomas D. Mrsic-Flogel Tobias Bonhoeffer Mark Hübener doi:10.1038/nature07487 Nature 2008-11-12 Nature 2008-11-12 Letter Regulation of ERBB2 by oestrogen receptor–PAX2 determines response to tamoxifen http://dx.doi.org/10.1038/nature07483 Crosstalk between the oestrogen receptor (ER) and ERBB2/HER-2 pathways has long been implicated in breast cancer aetiology and drug response, yet no direct connection at a transcriptional level has been shown. Here we show that oestrogen–ER and tamoxifen–ER complexes directly repress ERBB2 transcription by means of a cis-regulatory element within the ERBB2 gene in human cell lines. We implicate the paired box 2 gene product (PAX2), in a previously unrecognized role, as a crucial mediator of ER repression of ERBB2 by the anti-cancer drug tamoxifen. We show that PAX2 and the ER co-activator AIB-1/SRC-3 compete for binding and regulation of ERBB2 transcription, the outcome of which determines tamoxifen response in breast cancer cells. The repression of ERBB2 by ER-PAX2 links these two breast cancer subtypes and suggests that aggressive ERBB2-positive tumours can originate from ER-positive luminal tumours by circumventing this repressive mechanism. These data provide mechanistic insight into the molecular basis of endocrine resistance in breast cancer. Regulation of ERBB2 by oestrogen receptor–PAX2 determines response to tamoxifen

Nature advance online publication 12 November 2008. doi:10.1038/nature07483

Authors: Antoni Hurtado, Kelly A. Holmes, Timothy R. Geistlinger, Iain R. Hutcheson, Robert I. Nicholson, Myles Brown, Jie Jiang, William J. Howat, Simak Ali & Jason S. Carroll

Crosstalk between the oestrogen receptor (ER) and ERBB2/HER-2 pathways has long been implicated in breast cancer aetiology and drug response, yet no direct connection at a transcriptional level has been shown. Here we show that oestrogen–ER and tamoxifen–ER complexes directly repress ERBB2 transcription by means of a cis-regulatory element within the ERBB2 gene in human cell lines. We implicate the paired box 2 gene product (PAX2), in a previously unrecognized role, as a crucial mediator of ER repression of ERBB2 by the anti-cancer drug tamoxifen. We show that PAX2 and the ER co-activator AIB-1/SRC-3 compete for binding and regulation of ERBB2 transcription, the outcome of which determines tamoxifen response in breast cancer cells. The repression of ERBB2 by ER-PAX2 links these two breast cancer subtypes and suggests that aggressive ERBB2-positive tumours can originate from ER-positive luminal tumours by circumventing this repressive mechanism. These data provide mechanistic insight into the molecular basis of endocrine resistance in breast cancer.

]]> Regulation of ERBB2 by oestrogen receptor–PAX2 determines response to tamoxifen Antoni Hurtado Kelly A. Holmes Timothy R. Geistlinger Iain R. Hutcheson Robert I. Nicholson Myles Brown Jie Jiang William J. Howat Simak Ali Jason S. Carroll doi:10.1038/nature07483 Nature 2008-11-12 Nature 2008-11-12 Letter Neural processing of auditory feedback during vocal practice in a songbird http://dx.doi.org/10.1038/nature07467 Songbirds are capable of vocal learning and communication and are ideally suited to the study of neural mechanisms of complex sensory and motor processing. Vocal communication in a noisy bird colony and vocal learning of a specific song template both require the ability to monitor auditory feedback to distinguish self-generated vocalizations from external sounds and to identify mismatches between the developing song and a memorized template acquired from a tutor. However, neurons that respond to auditory feedback from vocal output have not been found in song-control areas despite intensive searching. Here we investigate feedback processing outside the traditional song system, in single auditory forebrain neurons of juvenile zebra finches that were in a late developmental stage of song learning. Overall, we found similarity of spike responses during singing and during playback of the bird’s own song, with song responses commonly leading by a few milliseconds. However, brief time-locked acoustic perturbations of auditory feedback revealed complex sensitivity that could not be predicted from passive playback responses. Some neurons that responded to playback perturbations did not respond to song perturbations, which is reminiscent of sensory-motor mirror neurons. By contrast, some neurons were highly feedback sensitive in that they responded vigorously to song perturbations, but not to unperturbed songs or perturbed playback. These findings suggest that a computational function of forebrain auditory areas may be to detect errors between actual feedback and mirrored feedback deriving from an internal model of the bird’s own song or that of its tutor. Such feedback-sensitive spikes could constitute the key signals that trigger adaptive motor responses to song disruptions or reinforce exploratory motor gestures for vocal learning. Neural processing of auditory feedback during vocal practice in a songbird

Nature advance online publication 12 November 2008. doi:10.1038/nature07467

Authors: Georg B. Keller & Richard H. R. Hahnloser

Songbirds are capable of vocal learning and communication and are ideally suited to the study of neural mechanisms of complex sensory and motor processing. Vocal communication in a noisy bird colony and vocal learning of a specific song template both require the ability to monitor auditory feedback to distinguish self-generated vocalizations from external sounds and to identify mismatches between the developing song and a memorized template acquired from a tutor. However, neurons that respond to auditory feedback from vocal output have not been found in song-control areas despite intensive searching. Here we investigate feedback processing outside the traditional song system, in single auditory forebrain neurons of juvenile zebra finches that were in a late developmental stage of song learning. Overall, we found similarity of spike responses during singing and during playback of the bird’s own song, with song responses commonly leading by a few milliseconds. However, brief time-locked acoustic perturbations of auditory feedback revealed complex sensitivity that could not be predicted from passive playback responses. Some neurons that responded to playback perturbations did not respond to song perturbations, which is reminiscent of sensory-motor mirror neurons. By contrast, some neurons were highly feedback sensitive in that they responded vigorously to song perturbations, but not to unperturbed songs or perturbed playback. These findings suggest that a computational function of forebrain auditory areas may be to detect errors between actual feedback and mirrored feedback deriving from an internal model of the bird’s own song or that of its tutor. Such feedback-sensitive spikes could constitute the key signals that trigger adaptive motor responses to song disruptions or reinforce exploratory motor gestures for vocal learning.

]]> Neural processing of auditory feedback during vocal practice in a songbird Georg B. Keller Richard H. R. Hahnloser doi:10.1038/nature07467 Nature 2008-11-12 Nature 2008-11-12 Letter Memory CD8 T-cell compartment grows in size with immunological experience http://dx.doi.org/10.1038/nature07486 Memory CD8 T cells, generated by natural pathogen exposure or intentional vaccination, protect the host against specific viral infections. It has long been proposed that the number of memory CD8 T cells in the host is inflexible, and that individual cells are constantly competing for limited space. Consequently, vaccines that introduce over-abundant quantities of memory CD8 T cells specific for an agent of interest could have catastrophic consequences for the host by displacing memory CD8 T cells specific for all previous infections. To test this paradigm, we developed a vaccination regimen in mice that introduced as many new long-lived memory CD8 T cells specific for a single vaccine antigen as there were memory CD8 T cells in the host before vaccination. Here we show that, in contrast to expectations, the size of the memory CD8 T-cell compartment doubled to accommodate these new cells, a change due solely to the addition of effector memory CD8 T cells. This increase did not affect the number of CD4 T cells, B cells or naive CD8 T cells, and pre-existing memory CD8 T cells specific for a previously encountered infection were largely preserved. Thus, the number of effector memory CD8 T cells in the mammalian host adapts according to immunological experience. Developing vaccines that abundantly introduce new memory CD8 T cells should not necessarily ablate pre-existing immunity to other infections. Memory CD8 T-cell compartment grows in size with immunological experience

Nature advance online publication 12 November 2008. doi:10.1038/nature07486

Authors: Vaiva Vezys, Andrew Yates, Kerry A. Casey, Gibson Lanier, Rafi Ahmed, Rustom Antia & David Masopust

Memory CD8 T cells, generated by natural pathogen exposure or intentional vaccination, protect the host against specific viral infections. It has long been proposed that the number of memory CD8 T cells in the host is inflexible, and that individual cells are constantly competing for limited space. Consequently, vaccines that introduce over-abundant quantities of memory CD8 T cells specific for an agent of interest could have catastrophic consequences for the host by displacing memory CD8 T cells specific for all previous infections. To test this paradigm, we developed a vaccination regimen in mice that introduced as many new long-lived memory CD8 T cells specific for a single vaccine antigen as there were memory CD8 T cells in the host before vaccination. Here we show that, in contrast to expectations, the size of the memory CD8 T-cell compartment doubled to accommodate these new cells, a change due solely to the addition of effector memory CD8 T cells. This increase did not affect the number of CD4 T cells, B cells or naive CD8 T cells, and pre-existing memory CD8 T cells specific for a previously encountered infection were largely preserved. Thus, the number of effector memory CD8 T cells in the mammalian host adapts according to immunological experience. Developing vaccines that abundantly introduce new memory CD8 T cells should not necessarily ablate pre-existing immunity to other infections.

]]> Memory CD8 T-cell compartment grows in size with immunological experience Vaiva Vezys Andrew Yates Kerry A. Casey Gibson Lanier Rafi Ahmed Rustom Antia David Masopust doi:10.1038/nature07486 Nature 2008-11-12 Nature 2008-11-12 Letter A role for VEGF as a negative regulator of pericyte function and vessel maturation http://dx.doi.org/10.1038/nature07424 Angiogenesis does not only depend on endothelial cell invasion and proliferation: it also requires pericyte coverage of vascular sprouts for vessel stabilization. These processes are coordinated by vascular endothelial growth factor (VEGF) and platelet-derived growth factor (PDGF) through their cognate receptors on endothelial cells and vascular smooth muscle cells (VSMCs), respectively. PDGF induces neovascularization by priming VSMCs/pericytes to release pro-angiogenic mediators. Although VEGF directly stimulates endothelial cell proliferation and migration, its role in pericyte biology is less clear. Here we define a role for VEGF as an inhibitor of neovascularization on the basis of its capacity to disrupt VSMC function. Specifically, under conditions of PDGF-mediated angiogenesis, VEGF ablates pericyte coverage of nascent vascular sprouts, leading to vessel destabilization. At the molecular level, VEGF-mediated activation of VEGF-R2 suppresses PDGF-Rβ signalling in VSMCs through the assembly of a previously undescribed receptor complex consisting of PDGF-Rβ and VEGF-R2. Inhibition of VEGF-R2 not only prevents assembly of this receptor complex but also restores angiogenesis in tissues exposed to both VEGF and PDGF. Finally, genetic deletion of tumour cell VEGF disrupts PDGF-Rβ/VEGF-R2 complex formation and increases tumour vessel maturation. These findings underscore the importance of VSMCs/pericytes in neovascularization and reveal a dichotomous role for VEGF and VEGF-R2 signalling as both a promoter of endothelial cell function and a negative regulator of VSMCs and vessel maturation. A role for VEGF as a negative regulator of pericyte function and vessel maturation

Nature advance online publication 09 November 2008. doi:10.1038/nature07424

Authors: Joshua I. Greenberg, David J. Shields, Samuel G. Barillas, Lisette M. Acevedo, Eric Murphy, Jianhua Huang, Lea Scheppke, Christian Stockmann, Randall S. Johnson, Niren Angle & David A. Cheresh

Angiogenesis does not only depend on endothelial cell invasion and proliferation: it also requires pericyte coverage of vascular sprouts for vessel stabilization. These processes are coordinated by vascular endothelial growth factor (VEGF) and platelet-derived growth factor (PDGF) through their cognate receptors on endothelial cells and vascular smooth muscle cells (VSMCs), respectively. PDGF induces neovascularization by priming VSMCs/pericytes to release pro-angiogenic mediators. Although VEGF directly stimulates endothelial cell proliferation and migration, its role in pericyte biology is less clear. Here we define a role for VEGF as an inhibitor of neovascularization on the basis of its capacity to disrupt VSMC function. Specifically, under conditions of PDGF-mediated angiogenesis, VEGF ablates pericyte coverage of nascent vascular sprouts, leading to vessel destabilization. At the molecular level, VEGF-mediated activation of VEGF-R2 suppresses PDGF-Rβ signalling in VSMCs through the assembly of a previously undescribed receptor complex consisting of PDGF-Rβ and VEGF-R2. Inhibition of VEGF-R2 not only prevents assembly of this receptor complex but also restores angiogenesis in tissues exposed to both VEGF and PDGF. Finally, genetic deletion of tumour cell VEGF disrupts PDGF-Rβ/VEGF-R2 complex formation and increases tumour vessel maturation. These findings underscore the importance of VSMCs/pericytes in neovascularization and reveal a dichotomous role for VEGF and VEGF-R2 signalling as both a promoter of endothelial cell function and a negative regulator of VSMCs and vessel maturation.

]]> A role for VEGF as a negative regulator of pericyte function and vessel maturation Joshua I. Greenberg David J. Shields Samuel G. Barillas Lisette M. Acevedo Eric Murphy Jianhua Huang Lea Scheppke Christian Stockmann Randall S. Johnson Niren Angle David A. Cheresh doi:10.1038/nature07424 Nature 2008-11-09 Nature 2008-11-09 Letter Immune control of an SIV challenge by a T-cell-based vaccine in rhesus monkeys http://dx.doi.org/10.1038/nature07469 A recombinant adenovirus serotype 5 (rAd5) vector-based vaccine for HIV-1 has recently failed in a phase 2b efficacy study in humans. Consistent with these results, preclinical studies have demonstrated that rAd5 vectors expressing simian immunodeficiency virus (SIV) Gag failed to reduce peak or setpoint viral loads after SIV challenge of rhesus monkeys (Macaca mulatta) that lacked the protective MHC class I allele Mamu-A*01 (ref. 3). Here we show that an improved T-cell-based vaccine regimen using two serologically distinct adenovirus vectors afforded substantially improved protective efficacy in this challenge model. In particular, a heterologous rAd26 prime/rAd5 boost vaccine regimen expressing SIV Gag elicited cellular immune responses with augmented magnitude, breadth and polyfunctionality as compared with the homologous rAd5 regimen. After SIVMAC251 challenge, monkeys vaccinated with the rAd26/rAd5 regimen showed a 1.4 log reduction of peak and a 2.4 log reduction of setpoint viral loads as well as decreased AIDS-related mortality as compared with control animals. These data demonstrate that durable partial immune control of a pathogenic SIV challenge for more than 500 days can be achieved by a T-cell-based vaccine in Mamu-A*01-negative rhesus monkeys in the absence of a homologous Env antigen. These findings have important implications for the development of next-generation T-cell-based vaccine candidates for HIV-1. Immune control of an SIV challenge by a T-cell-based vaccine in rhesus monkeys

Nature advance online publication 09 November 2008. doi:10.1038/nature07469

Authors: Jinyan Liu, Kara L. O’Brien, Diana M. Lynch, Nathaniel L. Simmons, Annalena La Porte, Ambryice M. Riggs, Peter Abbink, Rory T. Coffey, Lauren E. Grandpre, Michael S. Seaman, Gary Landucci, Donald N. Forthal, David C. Montefiori, Angela Carville, Keith G. Mansfield, Menzo J. Havenga, Maria G. Pau, Jaap Goudsmit & Dan H. Barouch

A recombinant adenovirus serotype 5 (rAd5) vector-based vaccine for HIV-1 has recently failed in a phase 2b efficacy study in humans. Consistent with these results, preclinical studies have demonstrated that rAd5 vectors expressing simian immunodeficiency virus (SIV) Gag failed to reduce peak or setpoint viral loads after SIV challenge of rhesus monkeys (Macaca mulatta) that lacked the protective MHC class I allele Mamu-A*01 (ref. 3). Here we show that an improved T-cell-based vaccine regimen using two serologically distinct adenovirus vectors afforded substantially improved protective efficacy in this challenge model. In particular, a heterologous rAd26 prime/rAd5 boost vaccine regimen expressing SIV Gag elicited cellular immune responses with augmented magnitude, breadth and polyfunctionality as compared with the homologous rAd5 regimen. After SIVMAC251 challenge, monkeys vaccinated with the rAd26/rAd5 regimen showed a 1.4 log reduction of peak and a 2.4 log reduction of setpoint viral loads as well as decreased AIDS-related mortality as compared with control animals. These data demonstrate that durable partial immune control of a pathogenic SIV challenge for more than 500 days can be achieved by a T-cell-based vaccine in Mamu-A*01-negative rhesus monkeys in the absence of a homologous Env antigen. These findings have important implications for the development of next-generation T-cell-based vaccine candidates for HIV-1.

]]> Immune control of an SIV challenge by a T-cell-based vaccine in rhesus monkeys Jinyan Liu Kara L. O’Brien Diana M. Lynch Nathaniel L. Simmons Annalena La Porte Ambryice M. Riggs Peter Abbink