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  • Biochemistry  (146)
  • Climate
  • Southern Ocean
  • American Association for the Advancement of Science (AAAS)  (158)
  • Frontiers Media  (6)
  • 2020-2022
  • 2015-2019  (164)
  • 1945-1949
  • 1
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Newman, L., Heil, P., Trebilco, R., Katsumata, K., Constable, A., van Wijk, E., Assmann, K., Beja, J., Bricher, P., Colemans, R., Costa, D., Diggs, S., Farneti, R., Fawcett, S., Gille, S. T., Hendry, K. R., Henley, S., Hofmann, E., Maksym, T., MazIoff, M., Meijers, A., Meredith, M. M., Moreau, S., Ozsor, B., Robertson, R., Schloss, I., Schofield, O., Shi, J., Sikes, E., Smith, I. J., Swart, S., Wahlin, A., Williams, G., Williams, M. J. M., Herraiz-Borreguero, L., Kern, S., Liesers, J., Massom, R. A., Melbourne-Thomas, J., Miloslavich, P., & Spreen, G. Delivering sustained, coordinated, and integrated observations of the Southern Ocean for global impact. Frontiers in Marine Science, 6, (2019): 433, doi:10.3389/fmars.2019.00433.
    Description: The Southern Ocean is disproportionately important in its effect on the Earth system, impacting climatic, biogeochemical, and ecological systems, which makes recent observed changes to this system cause for global concern. The enhanced understanding and improvements in predictive skill needed for understanding and projecting future states of the Southern Ocean require sustained observations. Over the last decade, the Southern Ocean Observing System (SOOS) has established networks for enhancing regional coordination and research community groups to advance development of observing system capabilities. These networks support delivery of the SOOS 20-year vision, which is to develop a circumpolar system that ensures time series of key variables, and delivers the greatest impact from data to all key end-users. Although the Southern Ocean remains one of the least-observed ocean regions, enhanced international coordination and advances in autonomous platforms have resulted in progress toward sustained observations of this region. Since 2009, the Southern Ocean community has deployed over 5700 observational platforms south of 40°S. Large-scale, multi-year or sustained, multidisciplinary efforts have been supported and are now delivering observations of essential variables at space and time scales that enable assessment of changes being observed in Southern Ocean systems. The improved observational coverage, however, is predominantly for the open ocean, encompasses the summer, consists of primarily physical oceanographic variables, and covers surface to 2000 m. Significant gaps remain in observations of the ice-impacted ocean, the sea ice, depths 〉2000 m, the air-ocean-ice interface, biogeochemical and biological variables, and for seasons other than summer. Addressing these data gaps in a sustained way requires parallel advances in coordination networks, cyberinfrastructure and data management tools, observational platform and sensor technology, two-way platform interrogation and data-transmission technologies, modeling frameworks, intercalibration experiments, and development of internationally agreed sampling standards and requirements of key variables. This paper presents a community statement on the major scientific and observational progress of the last decade, and importantly, an assessment of key priorities for the coming decade, toward achieving the SOOS vision and delivering essential data to all end-users.
    Description: PH was supported by the Australian Government’s Cooperative Research Centers Program through the Antarctica Climate and Ecosystems Cooperative Research Centre, and the International Space Science Institute’s team grant #406. This work contributes to the Australian Antarctica Science projects 4301 and 4390.
    Keywords: Southern Ocean ; observations ; modeling ; ocean–climate interactions ; ecosystem-based management ; long-term monitoring ; international coordination
    Repository Name: Woods Hole Open Access Server
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  • 2
    Publication Date: 2022-10-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Foltz, G. R., Brandt, P., Richter, I., Rodriguez-Fonsecao, B., Hernandez, F., Dengler, M., Rodrigues, R. R., Schmidt, J. O., Yu, L., Lefevre, N., Da Cunha, L. C., Mcphaden, M. J., Araujo, M., Karstensen, J., Hahn, J., Martin-Rey, M., Patricola, C. M., Poli, P., Zuidema, P., Hummels, R., Perez, R. C., Hatje, V., Luebbecke, J. F., Palo, I., Lumpkin, R., Bourles, B., Asuquo, F. E., Lehodey, P., Conchon, A., Chang, P., Dandin, P., Schmid, C., Sutton, A., Giordani, H., Xue, Y., Illig, S., Losada, T., Grodsky, S. A., Gasparinss, F., Lees, T., Mohino, E., Nobre, P., Wanninkhof, R., Keenlyside, N., Garcon, V., Sanchez-Gomez, E., Nnamchi, H. C., Drevillon, M., Storto, A., Remy, E., Lazar, A., Speich, S., Goes, M., Dorrington, T., Johns, W. E., Moum, J. N., Robinson, C., Perruches, C., de Souza, R. B., Gaye, A. T., Lopez-Paragess, J., Monerie, P., Castellanos, P., Benson, N. U., Hounkonnou, M. N., Trotte Duha, J., Laxenairess, R., & Reul, N. The tropical Atlantic observing system. Frontiers in Marine Science, 6(206), (2019), doi:10.3389/fmars.2019.00206.
    Description: he tropical Atlantic is home to multiple coupled climate variations covering a wide range of timescales and impacting societally relevant phenomena such as continental rainfall, Atlantic hurricane activity, oceanic biological productivity, and atmospheric circulation in the equatorial Pacific. The tropical Atlantic also connects the southern and northern branches of the Atlantic meridional overturning circulation and receives freshwater input from some of the world’s largest rivers. To address these diverse, unique, and interconnected research challenges, a rich network of ocean observations has developed, building on the backbone of the Prediction and Research Moored Array in the Tropical Atlantic (PIRATA). This network has evolved naturally over time and out of necessity in order to address the most important outstanding scientific questions and to improve predictions of tropical Atlantic severe weather and global climate variability and change. The tropical Atlantic observing system is motivated by goals to understand and better predict phenomena such as tropical Atlantic interannual to decadal variability and climate change; multidecadal variability and its links to the meridional overturning circulation; air-sea fluxes of CO2 and their implications for the fate of anthropogenic CO2; the Amazon River plume and its interactions with biogeochemistry, vertical mixing, and hurricanes; the highly productive eastern boundary and equatorial upwelling systems; and oceanic oxygen minimum zones, their impacts on biogeochemical cycles and marine ecosystems, and their feedbacks to climate. Past success of the tropical Atlantic observing system is the result of an international commitment to sustained observations and scientific cooperation, a willingness to evolve with changing research and monitoring needs, and a desire to share data openly with the scientific community and operational centers. The observing system must continue to evolve in order to meet an expanding set of research priorities and operational challenges. This paper discusses the tropical Atlantic observing system, including emerging scientific questions that demand sustained ocean observations, the potential for further integration of the observing system, and the requirements for sustaining and enhancing the tropical Atlantic observing system.
    Description: MM-R received funding from the MORDICUS grant under contract ANR-13-SENV-0002-01 and the MSCA-IF-EF-ST FESTIVAL (H2020-EU project 797236). GF, MG, RLu, RP, RW, and CS were supported by NOAA/OAR through base funds to AOML and the Ocean Observing and Monitoring Division (OOMD; fund reference 100007298). This is NOAA/PMEL contribution #4918. PB, MDe, JH, RH, and JL are grateful for continuing support from the GEOMAR Helmholtz Centre for Ocean Research Kiel. German participation is further supported by different programs funded by the Deutsche Forschungsgemeinschaft, the Deutsche Bundesministerium für Bildung und Forschung (BMBF), and the European Union. The EU-PREFACE project funded by the EU FP7/2007–2013 programme (Grant No. 603521) contributed to results synthesized here. LCC was supported by the UERJ/Prociencia-2018 research grant. JOS received funding from the Cluster of Excellence Future Ocean (EXC80-DFG), the EU-PREFACE project (Grant No. 603521) and the BMBF-AWA project (Grant No. 01DG12073C).
    Keywords: Tropical Atlantic Ocean ; Observing system ; Weather ; Climate ; Hurricanes ; Biogeochemistry ; Ecosystems ; Coupled model bias
    Repository Name: Woods Hole Open Access Server
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  • 3
    Publication Date: 2022-10-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in [citation], doi:[doi]. Swart, S., Gille, S. T., Delille, B., Josey, S., Mazloff, M., Newman, L., Thompson, A. F., Thomson, J., Ward, B., du Plessis, M. D., Kent, E. C., Girton, J., Gregor, L., Heil, P., Hyder, P., Pezzi, L. P., de Souza, R. B., Tamsitt, V., Weller, R. A., & Zappa, C. J. Constraining Southern Ocean air-sea-ice fluxes through enhanced observations. Frontiers in Marine Science, 6, (2019): 421, doi:10.3389/fmars.2019.00421.
    Description: Air-sea and air-sea-ice fluxes in the Southern Ocean play a critical role in global climate through their impact on the overturning circulation and oceanic heat and carbon uptake. The challenging conditions in the Southern Ocean have led to sparse spatial and temporal coverage of observations. This has led to a “knowledge gap” that increases uncertainty in atmosphere and ocean dynamics and boundary-layer thermodynamic processes, impeding improvements in weather and climate models. Improvements will require both process-based research to understand the mechanisms governing air-sea exchange and a significant expansion of the observing system. This will improve flux parameterizations and reduce uncertainty associated with bulk formulae and satellite observations. Improved estimates spanning the full Southern Ocean will need to take advantage of ships, surface moorings, and the growing capabilities of autonomous platforms with robust and miniaturized sensors. A key challenge is to identify observing system sampling requirements. This requires models, Observing System Simulation Experiments (OSSEs), and assessments of the specific spatial-temporal accuracy and resolution required for priority science and assessment of observational uncertainties of the mean state and direct flux measurements. Year-round, high-quality, quasi-continuous in situ flux measurements and observations of extreme events are needed to validate, improve and characterize uncertainties in blended reanalysis products and satellite data as well as to improve parameterizations. Building a robust observing system will require community consensus on observational methodologies, observational priorities, and effective strategies for data management and discovery.
    Description: SS was funded by a Wallenberg Academy Fellowship (WAF 2015.0186). EK was funded by the NERC ORCHESTRA Project (NE/N018095/1). LP was funded by the Advanced Studies in Oceanography of Medium and High Latitudes (CAPES 23038.004304/2014-28) and the Research Productivity Program (CNPq 304009/2016-4). BdS was a research associate at the F.R.S-FNRS. PeH was supported by the Australian Antarctic Science Projects 4301 and 4390, and the Australian Government’s Cooperative Research Centres Programme through the Antarctic Climate and Ecosystems Cooperative Research Centre and the International Space Science Institute Project 406. SG and MM were funded by National Science Foundation awards OCE-1658001 and PLR-1425989. AT was supported by NASA (NNX15AG42G) and NSF (OCE-1756956).
    Keywords: Air-sea/air-sea-ice fluxes ; Southern Ocean ; Ocean-atmosphere interaction ; Climate ; Ocean-ice interaction
    Repository Name: Woods Hole Open Access Server
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  • 4
    Publication Date: 2022-05-26
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 6 (2015): 1090, doi:10.3389/fmicb.2015.01090.
    Description: Antarctica polynyas support intense phytoplankton blooms, impacting their environment by a substantial depletion of inorganic carbon and nutrients. These blooms are dominated by the colony-forming haptophyte Phaeocystis antarctica and they are accompanied by a distinct bacterial population. Yet, the ecological role these bacteria may play in P. antarctica blooms awaits elucidation of their functional gene pool and of the geochemical activities they support. Here, we report on a metagenome (~160 million reads) analysis of the microbial community associated with a P. antarctica bloom event in the Amundsen Sea polynya (West Antarctica). Genomes of the most abundant Bacteroidetes and Proteobacteria populations have been reconstructed and a network analysis indicates a strong functional partitioning of these bacterial taxa. Three of them (SAR92, and members of the Oceanospirillaceae and Cryomorphaceae) are found in close association with P. antarctica colonies. Distinct features of their carbohydrate, nitrogen, sulfur and iron metabolisms may serve to support mutualistic relationships with P. antarctica. The SAR92 genome indicates a specialization in the degradation of fatty acids and dimethylsulfoniopropionate (compounds released by P. antarctica) into dimethyl sulfide, an aerosol precursor. The Oceanospirillaceae genome carries genes that may enhance algal physiology (cobalamin synthesis). Finally, the Cryomorphaceae genome is enriched in genes that function in cell or colony invasion. A novel pico-eukaryote, Micromonas related genome (19.6 Mb, ~94% completion) was also recovered. It contains the gene for an anti-freeze protein, which is lacking in Micromonas at lower latitudes. These draft genomes are representative for abundant microbial taxa across the Southern Ocean surface.
    Description: This work was performed with financial support from NSF Antarctic Sciences awards ANT-1142095 to AP.
    Keywords: Southern Ocean ; Amundsen Sea Polynya ; Phytoplankton bloom ; Phaeocystis ; Micromonas ; Microbial communities ; Metagenomics ; Genome reconstruction
    Repository Name: Woods Hole Open Access Server
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  • 5
    Publication Date: 2022-10-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Sloyan, B. M., Wilkin, J., Hill, K. L., Chidichimo, M. P., Cronin, M. F., Johannessen, J. A., Karstensen, J., Krug, M., Lee, T., Oka, E., Palmer, M. D., Rabe, B., Speich, S., von Schuckmann, K., Weller, R. A., & Yu, W. Evolving the physical global ocean observing system for research and application services through international coordination. Frontiers in Marine Science, 6, (2019): 449, doi:10.3389/fmars.2019.00449.
    Description: Climate change and variability are major societal challenges, and the ocean is an integral part of this complex and variable system. Key to the understanding of the ocean’s role in the Earth’s climate system is the study of ocean and sea-ice physical processes, including its interactions with the atmosphere, cryosphere, land, and biosphere. These processes include those linked to ocean circulation; the storage and redistribution of heat, carbon, salt and other water properties; and air-sea exchanges of heat, momentum, freshwater, carbon, and other gasses. Measurements of ocean physics variables are fundamental to reliable earth prediction systems for a range of applications and users. In addition, knowledge of the physical environment is fundamental to growing understanding of the ocean’s biogeochemistry and biological/ecosystem variability and function. Through the progress from OceanObs’99 to OceanObs’09, the ocean observing system has evolved from a platform centric perspective to an integrated observing system. The challenge now is for the observing system to evolve to respond to an increasingly diverse end user group. The Ocean Observations Physics and Climate panel (OOPC), formed in 1995, has undertaken many activities that led to observing system-related agreements. Here, OOPC will explore the opportunities and challenges for the development of a fit-for-purpose, sustained and prioritized ocean observing system, focusing on physical variables that maximize support for fundamental research, climate monitoring, forecasting on different timescales, and society. OOPC recommendations are guided by the Framework for Ocean Observing which emphasizes identifying user requirements by considering time and space scales of the Essential Ocean Variables. This approach provides a framework for reviewing the adequacy of the observing system, looking for synergies in delivering an integrated observing system for a range of applications and focusing innovation in areas where existing technologies do not meet these requirements.
    Description: BS received support from the Centre for Southern Hemisphere Oceans Research, a collaboration between the CSIRO and the Qingdao National Laboratory for Marine Science and Technology and the Australian Government Department of the Environment and CSIRO through the Australian Climate Change Science Programme and by the National Environmental Science Program. JK was supported by the European Union’s Horizon 2020 Research and Innovation Programme under the grant agreement no. 633211 (AtlantOS). MP was supported by the Met Office Hadley Centre Climate Programme funded by the BEIS and Defra. SS was supported by the Ecole Normale Supérieure, CNRS, and Ifremer funded by the European Union’s Horizon 2020 Research and Innovation Programme under the grant agreement no. 633211 (AtlantOS), CNES, and ANR grants.
    Keywords: Observing system evaluation ; Observing system design ; Sustained observations ; Observing networks ; Observation platforms ; Climate ; Weather ; Operational services
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  • 6
    Publication Date: 2022-10-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Benway, H. M., Lorenzoni, L., White, A. E., Fiedler, B., Levine, N. M., Nicholson, D. P., DeGrandpre, M. D., Sosik, H. M., Church, M. J., O'Brien, T. D., Leinen, M., Weller, R. A., Karl, D. M., Henson, S. A., & Letelier, R. M. Ocean time series observations of changing marine ecosystems: An era of integration, synthesis, and societal applications. Frontiers in Marine Science, 6, (2019): 393, doi:10.3389/fmars.2019.00393.
    Description: Sustained ocean time series are critical for characterizing marine ecosystem shifts in a time of accelerating, and at times unpredictable, changes. They represent the only means to distinguish between natural and anthropogenic forcings, and are the best tools to explore causal links and implications for human communities that depend on ocean resources. Since the inception of sustained ocean observations, ocean time series have withstood many challenges, most prominently availability of uninterrupted funding and retention of trained personnel. This OceanObs’19 review article provides an overarching vision for sustained ocean time series observations for the next decade, focusing on the growing challenges of maintaining sustained ocean time series, including ship-based and autonomous coastal and open-ocean platforms, as well as remote sensing. In addition to increased diversification of funding sources to include the private sector, NGOs, and other groups, more effective engagement of stakeholders and other end-users will be critical to ensure the sustainability of ocean time series programs. Building a cohesive international time series network will require dedicated capacity to coordinate across observing programs and leverage existing infrastructure and platforms of opportunity. This review article outlines near-term observing priorities and technology needs; explores potential mechanisms to broaden ocean time series data applications and end-user communities; and describes current tools and future requirements for managing increasingly complex multi-platform data streams and developing synthesis products that support science and society. The actionable recommendations outlined herein ultimately form the basis for a robust, sustainable, fit-for-purpose time series network that will foster a predictive understanding of changing ocean systems for the benefit of society.
    Description: This work was led by HB in the Ocean Carbon and Biogeochemistry (OCB) Project Office, which is supported by the NSF OCE (1558412) and the NASA (NNX17AB17G).
    Keywords: Ocean time series ; Marine ecosystems ; Climate ; End-users ; Synthesis ; Sustained observations
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  • 7
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-07-15
    Description: Author: Leslie K. Ferrarelli
    Keywords: Biochemistry
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 8
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-06-24
    Description: Author: Guy Riddihough
    Keywords: Biochemistry
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    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 9
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-05-27
    Description: Staphylococcus aureus is a Gram-positive bacterium that is a leading cause of life-threatening infections in humans. Knowledge of how this pathogen colonizes the human host and causes disease is crucial for the development of strategies to prevent and treat S. aureus infections (see the image, next page). On page 1105 of this issue, Ghssein et al. report the discovery, isolation, and functional evaluation of staphylopine (see the figure), a compound biosynthesized by S. aureus that captures metal ions from the pathogen's surroundings and thereby enables it to grow (1). Author: Elizabeth M. Nolan
    Keywords: Biochemistry
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  • 10
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-05-27
    Description: Author: Nicolas S. Wigginton
    Keywords: Biochemistry
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    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 11
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-06-24
    Description: The 14-month El Niño climate event that ended this month brought impacts across the globe, from wildfires in Indonesia to drought in Peru. The main drivers of El Niño conditions, ocean temperatures in the central and eastern Pacific, were as high as 3°C above the average, making this event one of the three most intense El Niños on record. For the most part, forecasts of its impacts on weather patterns were borne out, but forecasters fared relatively poorly in California, which relies on El Niños to deliver rains to parched areas. Along the U.S. West Coast, the jet stream was shifted hundreds of kilometers north last winter, which had the effect of dousing the Pacific Northwest with extraordinary precipitation while Southern California experienced its fourth straight year of drought. Now, scientists are analyzing why their climate models were blindsided and how they can be improved. Author: Eli Kintisch
    Keywords: Climate
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    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 12
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-06-17
    Description: Last summer the northern parts of the Greenland Ice Sheet experienced record melting as summer temperatures rose as high as 19°C (66°F), while southern Greenland was unusually cold, with just average melting. Now, scientists have linked the melt pattern with a 500-kilometer-wide, high-pressure vortex, known as a block, that loitered north of the island during June and July 2015, wreaking weather havoc. Such atmospheric blocks are expected to result from melting sea ice, some researchers say—a claim that has added fuel to a contentious dispute over the global influence of the warming Arctic. Until now, the dispute has focused on how disappearing sea ice might be favoring extreme midlatitude weather, such as floods in Texas or heat waves in Russia. The new study is one of three recent papers that have expanded the debate to the melting of Greenland. Author: Eli Kintisch
    Keywords: Climate
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  • 13
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-06-03
    Description: Author: Guy Riddihough
    Keywords: Biochemistry
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    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 14
    Publication Date: 2018-12-14
    Description: Primordial sequence signatures in modern proteins imply ancestral origins tracing back to simple peptides. Although short peptides seldom adopt unique folds, metal ions might have templated their assembly into higher-order structures in early evolution and imparted useful chemical reactivity. Recapitulating such a biogenetic scenario, we have combined design and laboratory evolution to transform a zinc-binding peptide into a globular enzyme capable of accelerating ester cleavage with exacting enantiospecificity and high catalytic efficiency ( k cat / K M ~ 10 6 M –1 s –1 ). The simultaneous optimization of structure and function in a naïve peptide scaffold not only illustrates a plausible enzyme evolutionary pathway from the distant past to the present but also proffers exciting future opportunities for enzyme design and engineering.
    Keywords: Biochemistry
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  • 15
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-08-31
    Description: Cryo–electron microscopy, or simply cryo-EM, refers mainly to three very different yet closely related techniques: electron crystallography, single-particle cryo-EM, and electron cryotomography. In the past few years, single-particle cryo-EM in particular has triggered a revolution in structural biology and has become a newly dominant discipline. This Review examines the fascinating story of its start and evolution over the past 40-plus years, delves into how and why the recent technological advances have been so groundbreaking, and briefly considers where the technique may be headed in the future.
    Keywords: Biochemistry
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  • 16
    Publication Date: 2018-08-31
    Description: Riback et al . (Reports, 13 October 2017, p. 238) used small-angle x-ray scattering (SAXS) experiments to infer a degree of compaction for unfolded proteins in water versus chemical denaturant that is highly consistent with the results from Förster resonance energy transfer (FRET) experiments. There is thus no "contradiction" between the two methods, nor evidence to support their claim that commonly used FRET fluorophores cause protein compaction.
    Keywords: Biochemistry
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  • 17
    Publication Date: 2018-08-31
    Description: Best et al . claim that we provide no convincing basis to assert that a discrepancy remains between FRET and SAXS results on the dimensions of disordered proteins under physiological conditions. We maintain that a clear discrepancy is apparent in our and other recent publications, including results shown in the Best et al . comment. A plausible origin is fluorophore interactions in FRET experiments.
    Keywords: Biochemistry
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  • 18
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-09-28
    Keywords: Biochemistry
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    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 19
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-10-05
    Keywords: Biochemistry
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    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 20
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-10-12
    Keywords: Biochemistry
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  • 21
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-12-21
    Keywords: Biochemistry
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    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 22
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-12-21
    Keywords: Biochemistry
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    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 23
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-03-18
    Description: Author: Nicholas S. Wigginton
    Keywords: Biochemistry
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  • 24
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-03-18
    Description: The S-adenosylmethionine (SAM) radical enzyme superfamily plays a central role in the biosynthesis of many vitamins, cofactors, and antibiotics. Radical SAM enzymes catalyze challenging chemical reactions such as C-H bond activation (1), ring contraction (2), and molecular skeletal rearrangements (3, 4). They overcome the dif culty of these reactions by forming a highly oxidizing radical species, 5′-deoxyadenosyl (5′-dAdo·), from SAM and a reduced iron-sulfur cluster (5). This radical species can selectively abstract a hydrogen atom from a substrate, enabling complex chemical transformations. There are more than 113,000 radical SAM enzymes, but only a small number are both biochemically and structurally characterized, and many of the reaction mechanisms remain enigmatic. On page 1320 of this issue, Sicoli et al. provide evidence for unexpected radical intermediates in the mechanism of the radical SAM enzyme NosL (6). Authors: Jennifer Bridwell-Rabb, Catherine L. Drennan
    Keywords: Biochemistry
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  • 25
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-05-20
    Description: About 500 to 600 million metric tons of methane, a potent greenhouse gas, are emitted annually worldwide; ~69% of this methane is produced biologically by anaerobic archaea known as methanogens (1). In some environments, methane emissions are partly offset by anaerobic methane oxidizing archaea (ANME) and aerobic methanotrophic bacteria (1). In methanogens, the methyl-coenzyme M reductase (MCR) enzyme uses a nickel-containing cofactor (F430) to catalyze the final step of methane synthesis (see the figure, panels A and B) (2, 3). The MCR reaction is reversible, and MCR may also catalyze the first step of methane oxidation by ANME (2). The MCR catalytic cycle begins with F430 in the reduced Ni(I) form (4), but what happens next has been unclear. On page 953 of this issue, Wongnate et al. (5) report evidence for a Ni(II)-thiolate intermediate. Authors: Thomas J. Lawton, Amy C. Rosenzweig
    Keywords: Biochemistry
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  • 26
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-04-29
    Description: Most biological oxygen consumption is carried out by membrane-integrated oxidases, which fall into three main classes. The heme-copper oxidases (HCOs) of mitochondria and many bacteria (1) have a binuclear active site that contains a heme and a copper atom. They achieve rapid, virtually complete reduction of oxygen to water. The alternative oxidases (AOXs) found in certain plants, fungi, and bacteria have a heme-free iron-iron reactive site (2) that confers nitric oxide–resistant respiration (3). The last class, the bacterial cytochrome bd–type oxidases (4), are found in many pathogenic bacteria and have a distinctive heme composition consisting of two hemes b and one heme d. On page 583 of this issue, Safarian et al. report the atomic-resolution structure of a cytochrome bd–type oxidase from Geobacillus thermodenitrificans (5). The structure will facilitate targeted and rational drug development against cytochrome bd–type oxidases. Authors: Gregory M. Cook, Robert K. Poole
    Keywords: Biochemistry
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  • 27
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-04-01
    Description: Ice sheets such as those on Greenland and Antarctica today not only respond to changing climate but can also cause climate to change. Their sizes have fluctuated substantially in the past. In particular, Antarctica was effectively ice-free until its ice cover began to expand rapidly at the Eocene-Oligocene boundary around 34 million years ago (see the figure). Recent research, including a report by Galeotti et al. on page 76 of this issue (1), helps to identify the mechanisms that led to this rapid ice sheet growth. Authors: Caroline H. Lear, Dan J. Lunt
    Keywords: Climate
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  • 28
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-11-02
    Keywords: Biochemistry
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  • 29
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-12-14
    Keywords: Biochemistry
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  • 30
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-10-19
    Keywords: Biochemistry
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  • 31
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-11-16
    Keywords: Biochemistry
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  • 32
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-11-30
    Keywords: Biochemistry
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  • 33
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-11-30
    Keywords: Biochemistry
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  • 34
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-08-10
    Keywords: Biochemistry
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  • 35
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-08-10
    Description: The Hedgehog (Hh) pathway involved in development and regeneration is activated by the extracellular binding of Hh to the membrane receptor Patched (Ptch). We report the structures of human Ptch1 alone and in complex with the N-terminal domain of human Sonic hedgehog (ShhN) at resolutions of 3.9 and 3.6 angstroms, respectively, as determined by cryo–electron microscopy. Ptch1 comprises two interacting extracellular domains, ECD1 and ECD2, and 12 transmembrane segments (TMs), with TMs 2 to 6 constituting the sterol-sensing domain (SSD). Two steroid-shaped densities are resolved in both structures, one enclosed by ECD1/2 and the other in the membrane-facing cavity of the SSD. Structure-guided mutational analysis shows that interaction between ShhN and Ptch1 is steroid-dependent. The structure of a steroid binding–deficient Ptch1 mutant displays pronounced conformational rearrangements.
    Keywords: Biochemistry
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  • 36
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-08-31
    Description: Super-resolution microscopy has overcome a long-held resolution barrier—the diffraction limit—in light microscopy and enabled visualization of previously invisible molecular details in biological systems. Since their conception, super-resolution imaging methods have continually evolved and can now be used to image cellular structures in three dimensions, multiple colors, and living systems with nanometer-scale resolution. These methods have been applied to answer questions involving the organization, interaction, stoichiometry, and dynamics of individual molecular building blocks and their integration into functional machineries in cells and tissues. In this Review, we provide an overview of super-resolution methods, their state-of-the-art capabilities, and their constantly expanding applications to biology, with a focus on the latter. We will also describe the current technical challenges and future advances anticipated in super-resolution imaging.
    Keywords: Biochemistry
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  • 37
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-05-11
    Keywords: Biochemistry
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  • 38
    Publication Date: 2018-11-02
    Description: Genomic DNA forms chromatin, in which the nucleosome is the repeating unit. The mechanism by which RNA polymerase II (RNAPII) transcribes the nucleosomal DNA remains unclear. Here we report the cryo–electron microscopy structures of RNAPII-nucleosome complexes in which RNAPII pauses at the superhelical locations SHL(–6), SHL(–5), SHL(–2), and SHL(–1) of the nucleosome. RNAPII pauses at the major histone-DNA contact sites, and the nucleosome interactions with the RNAPII subunits stabilize the pause. These structures reveal snapshots of nucleosomal transcription, in which RNAPII gradually tears DNA from the histone surface while preserving the histone octamer. The nucleosomes in the SHL(–1) complexes are bound to a "foreign" DNA segment, which might explain the histone transfer mechanism. These results provide the foundations for understanding chromatin transcription and epigenetic regulation.
    Keywords: Biochemistry
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  • 39
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-11-09
    Keywords: Biochemistry
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  • 40
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-11-09
    Keywords: Biochemistry
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  • 41
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-11-09
    Keywords: Biochemistry
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  • 42
    Publication Date: 2018-11-09
    Description: We describe a general computational approach to designing self-assembling helical filaments from monomeric proteins and use this approach to design proteins that assemble into micrometer-scale filaments with a wide range of geometries in vivo and in vitro. Cryo–electron microscopy structures of six designs are close to the computational design models. The filament building blocks are idealized repeat proteins, and thus the diameter of the filaments can be systematically tuned by varying the number of repeat units. The assembly and disassembly of the filaments can be controlled by engineered anchor and capping units built from monomers lacking one of the interaction surfaces. The ability to generate dynamic, highly ordered structures that span micrometers from protein monomers opens up possibilities for the fabrication of new multiscale metamaterials.
    Keywords: Biochemistry
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  • 43
    Publication Date: 2018-11-16
    Description: Membrane proteins reside in lipid bilayers and are typically extracted from this environment for study, which often compromises their integrity. In this work, we ejected intact assemblies from membranes, without chemical disruption, and used mass spectrometry to define their composition. From Escherichia coli outer membranes, we identified a chaperone-porin association and lipid interactions in the β-barrel assembly machinery. We observed efflux pumps bridging inner and outer membranes, and from inner membranes we identified a pentameric pore of TonB, as well as the protein-conducting channel SecYEG in association with F 1 F O adenosine triphosphate (ATP) synthase. Intact mitochondrial membranes from Bos taurus yielded respiratory complexes and fatty acid–bound dimers of the ADP (adenosine diphosphate)/ATP translocase (ANT-1). These results highlight the importance of native membrane environments for retaining small-molecule binding, subunit interactions, and associated chaperones of the membrane proteome.
    Keywords: Biochemistry
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  • 44
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-06-29
    Description: The precatalytic spliceosome (B complex) is preceded by the pre-B complex. Here we report the cryo–electron microscopy structures of the Saccharomyces cerevisiae pre-B and B complexes at average resolutions of 3.3 to 4.6 and 3.9 angstroms, respectively. In the pre-B complex, the duplex between the 5' splice site (5'SS) and U1 small nuclear RNA (snRNA) is recognized by Yhc1, Luc7, and the Sm ring. In the B complex, U1 small nuclear ribonucleoprotein is dissociated, the 5'-exon–5'SS sequences are translocated near U6 snRNA, and three B-specific proteins may orient the precursor messenger RNA. In both complexes, U6 snRNA is anchored to loop I of U5 snRNA, and the duplex between the branch point sequence and U2 snRNA is recognized by the SF3b complex. Structural analysis reveals the mechanism of assembly and activation for the yeast spliceosome.
    Keywords: Biochemistry
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  • 45
    Publication Date: 2015-01-17
    Description: Our understanding of when and how humans adapted to living on the Tibetan Plateau at altitudes above 2000 to 3000 meters has been constrained by a paucity of archaeological data. Here we report data sets from the northeastern Tibetan Plateau indicating that the first villages were established only by 5200 calendar years before the present (cal yr B.P.). Using these data, we tested the hypothesis that a novel agropastoral economy facilitated year-round living at higher altitudes since 3600 cal yr B.P. This successful subsistence strategy facilitated the adaptation of farmers-herders to the challenges of global temperature decline during the late Holocene.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chen, F H -- Dong, G H -- Zhang, D J -- Liu, X Y -- Jia, X -- An, C B -- Ma, M M -- Xie, Y W -- Barton, L -- Ren, X Y -- Zhao, Z J -- Wu, X H -- Jones, M K -- New York, N.Y. -- Science. 2015 Jan 16;347(6219):248-50. doi: 10.1126/science.1259172. Epub 2014 Nov 20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Key Laboratory of Western China's Environmental Systems (Ministry of Education), Lanzhou University, Lanzhou 730000, China. fhchen@lzu.edu.cn ghdong@lzu.edu.cn. ; Key Laboratory of Western China's Environmental Systems (Ministry of Education), Lanzhou University, Lanzhou 730000, China. ; Department of Anthropology, Washington University in St. Louis, St. Louis, MO 63130-48, USA. ; Center for Comparative Archaeology, Department of Anthropology, University of Pittsburgh, Pittsburgh, PA 15260, USA. ; Qinghai Provincial Institute of Cultural Relics and Archaeology, Xining 810007, China. ; Institute of Archaeology, Chinese Academy of Social Sciences, Beijing 100710, China. ; School of Archaeology and Museology, Peking University, Beijing 100871, China. ; McDonald Institute of Archaeological Research, University of Cambridge, Cambridge CB2 3ER, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25593179" target="_blank"〉PubMed〈/a〉
    Keywords: Acclimatization ; Agriculture/*history ; *Altitude ; Archaeology ; Climate ; History, Ancient ; Humans ; Radiometric Dating ; Temperature ; Tibet
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  • 46
    Publication Date: 2015-09-26
    Description: Antarctic ice-core data reveal that the atmosphere experienced abrupt centennial increases in CO2 concentration during the last deglaciation (~18 thousand to 11 thousand years ago). Establishing the role of ocean circulation in these changes requires high-resolution, accurately dated marine records. Here, we report radiocarbon data from uranium-thorium-dated deep-sea corals in the Equatorial Atlantic and Drake Passage over the past 25,000 years. Two major deglacial radiocarbon shifts occurred in phase with centennial atmospheric CO2 rises at 14.8 thousand and 11.7 thousand years ago. We interpret these radiocarbon-enriched signals to represent two short-lived (less than 500 years) "overshoot" events, with Atlantic meridional overturning stronger than that of the modern era. These results provide compelling evidence for a close coupling of ocean circulation and centennial climate events during the last deglaciation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chen, Tianyu -- Robinson, Laura F -- Burke, Andrea -- Southon, John -- Spooner, Peter -- Morris, Paul J -- Ng, Hong Chin -- New York, N.Y. -- Science. 2015 Sep 25;349(6255):1537-41. doi: 10.1126/science.aac6159.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Bristol Isotope Group, School of Earth Sciences, University of Bristol, Bristol, UK. tc14502@bristol.ac.uk. ; Bristol Isotope Group, School of Earth Sciences, University of Bristol, Bristol, UK. ; Department of Earth and Environmental Sciences, University of St Andrews, St. Andrews, UK. ; School of Physical Sciences, University of California, Irvine, Irvine, CA, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26404835" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Anthozoa/*chemistry ; Atmosphere/*chemistry ; Climate ; *Global Warming ; *Ice Cover ; Oceans and Seas ; Radiometric Dating ; Thorium/analysis ; Uranium/analysis
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  • 47
    Publication Date: 2015-09-19
    Description: The indigenous people of Greenland, the Inuit, have lived for a long time in the extreme conditions of the Arctic, including low annual temperatures, and with a specialized diet rich in protein and fatty acids, particularly omega-3 polyunsaturated fatty acids (PUFAs). A scan of Inuit genomes for signatures of adaptation revealed signals at several loci, with the strongest signal located in a cluster of fatty acid desaturases that determine PUFA levels. The selected alleles are associated with multiple metabolic and anthropometric phenotypes and have large effect sizes for weight and height, with the effect on height replicated in Europeans. By analyzing membrane lipids, we found that the selected alleles modulate fatty acid composition, which may affect the regulation of growth hormones. Thus, the Inuit have genetic and physiological adaptations to a diet rich in PUFAs.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fumagalli, Matteo -- Moltke, Ida -- Grarup, Niels -- Racimo, Fernando -- Bjerregaard, Peter -- Jorgensen, Marit E -- Korneliussen, Thorfinn S -- Gerbault, Pascale -- Skotte, Line -- Linneberg, Allan -- Christensen, Cramer -- Brandslund, Ivan -- Jorgensen, Torben -- Huerta-Sanchez, Emilia -- Schmidt, Erik B -- Pedersen, Oluf -- Hansen, Torben -- Albrechtsen, Anders -- Nielsen, Rasmus -- R01-HG003229/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2015 Sep 18;349(6254):1343-7. doi: 10.1126/science.aab2319.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics, Evolution, and Environment, University College London, London WC1E 6BT, UK. Department of Integrative Biology, University of California-Berkeley, Berkeley, CA 94720, USA. ; The Bioinformatics Centre, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark. ; The Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark. ; Department of Integrative Biology, University of California-Berkeley, Berkeley, CA 94720, USA. ; National Institute of Public Health, University of Southern Denmark, 1353 Copenhagen, Denmark. Greenland Center for Health Research, University of Greenland, Nuuk, Greenland. ; National Institute of Public Health, University of Southern Denmark, 1353 Copenhagen, Denmark. Steno Diabetes Center, 2820 Gentofte, Denmark. ; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark. ; Department of Genetics, Evolution, and Environment, University College London, London WC1E 6BT, UK. Department of Anthropology, University College London, London WC1H 0BW, UK. ; Research Centre for Prevention and Health, Capital Region of Denmark, Copenhagen, Denmark. Department of Clinical Experimental Research, Rigshospitalet, Glostrup, Denmark. Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. ; Department of Medicine, Lillebaelt Hospital, Vejle, Denmark. ; Department of Clinical Biochemistry, Lillebaelt Hospital, Vejle, Denmark. Institute of Regional Health Research, University of Southern Denmark, Odense, Denmark. ; Research Centre for Prevention and Health, Capital Region of Denmark, Copenhagen, Denmark. Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. Faculty of Medicine, University of Aalborg, Aalborg, Denmark. ; School of Natural Sciences, University of California-Merced, Merced, CA 95343, USA. ; Faculty of Medicine, University of Aalborg, Aalborg, Denmark. Department of Cardiology, Aalborg University Hospital, 9100 Aalborg, Denmark. ; The Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark. torben.hansen@sund.ku.dk albrecht@binf.ku.dk rasmus_nielsen@berkeley.edu. ; The Bioinformatics Centre, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark. torben.hansen@sund.ku.dk albrecht@binf.ku.dk rasmus_nielsen@berkeley.edu. ; Department of Integrative Biology, University of California-Berkeley, Berkeley, CA 94720, USA. Department of Statistics, University of California-Berkeley, Berkeley, CA 94720, USA. torben.hansen@sund.ku.dk albrecht@binf.ku.dk rasmus_nielsen@berkeley.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26383953" target="_blank"〉PubMed〈/a〉
    Keywords: Acclimatization/*genetics ; Alleles ; Arctic Regions ; Body Height/genetics ; Body Weight/genetics ; Chromosomes, Human, Pair 11/genetics ; Climate ; *Diet, High-Fat ; Fatty Acids, Omega-3/*administration & dosage/analysis ; Female ; Genetic Loci ; Genome, Human/genetics ; Genome-Wide Association Study ; Greenland ; Humans ; Inuits/*genetics ; Linkage Disequilibrium ; Male ; Membrane Lipids/analysis/genetics ; Polymorphism, Single Nucleotide ; Selection, Genetic
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  • 48
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2016-01-20
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Amigo, Ignacio -- New York, N.Y. -- Science. 2015 Dec 4;350(6265):1286. doi: 10.1126/science.350.6265.1286.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Ignacio Amigo is a postdoctoral researcher in the biochemistry department of the Chemistry Institute at the University of Sao Paulo in Brazil. Send your story to SciCareerEditor@aaas.org.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26785493" target="_blank"〉PubMed〈/a〉
    Keywords: Biochemistry ; Humans ; Molecular Biology ; Parenting/*psychology ; *Paternal Behavior
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  • 49
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2015-06-13
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Qiu, Jane -- New York, N.Y. -- Science. 2015 Jun 12;348(6240):1185. doi: 10.1126/science.348.6240.1185.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26068817" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; China ; Climate ; *Dinosaurs ; *Extinction, Biological ; *Geologic Sediments ; *Global Warming ; *Greenhouse Effect ; *Lakes ; Temperature
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  • 50
    Publication Date: 2015-10-10
    Description: The landforms of northern Gale crater on Mars expose thick sequences of sedimentary rocks. Based on images obtained by the Curiosity rover, we interpret these outcrops as evidence for past fluvial, deltaic, and lacustrine environments. Degradation of the crater wall and rim probably supplied these sediments, which advanced inward from the wall, infilling both the crater and an internal lake basin to a thickness of at least 75 meters. This intracrater lake system probably existed intermittently for thousands to millions of years, implying a relatively wet climate that supplied moisture to the crater rim and transported sediment via streams into the lake basin. The deposits in Gale crater were then exhumed, probably by wind-driven erosion, creating Aeolis Mons (Mount Sharp).〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Grotzinger, J P -- Gupta, S -- Malin, M C -- Rubin, D M -- Schieber, J -- Siebach, K -- Sumner, D Y -- Stack, K M -- Vasavada, A R -- Arvidson, R E -- Calef, F 3rd -- Edgar, L -- Fischer, W F -- Grant, J A -- Griffes, J -- Kah, L C -- Lamb, M P -- Lewis, K W -- Mangold, N -- Minitti, M E -- Palucis, M -- Rice, M -- Williams, R M E -- Yingst, R A -- Blake, D -- Blaney, D -- Conrad, P -- Crisp, J -- Dietrich, W E -- Dromart, G -- Edgett, K S -- Ewing, R C -- Gellert, R -- Hurowitz, J A -- Kocurek, G -- Mahaffy, P -- McBride, M J -- McLennan, S M -- Mischna, M -- Ming, D -- Milliken, R -- Newsom, H -- Oehler, D -- Parker, T J -- Vaniman, D -- Wiens, R C -- Wilson, S A -- New York, N.Y. -- Science. 2015 Oct 9;350(6257):aac7575. doi: 10.1126/science.aac7575.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Geologic and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA. ; Department of Earth Science and Engineering, Imperial College London, London SW7 2AZ, UK. ; Malin Space Science Systems, Post Office Box 910148, San Diego, CA 92121, USA. ; Department of Earth and Planetary Sciences, University of California-Santa Cruz, Santa Cruz, CA 95064, USA. ; Department of Geological Sciences, Indiana University, Bloomington, IN 47405, USA. ; Department of Earth and Planetary Sciences, University of California-Davis, Davis, CA 95616, USA. ; Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA. ; Department of Earth and Planetary Sciences, Washington University in St. Louis, St. Louis, MO 63130, USA. ; Astrogeology Science Center, U.S. Geological Survey, Flagstaff, AZ 86001, USA. ; Center for Earth and Planetary Studies, National Air and Space Museum, Smithsonian Institution, Washington, DC 20560, USA. ; Department of Earth and Planetary Sciences, University of Tennessee, Knoxville, TN 37996, USA. ; Department of Earth and Planetary Sciences, Johns Hopkins University, Baltimore, MD 21218, USA. ; Laboratoire Planetologie et Geodynamique de Nantes-Le Centre National de la Recherche, Unite Mixte de Recherche 6112 and Universite de Nantes, 44322 Nantes, France. ; Planetary Science Institute, Tucson, AZ 85719, USA. ; Department of Geology, Western Washington University, Bellingham, WA 98225, USA. ; Department of Space Sciences, NASA Ames Research Center, Moffett Field, CA 94035, USA. ; NASA Goddard Space Flight Center, Greenbelt, MD 20771, USA. ; Department of Earth and Planetary Science, University of California-Berkeley, Berkeley, CA 94720, USA. ; Laboratoire de Geologie de Lyon, Universite de Lyon, 69364 Lyon, France. ; Department of Geology and Geophysics, Texas A&M University, College Station, TX 77843, USA. ; Department of Physics, University of Guelph, Guelph, Ontario N1G 2W1, Canada. ; Department of Geosciences, Stony Brook University, Stony Brook, NY 11794-2100, USA. ; Department of Geological Sciences, University of Texas at Austin, Austin, TX 78712, USA. ; Astromaterials Research and Exploration Science Division, NASA Johnson Space Center, Houston, TX 77058, USA. ; Department of Geological Sciences, Brown University, Providence, RI 02912, USA. ; Institute of Meteoritics, University of New Mexico, Albuquerque, NM 87131 USA. ; LZ Technology, NASA Johnson Space Center, Houston, TX 77058, USA. ; Space Remote Sensing, Los Alamos National Laboratory, Los Alamos, NM 87544, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26450214" target="_blank"〉PubMed〈/a〉
    Keywords: Climate ; Exhumation ; *Lakes ; *Mars ; Paleontology
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  • 51
    Publication Date: 2016-01-09
    Description: Human activity is leaving a pervasive and persistent signature on Earth. Vigorous debate continues about whether this warrants recognition as a new geologic time unit known as the Anthropocene. We review anthropogenic markers of functional changes in the Earth system through the stratigraphic record. The appearance of manufactured materials in sediments, including aluminum, plastics, and concrete, coincides with global spikes in fallout radionuclides and particulates from fossil fuel combustion. Carbon, nitrogen, and phosphorus cycles have been substantially modified over the past century. Rates of sea-level rise and the extent of human perturbation of the climate system exceed Late Holocene changes. Biotic changes include species invasions worldwide and accelerating rates of extinction. These combined signals render the Anthropocene stratigraphically distinct from the Holocene and earlier epochs.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Waters, Colin N -- Zalasiewicz, Jan -- Summerhayes, Colin -- Barnosky, Anthony D -- Poirier, Clement -- Galuszka, Agnieszka -- Cearreta, Alejandro -- Edgeworth, Matt -- Ellis, Erle C -- Ellis, Michael -- Jeandel, Catherine -- Leinfelder, Reinhold -- McNeill, J R -- Richter, Daniel deB -- Steffen, Will -- Syvitski, James -- Vidas, Davor -- Wagreich, Michael -- Williams, Mark -- Zhisheng, An -- Grinevald, Jacques -- Odada, Eric -- Oreskes, Naomi -- Wolfe, Alexander P -- New York, N.Y. -- Science. 2016 Jan 8;351(6269):aad2622. doi: 10.1126/science.aad2622.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉British Geological Survey, Keyworth, Nottingham NG12 5GG, UK. ; Department of Geology, University of Leicester, University Road, Leicester LE1 7RH, UK. ; Scott Polar Research Institute, Cambridge University, Lensfield Road, Cambridge CB2 1ER, UK. ; Department of Integrative Biology, Museum of Paleontology, and Museum of Vertebrate Zoology, University of California-Berkeley, Berkeley, CA 94720, USA. ; Morphodynamique Continentale et Cotiere, Universite de Caen Normandie, Centre National de la Recherche Scientifique (CNRS), 24 Rue des Tilleuls, F-14000 Caen, France. ; Geochemistry and the Environment Division, Institute of Chemistry, Jan Kochanowski University, 15G Swietokrzyska Street, 25-406 Kielce, Poland. ; Departamento de Estratigrafia y Paleontologia, Facultad de Ciencia y Tecnologia, Universidad del Pais Vasco/Euskal Herriko Unibertsitatea, Apartado 644, 48080 Bilbao, Spain. ; School of Archaeology and Ancient History, University of Leicester, University Road, Leicester LE1 7RH, UK. ; Department of Geography and Environmental Systems, University of Maryland-Baltimore County, Baltimore, MD 21250, USA. ; Laboratoire d'Etudes en Geophysique et Oceanographie Spatiales (CNRS, Centre National d'Etudes Spatiales, Institut de Recherche pour le Developpement, Universite Paul Sabatier), 14 Avenue Edouard Belin, 31400 Toulouse, France. ; Department of Geological Sciences, Freie Universitat Berlin, Malteserstrasse 74-100/D, 12249 Berlin, Germany. ; Georgetown University, Washington, DC, USA. ; Nicholas School of the Environment, Duke University, Box 90233, Durham, NC 27516, USA. ; The Australian National University, Canberra, Australian Capital Territory 0200, Australia. ; Department of Geological Sciences, University of Colorado-Boulder, Box 545, Boulder, CO 80309-0545, USA. ; Marine Affairs and Law of the Sea Programme, The Fridtjof Nansen Institute, Lysaker, Norway. ; Department of Geodynamics and Sedimentology, University of Vienna, A-1090 Vienna, Austria. ; State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an 710061, Beijing Normal University, Beijing 100875, China. ; Institut de Hautes Etudes Internationales et du Developpement, Chemin Eugene Rigot 2, 1211 Geneve 11, Switzerland. ; Department of Geology, University of Nairobi, Nairobi, Kenya. ; Department of the History of Science, Harvard University, Cambridge, MA 02138, USA. ; Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26744408" target="_blank"〉PubMed〈/a〉
    Keywords: Aluminum/analysis ; *Biota ; Carbon Cycle ; Climate ; Construction Materials/analysis ; *Earth (Planet) ; Fossil Fuels/adverse effects ; Geologic Sediments/*chemistry ; *Human Activities ; Humans ; Ice/analysis ; Introduced Species ; Plastics/analysis ; Radioactive Fallout/analysis ; Radioisotopes/analysis
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  • 52
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-08-11
    Description: A parabolic relationship between lens radius and refractive index allows spherical lenses to avoid spherical aberration. We show that in squid, patchy colloidal physics resulted from an evolutionary radiation of globular S-crystallin proteins. Small-angle x-ray scattering experiments on lens tissue show colloidal gels of S-crystallins at all radial positions. Sparse lens materials form via low-valence linkages between disordered loops protruding from the protein surface. The loops are polydisperse and bind via a set of hydrogen bonds between disordered side chains. Peripheral lens regions with low particle valence form stable, volume-spanning gels at low density, whereas central regions with higher average valence gel at higher densities. The proteins demonstrate an evolved set of linkers for self-assembly of nanoparticles into volumetric materials.
    Keywords: Biochemistry
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  • 53
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-08-18
    Keywords: Biochemistry
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  • 54
    Publication Date: 2017-09-01
    Description: In the early stage of transcription, eukaryotic RNA polymerase II (Pol II) exchanges initiation factors with elongation factors to form an elongation complex for processive transcription. Here we report the structure of the Pol II elongation complex bound with the basal elongation factors Spt4/5, Elf1, and TFIIS. Spt4/5 (the Spt4/Spt5 complex) and Elf1 modify a wide area of the Pol II surface. Elf1 bridges the Pol II central cleft, completing a "DNA entry tunnel" for downstream DNA. Spt4 and the Spt5 NGN and KOW1 domains encircle the upstream DNA, constituting a "DNA exit tunnel." The Spt5 KOW4 and KOW5 domains augment the "RNA exit tunnel," directing the exiting nascent RNA. Thus, the elongation complex establishes a completely different transcription and regulation platform from that of the initiation complexes.
    Keywords: Biochemistry
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  • 55
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-09-01
    Keywords: Biochemistry
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  • 56
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-09-01
    Keywords: Biochemistry
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  • 57
    Publication Date: 2017-09-01
    Description: NAD + (oxidized form of NAD:nicotinamide adenine dinucleotide)–reducing soluble [NiFe]-hydrogenase (SH) is phylogenetically related to NADH (reduced form of NAD + ):quinone oxidoreductase (complex I), but the geometrical arrangements of the subunits and Fe–S clusters are unclear. Here, we describe the crystal structures of SH in the oxidized and reduced states. The cluster arrangement is similar to that of complex I, but the subunits orientation is not, which supports the hypothesis that subunits evolved as prebuilt modules. The oxidized active site includes a six-coordinate Ni, which is unprecedented for hydrogenases, whose coordination geometry would prevent O 2 from approaching. In the reduced state showing the normal active site structure without a physiological electron acceptor, the flavin mononucleotide cofactor is dissociated, which may be caused by the oxidation state change of nearby Fe–S clusters and may suppress production of reactive oxygen species.
    Keywords: Biochemistry
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  • 58
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-09-15
    Keywords: Biochemistry
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  • 59
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-06-23
    Keywords: Biochemistry
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  • 60
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-06-23
    Keywords: Biochemistry
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  • 61
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-11-25
    Description: Silicon is found in nature in many inorganic forms, some of which are constructed by living organisms. Yet, no known biological molecule contains a carbon–silicon (C–Si) bond, and no biological processes to form C–Si bonds have been identified. On page 1048 of this issue, Kan et al. (1) show that natural as well as reengineered enzymes can promote C–Si bond formation. The resulting chiral compounds mostly consist of one of the two possible stereoisomers (enantiomers). Authors: Hendrik F. T. Klare, Martin Oestreich
    Keywords: Biochemistry
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  • 62
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-08-11
    Keywords: Biochemistry
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  • 63
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-08-11
    Keywords: Biochemistry
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  • 64
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-08-11
    Keywords: Biochemistry
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  • 65
    Publication Date: 2017-08-11
    Description: Small basic proteins present in most Archaea share a common ancestor with the eukaryotic core histones. We report the crystal structure of an archaeal histone-DNA complex. DNA wraps around an extended polymer, formed by archaeal histone homodimers, in a quasi-continuous superhelix with the same geometry as DNA in the eukaryotic nucleosome. Substitutions of a conserved glycine at the interface of adjacent protein layers destabilize archaeal chromatin, reduce growth rate, and impair transcription regulation, confirming the biological importance of the polymeric structure. Our data establish that the histone-based mechanism of DNA compaction predates the nucleosome, illuminating the origin of the nucleosome.
    Keywords: Biochemistry
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  • 66
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-08-18
    Description: Vinculin is an actin-binding protein thought to reinforce cell-cell and cell-matrix adhesions. However, how mechanical load affects the vinculin–F-actin bond is unclear. Using a single-molecule optical trap assay, we found that vinculin forms a force-dependent catch bond with F-actin through its tail domain, but with lifetimes that depend strongly on the direction of the applied force. Force toward the pointed (–) end of the actin filament resulted in a bond that was maximally stable at 8 piconewtons, with a mean lifetime (12 seconds) 10 times as long as the mean lifetime when force was applied toward the barbed (+) end. A computational model of lamellipodial actin dynamics suggests that the directionality of the vinculin–F-actin bond could establish long-range order in the actin cytoskeleton. The directional and force-stabilized binding of vinculin to F-actin may be a mechanism by which adhesion complexes maintain front-rear asymmetry in migrating cells.
    Keywords: Biochemistry
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  • 67
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-09-01
    Keywords: Biochemistry
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  • 68
    Publication Date: 2017-06-02
    Description: The arenavirus Lassa causes severe hemorrhagic fever and a significant disease burden in West Africa every year. The glycoprotein, GPC, is the sole antigen expressed on the viral surface and the critical target for antibody-mediated neutralization. Here we present the crystal structure of the trimeric, prefusion ectodomain of Lassa GP bound to a neutralizing antibody from a human survivor at 3.2-angstrom resolution. The antibody extensively anchors two monomers together at the base of the trimer, and biochemical analysis suggests that it neutralizes by inhibiting conformational changes required for entry. This work illuminates pH-driven conformational changes in both receptor-binding and fusion subunits of Lassa virus, illustrates the unique assembly of the arenavirus glycoprotein spike, and provides a much-needed template for vaccine design against these threats to global health.
    Keywords: Biochemistry
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  • 69
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-06-02
    Keywords: Biochemistry
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  • 70
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-06-23
    Keywords: Biochemistry
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  • 71
    Publication Date: 2017-06-23
    Description: Hormones can transmit signals through adenosine 3',5'-monophosphate (cAMP) to precise intracellular locations. The fidelity of these responses relies on the activation of localized protein kinase A (PKA) holoenzymes. Association of PKA regulatory type II (RII) subunits with A-kinase–anchoring proteins (AKAPs) confers location, and catalytic (C) subunits phosphorylate substrates. Single-particle electron microscopy demonstrated that AKAP79 constrains RII-C subassemblies within 150 to 250 angstroms of its targets. Native mass spectrometry established that these macromolecular assemblies incorporated stoichiometric amounts of cAMP. Chemical-biology– and live cell–imaging techniques revealed that catalytically active PKA holoenzymes remained intact within the cytoplasm. These findings indicate that the parameters of anchored PKA holoenzyme action are much more restricted than originally anticipated.
    Keywords: Biochemistry
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  • 72
    Publication Date: 2017-06-23
    Description: The multifunctional protein cytochrome c (cyt c) plays key roles in electron transport and apoptosis, switching function by modulating bonding between a heme iron and the sulfur in a methionine residue. This Fe–S(Met) bond is too weak to persist in the absence of protein constraints. We ruptured the bond in ferrous cyt c using an optical laser pulse and monitored the bond reformation within the protein active site using ultrafast x-ray pulses from an x-ray free-electron laser, determining that the Fe–S(Met) bond enthalpy is ~4 kcal/mol stronger than in the absence of protein constraints. The 4 kcal/mol is comparable with calculations of stabilization effects in other systems, demonstrating how biological systems use an entatic state for modest yet accessible energetics to modulate chemical function.
    Keywords: Biochemistry
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  • 73
    Publication Date: 2017-07-21
    Description: Hsp100 polypeptide translocases are conserved members of the AAA+ family (adenosine triphosphatases associated with diverse cellular activities) that maintain proteostasis by unfolding aberrant and toxic proteins for refolding or proteolytic degradation. The Hsp104 disaggregase from Saccharomyces cerevisiae solubilizes stress-induced amorphous aggregates and amyloids. The structural basis for substrate recognition and translocation is unknown. Using a model substrate (casein), we report cryo–electron microscopy structures at near-atomic resolution of Hsp104 in different translocation states. Substrate interactions are mediated by conserved, pore-loop tyrosines that contact an 80-angstrom-long unfolded polypeptide along the axial channel. Two protomers undergo a ratchet-like conformational change that advances pore loop–substrate interactions by two amino acids. These changes are coupled to activation of specific nucleotide hydrolysis sites and, when transmitted around the hexamer, reveal a processive rotary translocation mechanism and substrate-responsive flexibility during Hsp104-catalyzed disaggregation.
    Keywords: Biochemistry
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  • 74
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-07-28
    Keywords: Biochemistry
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  • 75
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-07-28
    Keywords: Biochemistry
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  • 76
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-07-28
    Keywords: Biochemistry
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  • 77
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-07-28
    Keywords: Biochemistry
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  • 78
    Publication Date: 2017-07-28
    Description: Ribosome stalling leads to recruitment of the ribosome quality control complex (RQC), which targets the partially synthesized polypeptide for proteasomal degradation through the action of the ubiquitin ligase Ltn1p. A second core RQC component, Rqc2p, modifies the nascent polypeptide by adding a carboxyl-terminal alanine and threonine (CAT) tail through a noncanonical elongation reaction. Here we examined the role of CAT-tailing in nascent-chain degradation in budding yeast. We found that Ltn1p efficiently accessed only nascent-chain lysines immediately proximal to the ribosome exit tunnel. For substrates without Ltn1p-accessible lysines, CAT-tailing enabled degradation by exposing lysines sequestered in the ribosome exit tunnel. Thus, CAT-tails do not serve as a degron, but rather provide a fail-safe mechanism that expands the range of RQC-degradable substrates.
    Keywords: Biochemistry
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  • 79
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-07-28
    Keywords: Biochemistry
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  • 80
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-09-30
    Keywords: Biochemistry
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  • 81
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-09-30
    Description: How fast can a cell locate a specific chromosomal DNA sequence specified by a single-stranded oligonucleotide? To address this question, we investigate the intracellular search processes of the Cas9 protein, which can be programmed by a guide RNA to bind essentially any DNA sequence. This targeting flexibility requires Cas9 to unwind the DNA double helix to test for correct base pairing to the guide RNA. Here we study the search mechanisms of the catalytically inactive Cas9 (dCas9) in living Escherichia coli by combining single-molecule fluorescence microscopy and bulk restriction-protection assays. We find that it takes a single fluorescently labeled dCas9 6 hours to find the correct target sequence, which implies that each potential target is bound for less than 30 milliseconds. Once bound, dCas9 remains associated until replication. To achieve fast targeting, both Cas9 and its guide RNA have to be present at high concentrations.
    Keywords: Biochemistry
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  • 82
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-10-13
    Keywords: Biochemistry
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    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 83
    Publication Date: 2017-10-13
    Description: A substantial fraction of the proteome is intrinsically disordered, and even well-folded proteins adopt non-native geometries during synthesis, folding, transport, and turnover. Characterization of intrinsically disordered proteins (IDPs) is challenging, in part because of a lack of accurate physical models and the difficulty of interpreting experimental results. We have developed a general method to extract the dimensions and solvent quality (self-interactions) of IDPs from a single small-angle x-ray scattering measurement. We applied this procedure to a variety of IDPs and found that even IDPs with low net charge and high hydrophobicity remain highly expanded in water, contrary to the general expectation that protein-like sequences collapse in water. Our results suggest that the unfolded state of most foldable sequences is expanded; we conjecture that this property was selected by evolution to minimize misfolding and aggregation.
    Keywords: Biochemistry
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  • 84
    Publication Date: 2017-10-06
    Description: Amyloids are implicated in neurodegenerative diseases. Fibrillar aggregates of the amyloid-β protein (Aβ) are the main component of the senile plaques found in brains of Alzheimer’s disease patients. We present the structure of an Aβ(1–42) fibril composed of two intertwined protofilaments determined by cryo–electron microscopy (cryo-EM) to 4.0-angstrom resolution, complemented by solid-state nuclear magnetic resonance experiments. The backbone of all 42 residues and nearly all side chains are well resolved in the EM density map, including the entire N terminus, which is part of the cross-β structure resulting in an overall "LS"-shaped topology of individual subunits. The dimer interface protects the hydrophobic C termini from the solvent. The characteristic staggering of the nonplanar subunits results in markedly different fibril ends, termed "groove" and "ridge," leading to different binding pathways on both fibril ends, which has implications for fibril growth.
    Keywords: Biochemistry
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  • 85
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-10-06
    Keywords: Biochemistry
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    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 86
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-03-30
    Keywords: Biochemistry
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    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 87
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-04-06
    Keywords: Biochemistry
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    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 88
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-04-06
    Keywords: Biochemistry
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    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 89
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-04-06
    Description: Small carbocycles are structurally rigid and possess high intrinsic energy due to their ring strain. These features lead to broad applications but also create challenges for their construction. We report the engineering of hemeproteins that catalyze the formation of chiral bicyclobutanes, one of the most strained four-membered systems, via successive carbene addition to unsaturated carbon-carbon bonds. Enzymes that produce cyclopropenes, putative intermediates to the bicyclobutanes, were also identified. These genetically encoded proteins are readily optimized by directed evolution, function in Escherichia coli , and act on structurally diverse substrates with high efficiency and selectivity, providing an effective route to many chiral strained structures. This biotransformation is easily performed at preparative scale, and the resulting strained carbocycles can be derivatized, opening myriad potential applications.
    Keywords: Biochemistry
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  • 90
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-04-13
    Keywords: Biochemistry
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    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 91
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-11-17
    Keywords: Biochemistry
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    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 92
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-11-24
    Keywords: Biochemistry
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  • 93
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-11-17
    Description: Mitochondrial adenosine triphosphate (ATP) synthase produces the majority of ATP in eukaryotic cells, and its dimerization is necessary to create the inner membrane folds, or cristae, characteristic of mitochondria. Proton translocation through the membrane-embedded F O region turns the rotor that drives ATP synthesis in the soluble F 1 region. Although crystal structures of the F 1 region have illustrated how this rotation leads to ATP synthesis, understanding how proton translocation produces the rotation has been impeded by the lack of an experimental atomic model for the F O region. Using cryo–electron microscopy, we determined the structure of the dimeric F O complex from Saccharomyces cerevisiae at a resolution of 3.6 angstroms. The structure clarifies how the protons travel through the complex, how the complex dimerizes, and how the dimers bend the membrane to produce cristae.
    Keywords: Biochemistry
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  • 94
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-11-17
    Description: In bacteria, the activation of gene transcription at many promoters is simple and only involves a single activator. The cyclic adenosine 3',5'-monophosphate receptor protein (CAP), a classic activator, is able to activate transcription independently through two different mechanisms. Understanding the class I mechanism requires an intact transcription activation complex (TAC) structure at a high resolution. Here we report a high-resolution cryo–electron microscopy structure of an intact Escherichia coli class I TAC containing a CAP dimer, a 70 –RNA polymerase (RNAP) holoenzyme, a complete class I CAP-dependent promoter DNA, and a de novo synthesized RNA oligonucleotide. The structure shows how CAP wraps the upstream DNA and how the interactions recruit RNAP. Our study provides a structural basis for understanding how activators activate transcription through the class I recruitment mechanism.
    Keywords: Biochemistry
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  • 95
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-11-24
    Keywords: Biochemistry
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  • 96
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-11-17
    Keywords: Biochemistry
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  • 97
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-11-03
    Keywords: Biochemistry
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  • 98
    Publication Date: 2017-11-03
    Description: The Rift Valley fever virus (RVFV) is transmitted by infected mosquitoes, causing severe disease in humans and livestock across Africa. We determined the x-ray structure of the RVFV class II fusion protein Gc in its postfusion form and in complex with a glycerophospholipid (GPL) bound in a conserved cavity next to the fusion loop. Site-directed mutagenesis and molecular dynamics simulations further revealed a built-in motif allowing en bloc insertion of the fusion loop into membranes, making few nonpolar side-chain interactions with the aliphatic moiety and multiple polar interactions with lipid head groups upon membrane restructuring. The GPL head-group recognition pocket is conserved in the fusion proteins of other arthropod-borne viruses, such as Zika and chikungunya viruses, which have recently caused major epidemics worldwide.
    Keywords: Biochemistry
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  • 99
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-03-23
    Keywords: Biochemistry
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    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 100
    Publication Date: 2018-03-23
    Description: Metal homeostasis poses a major challenge to microbes, which must acquire scarce elements for core metabolic processes. Methanobactin, an extensively modified copper-chelating peptide, was one of the earliest natural products shown to enable microbial acquisition of a metal other than iron. We describe the core biosynthetic machinery responsible for the characteristic posttranslational modifications that grant methanobactin its specificity and affinity for copper. A heterodimer comprising MbnB, a DUF692 family iron enzyme, and MbnC, a protein from a previously unknown family, performs a dioxygen-dependent four-electron oxidation of the precursor peptide (MbnA) to install an oxazolone and an adjacent thioamide, the characteristic methanobactin bidentate copper ligands. MbnB and MbnC homologs are encoded together and separately in many bacterial genomes, suggesting functions beyond their roles in methanobactin biosynthesis.
    Keywords: Biochemistry
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