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  • Articles  (79)
  • Evolution  (68)
  • Models, Molecular
  • American Association for the Advancement of Science (AAAS)  (79)
  • American Association of Petroleum Geologists (AAPG)
  • American Geophysical Union (AGU)
  • Elsevier
  • 2015-2019  (79)
  • Science  (68)
  • Science. 347(6221): 548-51. doi: 10.1126/science.aaa0986.  (1)
  • Science. 347(6221): 555-8. doi: 10.1126/science.1260590.  (1)
  • Science. 347(6227): 1256-9. doi: 10.1126/science.1261512.  (1)
  • Science. 349(6253): 1182-91. doi: 10.1126/science.aac7629.  (1)
  • Science. 350(6267): aac5464. doi: 10.1126/science.aac5464.  (1)
  • Science. 351(6275) doi: 10.1126/science.aad9421.  (1)
  • Science. 351(6275): 871-5. doi: 10.1126/science.aad7974.  (1)
  • Science. 351(6278): aad2001. doi: 10.1126/science.aad2001.  (1)
  • Science. 351(6280): 1416-20. doi: 10.1126/science.aad2085.  (1)
  • Science. 352(6283): 363-5. doi: 10.1126/science.aaf0643.  (1)
  • Science. 352(6285): aad3873. doi: 10.1126/science.aad3873.  (1)
  • 25
Collection
  • Articles  (79)
Keywords
Publisher
  • American Association for the Advancement of Science (AAAS)  (79)
  • American Association of Petroleum Geologists (AAPG)
  • American Geophysical Union (AGU)
  • Elsevier
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Year
Journal
  • 1
    Publication Date: 2018-08-10
    Description: Mammals diversified by colonizing drastically different environments, with each transition yielding numerous molecular changes, including losses of protein function. Though not initially deleterious, these losses could subsequently carry deleterious pleiotropic consequences. We have used phylogenetic methods to identify convergent functional losses across independent marine mammal lineages. In one extreme case, Paraoxonase 1 ( PON1 ) accrued lesions in all marine lineages, while remaining intact in all terrestrial mammals. These lesions coincide with PON1 enzymatic activity loss in marine species’ blood plasma. This convergent loss is likely explained by parallel shifts in marine ancestors’ lipid metabolism and/or bloodstream oxidative environment affecting PON1’s role in fatty acid oxidation. PON1 loss also eliminates marine mammals’ main defense against neurotoxicity from specific man-made organophosphorus compounds, implying potential risks in modern environments.
    Keywords: Evolution
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  • 2
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-08-10
    Description: The turbulent surfaces of rivers and streams are natural hotspots of biogeochemical exchange with the atmosphere. At the global scale, the total river-atmosphere flux of trace gasses such as carbon dioxide depends on the proportion of Earth’s surface that is covered by the fluvial network, yet the total surface area of rivers and streams is poorly constrained. We used a global database of planform river hydromorphology and a statistical approach to show that global river and stream surface area at mean annual discharge is 773,000 ± 79,000 square kilometers (0.58 ± 0.06%) of Earth’s nonglaciated land surface, an area 44 ± 15% larger than previous spatial estimates. We found that rivers and streams likely play a greater role in controlling land-atmosphere fluxes than is currently represented in global carbon budgets.
    Keywords: Evolution
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  • 3
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-10-05
    Keywords: Evolution
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  • 4
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-12-14
    Keywords: Evolution
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  • 5
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-10-26
    Keywords: Evolution
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  • 6
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-10-26
    Keywords: Evolution
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  • 7
    Publication Date: 2018-10-26
    Description: The color patterns of African cichlid fishes provide notable examples of phenotypic convergence. Across the more than 1200 East African rift lake species, melanic horizontal stripes have evolved numerous times. We discovered that regulatory changes of the gene agouti-related peptide 2 ( agrp2 ) act as molecular switches controlling this evolutionarily labile phenotype. Reduced agrp2 expression is convergently associated with the presence of stripe patterns across species flocks. However, cis-regulatory mutations are not predictive of stripes across radiations, suggesting independent regulatory mechanisms. Genetic mapping confirms the link between the agrp2 locus and stripe patterns. The crucial role of agrp2 is further supported by a CRISPR-Cas9 knockout that reconstitutes stripes in a nonstriped cichlid. Thus, we unveil how a single gene affects the convergent evolution of a complex color pattern.
    Keywords: Evolution
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  • 8
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-11-30
    Keywords: Evolution
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  • 9
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-08-10
    Keywords: Evolution
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  • 10
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-08-10
    Keywords: Evolution
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  • 11
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-08-10
    Keywords: Evolution
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  • 12
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-10-26
    Keywords: Evolution
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  • 13
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-11-09
    Keywords: Evolution
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  • 14
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-07-13
    Keywords: Evolution
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  • 15
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-06-22
    Keywords: Evolution
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  • 16
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-04-13
    Keywords: Evolution
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  • 17
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-07-06
    Keywords: Evolution
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  • 18
    Publication Date: 2018-06-22
    Description: Snowshoe hares ( Lepus americanus ) maintain seasonal camouflage by molting to a white winter coat, but some hares remain brown during the winter in regions with low snow cover. We show that cis-regulatory variation controlling seasonal expression of the Agouti gene underlies this adaptive winter camouflage polymorphism. Genetic variation at Agouti clustered by winter coat color across multiple hare and jackrabbit species, revealing a history of recurrent interspecific gene flow. Brown winter coats in snowshoe hares likely originated from an introgressed black-tailed jackrabbit allele that has swept to high frequency in mild winter environments. These discoveries show that introgression of genetic variants that underlie key ecological traits can seed past and ongoing adaptation to rapidly changing environments.
    Keywords: Evolution
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  • 19
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-02-10
    Keywords: Evolution
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  • 20
    Publication Date: 2018-03-06
    Description: Maintenance of biodiversity in a rapidly changing climate will depend on the efficacy of evolutionary rescue, whereby population declines due to abrupt environmental change are reversed by shifts in genetically driven adaptive traits. However, a lack of traits known to be under direct selection by anthropogenic climate change has limited the incorporation of evolutionary processes into global conservation efforts. In 21 vertebrate species, some individuals undergo a seasonal color molt from summer brown to winter white as camouflage against snow, whereas other individuals remain brown. Seasonal snow duration is decreasing globally, and fitness is lower for winter white animals on snowless backgrounds. Based on 2713 georeferenced samples of known winter coat color—from eight species across trophic levels—we identify environmentally driven clinal gradients in winter coat color, including polymorphic zones where winter brown and white morphs co-occur. These polymorphic zones, underrepresented by existing global protected area networks, indicate hot spots for evolutionary rescue in a changing climate.
    Keywords: Evolution
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  • 21
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-03-06
    Keywords: Evolution
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  • 22
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-03-06
    Keywords: Evolution
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  • 23
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-03-17
    Description: Anyone awed by towering redwoods should offer thanks to stomata, the tiny pores on the leaves of all trees and other vascular plants. These microscopic mouths allow plants to grow tall and to regulate carbon dioxide intake and water loss. Stomata, in short, helped plants colonize the landscape and transform the planet. Now, molecular studies are giving scientists glimpses of the early days of stomata and how they have changed since then. They suggest complex stomata evolved to help early plants control moisture in their spore capsules and that other plants later exploited these pores to breathe in carbon dioxide and exhale water vapor. And hundreds of millions of years later, more sophisticated stomata evolved in grasses, enabling them to tightly control water loss—a feature that helped them dominate dry landscapes around the world. Author: Elizabeth Pennisi
    Keywords: Evolution
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  • 24
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-08-11
    Keywords: Evolution
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  • 25
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-09-15
    Keywords: Evolution
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  • 26
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-06-23
    Keywords: Evolution
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  • 27
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-09-22
    Keywords: Evolution
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  • 28
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-09-01
    Keywords: Evolution
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  • 29
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-02-24
    Description: Author: Julia Fahrenkamp-Uppenbrink
    Keywords: Evolution
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  • 30
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-06-02
    Keywords: Evolution
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  • 31
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-06-23
    Keywords: Evolution
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  • 32
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-06-23
    Description: Avian egg shape is generally explained as an adaptation to life history, yet we currently lack a global synthesis of how egg-shape differences arise and evolve. Here, we apply morphometric, mechanistic, and macroevolutionary analyses to the egg shapes of 1400 bird species. We characterize egg-shape diversity in terms of two biologically relevant variables, asymmetry and ellipticity, allowing us to quantify the observed morphologies in a two-dimensional morphospace. We then propose a simple mechanical model that explains the observed egg-shape diversity based on geometric and material properties of the egg membrane. Finally, using phylogenetic models, we show that egg shape correlates with flight ability on broad taxonomic scales, suggesting that adaptations for flight may have been critical drivers of egg-shape variation in birds.
    Keywords: Evolution
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  • 33
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-07-28
    Keywords: Evolution
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  • 34
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-08-04
    Keywords: Evolution
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  • 35
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-08-04
    Keywords: Evolution
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  • 36
    Publication Date: 2017-08-04
    Description: Extreme environmental perturbations offer opportunities to observe the effects of natural selection in wild populations. During the winter of 2013–2014, the southeastern United States endured an extreme cold event. We used thermal performance, transcriptomics, and genome scans to measure responses of lizard populations to storm-induced selection. We found significant increases in cold tolerance at the species’ southern limit. Gene expression in southern survivors shifted toward patterns characteristic of northern populations. Comparing samples before and after the extreme winter, 14 genomic regions were differentiated in the surviving southern population; four also exhibited signatures of local adaptation across the latitudinal gradient and implicate genes involved in nervous system function. Together, our results suggest that extreme winter events can rapidly produce strong selection on natural populations at multiple biological levels that recapitulate geographic patterns of local adaptation.
    Keywords: Evolution
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  • 37
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-11-17
    Keywords: Evolution
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  • 38
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-11-17
    Keywords: Evolution
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  • 39
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-11-03
    Keywords: Evolution
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  • 40
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-05-05
    Keywords: Evolution
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  • 41
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-02-10
    Description: Author: Sacha Vignieri
    Keywords: Evolution
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  • 42
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-01-06
    Description: The phrase “perception is reality” is used in many contexts but is often not true. For example, human inability to perceive ultraviolet light does not negate its reality. Nevertheless, perception can cause reality to evolve. This is the insight of the study by Nachev et al. on page 75 of this issue (1). The authors integrated field and laboratory experiments with computer simulations to explain how perceptual mechanisms in a pollinator—a bat—can cause the evolution of counterintuitive traits in flowers. Author: Hamilton Farris
    Keywords: Evolution
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  • 43
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-03-03
    Description: Charles Darwin closed his first edition of On the Origin of Species with the poetic words: “There is grandeur in this view of life,…whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved” (1). Today, scientists are using genetics to understand how species multiply, and ecological and behavioral knowledge to understand why they do so. However, many questions remain about the sources of genetic variation and how new phenotypes arise in response to environmental change. Recent research has revealed unexpected origins of genetic variation, providing crucial insights into phenotypic divergence and the evolutionary effects of rare events triggered by global climatic change. Authors: B. Rosemary Grant, Peter R. Grant
    Keywords: Evolution
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  • 44
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-03-03
    Description: Author: Julia Fahrenkamp-Uppenbrink
    Keywords: Evolution
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  • 45
    Publication Date: 2017-10-20
    Description: We used extensive data from a long-term study of great tits ( Parus major ) in the United Kingdom and Netherlands to better understand how genetic signatures of selection translate into variation in fitness and phenotypes. We found that genomic regions under differential selection contained candidate genes for bill morphology and used genetic architecture analyses to confirm that these genes, especially the collagen gene COL4A5 , explained variation in bill length. COL4A5 variation was associated with reproductive success, which, combined with spatiotemporal patterns of bill length, suggested ongoing selection for longer bills in the United Kingdom. Last, bill length and COL4A5 variation were associated with usage of feeders, suggesting that longer bills may have evolved in the United Kingdom as a response to supplementary feeding.
    Keywords: Evolution
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  • 46
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-12-08
    Description: Nachev et al . (Reports, 6 January 2017, p. 75) present dilute nectar in bat-pollinated plants as "paradoxical" because bats prefer concentrated nectar, but paradox disappears with realistic assumptions about nectar evolution. We argue that they make unrealistic assumptions about the cognitive abilities of bat pollinators, invoke Weber’s law inappropriately, and cannot predict observed nectar concentrations of bat flowers or negative correlations between pollinator body size and average concentration.
    Keywords: Evolution
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  • 47
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-12-08
    Description: Pyke and Waser claim that our virtual pollination ecology model makes unrealistic assumptions and fails to predict observed nectar concentrations of bat flowers and negative correlations between pollinator body size and sugar concentration. In their comment, crucial model features are misrepresented, misunderstood, or ignored. Sensitivity to the supply/demand ratio explains both the equilibrium concentrations and the selection for lower concentrations by larger pollinators.
    Keywords: Evolution
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  • 48
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-07-07
    Keywords: Evolution
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  • 49
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-04-01
    Description: One of the most important developments in Earth's history is the change from the anaerobic environment of the early Earth to the aerobic and highly oxidizing environment that we have today, with 21% atmospheric oxygen (O2) (1). Many geologists, atmospheric scientists, and biologists have studied this dramatic change in the redox state of Earth—the “great oxidation event” (2)—to understand when and how it took place. On page 1436 of this issue, Soo et al. report exciting new evidence toward answers to both these questions (3). Author: Robert E. Blankenship
    Keywords: Evolution
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  • 50
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-05-26
    Keywords: Evolution
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  • 51
    Publication Date: 2017-09-22
    Description: Animals that wield toxins face self-intoxication. Poison frogs have a diverse arsenal of defensive alkaloids that target the nervous system. Among them is epibatidine, a nicotinic acetylcholine receptor (nAChR) agonist that is lethal at microgram doses. Epibatidine shares a highly conserved binding site with acetylcholine, making it difficult to evolve resistance yet maintain nAChR function. Electrophysiological assays of human and frog nAChR revealed that one amino acid replacement, which evolved three times in poison frogs, decreased epibatidine sensitivity but at a cost of acetylcholine sensitivity. However, receptor functionality was rescued by additional amino acid replacements that differed among poison frog lineages. Our results demonstrate how resistance to agonist toxins can evolve and that such genetic changes propel organisms toward an adaptive peak of chemical defense.
    Keywords: Evolution
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  • 52
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-10-20
    Keywords: Evolution
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  • 53
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-07-22
    Description: Mutualistic symbiotic relationships are those in which both species benefit; for example, the vivid colors of coral reefs come from symbiotic algae that provide their living coral hosts with nutrients and oxygen through photosynthesis in exchange for protection. A similar mutualistic relationship exists between gut-dwelling bacteria and their animal hosts (1). It remains unclear, however, to what degree symbiosis has shaped host-microbial interactions and coevolution. On page 380 of this issue, Moeller et al. show that gut bacterial strains cospeciated with hominids (apes and humans) over the past 15 million years (2). These findings set the stage for exploring the evolutionary processes that underlie the symbiotic relationship between hominids and their gut-dwelling microbes. Authors: Julia A. Segre, Nick Salafsky
    Keywords: Evolution
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  • 54
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-07-22
    Description: Author: Caroline Ash
    Keywords: Evolution
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  • 55
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-03-25
    Description: Several unprecedented videos of gelatinous sea creatures called comb jellies, or ctenophores, now threaten to upend the standard view of the evolution of the so-called through-gut. Comb jellies, jellyfish, sea sponges, and a few other creatures all were thought to lack an anus, which meant they had to eat and defecate through a single hole. These are descendants of some of the first animals to arise, so it has been thought that the through-gut and anus were an innovation that came after those lineages emerged—and perhaps something that drove the diversity of new animal forms. But on 15 March, at the Ctenopolooza meeting in St. Augustine, Florida, evolutionary biologist William Browne of the University of Miami in Florida debuted films of comb jellies pooping—and it wasn't through their mouths. Browne's videos elicited gasps from the audience, who is now rethinking when the through-gut first evolved—and whether it may have emerged more than once. Author: Amy Maxmen
    Keywords: Evolution
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  • 56
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-06-03
    Description: For years, scientists have debated where dogs came from. Did wolves first forge their special relationship with humans in Europe, or in Asia? The answer, according to a new study, is yes. Researchers report that genetic analysis of hundreds of canines—including a nearly 5000-year-old dog unearthed on the east coast of Ireland—reveals that dogs may have been domesticated twice, once in Asia and once in Europe or the Near East, although European ancestry has mostly vanished from today's dogs. The findings could resolve a rift that has roiled the canine origins community—but experts say a lot more work needs to be done to confirm them. Author: David Grimm
    Keywords: Evolution
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  • 57
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-09-09
    Description: One of the greatest symbols of the birth of evolutionary biology is Darwin's first sketch of an evolutionary tree, above which he wrote: “I think.” Not only are evolutionary trees central to how scientists conceptualize evolutionary processes, Darwin's words also capture a key aspect of evolutionary science: It is difficult to observe, forcing researchers to rely heavily on inference. In recent decades, studies of fast-growing microorganisms have allowed hypotheses about evolutionary processes to be tested experimentally (1). On page 1147 of this issue, Baym et al. (2) report a device for visualizing evolutionary branching as bacteria grow across a meter-scale agar slab. The results offer important insights into evolutionary dynamics in spatially extended systems. Authors: Luke McNally, Sam P. Brown
    Keywords: Evolution
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  • 58
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-05-13
    Description: The field of molecular evolution is concerned with evolutionary changes in genes and genomes and the underlying driving forces behind those changes. Current studies in molecular evolution are almost entirely retrospective, with a focus on the mutations that were fixed during evolution, and the conclusions are often explanatory, offering no predictive insights. Because only a tiny fraction of all mutations that have ever occurred during evolution have been fixed, the “successes” that we see today provide an incomplete or even biased understanding of the evolutionary process. One way to circumvent this problem is to obtain the whole fitness landscape of a gene to understand, prospectively, chance and necessity in evolution (see the figure). Two studies in this issue, by Li et al. on page 837 (1) and Puchta et al. on page 840 (2), each take on this challenge by characterizing the in vivo fitness landscape of two RNA genes. Authors: Xionglei He, Li Liu
    Keywords: Evolution
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  • 59
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-03-18
    Description: Author: Sacha Vignieri
    Keywords: Evolution
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  • 60
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-04-22
    Description: For many evolutionary biologists, nothing gets their dander up faster than suggesting evolution is anything other than the process of natural selection, acting on random mutations. So some are uneasy that the John Templeton Foundation has awarded $8.7 million to U.K., Swedish, and U.S. researchers for experimental and theoretical work intended to put a revisionist view of evolution, the so-called extended evolutionary synthesis, on a sounder footing. Using a variety of plants, animals, and microbes, the researchers will study the possibility that organisms can influence their own evolution and that inheritance can take place through routes other than the genetic material. Critics are against evolutionary biologists accepting this money and argue that evolutionary theory already embraces the best of these ideas. But others are pleased as the money should help clarify the importance of different aspects of the extended synthesis. Author: Elizabeth Pennisi
    Keywords: Evolution
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  • 61
    Publication Date: 2016-02-26
    Description: Hundreds of pathways for degradation converge at ubiquitin recognition by a proteasome. Here, we found that the five known proteasomal ubiquitin receptors in yeast are collectively nonessential for ubiquitin recognition and identified a sixth receptor, Rpn1. A site ( T1: ) in the Rpn1 toroid recognized ubiquitin and ubiquitin-like ( UBL: ) domains of substrate shuttling factors. T1 structures with monoubiquitin or lysine 48 diubiquitin show three neighboring outer helices engaging two ubiquitins. T1 contributes a distinct substrate-binding pathway with preference for lysine 48-linked chains. Proximal to T1 within the Rpn1 toroid is a second UBL-binding site ( T2: ) that assists in ubiquitin chain disassembly, by binding the UBL of deubiquitinating enzyme Ubp6. Thus, a two-site recognition domain intrinsic to the proteasome uses distinct ubiquitin-fold ligands to assemble substrates, shuttling factors, and a deubiquitinating enzyme.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shi, Yuan -- Chen, Xiang -- Elsasser, Suzanne -- Stocks, Bradley B -- Tian, Geng -- Lee, Byung-Hoon -- Shi, Yanhong -- Zhang, Naixia -- de Poot, Stefanie A H -- Tuebing, Fabian -- Sun, Shuangwu -- Vannoy, Jacob -- Tarasov, Sergey G -- Engen, John R -- Finley, Daniel -- Walters, Kylie J -- New York, N.Y. -- Science. 2016 Feb 19;351(6275). pii: aad9421. doi: 10.1126/science.aad9421.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA. ; Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA. ; Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA. ; Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA. Department of Analytical Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, P. R. China. ; Department of Analytical Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, P. R. China. ; Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA. Linganore High School, Frederick, MD 21701, USA. ; Biophysics Resource, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA. ; Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA. j.engen@neu.edu kylie.walters@nih.gov daniel_finley@hms.harvard.edu. ; Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA. j.engen@neu.edu kylie.walters@nih.gov daniel_finley@hms.harvard.edu. ; Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA. j.engen@neu.edu kylie.walters@nih.gov daniel_finley@hms.harvard.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26912900" target="_blank"〉PubMed〈/a〉
    Keywords: DNA-Binding Proteins/metabolism ; Endopeptidases/metabolism ; Metabolic Networks and Pathways ; Models, Molecular ; Mutation ; Proteasome Endopeptidase Complex/chemistry/genetics/*metabolism ; Saccharomyces cerevisiae/*metabolism ; Saccharomyces cerevisiae Proteins/*chemistry/genetics/*metabolism ; Ubiquitin-Specific Proteases/metabolism ; Ubiquitination
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  • 62
    Publication Date: 2016-02-26
    Description: The U4/U6.U5 triple small nuclear ribonucleoprotein (tri-snRNP) is a major spliceosome building block. We obtained a three-dimensional structure of the 1.8-megadalton human tri-snRNP at a resolution of 7 angstroms using single-particle cryo-electron microscopy (cryo-EM). We fit all known high-resolution structures of tri-snRNP components into the EM density map and validated them by protein cross-linking. Our model reveals how the spatial organization of Brr2 RNA helicase prevents premature U4/U6 RNA unwinding in isolated human tri-snRNPs and how the ubiquitin C-terminal hydrolase-like protein Sad1 likely tethers the helicase Brr2 to its preactivation position. Comparison of our model with cryo-EM three-dimensional structures of the Saccharomyces cerevisiae tri-snRNP and Schizosaccharomyces pombe spliceosome indicates that Brr2 undergoes a marked conformational change during spliceosome activation, and that the scaffolding protein Prp8 is also rearranged to accommodate the spliceosome's catalytic RNA network.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Agafonov, Dmitry E -- Kastner, Berthold -- Dybkov, Olexandr -- Hofele, Romina V -- Liu, Wen-Ti -- Urlaub, Henning -- Luhrmann, Reinhard -- Stark, Holger -- New York, N.Y. -- Science. 2016 Mar 25;351(6280):1416-20. doi: 10.1126/science.aad2085. Epub 2016 Feb 18.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, D-37077 Gottingen, Germany. ; Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, D-37077 Gottingen, Germany. Bioanalytics Group, Institute for Clinical Chemistry, University Medical Center Gottingen, D-37075 Gottingen, Germany. ; Department of 3D Electron Cryomicroscopy, Georg-August Universitat Gottingen, D-37077 Gottingen, Germany. Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, D-37077 Gottingen, Germany. ; Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, D-37077 Gottingen, Germany. Bioanalytics Group, Institute for Clinical Chemistry, University Medical Center Gottingen, D-37075 Gottingen, Germany. reinhard.luehrmann@mpi-bpc.mpg.de hstark1@gwdg.de henning.urlaub@mpibpc.mpg.de. ; Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, D-37077 Gottingen, Germany. reinhard.luehrmann@mpi-bpc.mpg.de hstark1@gwdg.de henning.urlaub@mpibpc.mpg.de. ; Department of 3D Electron Cryomicroscopy, Georg-August Universitat Gottingen, D-37077 Gottingen, Germany. Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, D-37077 Gottingen, Germany. reinhard.luehrmann@mpi-bpc.mpg.de hstark1@gwdg.de henning.urlaub@mpibpc.mpg.de.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26912367" target="_blank"〉PubMed〈/a〉
    Keywords: Cryoelectron Microscopy ; Crystallography, X-Ray ; DEAD-box RNA Helicases/chemistry ; Enzyme Activation ; HeLa Cells ; Humans ; Models, Molecular ; Peptide Elongation Factors/chemistry ; Protein Conformation ; RNA Helicases/chemistry ; RNA-Binding Proteins/chemistry ; Ribonucleoprotein, U4-U6 Small Nuclear/*chemistry ; Ribonucleoprotein, U5 Small Nuclear/*chemistry ; Ribonucleoproteins, Small Nuclear/chemistry ; Saccharomyces cerevisiae Proteins/chemistry ; Schizosaccharomyces/metabolism ; Ubiquitin Thiolesterase/chemistry
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  • 63
    Publication Date: 2016-03-12
    Description: AMPA-type glutamate receptors (AMPARs), which are central mediators of rapid neurotransmission and synaptic plasticity, predominantly exist as heteromers of the subunits GluA1 to GluA4. Here we report the first AMPAR heteromer structures, which deviate substantially from existing GluA2 homomer structures. Crystal structures of the GluA2/3 and GluA2/4 N-terminal domains reveal a novel compact conformation with an alternating arrangement of the four subunits around a central axis. This organization is confirmed by cysteine cross-linking in full-length receptors, and it permitted us to determine the structure of an intact GluA2/3 receptor by cryogenic electron microscopy. Two models in the ligand-free state, at resolutions of 8.25 and 10.3 angstroms, exhibit substantial vertical compression and close associations between domain layers, reminiscent of N-methyl-D-aspartate receptors. Model 1 resembles a resting state and model 2 a desensitized state, thus providing snapshots of gating transitions in the nominal absence of ligand. Our data reveal organizational features of heteromeric AMPARs and provide a framework to decipher AMPAR architecture and signaling.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4852135/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4852135/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Herguedas, Beatriz -- Garcia-Nafria, Javier -- Cais, Ondrej -- Fernandez-Leiro, Rafael -- Krieger, James -- Ho, Hinze -- Greger, Ingo H -- MC_U105174197/Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2016 Apr 29;352(6285):aad3873. doi: 10.1126/science.aad3873. Epub 2016 Mar 10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Neurobiology Division, Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge, UK. ; Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26966189" target="_blank"〉PubMed〈/a〉
    Keywords: Brain/metabolism ; Cryoelectron Microscopy ; Crystallography, X-Ray ; HEK293 Cells ; Humans ; Ligands ; Models, Molecular ; *Protein Multimerization ; Protein Structure, Tertiary ; Receptors, AMPA/*chemistry/ultrastructure
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  • 64
    Publication Date: 2016-01-30
    Description: p97 is a hexameric AAA+ adenosine triphosphatase (ATPase) that is an attractive target for cancer drug development. We report cryo-electron microscopy (cryo-EM) structures for adenosine diphosphate (ADP)-bound, full-length, hexameric wild-type p97 in the presence and absence of an allosteric inhibitor at resolutions of 2.3 and 2.4 angstroms, respectively. We also report cryo-EM structures (at resolutions of ~3.3, 3.2, and 3.3 angstroms, respectively) for three distinct, coexisting functional states of p97 with occupancies of zero, one, or two molecules of adenosine 5'-O-(3-thiotriphosphate) (ATPgammaS) per protomer. A large corkscrew-like change in molecular architecture, coupled with upward displacement of the N-terminal domain, is observed only when ATPgammaS is bound to both the D1 and D2 domains of the protomer. These cryo-EM structures establish the sequence of nucleotide-driven structural changes in p97 at atomic resolution. They also enable elucidation of the binding mode of an allosteric small-molecule inhibitor to p97 and illustrate how inhibitor binding at the interface between the D1 and D2 domains prevents propagation of the conformational changes necessary for p97 function.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Banerjee, Soojay -- Bartesaghi, Alberto -- Merk, Alan -- Rao, Prashant -- Bulfer, Stacie L -- Yan, Yongzhao -- Green, Neal -- Mroczkowski, Barbara -- Neitz, R Jeffrey -- Wipf, Peter -- Falconieri, Veronica -- Deshaies, Raymond J -- Milne, Jacqueline L S -- Huryn, Donna -- Arkin, Michelle -- Subramaniam, Sriram -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2016 Feb 19;351(6275):871-5. doi: 10.1126/science.aad7974. Epub 2016 Jan 28.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Cell Biology, National Cancer Institute, Bethesda, MD 20892, USA. ; Small Molecule Discovery Center, Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA 94143, USA. ; University of Pittsburgh Chemical Diversity Center, University of Pittsburgh, Pittsburgh, PA 15260, USA. ; Leidos Biomedical Research Inc., Frederick, MD 21702, USA. ; Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA. ; Division of Biology and Biological Engineering and Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91107, USA. ; Laboratory of Cell Biology, National Cancer Institute, Bethesda, MD 20892, USA. ss1@nih.gov.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26822609" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Diphosphate/chemistry ; Adenosine Triphosphatases/*antagonists & inhibitors/*chemistry ; Adenosine Triphosphate/analogs & derivatives/chemistry ; Allosteric Regulation ; Binding Sites ; Cryoelectron Microscopy ; Enzyme Inhibitors ; Humans ; Models, Molecular ; Nuclear Proteins/*antagonists & inhibitors/*chemistry ; Protein Structure, Tertiary
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  • 65
    Publication Date: 2016-03-12
    Description: Type IVa pili are filamentous cell surface structures observed in many bacteria. They pull cells forward by extending, adhering to surfaces, and then retracting. We used cryo-electron tomography of intact Myxococcus xanthus cells to visualize type IVa pili and the protein machine that assembles and retracts them (the type IVa pilus machine, or T4PM) in situ, in both the piliated and nonpiliated states, at a resolution of 3 to 4 nanometers. We found that T4PM comprises an outer membrane pore, four interconnected ring structures in the periplasm and cytoplasm, a cytoplasmic disc and dome, and a periplasmic stem. By systematically imaging mutants lacking defined T4PM proteins or with individual proteins fused to tags, we mapped the locations of all 10 T4PM core components and the minor pilins, thereby providing insights into pilus assembly, structure, and function.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chang, Yi-Wei -- Rettberg, Lee A -- Treuner-Lange, Anke -- Iwasa, Janet -- Sogaard-Andersen, Lotte -- Jensen, Grant J -- R01 GM094800B/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2016 Mar 11;351(6278):aad2001. doi: 10.1126/science.aad2001. Epub 2016 Mar 10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉California Institute of Technology, Pasadena, CA 91125, USA. Howard Hughes Medical Institute, Pasadena, CA 91125, USA. ; Howard Hughes Medical Institute, Pasadena, CA 91125, USA. ; Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany. ; University of Utah, Salt Lake City, UT 84112, USA. ; California Institute of Technology, Pasadena, CA 91125, USA. Howard Hughes Medical Institute, Pasadena, CA 91125, USA. jensen@caltech.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26965631" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Adhesion ; Cryoelectron Microscopy ; Fimbriae, Bacterial/genetics/*ultrastructure ; Microscopy, Electron, Transmission ; Models, Molecular ; Mutation ; Myxococcus xanthus/genetics/physiology/*ultrastructure
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  • 66
    Publication Date: 2016-04-16
    Description: Nuclear pore complexes (NPCs) are 110-megadalton assemblies that mediate nucleocytoplasmic transport. NPCs are built from multiple copies of ~30 different nucleoporins, and understanding how these nucleoporins assemble into the NPC scaffold imposes a formidable challenge. Recently, it has been shown how the Y complex, a prominent NPC module, forms the outer rings of the nuclear pore. However, the organization of the inner ring has remained unknown until now. We used molecular modeling combined with cross-linking mass spectrometry and cryo-electron tomography to obtain a composite structure of the inner ring. This architectural map explains the vast majority of the electron density of the scaffold. We conclude that despite obvious differences in morphology and composition, the higher-order structure of the inner and outer rings is unexpectedly similar.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kosinski, Jan -- Mosalaganti, Shyamal -- von Appen, Alexander -- Teimer, Roman -- DiGuilio, Amanda L -- Wan, William -- Bui, Khanh Huy -- Hagen, Wim J H -- Briggs, John A G -- Glavy, Joseph S -- Hurt, Ed -- Beck, Martin -- 1R21AG047433-01/AG/NIA NIH HHS/ -- R21 AG047433/AG/NIA NIH HHS/ -- New York, N.Y. -- Science. 2016 Apr 15;352(6283):363-5. doi: 10.1126/science.aaf0643.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany. ; Biochemistry Center of Heidelberg University, Im Neuenheimer Feld 328, D-69120 Heidelberg, Germany. ; Department of Chemistry, Chemical Biology and Biomedical Engineering, Stevens Institute of Technology, 507 River Street, Hoboken, NJ 07030, USA. ; Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada. ; Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany. Cell Biology and Biophysics Unit, EMBL, Heidelberg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/27081072" target="_blank"〉PubMed〈/a〉
    Keywords: Active Transport, Cell Nucleus ; Cryoelectron Microscopy ; Electron Microscope Tomography ; HeLa Cells ; Humans ; Mass Spectrometry ; Models, Molecular ; Nuclear Matrix/metabolism/ultrastructure ; Nuclear Pore/*metabolism/*ultrastructure ; Nuclear Pore Complex Proteins/chemistry/genetics/*metabolism
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  • 67
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-10-21
    Description: Dinosaurs were once widely considered an evolutionary dead end without much bearing on the evolution of living animals. Yet, today it is clear that theropod dinosaurs gave rise to birds, and that dinosaurs are therefore still alive today. Similarly, placoderms, a group of extinct armored fishes, long held little or no interest to evolutionary biologists. However, discoveries from China are changing that by showing how important placoderms are to understanding the early assembly of the vertebrate body plan. On page 334 of this issue, Zhu et al. (1) report the discovery of a placoderm from Qujing in Yunnan, China, that fills a big gap in our understanding of how vertebrate jaws evolved. Author: John A. Long
    Keywords: Evolution
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  • 68
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-10-21
    Description: Repeated evolution of similar traits in organisms facing the same ecological challenges has long captured the interest of evolutionary biologists (1–4). Naturally occurring examples of “convergent evolution” offer new opportunities to ask about predictability in evolution. Do complex genomes mean that there are endless possibilities for adapting to an ecological challenge? Or must evolution target the same genes, or even the same amino acids in the same proteins, in order to increase the fitness and therefore survival of different species facing similar challenges? Natarajan et al. (5), on page 336 of this issue, provide an example of an integrated approach to answer these questions. By using a combination of genetic data with experimental tests, they show that evolution of a new protein function in response to low-oxygen, high-altitude conditions can occur through different genetic mechanisms across a wide diversity of avian species living at high and low elevations. Author: Jamie T. Bridgham
    Keywords: Evolution
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  • 69
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-10-21
    Description: Author: Sacha Vignieri
    Keywords: Evolution
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    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 70
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-10-28
    Description: Some species, such as the giraffe or bottlenose dolphin, are immediately recognizable and might seem immutable. In fact, their evolutionary stories are often more complicated. Regional populations of giraffe with distinct pelage patterns have only recently been recognized as four different species (1), and the number of species represented by what we recognize as the bottlenose dolphin was historically as many as 20, refined down to one, then two, and the question is still being resolved (2). On page 477 of this issue, de Manuel et al. (3) describe the relationship between two other iconic species in unprecedented detail, comparing whole genomes from populations of bonobo (Pan paniscus) and chimpanzee (Pan troglodytes). They report evidence for gene flow between these species, contributing to our increasing appreciation for the complexities of the process of speciation. Author: A. Rus Hoelzel
    Keywords: Evolution
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  • 71
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-09-23
    Description: In convergent evolution, different species independently acquire similar traits. Knowing whether divergent species use the same or different genetic solutions to adapt to similar selection pressures can illuminate innate constraints on underlying molecular networks. Most cases of convergence that are understood at the genetic level are relatively simple, involving one or a few genes. On page 1431 of this issue, Yeaman et al. (1) report mapping of locally adaptive genes in lodgepole pine (Pinus contorta) and interior spruce (the species complex that includes Picea engelmannii and Picea glauca) (see the photo). The authors show that many genes implicated in local adaptation are shared among the two species. Author: Angela M. Hancock
    Keywords: Evolution
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  • 72
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-09-23
    Description: Author: Annalisa VanHook
    Keywords: Evolution
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  • 73
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-09-30
    Description: Author: Sacha Vignieri
    Keywords: Evolution
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    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 74
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-12-09
    Description: Human activities alter ecosystems around the planet, often rendering environmental conditions unfavorable for plant and animal survival. In the salt marshes along North America's Atlantic coast, the influx of industrial waste has caused chemical pollutants to accumulate at lethal levels, causing the disappearance of many species from affected sites. Yet, multiple populations of the Atlantic killifish (Fundulus heteroclitus) have adapted to cope with levels of pollution orders of magnitude higher than those that members of the same species from unaffected habitats can tolerate. On page 1305 of this issue, Reid et al. (1) provide strong evidence that adaptation has occurred rapidly and through similar genetic changes in multiple populations of killifish that have independently colonized polluted habitats. Authors: Michael Tobler, Zachary W. Culumber
    Keywords: Evolution
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  • 75
    Publication Date: 2015-03-15
    Description: TREK-2 (KCNK10/K2P10), a two-pore domain potassium (K2P) channel, is gated by multiple stimuli such as stretch, fatty acids, and pH and by several drugs. However, the mechanisms that control channel gating are unclear. Here we present crystal structures of the human TREK-2 channel (up to 3.4 angstrom resolution) in two conformations and in complex with norfluoxetine, the active metabolite of fluoxetine (Prozac) and a state-dependent blocker of TREK channels. Norfluoxetine binds within intramembrane fenestrations found in only one of these two conformations. Channel activation by arachidonic acid and mechanical stretch involves conversion between these states through movement of the pore-lining helices. These results provide an explanation for TREK channel mechanosensitivity, regulation by diverse stimuli, and possible off-target effects of the serotonin reuptake inhibitor Prozac.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dong, Yin Yao -- Pike, Ashley C W -- Mackenzie, Alexandra -- McClenaghan, Conor -- Aryal, Prafulla -- Dong, Liang -- Quigley, Andrew -- Grieben, Mariana -- Goubin, Solenne -- Mukhopadhyay, Shubhashish -- Ruda, Gian Filippo -- Clausen, Michael V -- Cao, Lishuang -- Brennan, Paul E -- Burgess-Brown, Nicola A -- Sansom, Mark S P -- Tucker, Stephen J -- Carpenter, Elisabeth P -- 084655/Wellcome Trust/United Kingdom -- 092809/Z/10/Z/Wellcome Trust/United Kingdom -- Biotechnology and Biological Sciences Research Council/United Kingdom -- New York, N.Y. -- Science. 2015 Mar 13;347(6227):1256-9. doi: 10.1126/science.1261512.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK. ; Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK. Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK. ; Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK. OXION Initiative in Ion Channels and Disease, University of Oxford, Oxford OX1 3PN, UK. ; Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK. OXION Initiative in Ion Channels and Disease, University of Oxford, Oxford OX1 3PN, UK. Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK. ; Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK. Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK. ; Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK. ; Pfizer Neusentis, Granta Park, Cambridge CB21 6GS, UK. ; OXION Initiative in Ion Channels and Disease, University of Oxford, Oxford OX1 3PN, UK. Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK. ; Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK. OXION Initiative in Ion Channels and Disease, University of Oxford, Oxford OX1 3PN, UK. liz.carpenter@sgc.ox.ac.uk stephen.tucker@physics.ox.ac.uk. ; Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK. OXION Initiative in Ion Channels and Disease, University of Oxford, Oxford OX1 3PN, UK. liz.carpenter@sgc.ox.ac.uk stephen.tucker@physics.ox.ac.uk.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25766236" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Arachidonic Acid/pharmacology ; Binding Sites ; Crystallography, X-Ray ; Fluoxetine/analogs & derivatives/chemistry/metabolism/pharmacology ; Humans ; *Ion Channel Gating ; Models, Molecular ; Molecular Dynamics Simulation ; Molecular Sequence Data ; Potassium/metabolism ; Potassium Channels, Tandem Pore Domain/antagonists & ; inhibitors/*chemistry/metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary
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  • 76
    Publication Date: 2015-01-31
    Description: The 18-kilodalton translocator protein (TSPO), proposed to be a key player in cholesterol transport into mitochondria, is highly expressed in steroidogenic tissues, metastatic cancer, and inflammatory and neurological diseases such as Alzheimer's and Parkinson's. TSPO ligands, including benzodiazepine drugs, are implicated in regulating apoptosis and are extensively used in diagnostic imaging. We report crystal structures (at 1.8, 2.4, and 2.5 angstrom resolution) of TSPO from Rhodobacter sphaeroides and a mutant that mimics the human Ala(147)--〉Thr(147) polymorphism associated with psychiatric disorders and reduced pregnenolone production. Crystals obtained in the lipidic cubic phase reveal the binding site of an endogenous porphyrin ligand and conformational effects of the mutation. The three crystal structures show the same tightly interacting dimer and provide insights into the controversial physiological role of TSPO and how the mutation affects cholesterol binding.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Li, Fei -- Liu, Jian -- Zheng, Yi -- Garavito, R Michael -- Ferguson-Miller, Shelagh -- ACB-12002/PHS HHS/ -- AGM-12006/PHS HHS/ -- GM094625/GM/NIGMS NIH HHS/ -- GM26916/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2015 Jan 30;347(6221):555-8. doi: 10.1126/science.1260590.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA. ; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA. fergus20@msu.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25635101" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/*chemistry/*metabolism ; Binding Sites ; Cholesterol/metabolism ; Crystallography, X-Ray ; Humans ; Hydrogen Bonding ; Isoquinolines/metabolism ; Ligands ; Membrane Transport Proteins/*chemistry/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Mutant Proteins/chemistry ; Polymorphism, Single Nucleotide ; Porphyrins/metabolism ; Protein Conformation ; Protein Multimerization ; Protein Structure, Secondary ; Protoporphyrins/metabolism ; Receptors, GABA/chemistry/genetics ; Rhodobacter sphaeroides/*chemistry
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  • 77
    Publication Date: 2015-01-31
    Description: Coordinated replication and expression of the mitochondrial genome is critical for metabolically active cells during various stages of development. However, it is not known whether replication and transcription can occur simultaneously without interfering with each other and whether mitochondrial DNA copy number can be regulated by the transcription machinery. We found that interaction of human transcription elongation factor TEFM with mitochondrial RNA polymerase and nascent transcript prevents the generation of replication primers and increases transcription processivity and thereby serves as a molecular switch between replication and transcription, which appear to be mutually exclusive processes in mitochondria. TEFM may allow mitochondria to increase transcription rates and, as a consequence, respiration and adenosine triphosphate production without the need to replicate mitochondrial DNA, as has been observed during spermatogenesis and the early stages of embryogenesis.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4677687/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4677687/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Agaronyan, Karen -- Morozov, Yaroslav I -- Anikin, Michael -- Temiakov, Dmitry -- R01 GM104231/GM/NIGMS NIH HHS/ -- R01GM104231/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2015 Jan 30;347(6221):548-51. doi: 10.1126/science.aaa0986.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell Biology, School of Osteopathic Medicine, Rowan University, 2 Medical Center Drive, Stratford, NJ 08084, USA. ; Department of Cell Biology, School of Osteopathic Medicine, Rowan University, 2 Medical Center Drive, Stratford, NJ 08084, USA. temiakdm@rowan.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25635099" target="_blank"〉PubMed〈/a〉
    Keywords: *DNA Replication ; DNA, Mitochondrial/*genetics/*metabolism ; DNA-Directed RNA Polymerases/chemistry/*metabolism ; G-Quadruplexes ; Genome, Mitochondrial ; Humans ; Mitochondria/genetics/metabolism ; Mitochondrial Proteins/chemistry/*metabolism ; Models, Genetic ; Models, Molecular ; RNA/chemistry/*metabolism ; Transcription Factors/*metabolism ; Transcription Termination, Genetic ; *Transcription, Genetic
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  • 78
    Publication Date: 2015-12-19
    Description: Voltage-gated sodium (Nav) channels propagate action potentials in excitable cells. Accordingly, Nav channels are therapeutic targets for many cardiovascular and neurological disorders. Selective inhibitors have been challenging to design because the nine mammalian Nav channel isoforms share high sequence identity and remain recalcitrant to high-resolution structural studies. Targeting the human Nav1.7 channel involved in pain perception, we present a protein-engineering strategy that has allowed us to determine crystal structures of a novel receptor site in complex with isoform-selective antagonists. GX-936 and related inhibitors bind to the activated state of voltage-sensor domain IV (VSD4), where their anionic aryl sulfonamide warhead engages the fourth arginine gating charge on the S4 helix. By opposing VSD4 deactivation, these compounds inhibit Nav1.7 through a voltage-sensor trapping mechanism, likely by stabilizing inactivated states of the channel. Residues from the S2 and S3 helices are key determinants of isoform selectivity, and bound phospholipids implicate the membrane as a modulator of channel function and pharmacology. Our results help to elucidate the molecular basis of voltage sensing and establish structural blueprints to design selective Nav channel antagonists.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ahuja, Shivani -- Mukund, Susmith -- Deng, Lunbin -- Khakh, Kuldip -- Chang, Elaine -- Ho, Hoangdung -- Shriver, Stephanie -- Young, Clint -- Lin, Sophia -- Johnson, J P Jr -- Wu, Ping -- Li, Jun -- Coons, Mary -- Tam, Christine -- Brillantes, Bobby -- Sampang, Honorio -- Mortara, Kyle -- Bowman, Krista K -- Clark, Kevin R -- Estevez, Alberto -- Xie, Zhiwei -- Verschoof, Henry -- Grimwood, Michael -- Dehnhardt, Christoph -- Andrez, Jean-Christophe -- Focken, Thilo -- Sutherlin, Daniel P -- Safina, Brian S -- Starovasnik, Melissa A -- Ortwine, Daniel F -- Franke, Yvonne -- Cohen, Charles J -- Hackos, David H -- Koth, Christopher M -- Payandeh, Jian -- New York, N.Y. -- Science. 2015 Dec 18;350(6267):aac5464. doi: 10.1126/science.aac5464.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Structural Biology, Genentech Inc., South San Francisco, CA 94080, USA. ; Department of Neuroscience, Genentech Inc., South San Francisco, CA 94080, USA. ; Department of Biology, Xenon Pharmaceuticals Inc., Burnaby, British Columbia, V5G 4W8, Canada. ; Department of Discovery Chemistry, Genentech Inc., South San Francisco, CA 94080, USA. ; Department of Biochemical and Cellular Pharmacology, Genentech Inc., South San Francisco, CA 94080, USA. ; Department of Chemistry, Xenon Pharmaceuticals Inc., Burnaby, British Columbia, V5G 4W8, Canada. ; Department of Neuroscience, Genentech Inc., South San Francisco, CA 94080, USA. hackos.david@gene.com koth.christopher@gene.com payandeh.jian@gene.com. ; Department of Structural Biology, Genentech Inc., South San Francisco, CA 94080, USA. hackos.david@gene.com koth.christopher@gene.com payandeh.jian@gene.com.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26680203" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Cell Membrane/chemistry ; Crystallization/methods ; Crystallography, X-Ray ; DNA Mutational Analysis ; Humans ; Models, Molecular ; Molecular Sequence Data ; NAV1.7 Voltage-Gated Sodium Channel/*chemistry/genetics ; Pain Perception/drug effects ; Protein Engineering ; Protein Isoforms/antagonists & inhibitors/chemistry ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Sodium Channel Blockers/*chemistry/*pharmacology ; Sulfonamides/*chemistry/*pharmacology ; Thiadiazoles/*chemistry/*pharmacology
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  • 79
    Publication Date: 2015-08-22
    Description: Splicing of precursor messenger RNA (pre-mRNA) in yeast is executed by the spliceosome, which consists of five small nuclear ribonucleoproteins (snRNPs), NTC (nineteen complex), NTC-related proteins (NTR), and a number of associated enzymes and cofactors. Here, we report the three-dimensional structure of a Schizosaccharomyces pombe spliceosome at 3.6-angstrom resolution, revealed by means of single-particle cryogenic electron microscopy. This spliceosome contains U2 and U5 snRNPs, NTC, NTR, U6 small nuclear RNA, and an RNA intron lariat. The atomic model includes 10,574 amino acids from 37 proteins and four RNA molecules, with a combined molecular mass of approximately 1.3 megadaltons. Spp42 (Prp8 in Saccharomyces cerevisiae), the key protein component of the U5 snRNP, forms a central scaffold and anchors the catalytic center. Both the morphology and the placement of protein components appear to have evolved to facilitate the dynamic process of pre-mRNA splicing. Our near-atomic-resolution structure of a central spliceosome provides a molecular framework for mechanistic understanding of pre-mRNA splicing.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yan, Chuangye -- Hang, Jing -- Wan, Ruixue -- Huang, Min -- Wong, Catherine C L -- Shi, Yigong -- New York, N.Y. -- Science. 2015 Sep 11;349(6253):1182-91. doi: 10.1126/science.aac7629. Epub 2015 Aug 20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China. ; National Center for Protein Science Shanghai, Institute of Biochemistry and Cell Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26292707" target="_blank"〉PubMed〈/a〉
    Keywords: Catalytic Domain ; Cryoelectron Microscopy ; Models, Molecular ; Protein Structure, Secondary ; RNA, Small Nuclear/chemistry ; Repressor Proteins/chemistry ; Ribonucleoprotein, U5 Small Nuclear/chemistry ; Schizosaccharomyces/*ultrastructure ; Schizosaccharomyces pombe Proteins/chemistry ; Spliceosomes/*chemistry/*ultrastructure
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