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Interview: Telling the Life Story of The Ginkgo, The Oldest Tree on Earth

Yale Environment 360 - Wed, 05/01/2013 - 08:57

Botanist Peter Crane sees the ginkgo as more than just a distinctive tree with foul-smelling fruits and nuts prized AJYIGinkgo leaves in autumn for reputed medicinal properties. To Crane, author of a new book, Ginkgo, the tree is an oddity in nature because it is a single species with no known living relatives; a living fossil that has been essentially unchanged for more than 200 million years; and an inspiring example of how humans can help a species survive. In an interview with Yale Environment 360, Crane, dean of the Yale School of Forestry & Environmental Studies, talks about what makes the ginkgo unique and what makes it smell, how its toughness and resilience has enabled it to thrive as a street tree, and what the ginkgo’s long history says about human life on earth. The ginkgo, which co-existed with the dinosaurs, “really puts our own species — let alone our individual existence — into a broader context,” says Crane.
Read the interview

Categories: Environmental News

Evolution: Stuck between the teeth

Nature - Wed, 05/01/2013 - 00:00

Evolution: Stuck between the teeth

Nature 497, 7449 (2013). doi:10.1038/nature12099

Authors: P. David Polly

A computer model of tooth evolution designed to assess the impact of developmental dynamics on natural selection reveals that complexity reduces the likelihood of maximum fitness being attained. See Letter p.361

Categories: Literature

Structure of the human smoothened receptor bound to an antitumour agent

Nature - Wed, 05/01/2013 - 00:00

Structure of the human smoothened receptor bound to an antitumour agent

Nature 497, 7449 (2013). doi:10.1038/nature12167

Authors: Chong Wang, Huixian Wu, Vsevolod Katritch, Gye Won Han, Xi-Ping Huang, Wei Liu, Fai Yiu Siu, Bryan L. Roth, Vadim Cherezov & Raymond C. Stevens

The smoothened (SMO) receptor, a key signal transducer in the hedgehog signalling pathway, is responsible for the maintenance of normal embryonic development and is implicated in carcinogenesis. It is classified as a class frizzled (class F) G-protein-coupled receptor (GPCR), although the canonical hedgehog signalling pathway

Categories: Literature

Adaptive dynamics under development-based genotype–phenotype maps

Nature - Wed, 05/01/2013 - 00:00

Adaptive dynamics under development-based genotype–phenotype maps

Nature 497, 7449 (2013). doi:10.1038/nature12142

Authors: Isaac Salazar-Ciudad & Miquel Marín-Riera

It is not known whether natural selection can encounter any given phenotype that can be produced by genetic variation. There has been a long-lasting debate about the processes that limit adaptation and, consequently, about how well adapted phenotypes are. Here we examine how development may affect adaptation, by decomposing the genotype–fitness map—the association between each genotype and its fitness—into two: one mapping genotype to phenotype by means of a computational model of organ development, and one mapping phenotype to fitness. In the map of phenotype and fitness, the fitness of each individual is based on the similarity between realized morphology and optimal morphology. We use three different simulations to map phenotype to fitness, and these differ in the way in which similarity is calculated: similarity is calculated for each trait (in terms of each cell position individually), for a large or a small number of phenotypic landmarks (the ‘many-traits’ and ‘few-traits’ phenotype–fitness maps), and by measuring the overall surface roughness of morphology (the ‘roughness’ phenotype–fitness map). Evolution is simulated by applying the genotype–phenotype map and one phenotype–fitness map to each individual in the population, as well as random mutation and drift. We show that the complexity of the genotype–phenotype map prevents substantial adaptation in some of the phenotype–fitness maps: sustained adaptation is only possible using ‘roughness’ or ‘few-traits’ phenotype–fitness maps. The results contribute developmental understanding to the long-standing question of which aspects of phenotype can be effectively optimized by natural selection.

Categories: Literature

EGFR modulates microRNA maturation in response to hypoxia through phosphorylation of AGO2

Nature - Wed, 05/01/2013 - 00:00

EGFR modulates microRNA maturation in response to hypoxia through phosphorylation of AGO2

Nature 497, 7449 (2013). doi:10.1038/nature12080

Authors: Jia Shen, Weiya Xia, Yekaterina B. Khotskaya, Longfei Huo, Kotaro Nakanishi, Seung-Oe Lim, Yi Du, Yan Wang, Wei-Chao Chang, Chung-Hsuan Chen, Jennifer L. Hsu, Yun Wu, Yung Carmen Lam, Brian P. James, Xiuping Liu, Chang-Gong Liu, Dinshaw J. Patel & Mien-Chie Hung

MicroRNAs (miRNAs) are generated by two-step processing to yield small RNAs that negatively regulate target gene expression at the post-transcriptional level. Deregulation of miRNAs has been linked to diverse pathological processes, including cancer. Recent studies have also implicated miRNAs in the regulation of cellular response to a spectrum of stresses, such as hypoxia, which is frequently encountered in the poorly angiogenic core of a solid tumour. However, the upstream regulators of miRNA biogenesis machineries remain obscure, raising the question of how tumour cells efficiently coordinate and impose specificity on miRNA expression and function in response to stresses. Here we show that epidermal growth factor receptor (EGFR), which is the product of a well-characterized oncogene in human cancers, suppresses the maturation of specific tumour-suppressor-like miRNAs in response to hypoxic stress through phosphorylation of argonaute 2 (AGO2) at Tyr 393. The association between EGFR and AGO2 is enhanced by hypoxia, leading to elevated AGO2-Y393 phosphorylation, which in turn reduces the binding of Dicer to AGO2 and inhibits miRNA processing from precursor miRNAs to mature miRNAs. We also identify a long-loop structure in precursor miRNAs as a critical regulatory element in phospho-Y393-AGO2-mediated miRNA maturation. Furthermore, AGO2-Y393 phosphorylation mediates EGFR-enhanced cell survival and invasiveness under hypoxia, and correlates with poorer overall survival in breast cancer patients. Our study reveals a previously unrecognized function of EGFR in miRNA maturation and demonstrates how EGFR is likely to function as a regulator of AGO2 through novel post-translational modification. These findings suggest that modulation of miRNA biogenesis is important for stress response in tumour cells and has potential clinical implications.

Categories: Literature

Structural biology: Security measures of a master regulator

Nature - Wed, 05/01/2013 - 00:00

Structural biology: Security measures of a master regulator

Nature 497, 7448 (2013). doi:10.1038/nature12101

Authors: Dario R. Alessi & Yogesh Kulathu

At last, the crystal structure is revealed for the catalytically active mTOR kinase enzyme, a master regulator of cell growth. The structure indicates a gatekeeper mechanism that controls substrate access to the active site. See Article p.217

Categories: Literature

Physiology: Inflammation links ageing to the brain

Nature - Wed, 05/01/2013 - 00:00

Physiology: Inflammation links ageing to the brain

Nature 497, 7448 (2013). doi:10.1038/nature12100

Authors: Dana Gabuzda & Bruce A. Yankner

Inflammation-activated signalling pathways in the brain's hypothalamus control the production of ageing-related hormones. This finding provides a link between inflammation, stress responses and systemic ageing. See Article p.211

Categories: Literature

Hypothalamic programming of systemic ageing involving IKK-β, NF-κB and GnRH

Nature - Wed, 05/01/2013 - 00:00

Hypothalamic programming of systemic ageing involving IKK-β, NF-κB and GnRH

Nature 497, 7448 (2013). doi:10.1038/nature12143

Authors: Guo Zhang, Juxue Li, Sudarshana Purkayastha, Yizhe Tang, Hai Zhang, Ye Yin, Bo Li, Gang Liu & Dongsheng Cai

Ageing is a result of gradual and overall functional deteriorations across the body; however, it is unknown whether an individual tissue primarily works to mediate the ageing progress and control lifespan. Here we show that the hypothalamus is important for the development of whole-body ageing

Categories: Literature

mTOR kinase structure, mechanism and regulation

Nature - Wed, 05/01/2013 - 00:00

mTOR kinase structure, mechanism and regulation

Nature 497, 7448 (2013). doi:10.1038/nature12122

Authors: Haijuan Yang, Derek G. Rudge, Joseph D. Koos, Bhamini Vaidialingam, Hyo J. Yang & Nikola P. Pavletich

The mammalian target of rapamycin (mTOR), a phosphoinositide 3-kinase-related protein kinase, controls cell growth in response to nutrients and growth factors and is frequently deregulated in cancer. Here we report co-crystal structures of a complex of truncated mTOR and mammalian lethal with SEC13 protein 8

Categories: Literature

Formation of a topological non-Fermi liquid in MnSi

Nature - Wed, 05/01/2013 - 00:00

Formation of a topological non-Fermi liquid in MnSi

Nature 497, 7448 (2013). doi:10.1038/nature12023

Authors: R. Ritz, M. Halder, M. Wagner, C. Franz, A. Bauer & C. Pfleiderer

Fermi liquid theory provides a remarkably powerful framework for the description of the conduction electrons in metals and their ordering phenomena, such as superconductivity, ferromagnetism, and spin- and charge-density-wave order. A different class of ordering phenomena of great interest concerns spin configurations that are topologically protected, that is, their topology can be destroyed only by forcing the average magnetization locally to zero. Examples of such configurations are hedgehogs (points at which all spins are either pointing inwards or outwards) and vortices. A central question concerns the nature of the metallic state in the presence of such topologically distinct spin textures. Here we report a high-pressure study of the metallic state at the border of the skyrmion lattice in MnSi, which represents a new form of magnetic order composed of topologically non-trivial vortices. When long-range magnetic order is suppressed under pressure, the key characteristic of the skyrmion lattice—that is, the topological Hall signal due to the emergent magnetic flux associated with the topological winding—is unaffected in sign or magnitude and becomes an important characteristic of the metallic state. The regime of the topological Hall signal in temperature, pressure and magnetic field coincides thereby with the exceptionally extended regime of a pronounced non-Fermi-liquid resistivity. The observation of this topological Hall signal in the regime of the NFL resistivity suggests empirically that spin correlations with non-trivial topological character may drive a breakdown of Fermi liquid theory in pure metals.

Categories: Literature

Fields of gold

Nature - Wed, 05/01/2013 - 00:00

Fields of gold

Nature 497, 7447 (2013). doi:10.1038/497005b

Research on transgenic crops must be done outside industry if it is to fulfil its early promise.

Categories: Literature

Freed speech

Nature - Wed, 05/01/2013 - 00:00

Freed speech

Nature 497, 7447 (2013). doi:10.1038/497006a

The reform of English libel law is a victory, even if it doesn’t achieve everything that was hoped.

Categories: Literature

Australian science needs more female fellows

Nature - Wed, 05/01/2013 - 00:00

Australian science needs more female fellows

Nature 497, 7447 (2013). http://www.nature.com/doifinder/10.1038/497007a

Author: Douglas Hilton

The Australian Academy of Science must take urgent steps to address the lack of gender equality among its elected fellows, warns Douglas Hilton.

Categories: Literature

Archaeology: Monkeys make their mark

Nature - Wed, 05/01/2013 - 00:00

Archaeology: Monkeys make their mark

Nature 497, 7447 (2013). doi:10.1038/497008a

Wild monkeys leave behind long-lasting traces of their efforts to crack nuts with tools — evidence that could be useful to archaeologists.Bearded capuchin monkeys (Sapajus libidinosus, pictured) open seeds such as palm nuts by placing them on stone and wood surfaces, or

Categories: Literature

Urban growth: The shape of cities to come

Nature - Wed, 05/01/2013 - 00:00

Urban growth: The shape of cities to come

Nature 497, 7447 (2013). doi:10.1038/497008b

The physical features of the world's largest cities are shifting as urban centres in Asia expand upwards and outwards.Steve Frolking at the University of New Hampshire in Durham and his colleagues combined satellite observations of night-time illumination and urban backscatter — the reflection of

Categories: Literature

Gene therapy: Enzymes fix disease genes

Nature - Wed, 05/01/2013 - 00:00

Gene therapy: Enzymes fix disease genes

Nature 497, 7447 (2013). doi:10.1038/497008c

Genome-editing enzymes can be used to correct patient-specific genetic defects.Mutations in the COL7A1 gene cause the skin-blistering disease recessive dystrophic epidermolysis bullosa, which can be fatal. A team led by Jakub Tolar at the University of Minnesota in Minneapolis engineered enzymes called transcription

Categories: Literature

Disease research: New hormone for diabetes

Nature - Wed, 05/01/2013 - 00:00

Disease research: New hormone for diabetes

Nature 497, 7447 (2013). doi:10.1038/497008d

A newly identified hormone stimulates growth of insulin-producing cells in the mouse pancreas.Douglas Melton and his colleagues at Harvard University in Cambridge, Massachusetts, identified the hormone, which they call betatrophin, by searching for genes that became more active in fat and liver tissue when

Categories: Literature

Conservation biology: Bigger is better for protecting seas

Nature - Wed, 05/01/2013 - 00:00

Conservation biology: Bigger is better for protecting seas

Nature 497, 7447 (2013). doi:10.1038/497008e

Although small protected marine zones are important for conservation, they do not protect fish as well as larger areas do.Nicholas Graham at James Cook University in Townsville, Australia, and Tim McClanahan at the Wildlife Conservation Society in New York assessed biomass and composition of

Categories: Literature

Palaeontology: Winged raptor dined on fish

Nature - Wed, 05/01/2013 - 00:00

Palaeontology: Winged raptor dined on fish

Nature 497, 7447 (2013). doi:10.1038/497009a

A fossil of a dinosaur that was thought to feed on tree-living animals has been found with a fish in its belly.Used to understand the origins of flight, fossils of the four-winged feathered raptor Microraptor gui, which lived 120 million years ago have

Categories: Literature

Quantum mechanics: Exchange-free communication

Nature - Wed, 05/01/2013 - 00:00

Quantum mechanics: Exchange-free communication

Nature 497, 7447 (2013). doi:10.1038/497009b

Researchers have proposed a mode of quantum communication whereby information could travel between two parties without the exchange of physical particles.Quantum communication holds the promise of ultrasecure encryption, but most schemes proposed so far require the communicating parties to exchange particles. Hatim Salih at

Categories: Literature