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  • Springer Nature  (365,529)
  • American Association of Petroleum Geologists (AAPG)
  • Annual Reviews
  • 2015-2019  (253,159)
  • 2000-2004  (50,445)
  • 1980-1984  (25,156)
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  • 1
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    South Atlantic paleobathymetry since early Creteceous (2017)
    Springer Nature
    In:  EPIC3Scientific Reports, Springer Nature, 7(11819)
    Details
    Publication Date: 2017-09-24
    Description: We present early Cretaceous to present paleobathymetric reconstructions and quantitative uncertainty estimates for the South Atlantic, offering a strong basis for studies of paleocirculation, paleoclimate and paleobiogeography. Circulation in an initially salty and anoxic ocean, restricted by the topography of the Falkland Plateau, Rio Grande Ridge and Walvis Rise, favoured deposition of thick evaporites in shallow water of the Brazilian-Angolan margins. This ceased as sea oor spreading propagated northwards, opening an equatorial gateway to shallow and intermediate circulation. This gateway, together with subsiding volcano-tectonic barriers would have played a key role in Late Cretaceous climate changes. Later deepening and widening of the South Atlantic, together with gateway opening at Drake Passage would lead, by mid-Miocene (∼15 Ma) to the establishment of modern-style thermohaline circulation.
    Repository Name: EPIC Alfred Wegener Institut
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  • 2
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    Evidence of long-term NAO influence on East-Central Europe winter precipitation from a guano-derived δ15N record (2017)
    Springer Nature
    In:  EPIC3Scientific Reports, Springer Nature, 7(1), ISSN: 2045-2322
    Details
    Publication Date: 2017-11-06
    Description: Currently there is a scarcity of paleo-records related to the North Atlantic Oscillation (NAO), particularly in East-Central Europe (ECE). Here we report δ15N analysis of guano from a cave in NW Romania with the intent of reconstructing past variation in ECE hydroclimate and examine NAO impacts on winter precipitation. We argue that the δ15N values of guano indicate that the nitrogen cycle is hydrologically controlled and the δ15N values likely reflect winter precipitation related to nitrogen mineralization prior to the growing season. Drier conditions indicated by δ15N values at AD 1848–1852 and AD 1880–1930 correspond to the positive phase of the NAO. The increased frequency of negative phases of the NAO between AD 1940–1975 is contemporaneous with higher δ15N values (wetter conditions). A 4‰ decrease in δ15N values at the end of the 1970’s corresponds to a strong reduction in precipitation associated with a shift from negative to positive phase of the NAO. Using the relationship between NAO index and δ15N values in guano for the instrumental period, we reconstructed NAO-like phases back to AD 1650. Our results advocate that δ15N values of guano offer a proxy of the NAO conditions in the more distant past, helping assess its predictability.
    Repository Name: EPIC Alfred Wegener Institut
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  • 3
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    Along-shelf connectivity and circumpolar gene flow in Antarctic silverfish (Pleuragramma antarctica) (2018)
    Springer Nature
    In:  EPIC3Scientific reports, Springer Nature, 8(17856), pp. 1-16
    Details
    Publication Date: 2019-10-04
    Description: The Antarctic silverfish (Pleuragramma antarctica) is a critically important forage species with a circumpolar distribution and is unique among other notothenioid species for its wholly pelagic life cycle. Previous studies have provided mixed evidence of population structure over regional and circumpolar scales. The aim of the present study was to test the recent population hypothesis for Antarctic silverfish, which emphasizes the interplay between life history and hydrography in shaping connectivity. A total of 1067 individuals were collected over 25 years from different locations on a circumpolar scale. Samples were genotyped at fifteen microsatellites to assess population differentiation and genetic structuring using clustering methods, F-statistics, and hierarchical analysis of variance. A lack of differentiation was found between locations connected by the Antarctic Slope Front Current (ASF), indicative of high levels of gene flow. However, gene flow was significantly reduced at the South Orkney Islands and the western Antarctic Peninsula where the ASF is absent. This pattern of gene flow emphasized the relevance of large-scale circulation as a mechanism for circumpolar connectivity. Chaotic genetic patchiness characterized population structure over time, with varying patterns of differentiation observed between years, accompanied by heterogeneous standard length distributions. The present study supports a more nuanced version of the genetic panmixia hypothesis that reflects physical-biological interactions over the life history.
    Repository Name: EPIC Alfred Wegener Institut
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  • 4
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    Arctic megaslide at presumed rest (2016)
    Springer Nature
    In:  EPIC3Scientific Reports, Springer Nature, 6(38529), ISSN: 2045-2322
    Details
    Publication Date: 2016-12-16
    Description: Slope failure like in the Hinlopen/Yermak Megaslide is one of the major geohazards in a changing Arctic environment. We analysed hydroacoustic and 2D high-resolution seismic data from the apparently intact continental slope immediately north of the Hinlopen/Yermak Megaslide for signs of past and future instabilities. Our new bathymetry and seismic data show clear evidence for incipient slope instability. Minor slide deposits and an internally-deformed sedimentary layer near the base of the gas hydrate stability zone imply an incomplete failure event, most probably about 30000 years ago, contemporaneous to or shortly after the Hinlopen/Yermak Megaslide. An active gas reservoir at the base of the gas hydrate stability zone demonstrate that over-pressured fluids might have played a key role in the initiation of slope failure at the studied slope, but more importantly also for the giant HYM slope failure. To date, it is not clear, if the studied slope is fully preconditioned to fail completely in future or if it might be slowly deforming and creeping at present. We detected widespread methane seepage on the adjacent shallow shelf areas not sealed by gas hydrates.
    Repository Name: EPIC Alfred Wegener Institut
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  • 5
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    Production of fluorescent dissolved organic matter in Arctic Ocean sediments (2016)
    Springer Nature
    In:  EPIC3Scientific Reports, Springer Nature, (39213), pp. 1-10
    Details
    Publication Date: 2017-07-05
    Description: Little is known about the production of fluorescent dissolved organic matter (FDOM) in the anoxic oceanic sediments. In this study, sediment pore waters were sampled from four different sites in the Chukchi-East Siberian Seas area to examine the bulk dissolved organic carbon (DOC) and their optical properties. The production of FDOM, coupled with the increase of nutrients, was observed above the sulfate-methane-transition-zone (SMTZ). The presence of FDOM was concurrent with sulfate reduction and increased alkalinity (R2 〉 0.96, p 〈 0.0001), suggesting a link to organic matter degradation. This inference was supported by the positive correlation (R2 〉 0.95, p 〈 0.0001) between the net production of FDOM and the modeled degradation rates of particulate organic carbon sulfate reduction. The production of FDOM was more pronounced in a shallow shelf site S1 with a total net production ranging from 17.9 to 62.3 RU for different FDOM components above the SMTZ depth of ca. 4.1 mbsf, which presumably underwent more accumulation of particulate organic matter than the other three deeper sites. The sediments were generally found to be the sources of CDOM and FDOM to the overlying water column, unearthing a channel of generally bio-refractory and pre-aged DOM to the oceans.
    Repository Name: EPIC Alfred Wegener Institut
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  • 6
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    Reconciling glacial Antarctic water stable isotopes with ice sheet topography and the isotopic paleothermometer (2018)
    Springer Nature
    In:  EPIC3Nature Communications, Springer Nature, 9(3537), ISSN: 2041-1723
    Details
    Publication Date: 2018-09-17
    Description: Stable water isotope records from Antarctica are key for our understanding of Quaternary climate variations. However, the exact quantitative interpretation of these important climate proxy records in terms of surface temperature, ice sheet height and other climatic changes is still a matter of debate. Here we report results obtained with an atmospheric general circulation model equipped with water isotopes, run at a high-spatial horizontal resolution of one-by-one degree. Comparing different glacial maximum ice sheet reconstructions, a best model data match is achieved for the PMIP3 reconstruction. Reduced West Antarctic elevation changes between 400 and 800 m lead to further improved agreement with ice core data. Our modern and glacial climate simulations support the validity of the isotopic paleothermometer approach based on the use of present-day observations and reveal that a glacial ocean state as displayed in the GLAMAP reconstruction is suitable for capturing the observed glacial isotope changes in Antarctic ice cores.
    Repository Name: EPIC Alfred Wegener Institut
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  • 7
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    The winter pack-ice zone provides a sheltered but food-poor habitat for larval Antarctic krill (2017)
    Springer Nature
    In:  EPIC3Nature Ecology & Evolution, Springer Nature, 1, pp. 1853-1861, ISSN: 2397-334X
    Details
    Publication Date: 2018-01-03
    Description: A dominant Antarctic ecological paradigm suggests that winter sea ice is generally the main feeding ground for krill larvae. Observations from our winter cruise to the southwest Atlantic sector of the Southern Ocean contradict this view and present the first evidence that the pack-ice zone is a food-poor habitat for larval development. In contrast, the more open marginal ice zone provides a more favourable food environment for high larval krill growth rates. We found that complex under-ice habitats are, however, vital for larval krill when water column productivity is limited by light, by providing structures that offer protec- tion from predators and to collect organic material released from the ice. The larvae feed on this sparse ice-associated food during the day. After sunset, they migrate into the water below the ice (upper 20 m) and drift away from the ice areas where they have previously fed. Model analyses indicate that this behaviour increases both food uptake in a patchy food environment and the likelihood of overwinter transport to areas where feeding conditions are more favourable in spring.
    Repository Name: EPIC Alfred Wegener Institut
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  • 8
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    Submarine slope failures due to pipe structure formation (2018)
    Springer Nature
    In:  EPIC3Nature Communications, Springer Nature, 9(1), pp. 715, ISSN: 2041-1723
    Details
    Publication Date: 2018-03-04
    Description: There is a strong spatial correlation between submarine slope failures and the occurrence of gas hydrates. This has been attributed to the dynamic nature of gas hydrate systems and the potential reduction of slope stability due to bottom water warming or sea level drop. However, 30 years of research into this process found no solid supporting evidence. Here we present new reflection seismic data from the Arctic Ocean and numerical modelling results supporting a different link between hydrates and slope stability. Hydrates reduce sediment permeability and cause build-up of overpressure at the base of the gas hydrate stability zone. Resulting hydro-fracturing forms pipe structures as pathways for overpressured fluids to migrate upward. Where these pipe structures reach shallow permeable beds, this overpressure transfers laterally and destabilises the slope. This process reconciles the spatial correlation of submarine landslides and gas hydrate, and it is independent of environmental change and water depth.
    Repository Name: EPIC Alfred Wegener Institut
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  • 9
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    Tundra landform and vegetation productivity trend maps for the Arctic Coastal Plain of northern Alaska (2018)
    Springer Nature
    In:  EPIC3Scientific Data, Springer Nature, 5, pp. 180058, ISSN: 2052-4463
    Details
    Publication Date: 2018-04-15
    Description: Arctic tundra landscapes are composed of a complex mosaic of patterned ground features, varying in soil moisture, vegetation composition, and surface hydrology over small spatial scales (10–100 m). The importance of microtopography and associated geomorphic landforms in influencing ecosystem structure and function is well founded, however, spatial data products describing local to regional scale distribution of patterned ground or polygonal tundra geomorphology are largely unavailable. Thus, our understanding of local impacts on regional scale processes (e.g., carbon dynamics) may be limited. We produced two key spatiotemporal datasets spanning the Arctic Coastal Plain of northern Alaska (~60,000 km2) to evaluate climate-geomorphological controls on arctic tundra productivity change, using (1) a novel 30m classification of polygonal tundra geomorphology and (2) decadal-trends in surface greenness using the Landsat archive (1999–2014). These datasets can be easily integrated and adapted in an array of local to regional applications such as (1) upscaling plot-level measurements (e.g., carbon/energy fluxes), (2) mapping of soils, vegetation, or permafrost, and/or (3) initializing ecosystem biogeochemistry, hydrology, and/or habitat modeling.
    Repository Name: EPIC Alfred Wegener Institut
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  • 10
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    Predictability of Arctic sea ice on weather time scales (2018)
    Springer Nature
    In:  EPIC3Scientific Reports, Springer Nature, 8(6514), pp. 1-7, ISSN: 2045-2322
    Details
    Publication Date: 2018-04-30
    Description: The field of Arctic sea ice prediction on “weather time scales” is still in its infancy with little existing understanding of the limits of predictability. This is especially true for sea ice deformation along so-called Linear Kinematic Features (LKFs) including leads that are relevant for marine operations. Here the potential predictability of the sea ice pack in the wintertime Arctic up to ten days ahead is determined, exploiting the fact that sea ice-ocean models start to show skill at representing sea ice deformation at high spatial resolutions. Results are based on ensemble simulations with a high-resolution sea ice-ocean model driven by atmospheric ensemble forecasts. The predictability of LKFs as measured by different metrics drops quickly, with predictability being almost completely lost after 4–8 days. In contrast, quantities such as sea ice concentration or the location of the ice edge retain high levels of predictability throughout the full 10-day forecast period. It is argued that the rapid error growth for LKFs is mainly due to the chaotic behaviour of the atmosphere associated with the low predictability of near surface wind divergence and vorticity; initial condition uncertainty for ice thickness is found to be of minor importance as long as LKFs are initialized at the right locations.
    Repository Name: EPIC Alfred Wegener Institut
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  • 11
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    Functional characterization of the circadian clock in the Antarctic krill, Euphausia superba (2017)
    Springer Nature
    In:  EPIC3Scientific Reports, Springer Nature, 7(17742), ISSN: 2045-2322
    Details
    Publication Date: 2018-01-08
    Description: Antarctic krill (Euphausia superba) is a key species in Southern Ocean ecosystem where it plays a central role in the Antarctic food web. Available information supports the existence of an endogenous timing system in krill enabling it to synchronize metabolism and behavior with an environment characterized by extreme seasonal changes in terms of day length, food availability, and surface ice extent. A screening of our transcriptome database “KrillDB” allowed us to identify the putative orthologues of 20 circadian clock components. Mapping of conserved domains and phylogenetic analyses strongly supported annotations of the identi ed sequences. Luciferase assays and co-immunoprecipitation experiments allowed us to de ne the role of the main clock components. Our ndings provide an overall picture of the molecular mechanisms underlying the functioning of the endogenous circadian clock in the Antarctic krill and shed light on their evolution throughout crustaceans speciation. Interestingly, the core clock machinery shows both mammalian and insect features that presumably contribute to an evolutionary strategy to cope with polar environment’s challenges. Moreover, despite the extreme variability characterizing the Antarctic seasonal day length, the conserved light mediated degradation of the photoreceptor EsCRY1 suggests a persisting pivotal role of light as a Zeitgeber.
    Repository Name: EPIC Alfred Wegener Institut
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  • 12
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    Reduced arctic tundra productivity linked with landform and climate change interactions (2018)
    Springer Nature
    In:  EPIC3Scientific Reports, Springer Nature, 8(1), pp. 2345, ISSN: 2045-2322
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    Publication Date: 2018-04-15
    Description: Arctic tundra ecosystems have experienced unprecedented change associated with climate warming over recent decades. Across the Pan-Arctic, vegetation productivity and surface greenness have trended positively over the period of satellite observation. However, since 2011 these trends have slowed considerably, showing signs of browning in many regions. It is unclear what factors are driving this change and which regions/landforms will be most sensitive to future browning. Here we provide evidence linking decadal patterns in arctic greening and browning with regional climate change and local permafrost-driven landscape heterogeneity. We analyzed the spatial variability of decadal-scale trends in surface greenness across the Arctic Coastal Plain of northern Alaska (~60,000 km²) using the Landsat archive (1999–2014), in combination with novel 30 m classifications of polygonal tundra and regional watersheds, finding landscape heterogeneity and regional climate change to be the most important factors controlling historical greenness trends. Browning was linked to increased temperature and precipitation, with the exception of young landforms (developed following lake drainage), which will likely continue to green. Spatiotemporal model forecasting suggests carbon uptake potential to be reduced in response to warmer and/or wetter climatic conditions, potentially increasing the net loss of carbon to the atmosphere, at a greater degree than previously expected.
    Repository Name: EPIC Alfred Wegener Institut
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  • 13
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    Competition-induced starvation drives large-scale population cycles in Antarctic krill (2017)
    Springer Nature
    In:  EPIC3Nature Ecology & Evolution, Springer Nature, 1(0177)
    Details
    Publication Date: 2017-11-29
    Description: Antarctic krill (Euphausia superba)—one of the most abundant animal species on Earth—exhibits a five to six year population cycle, with oscillations in biomass exceeding one order of magnitude. Previous studies have postulated that the krill cycle is induced by periodic climatological factors, but these postulated drivers neither show consistent agreement, nor are they supported by quantitative models. Here, using data analysis complemented with modelling of krill ontogeny and population dynamics, we identify intraspecific competition for food as the main driver of the krill cycle, while external climatological factors possibly modulate its phase and synchronization over large scales. Our model indicates that the cycle amplitude increases with reduction of krill loss rates. Thus, a decline of apex predators is likely to increase the oscillation amplitude, potentially destabilizing the marine food web, with drastic consequences for the entire Antarctic ecosystem.
    Repository Name: EPIC Alfred Wegener Institut
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  • 14
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    An innovative methodology for the non-destructive diagnosis of architectural elements of ancient historical buildings (2018)
    Springer Nature
    In:  This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
    Details
    Publication Date: 2019-03-26
    Description: In the following we present a new non-invasive methodology aimed at the diagnosis of stone building materials used in historical buildings and architectural elements. This methodology consists of the integrated sequential application of in situ proximal sensing methodologies such as the 3D Terrestrial Laser Scanner for the 3D modelling of investigated objects together with laboratory and in situ non-invasive multi-techniques acoustic data, preceded by an accurate petrographical study of the investigated stone materials by optical and scanning electron microscopy. The increasing necessity to integrate different types of techniques in the safeguard of the Cultural Heritage is the result of the following two interdependent factors: 1) The diagnostic process on the building stone materials of monuments is increasingly focused on difficult targets in critical situations. In these cases, the diagnosis using only one type of non-invasive technique may not be sufficient to investigate the conservation status of the stone materials of the superficial and inner parts of the studied structures 2) Recent technological and scientific developments in the field of non-invasive diagnostic techniques for different types of materials favors and supports the acquisition, processing and interpretation of huge multidisciplinary datasets.
    Description: Regione Autonoma della Sardegna (RAS) (Sardinian Autonomous Region), Regional Law 7th August 2007, no. 7, Promotion of scientific research and technological innovation in Sardinia (Italy).
    Description: Published
    Description: 4334
    Description: 5T. Sismologia, geofisica e geologia per l'ingegneria sismica
    Description: JCR Journal
    Keywords: Non-invasive methodology ; Stone building materials ; Diagnosis ; 3D Terrestrial Laser Scanner ; Non-invasive multi-techniques acoustic data ; Microscopy ; Methodology for the non-destructive diagnosis of architectural elements ; Cultural Heritage
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 15
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    Enhanced North Pacific deep-ocean stratification by stronger intermediate water formation during Heinrich Stadial 1 (2019)
    Springer Nature
    In:  EPIC3Nature Communications, Springer Nature, 10(656), ISSN: 2041-1723
    Details
    Publication Date: 2021-02-16
    Description: The deglacial history of CO2 release from the deep North Pacific remains unresolved. This is due to conflicting indications about subarctic Pacific ventilation changes based on various marine proxies, especially for Heinrich Stadial 1 (HS-1) when a rapid atmospheric CO2 rise occurs. Here, we use a complex Earth System Model to investigate the deglacial North Pacific overturning and its control on ocean stratification. Our results show an enhanced intermediate-to-deep ocean stratification coeval with intensified North Pacific Intermediate Water (NPIW) formation during HS-1, compared to the Last Glacial Maximum. The stronger NPIW formation causes lower salinities and higher temperatures at intermediate depths. By lowering NPIW densities, this enlarges vertical density gradient and thus enhances intermediate-to-deep ocean stratification during HS-1. Physically, this process prevents the North Pacific deep waters from a better communication with the upper oceans, thus prolongs the existing isolation of glacial Pacific abyssal carbons during HS-1.
    Repository Name: EPIC Alfred Wegener Institut
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  • 16
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    Studying the cardiovascular system of a marine crustacean with magnetic resonance imaging at 9.4 T (2019)
    Springer Nature
    In:  EPIC3Magnetic Resonance Materials in Physics, Biology and Medicine, Springer Nature, ISSN: 1352-8661
    Details
    Publication Date: 2019-05-27
    Description: An approach is presented for high-field MRI studies of the cardiovascular system (CVS) of a marine crustacean, the edible crab Cancer pagurus, submerged in highly conductive seawater. Structure and function of the CVS were investigated at 9.4 T. Cardiac motion was studied using self-gated CINE MRI. Imaging protocols and radio-frequency coil arrangements were tested for anatomical imaging. Haemolymph flow was quantified using phase-contrast angiography. Signal-to-noise-ratios and flow velocities in afferent and efferent branchial veins were compared with Student’s t test (n = 5). Seawater induced signal losses were dependent on imaging protocols and RF coil setup. Internal cardiac structures could be visualized with high spatial resolution within 8 min using a gradient-echo technique. Variations in haemolymph flow in different vessels could be determined over time. Maximum flow was similar within individual vessels and corresponded to literature values from Doppler measurements. Heart contractions were more pronounced in lateral and dorso-ventral directions than in the anterior–posterior direction. Choosing adequate imaging protocols in combination with a specific RF coil arrangement allows to monitor various parts of the crustacean CVS with exceptionally high spatial resolution despite the adverse effects of seawater at 9.4 T.
    Repository Name: EPIC Alfred Wegener Institut
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  • 17
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    Magma plumbing system and seismicity of an active mid-ocean ridge volcano (2017)
    Springer Nature
    In:  EPIC3Scientific Reports, Springer Nature, 7(42949), pp. 1-9
    Details
    Publication Date: 2017-03-23
    Description: At mid-ocean ridges volcanism generally decreases with spreading rate but surprisingly massive volcanic centres occur at the slowest spreading ridges. These volcanoes can host unexpectedly strong earthquakes and vigorous, explosive submarine eruptions. Our understanding of the geodynamic processes forming these volcanic centres is still incomplete due to a lack of geophysical data and the difficulty to capture their rare phases of magmatic activity. We present a local earthquake tomographic image of the magma plumbing system beneath the Segment 8 volcano at the ultraslow-spreading Southwest Indian Ridge. The tomography shows a confined domain of partial melt under the volcano. We infer that from there melt is horizontally transported to a neighbouring ridge segment at 35 km distance where microearthquake swarms and intrusion tremor occur that suggest ongoing magmatic activity. Teleseismic earthquakes around the Segment 8 volcano, prior to our study, indicate that the current magmatic spreading episode may already have lasted over a decade and hence its temporal extent greatly exceeds the frequent short-lived spreading episodes at faster opening mid-ocean ridges.
    Repository Name: EPIC Alfred Wegener Institut
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  • 18
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    Evidence for a palaeo-subglacial lake on the Antarctic continental shelf (2017)
    Springer Nature
    In:  EPIC3Nature Communications, Springer Nature, 8, pp. 15591, ISSN: 2041-1723
    Details
    Publication Date: 2018-08-10
    Description: Subglacial lakes are widespread beneath the Antarctic Ice Sheet but their control on ice-sheet dynamics and their ability to harbour life remain poorly characterized. Here we present evidence for a palaeo-subglacial lake on the Antarctic continental shelf. A distinct sediment facies recovered from a bedrock basin in Pine Island Bay indicates deposition within a low-energy lake environment. Diffusive-advection modelling demonstrates that low chloride concentrations in the pore water of the corresponding sediments can only be explained by initial deposition of this facies in a freshwater setting. These observations indicate that an active subglacial meltwater network, similar to that observed beneath the extant ice sheet, was also active during the last glacial period. It also provides a new framework for refining the exploration of these unique environments.
    Repository Name: EPIC Alfred Wegener Institut
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  • 19
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    West Antarctic Ice Sheet retreat driven by Holocene warm water incursions (2017)
    Springer Nature
    In:  EPIC3Nature, Springer Nature, 547(7661), pp. 43-48, ISSN: 0028-0836
    Details
    Publication Date: 2018-08-10
    Description: Glaciological and oceanographic observations coupled with numerical models show that warm Circumpolar Deep Water (CDW) incursions onto the West Antarctic continental shelf cause melting of the undersides of floating ice shelves. Because these ice shelves buttress glaciers feeding into them, their ocean-induced thinning is driving Antarctic ice-sheet retreat today. Here we present a multi-proxy data based reconstruction of variability in CDW inflow to the Amundsen Sea sector, the most vulnerable part of the West Antarctic Ice Sheet, during the Holocene epoch (from 11.7 thousand years ago to the present). The chemical compositions of foraminifer shells and benthic foraminifer assemblages in marine sediments indicate that enhanced CDW upwelling, controlled by the latitudinal position of the Southern Hemisphere westerly winds, forced deglaciation of this sector from at least 10,400 years ago until 7,500 years ago—when an ice-shelf collapse may have caused rapid ice-sheet thinning further upstream—and since the 1940s. These results increase confidence in the predictive capability of current ice-sheet models.
    Repository Name: EPIC Alfred Wegener Institut
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  • 20
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    Erratum to: Distribution, density and abundance of Antarctic ice seals off Queen Maud Land and the eastern Weddell Sea (2017)
    Springer Nature
    In:  EPIC3Polar Biology, Springer Nature, 40(5), pp. 1167-1168, ISSN: 0722-4060
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    Publication Date: 2017-10-20
    Repository Name: EPIC Alfred Wegener Institut
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  • 21
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    Slope stability, gas hydrates, and methane seepage at the shelf north of Svalbard (2015)
    American Association of Petroleum Geologists (AAPG)
    In:  EPIC33P Arctic: Polar Petroleum Potential Conference & Exhibition, Stavanger, Norway, 2015-09-29-2015-10-02American Association of Petroleum Geologists (AAPG)
    Details
    Publication Date: 2016-01-17
    Description: The Arctic changes rapidly in response to global warming and is expected to change even faster in the future (IPCC 2001, 2007, 2013). Large areas of the shelves and continental slopes bordering the Arctic Ocean are characterized by permafrost and the presence of gas hydrates. Future global warming and potential hydrate dissociation in the Arctic Ocean challenge the slope stability of these areas. This may lead to slope failures. The first, and so far only reported, large-scale slope failure in the Arctic Ocean is the Hinlopen/Yermak Megaslide (HYM), which is located in front of the Hinlopen glacial trough north of Svalbard. During cruise MSM31 onboard the German R/V MARIA S. MERIAN we investigated this giant slope failure and the deeper structure of the Sophia Basin in detail to elucidate the potential causes of the main and following failure events as well as to test existing hypotheses on the generation of this giant submarine landslide. We studied the megaslide and the adjacent so far not failed shelf areas by means of multibeam swath bathymetry, Parasound sediment echo sounder, low- and high-resolution multichannel seismic reflection profiling. The seismic data image bottom-simulating reflectors beneath not failed areas of the slope, as well as a buried gas escape pipe. On the shelf, shallower than the gas hydrate stability zone, we observed widespread gas seepage as flares in the Parasound echo sounder data. These flares rise from a seafloor highly disturbed by iceberg scouring. Therefore, we could not identify pockmarks in the multibeam data. At one location, we sampled a flare by means of a CTD probe close to the seafloor and proofed that the emanating gas has a high methane concentration. The new data indicate that the existence of gas and gas hydrates beneath the shelf north of Svalbard was one key factor causing slope instability in the past and may also cause further slope failures in the future.
    Repository Name: EPIC Alfred Wegener Institut
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    The Opening of the Arctic-Atlantic Gateway: Tectonic, Oceanographic and Climatic Dynamics - an IODP Initiative (2015)
    American Association of Petroleum Geologists (AAPG)
    In:  EPIC33P Arctic: Polar Petroleum Potential Conference & Exhibition, Stavanger, Norway, 2015-09-29-2015-10-02American Association of Petroleum Geologists (AAPG)
    Details
    Publication Date: 2016-01-21
    Description: The modern polar cryosphere reflects an extreme climate state with profound temperature gradients towards high-latitudes. It developed in association with stepwise Cenozoic cooling, beginning with ephemeral glaciations and the appearance of sea ice in the late middle Eocene. The polar ocean gateways played a pivotal role in changing the polar and global climate, along with declining greenhouse gas levels. The opening of the Drake Passage finalized the oceanographic isolation of Antarctica, some 40 Ma ago. The Arctic Ocean was an isolated basin until the early Miocene when rifting and subsequent sea-floor spreading started between Greenland and Svalbard, initiating the opening of the Fram Strait / Arctic-Atlantic Gateway (AAG). Although this gateway is known to be important in Earth’s past and modern climate, little is known about its Cenozoic development. However, the opening history and AAG’s consecutive widening and deepening must have had a strong impact on circulation and water mass exchange between the Arctic Ocean and the North Atlantic. To study the AAG’s complete history, ocean drilling at two primary sites and one alternate site located between 73°N and 78°N in the Boreas Basin and along the East Greenland continental margin are proposed. These sites will provide unprecedented sedimentary records that will unveil (1) the history of shallow-water exchange between the Arctic Ocean and the North Atlantic, and (2) the development of the AAG to a deep-water connection and its influence on the global climate system. The specific overarching goals of our proposal are to study: (1) the influence of distinct tectonic events in the development of the AAG and the formation of deep water passage on the North Atlantic and Arctic paleoceanography, and (2) the role of the AAG in the climate transition from the Paleogene greenhouse to the Neogene icehouse for the long-term (~50 Ma) climate history of the northern North Atlantic. Getting a continuous record of the Cenozoic sedimentary succession that recorded the evolution of the Arctic-North Atlantic horizontal and vertical motions, and land and water connections will also help better understanding the post-breakup evolution of the NE Atlantic conjugate margins and associated sedimentary basins.
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    Paleozoic diversification of terrestrial chitin-degrading bacterial lineages (2019)
    Springer Nature
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Gruen, D. S., Wolfe, J. M., & Fournier, G. P.. Paleozoic diversification of terrestrial chitin-degrading bacterial lineages. BMC Evolutionary Biology, 19, (2019): 34, doi:10.1186/s12862-019-1357-8.
    Description: Background Establishing the divergence times of groups of organisms is a major goal of evolutionary biology. This is especially challenging for microbial lineages due to the near-absence of preserved physical evidence (diagnostic body fossils or geochemical biomarkers). Horizontal gene transfer (HGT) can serve as a temporal scaffold between microbial groups and other fossil-calibrated clades, potentially improving these estimates. Specifically, HGT to or from organisms with fossil-calibrated age estimates can propagate these constraints to additional groups that lack fossils. While HGT is common between lineages, only a small subset of HGT events are potentially informative for dating microbial groups. Results Constrained by published fossil-calibrated studies of fungal evolution, molecular clock analyses show that multiple clades of Bacteria likely acquired chitinase homologs via HGT during the very late Neoproterozoic into the early Paleozoic. These results also show that, following these HGT events, recipient terrestrial bacterial clades likely diversified ~ 300–500 million years ago, consistent with established timescales of arthropod and plant terrestrialization. Conclusions We conclude that these age estimates are broadly consistent with the dispersal of chitinase genes throughout the microbial world in direct response to the evolution and ecological expansion of detrital-chitin producing groups. The convergence of multiple lines of evidence demonstrates the utility of HGT-based dating methods in microbial evolution. The pattern of inheritance of chitinase genes in multiple terrestrial bacterial lineages via HGT processes suggests that these genes, and possibly other genes encoding substrate-specific enzymes, can serve as a “standard candle” for dating microbial lineages across the Tree of Life.
    Description: This work was supported by a National Science Foundation (NSF) Graduate Research Fellowship Program Award to DSG., and Simons Collaboration on the Origins of Life Award #339603 and NSF Integrated Earth Systems Program Award #1615426 to GPF. The funding agencies for this study had no role in study design, data collection, data analysis and interpretation, or in writing the manuscript.
    Keywords: Horizontal gene transfer ; Chitinase ; Chitin ; Bacteria ; Fungi ; Arthropods
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    Superplume mantle tracked isotopically the length of Africa from the Indian Ocean to the Red Sea (2019)
    Springer Nature
    In:  EPIC3Nature Communications, Springer Nature, 10(5493), ISSN: 2041-1723
    Details
    Publication Date: 2019-12-02
    Description: Seismological findings show a complex scenario of plume upwellings from a deep thermo-chemical anomaly (superplume) beneath the East African Rift System (EARS). It is unclear if these geophysical observations represent a true picture of the superplume and its influence on magmatism along the EARS. Thus, it is essential to find a geochemical tracer to establish where upwellings are connected to the deep-seated thermo-chemical anomaly. Here we identify a unique non-volatile superplume isotopic signature (‘C’) in the youngest (after 10 Ma) phase of widespread EARS rift-related magmatism where it extends into the Indian Ocean and the Red Sea. This is the first sound evidence that the superplume influences the EARS far from the low seismic velocities in the magma-rich northern half. Our finding shows for the first time that superplume mantle exists beneath the rift the length of Africa from the Red Sea to the Indian Ocean offshore southern Mozambique
    Repository Name: EPIC Alfred Wegener Institut
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    Antarctic marine animal forests: three-dimensional communities in Southern Ocean ecosystems (2017)
    Springer Nature
    In:  EPIC3Marine Animal Forests - The Ecology of Benthic Biodiversity Hotspots, Marine Animal Forests - The Ecology of Benthic Biodiversity Hotspots, Cham, Switzerland, Springer Nature, 29 p., pp. 315-344, ISBN: 978-3-319-21011-7
    Details
    Publication Date: 2019-11-19
    Repository Name: EPIC Alfred Wegener Institut
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    Sediment characteristics of a thermokarst lagoon in the northeastern Siberian Arctic (Ivashkina Lagoon, Bykovsky Peninsula) (2018)
    Springer Nature
    In:  EPIC3Arktos, Springer Nature, 4(13), ISSN: ISSN: 2364-9461
    Details
    Publication Date: 2022-03-25
    Description: Lagoon development in ice-rich permafrost environments such as the Alaskan Beaufort Sea coastline and the Yedoma coastlines of northern Siberia represents a key mechanism of marine inundation of permafrost along the Arctic coastal plains. Here we show lithological, geochronological, and geochemical data from a core drilled in 1999 in Ivashkina Lagoon on the Bykovsky Peninsula in northeastern Siberia. This study extends previous studies of the Ivashkina Lagoon, and provides a first dated geochronological context for sedimentation and lithological characteristics. In addition, we report ground temperature measurements from different borehole sites in and around the lagoon to support our analysis of the thermokarst lagoon environment. Furthermore, a change detection study was carried out using historical aerial photography and modern satellite imagery for the 1982 to 2016 period. Several stages of landscape dynamics were reconstructed, starting with an initial Yedoma Ice Complex that covered the area during the late Pleistocene and which was locally thawed by thermokarst lake development during the Late Glacial with subsequent lacustrine sedimentation. A final stage completed the landscape dynamics during the last few hundreds of years. This stage was characterized by lake drainage and lagoon development, including strong reworking of surface sediments. By extrapolating the organic carbon data from Ivashkina Lagoon to the lagoons of the Bykovsky Peninsula, we estimate that lagoons contain 1.68 ± 0.04 Mt of organic carbon in their upper 6 m.
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    Quantifying population-specific growth in benthic bacterial communities under low oxygen using H218O (2019)
    Springer Nature
    Details
    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 ISME Journal (2019), doi:10.1038/s41396-019-0373-4.
    Description: The benthos in estuarine environments often experiences periods of regularly occurring hypoxic and anoxic conditions, dramatically impacting biogeochemical cycles. How oxygen depletion affects the growth of specific uncultivated microbial populations within these diverse benthic communities, however, remains poorly understood. Here, we applied H218O quantitative stable isotope probing (qSIP) in order to quantify the growth of diverse, uncultured bacterial populations in response to low oxygen concentrations in estuarine sediments. Over the course of 7- and 28-day incubations with redox conditions spanning from hypoxia to euxinia (sulfidic), 18O labeling of bacterial populations exhibited different patterns consistent with micro-aerophilic, anaerobic, facultative anaerobic, and aerotolerant anaerobic growth. 18O-labeled populations displaying anaerobic growth had a significantly non-random phylogenetic distribution, exhibited by numerous clades currently lacking cultured representatives within the Planctomycetes, Actinobacteria, Latescibacteria, Verrucomicrobia, and Acidobacteria. Genes encoding the beta-subunit of the dissimilatory sulfate reductase (dsrB) became 18O labeled only during euxinic conditions. Sequencing of these 18O-labeled dsrB genes showed that Acidobacteria were the dominant group of growing sulfate-reducing bacteria, highlighting their importance for sulfur cycling in estuarine sediments. Our findings provide the first experimental constraints on the redox conditions underlying increased growth in several groups of “microbial dark matter”, validating hypotheses put forth by earlier metagenomic studies.
    Description: This work was supported by a grant OR 417/1-1 from the Deutsche Forschungsgemeinschaft, and a Junior Researcher Fund grant from LMU Munich to WDO. This work was performed in part, through the Master’s Program in Geobiology and Paleontology (MGAP) at LMU Munich.
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    Ocean Colour Remote Sensing in the Laptev Sea (2018)
    Springer Nature
    In:  EPIC3Springer Nature, 15 p., ISBN: 978-3-319-94067-0
    Details
    Publication Date: 2022-06-16
    Description: The Laptev and Eastern Siberian shelves are the world’s broadest shallow shelf systems. Large Siberian rivers and coastal erosion of up to meters per summer deliver large volumes of terrestrial matter into the Arctic shelf seas. In this chapter we investigate the applicability of Ocean Colour Remote Sensing during the ice-free summer season in the Siberian Laptev Sea region. We show that the early summer river peak discharge may be traced using remote sensing in years characterized by early sea-ice retreat. In the summer time after the peak discharge, the spreading of the main Lena River plume east and north-east of the Lena River Delta into the shelf system becomes hardly traceable using optical remote sensing methods. Measurements of suspended particulate matter (SPM) and coloured dissolved organic matter (cDOM) are of the same magnitude in the coastal waters of Buor Khaya Bay as in the Lena River. Match-up analyses of in situ chlorophyll-a (Chl-a) show that standard Medium Resolution Imaging Spectrometer (MERIS) and Moderate Resolution Imaging Spectroradiometer (MODIS) satellite-derived Chl-a is not a valid remote sensing product for the coastal waters and the inner shelf region of the Laptev Sea. All MERIS and MODIS-derived Chl-a products are overestimated by at least a factor of ten, probably due to absorption by the extraordinarily high amount of non-algal particles and cDOM in these coastal and inner-shelf waters. Instead, Ocean Colour remote sensing provides information on wide-spread resuspension over shallows and lateral advection visible in satellite-derived turbidity. Satellite Sea Surface Temperature (SST) data clearly show hydrodynamics and delineate the outflow of the Lena River for hundreds of kilometres out into the shelf seas.
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    Active subseafloor microbial communities from Mariana back-arc venting fluids share metabolic strategies across different thermal niches and taxa (2019)
    Springer Nature
    Details
    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 Trembath-Reichert, E., Butterfield, D. A., & Huber, J. A. Active subseafloor microbial communities from Mariana back-arc venting fluids share metabolic strategies across different thermal niches and taxa. Isme Journal, 13(9), (2019): 2264-2279, doi: 10.1038/s41396-019-0431-y.
    Description: There are many unknowns regarding the distribution, activity, community composition, and metabolic repertoire of microbial communities in the subseafloor of deep-sea hydrothermal vents. Here we provide the first characterization of subseafloor microbial communities from venting fluids along the central Mariana back-arc basin (15.5–18°N), where the slow-spreading rate, depth, and variable geochemistry along the back-arc distinguish it from other spreading centers. Results indicated that diverse Epsilonbacteraeota were abundant across all sites, with a population of high temperature Aquificae restricted to the northern segment. This suggests that differences in subseafloor populations along the back-arc are associated with local geologic setting and resultant geochemistry. Metatranscriptomics coupled to stable isotope probing revealed bacterial carbon fixation linked to hydrogen oxidation, denitrification, and sulfide or thiosulfate oxidation at all sites, regardless of community composition. NanoSIMS (nanoscale secondary ion mass spectrometry) incubations at 80 °C show only a small portion of the microbial community took up bicarbonate, but those autotrophs had the highest overall rates of activity detected across all experiments. By comparison, acetate was more universally utilized to sustain growth, but within a smaller range of activity. Together, results indicate that microbial communities in venting fluids from the Mariana back-arc contain active subseafloor communities reflective of their local conditions with metabolisms commonly shared across geologically disparate spreading centers throughout the ocean.
    Description: This work was funded by the NOAA Ocean Exploration and Research (OER) Program, the NSF Center for Dark Energy Biosphere Investigations (C-DEBI) (OCE-0939564), and NOAA/PMEL and JISAO under NOAA Cooperative Agreement NA15OAR4320063. ETR was supported by a NASA Postdoctoral Fellowship with the NASA Astrobiology Institute and a L’Oréal USA For Women in Science Fellowship. The data collected in this study includes work supported by the Schmidt Ocean Institute during cruise FK161129 aboard R/V Falkor. We thank the captains and crews of the R/V Falkor and ROV SuBastian. Critical support in cruise planning and sampling at sea was carried out by Andra Bobbitt, Bill Chadwick, Bob Embley, Ben Larson, and Kevin Roe. Caroline Fortunato, Connor Skennerton, Rika Anderson, Karthik Anantharaman, Jaclyn Saunders, Hank Yu, Lewis Ward, Elaina Graham, and Ben Tully aided bioinformatics pipeline development and Victoria Orphan and Yunbin Guan aided with NanoSIMS analysis. This is C-DEBI Contribution 470, JISAO Contribution 2018-0173, and PMEL Contribution 4867.
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    Ocean acidification responses in paralarval squid swimming behavior using a novel 3D tracking system (2019)
    Springer Nature
    Details
    Publication Date: 2022-05-26
    Description: Author Posting. © The Author(s), 2019. This is the author's version of the work. It is posted here by permission of Springer Nature for personal use, not for redistribution. The definitive version was published in Zakroff, C., Mooney, T.A. & Wirth, C. Ocean acidification responses in paralarval squid swimming behavior using a novel 3D tracking system. Hydrobiologia, 808(1),(2018):83-106, doi:10.1007/s10750-017-3342-9.
    Description: Chronic embryonic exposure to ocean acidification (OA) has been shown to degrade the aragonitic statolith of paralarval squid, Doryteuthis pealeii, a key structure for their swimming behavior. This study examined if day-of-hatching paralarval D. pealeii from eggs reared under chronic OA demonstrated measurable impairments to swimming activity and control. This required the development of a novel, cost-effective, and robust method for 3D motion tracking and analysis. Squid eggs were reared in pCO2 levels in a dose-dependent manner ranging from 400 - 2200 ppm. Initial 2D experiments showed paralarvae in higher acidification environments spent more time at depth. In 3D experiments, velocity, particularly positive and negative vertical velocities, significantly decreased from 400 to 1000 ppm pCO2, but showed non-significant decreases at higher concentrations. Activity and horizontal velocity decreased linearly with increasing pCO2, indicating a subtle impact to paralarval energetics. Patterns may have been obscured by notable individual variability in the paralarvae. Responses were also seen to vary between trials on cohort or potentially annual scales. Overall, paralarval swimming appeared resilient to OA, with effects being slight. The newly developed 3D tracking system provides a powerful and accessible method for future studies to explore similar questions in the larvae of aquatic taxa.
    Description: We thank D. Remsen, the MBL Marine Resources Center staff, and MBL Gemma crew for their support in acquiring squid. R. Galat and the facilities staff of the WHOI ESL provided system support. D. McCorkle, KYK Chan, and M. White provided valuable insight on the OA system. E. Moberg, A. Beet, and A. Solow assisted in the development and coding of the 3D model system. We also thank E. Bonk, K. Hoering, M. Lee, D. Weiler, and A. Schlunk for their assistance and input with the experiments. This material is based upon work supported by the National Science Foundation Graduate Research Fellowship under Grant No. 1122374. This project is funded by NSF Grant No. 1220034.
    Keywords: Hypercapnia ; Cephalopod ; Larvae ; Movement analysis ; Stress physiology
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    Parkinson's disease protein DJ-1 regulates ATP synthase protein components to increase neuronal process outgrowth (2019)
    Springer Nature
    Details
    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 Chen, R.; Park, H. A.; Mnatsakanyan, N.; Niu, Y.; Licznerski, P.; Wu, J.; Miranda, P.; Graham, M.; Tang, J.; Boon, A. J. W.; Cossu, G.; Mandemakers, W.; Bonifati, V.; Smith, P. J. S.; Alavian, K. N.; Jonas, E. A. Parkinson's disease protein DJ-1 regulates ATP synthase protein components to increase neuronal process outgrowth. Cell Death & Disease, 10(6), (2019):469, doi:10.1038/s41419-019-1679-x.
    Description: Familial Parkinson’s disease (PD) protein DJ-1 mutations are linked to early onset PD. We have found that DJ-1 binds directly to the F1FO ATP synthase β subunit. DJ-1’s interaction with the β subunit decreased mitochondrial uncoupling and enhanced ATP production efficiency while in contrast mutations in DJ-1 or DJ-1 knockout increased mitochondrial uncoupling, and depolarized neuronal mitochondria. In mesencephalic DJ-1 KO cultures, there was a progressive loss of neuronal process extension. This was ameliorated by a pharmacological reagent, dexpramipexole, that binds to ATP synthase, closing a mitochondrial inner membrane leak and enhancing ATP synthase efficiency. ATP synthase c-subunit can form an uncoupling channel; we measured, therefore, ATP synthase F1 (β subunit) and c-subunit protein levels. We found that ATP synthase β subunit protein level in the DJ-1 KO neurons was approximately half that found in their wild-type counterparts, comprising a severe defect in ATP synthase stoichiometry and unmasking c-subunit. We suggest that DJ-1 enhances dopaminergic cell metabolism and growth by its regulation of ATP synthase protein components.
    Description: The research was supported by NIH (NS081746) to E.A.J., W.M. and V.B. are supported by the Stichting Parkinson Fonds (The Netherlands).
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    Fukushima Daiichi–derived radionuclides in the ocean : transport, fate, and impacts (2017)
    Annual Reviews
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Annual Review of Marine Science 9 (2017): 173-203, doi:10.1146/annurev-marine-010816-060733.
    Description: The events that followed the Tohoku earthquake and tsunami on March 11, 2011, included the loss of power and overheating at the Fukushima Daiichi nuclear power plants, which led to extensive releases of radioactive gases, volatiles, and liquids, particularly to the coastal ocean. The fate of these radionuclides depends in large part on their oceanic geochemistry, physical processes, and biological uptake. Whereas radioactivity on land can be resampled and its distribution mapped, releases to the marine environment are harder to characterize owing to variability in ocean currents and the general challenges of sampling at sea. Five years later, it is appropriate to review what happened in terms of the sources, transport, and fate of these radionuclides in the ocean. In addition to the oceanic behavior of these contaminants, this review considers the potential health effects and societal impacts.
    Description: K.B. was supported in part by the Gordon and Betty Moore Foundation and the Deerbrook Charitable Trust. P.M. was supported in part by the Generalitat de Catalunya through MERS (grant 2014 SGR 1356), the European Commission 7th Framework COMET-FRAME project (grant agreement 604974), and the Ministerio de Economía y Competitividad of Spain (project CTM2011-15152-E). S.C. was supported in part by the French program Investissement d'Avenir run by the National Research Agency (AMORAD project, grant ANR-11-RSNR-0002). D.O. was supported in part by the Center for Environmental Radioactivity (NFR Centers of Excellence grant 223268/F50). J.N.S. was supported in part by the Marine Environmental Observation, Prediction, and Response Network.
    Keywords: Cesium ; Caesium ; North Pacific ; Radioactivity ; Japan
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    Using spatial variability in the rate of change of chlorophyll a to improve water quality management in a subtropical oligotrophic estuary (2019)
    Springer Nature
    Details
    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 Millette, N. C., Kelble, C., Linhoss, A., Ashby, S., & Visser, L. Using spatial variability in the rate of change of chlorophyll a to improve water quality management in a subtropical oligotrophic estuary. Estuaries and Coasts, 42(7), (2019): 1792-1803, doi:10.1007/s12237-019-00610-5.
    Description: Anthropogenic eutrophication threatens numerous aquatic ecosystems across the globe. Proactive management that prevents a system from becoming eutrophied is more effective and cheaper than restoring a eutrophic system, but detecting early warning signs and problematic nutrient sources in a relatively healthy system can be difficult. The goal of this study was to investigate if rates of change in chlorophyll a and nutrient concentrations at individual stations can be used to identify specific areas that need to be targeted for management. Biscayne Bay is a coastal embayment in southeast Florida with primarily adequate water quality that has experienced rapid human population growth over the last century. Water quality data collected at 48 stations throughout Biscayne Bay over a 20-year period (1995–2014) were examined to identify any water quality trends associated with eutrophication. Chlorophyll a and phosphate concentrations have increased throughout Biscayne Bay, which is a primary indicator of eutrophication. Moreover, chlorophyll a concentrations throughout the northern area, where circulation is restricted, and in nearshore areas of central Biscayne Bay are increasing at a higher rate compared to the rest of the Bay. This suggests increases in chlorophyll a are due to local nutrient sources from the watershed. These areas are also where recent seagrass die-offs have occurred, suggesting an urgent need for management intervention. This is in contrast with the state of Florida listing of Biscayne Bay as a medium priority impaired body of water.
    Description: Data provided by the SERC-FIU/SFWMD Water Quality Monitoring Network is supported by SFWMD/SERC Cooperative Agreement #4600000352 as well as EPA Agreement #X7-96410603-3. This research was also funded by a NOAA/Atlantic Oceanographic and Meteorological Laboratory grant to the Northern Gulf Institute (award number NA160AR4320199).
    Keywords: Chlorophyll a ; Eutrophication ; Oligotrophic ; Ecological indicators
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    Marine litter: Sea change for plastic pollution (2017)
    Springer Nature
    In:  EPIC3Nature, Springer Nature, 544(7650), pp. 297-297, ISSN: 0028-0836
    Details
    Publication Date: 2023-06-21
    Repository Name: EPIC Alfred Wegener Institut
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    Living on Cold Substrata: New Insights and Approaches in the Study of Microphytobenthos Ecophysiology and Ecology in Kongsfjorden (2019)
    Springer Nature
    In:  EPIC3Advances in Polar Ecology 2, The Ecosystem of Kongsfjorden, Svalbard, Switzerland, Springer Nature, 2, pp. 303-330, ISSN: 2468-5712
    Details
    Publication Date: 2023-06-21
    Description: Organisms in shallow waters at high latitudes are under pressure due to climate change. These areas are typically inhabited by microphytobenthos (MPB) communities, composed mainly of diatoms. Only sparse information is available on the ecophysiology and acclimation processes within MPBs from Arctic regions. The physico-chemical environment and the ecology and ecophysiology of benthic diatoms in Kongsfjorden (Svalbard, Norway) are addressed in this review. MPB biofilms cover extensive areas of sediment. They show high rates of primary production, stabilise sediment surfaces against erosion under hydrodynamic forces,and affect the exchange of oxygen and nutrients across the sediment-water interface. Additionally, this phototrophic community represents a key component in the functioning of the Kongsfjorden trophic web, particularly as a major food source for benthic suspension- or deposit-feeders. MPB in Kongsfjorden is confronted with pronounced seasonal variations in solar radiation, low temperatures, and hyposaline (meltwater) conditions in summer, as well as long periods of ice and snow cover in winter. From the few data available, it seems that these organisms can easily cope with these environmental extremes. The underlying physiological mechanisms that allow growth and photosynthesis to continue under widely varying abiotic parameters, along with vertical migration and heterotrophy, and biochemical features such as a pronounced fatty-acid metabolism and silicate incorporation are discussed. Existing gaps in our knowledge of benthic diatoms in Kongsfjorden, such as the chemical ecology of biotic interactions, need to be filled. In addition, since many of the underlying molecular acclimation mechanisms are poorly understood, modern approaches based on transcriptomics, proteomics, and/or metabolomics, in conjunction with cell biological and biochemical techniques, are urgently needed. Climate change models for the Arctic predict other multifactorial stressors, such as an increase in precipitation and permafrost thawing, with consequences for the shallow-water regions. Both precipitation and permafrost thawing are likely to increase nutrient-enriched, turbid freshwater runoff and may locally counteract the expected increase in coastal radiation availability. So far, complex interactions among factors, as well as the full genetic diversity and physiological plasticity of Arctic benthic diatoms, have only rarely been considered. The limited existing information is described and discussed in this review.
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    Phytoplankton responses to temperature increases are constrained by abiotic conditions and community composition (2016)
    Springer Nature
    In:  EPIC3Oecologia, Springer Nature, 182(3), pp. 815-827, ISSN: 0029-8549
    Details
    Publication Date: 2023-09-22
    Description: Effects of temperature changes on phytoplankton communities seem to be highly context-specific, but few studies have analyzed whether this context specificity depends on differences in the abiotic conditions or in species composition between studies. We present an experiment that allows disentangling the contribution of abiotic and biotic differences in shaping the response to two aspects of temperature change: permanent increase of mean temperature versus pulse disturbance in form of a heat wave. We used natural communities from six different sites of a floodplain system as well as artificially mixed communities from laboratory cultures and grew both, artificial and natural communities, in water from the six different floodplain lakes (sites). All 12 contexts (2 communities × 6 sites) were first exposed to three different temperature levels (12, 18, 24 °C, respectively) and afterward to temperature pulses (4 °C increase for 7 h day(-1)). Temperature-dependent changes in biomass and community composition depended on the initial composition of phytoplankton communities. Abiotic conditions had a major effect on biomass of phytoplankton communities exposed to different temperature conditions, however, the effect of biotic and abiotic conditions together was even more pronounced. Additionally, phytoplankton community responses to pulse temperature effects depended on the warming history. By disentangling abiotic and biotic effects, our study shows that temperature-dependent effects on phytoplankton communities depend on both, biotic and abiotic constraints.
    Repository Name: EPIC Alfred Wegener Institut
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    The body-size structure of macrobenthos changes predictably along gradients of hydrodynamic stress and organic enrichment (2015)
    Springer Nature
    In:  EPIC3Marine Biology, Springer Nature, 162(3), pp. 675-685, ISSN: 0025-3162
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    Publication Date: 2023-09-22
    Repository Name: EPIC Alfred Wegener Institut
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    Far-ranging generalist top predators enhance the stability of meta-foodwebs (2019)
    Springer Nature
    In:  EPIC3Scientific Reports, Springer Nature, 9(1), pp. 12268-12268, ISSN: 2045-2322
    Details
    Publication Date: 2023-09-25
    Description: Identifying stabilizing factors in foodwebs is a long standing challenge with wide implications for community ecology and conservation. Here, we investigate the stability of spatially resolved meta-foodwebs with far-ranging super-predators for whom the whole meta-foodwebs appears to be a single habitat. By using a combination of generalized modeling with a master stability function approach, we are able to efficiently explore the asymptotic stability of large classes of realistic many-patch meta-foodwebs. We show that meta-foodwebs with far-ranging top predators are more stable than those with localized top predators. Moreover, adding far-ranging generalist top predators to a system can have a net stabilizing effect. These results highlight the importance of top predator conservation.
    Repository Name: EPIC Alfred Wegener Institut
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    Correction to: Resistance of Arctic phytoplankton to ocean acidification and enhanced irradiance (2018)
    Springer Nature
    In:  EPIC3Polar Biology, Springer Nature, 41(3), pp. 415-416, ISSN: 0722-4060
    Details
    Publication Date: 2024-05-08
    Description: The authors regret an error in the published article, where incorrect data was used to produce Figure 2, showing the temporal development of pH over the duration of the experiment. The corrected Fig. 2 shows that the error did not affect the interpretation of nor the conclusions drawn from the present dataset. The original article has been corrected.
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    Correction to: Sedimentary and geochemical characteristics of two small permafrost-dominated Arctic river deltas in northern Alaska (2018)
    Springer Nature
    In:  EPIC3arktos, Springer Nature, 4(1), pp. 1-1, ISSN: 2364-9453
    Details
    Publication Date: 2024-04-11
    Description: Arctic river deltas are highly dynamic environments in the northern circumpolar permafrost region that are affected by fluvial, coastal, and permafrost-thaw processes. They are characterized by thick sediment deposits containing large but poorly constrained amounts of frozen organic carbon and nitrogen. This study presents new data on soil organic carbon and nitrogen storage as well as accumulation rates from the Ikpikpuk and Fish Creek river deltas, two small, permafrost-dominated Arctic river deltas on the Arctic Coastal Plain of northern Alaska. A soil organic carbon storage of 42.4 ± 1.6 and 37.9 ± 3.5 kg C m− 2 and soil nitrogen storage of 2.1 ± 0.1 and 2.0 ± 0.2 kg N m− 2 was found for the first 2 m of soil for the Ikpikpuk and Fish Creek river delta, respectively. While the upper meter of soil contains 3.57 Tg C, substantial amounts of carbon (3.09 Tg C or 46%) are also stored within the second meter of soil (100–200 cm) in the two deltas. An increasing and inhomogeneous distribution of C with depth is indicative of the dominance of deltaic depositional rather than soil forming processes for soil organic carbon storage. Largely, mid- to late Holocene radiocarbon dates in our cores suggest different carbon accumulation rates for the two deltas for the last 2000 years. Rates up to 28 g C m− 2 year− 1 for the Ikpikpuk river delta are about twice as high as for the Fish Creek river delta. With this study, we highlight the importance of including these highly dynamic permafrost environments in future permafrost carbon estimations.
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    SILVA–Referenzdatensätze für den Nachweis von Mikroorganismen (2018)
    Springer Nature
    In:  EPIC3BIOspektrum, Springer Nature, 24(7), pp. 750-751, ISSN: 0947-0867
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    Publication Date: 2024-05-03
    Repository Name: EPIC Alfred Wegener Institut
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    Ein neuer Baum des Lebens? (2019)
    Springer Nature
    In:  EPIC3BIOspektrum, Springer Nature, 25(1), pp. 50-57, ISSN: 0947-0867
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    Publication Date: 2024-05-03
    Repository Name: EPIC Alfred Wegener Institut
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    STRUCTURE AND FUNCTION OF LIPID-DNA COMPLEXES FOR GENE DELIVERY (2000)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 29 (2000), S. 27-47 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Owing to the rapid development of in vivo applications for non-viral gene delivery vectors, it is necessary to have a better understanding of how the structure-activity relationships of these lipid-DNA complexes are affected by their environment. Indeed, research in gene therapy first focused on in vitro cell culture studies to determine the mechanisms involved in the delivery of DNA into the cell. New biophysical techniques such as electron microscopy and X-ray diffraction have been developed to discern the structure of the lipid-DNA complex. However, further studies have revealed discrepancies between optimal lipid-DNA formulations for in vitro transfection and for in vivo administration of these vectors. Furthermore, some immune stimulatory effects have been associated with in vivo lipid-DNA administration. This review summarizes the current state of knowledge on in vitro and in vivo lipid-DNA complex transfections. New prospects of vectors for in vivo gene transfer are also discussed.
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    GCN5-RELATED N-ACETYLTRANSFERASES: A Structural Overview (2000)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 29 (2000), S. 81-103 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Hundreds of acetyltransferases exist. All use a common acetyl donor-acetyl coenzyme A-and each exhibits remarkable specificity for acetyl acceptors, which include small molecules and proteins. Analysis of the primary sequences of these enzymes indicates that they can be sorted into several superfamilies. This review covers the three-dimensional structures of members of one of these superfamilies, now referred to in the literature as the GCN5-related N-acetyltransferases (GNAT), reflecting the importance of one functional category, the histone acetyltransferases. Despite the diversity of substrate specificities, members of the GNAT superfamily demonstrate remarkable similarity in protein topology and mode of acetyl coenzyme A binding, likely reflecting a conserved catalytic mechanism.
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    SIGNALING AND SUBCELLULAR TARGETING BY MEMBRANE-BINDING DOMAINS1 (2000)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 29 (2000), S. 49-79 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Protein kinase C homology-1 and -2, FYVE, and pleckstrin homology domains are ubiquitous in eukaryotic signal transduction and membrane-trafficking proteins. These domains regulate subcellular localization and protein function by binding to lipid ligands embedded in cell membranes. Structural and biochemical analysis of these domains has shown that their molecular mechanisms of membrane binding depend on a combination of specific and nonspecific interactions with membrane lipids. In vivo studies of green fluorescent protein fusions have highlighted the key roles of these domains in regulating protein localization to plasma and internal membranes in cells.
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    MEASURING THE FORCES THAT CONTROL PROTEIN INTERACTIONS (2000)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 29 (2000), S. 1-26 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Although the force fields and interaction energies that control protein behavior can be inferred indirectly from equilibrium and kinetic measurements, recent developments have made it possible to quantify directly (a) the ranges, magnitudes, and time dependence of the interaction energies and forces between biological materials; (b) the mechanical properties of isolated proteins; and (c) the strength of single receptor-ligand bonds. This review describes recent results obtained by using the atomic force microscope, optical tweezers, the surface force apparatus, and micropipette aspiration to quantify short-range protein-ligand interactions and the long-range, nonspecific forces that together control protein behavior. The examples presented illustrate the power of force measurements to quantify directly the force fields and energies that control protein behavior.
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    DNA RECOGNITION BY Cys2His2 ZINC FINGER PROTEINS (2000)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 29 (2000), S. 183-212 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Cys2His2 zinc fingers are one of the most common DNA-binding motifs found in eukaryotic transcription factors. These proteins typically contain several fingers that make tandem contacts along the DNA. Each finger has a conserved betabetaalpha structure, and amino acids on the surface of the alpha-helix contact bases in the major groove. This simple, modular structure of zinc finger proteins, and the wide variety of DNA sequences they can recognize, make them an attractive framework for attempts to design novel DNA-binding proteins. Several studies have selected fingers with new specificities, and there clearly are recurring patterns in the observed side chain-base interactions. However, the structural details of recognition are intricate enough that there are no general rules (a "recognition code") that would allow the design of an optimal protein for any desired target site. Construction of multifinger proteins is also complicated by interactions between neighboring fingers and the effect of the intervening linker. This review analyzes DNA recognition by Cys2His2 zinc fingers and summarizes progress in generating proteins with novel specificities from fingers selected by phage display.
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    FAST KINETICS AND MECHANISMS IN PROTEIN FOLDING1 (2000)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 29 (2000), S. 327-359 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract This review describes how kinetic experiments using techniques with dramatically improved time resolution have contributed to understanding mechanisms in protein folding. Optical triggering with nanosecond laser pulses has made it possible to study the fastest-folding proteins as well as fundamental processes in folding for the first time. These include formation of alpha-helices, beta-sheets, and contacts between residues distant in sequence, as well as overall collapse of the polypeptide chain. Improvements in the time resolution of mixing experiments and the use of dynamic nuclear magnetic resonance methods have also allowed kinetic studies of proteins that fold too fast (〉 103 s-1) to be observed by conventional methods. Simple statistical mechanical models have been extremely useful in interpreting the experimental results. One of the surprises is that models originally developed for explaining the fast kinetics of secondary structure formation in isolated peptides are also successful in calculating folding rates of single domain proteins from their native three-dimensional structure.
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    A DECADE OF CLC CHLORIDE CHANNELS: Structure, Mechanism, and Many Unsettled Questions (2000)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 29 (2000), S. 411-438 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract ClC-type chloride channels are ubiquitous throughout the biological world. Expressed in nearly every cell type, these proteins have a host of biological functions. With nine distinct homologues known in eukaryotes, the ClCs represent the only molecularly defined family of chloride channels. ClC channels exhibit features of molecular architecture and gating mechanisms unprecedented in other types of ion channels. They form two-pore homodimers, and their voltage-dependence arises not from charged residues in the protein, but rather via coupling of gating to the movement of chloride ions within the pore. Because the functional characteristics of only a few ClC channels have been studied in detail, we are still learning which properties are general to the whole family. New approaches, including structural analyses, will be crucial to an understanding of ClC architecture and function.
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    DESIGNED SEQUENCE-SPECIFIC MINOR GROOVE LIGANDS (2000)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 29 (2000), S. 439-461 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract In the past decade, a general design for sequence-specific minor groove ligands has evolved, based on the natural products distamycin and netropsin. By utilizing a basic set of design rules for connecting pyrrole, imidazole, and hydroxypyrrole modules, new ligands can be prepared to target almost any sequence of interest with both high affinity and specificity. In this review we present the design rules with a brief history of how they evolved. The structural basis for sequence-specific recognition is explained, together with developments that allow linking of recognition modules that enable targeting of long DNA sequences. Examples of the affinity and specificity that can be achieved with a number of variations on the basic design are given. Recently these molecules have been used to compete with proteins both in vitro and in vivo, and a brief description of the experimental results are given.
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    NMR PROBES OF MOLECULAR DYNAMICS: Overview and Comparison with Other Techniques (2001)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 30 (2001), S. 129-155 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract NMR spin relaxation spectroscopy is a powerful approach for characterizing intramolecular and overall rotational motions in proteins. This review describes experimental methods for measuring laboratory frame spin relaxation rate constants by high-resolution solution-state NMR spectroscopy, together with theoretical approaches for interpreting spin relaxation data in order to quantify protein conformational dynamics on picosecond-nanosecond time scales. Recent applications of these techniques to proteins are surveyed, and investigations of the contribution of conformational chain entropy to protein function are highlighted. Insights into the dynamical properties of proteins obtained from NMR spin relaxation spectroscopy are compared with results derived from other experimental and theoretical techniques.
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    STRUCTURE OF PROTEINS INVOLVED IN SYNAPTIC VESICLE FUSION IN NEURONS (2001)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 30 (2001), S. 157-171 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract The fusion of vesicles with target membranes is controlled by a complex network of protein-protein and protein-lipid interactions. Structures of the SNARE complex, synaptotagmin III, nSec1, domains of the NSF chaperone and its adaptor SNAP, and Rab3 and some of its effectors provide the framework for developing molecular models of vesicle fusion and for designing experiments to test these models.
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    AB INITIO PROTEIN STRUCTURE PREDICTION: Progress and Prospects (2001)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 30 (2001), S. 173-189 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Considerable recent progress has been made in the field of ab initio protein structure prediction, as witnessed by the third Critical Assessment of Structure Prediction (CASP3). In spite of this progress, much work remains, for the field has yet to produce consistently reliable ab initio structure prediction protocols. In this work, we review the features of current ab initio protocols in an attempt to highlight the foundations of recent progress in the field and suggest promising directions for future work.
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    STRUCTURAL RELATIONSHIPS AMONG REGULATED AND UNREGULATED PHOSPHORYLASES (2001)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 30 (2001), S. 191-209 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Species and tissue-specific isozymes of phosphorylase display differences in regulatory properties consistent with their distinct roles in particular organisms and tissues. In this review, we compare crystallographic structures of regulated and unregulated phosphorylases, including maltodextrin phosphorylase (MalP) from Escherichia coli, glycogen phosphorylase from yeast, and mammalian isozymes from muscle and liver tissues. Mutagenesis and functional studies supplement the structural work and provide insights into the structural basis for allosteric control mechanisms. MalP, a simple, unregulated enzyme, is contrasted with the more complicated yeast and mammalian phosphorylases that have evolved regulatory sites onto the basic catalytic architecture. The human liver and muscle isozymes show differences structurally in their means of invoking allosteric activation. Phosphorylation, though common to both the yeast and mammalian enzymes, occurs at different sites and activates the enzymes by surprisingly different mechanisms.
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    BIOMOLECULAR SIMULATIONS: Recent Developments in Force Fields, Simulations of Enzyme Catalysis, Protein-Ligand, Protein-Protein, and Protein-Nucleic Acid Noncovalent Interactions (2001)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 30 (2001), S. 211-243 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Computer modeling has been developed and widely applied in studying molecules of biological interest. The force field is the cornerstone of computer simulations, and many force fields have been developed and successfully applied in these simulations. Two interesting areas are (a) studying enzyme catalytic mechanisms using a combination of quantum mechanics and molecular mechanics, and (b) studying macromolecular dynamics and interactions using molecular dynamics (MD) and free energy (FE) calculation methods. Enzyme catalysis involves forming and breaking of covalent bonds and requires the use of quantum mechanics. Noncovalent interactions appear ubiquitously in biology, but here we confine ourselves to review only noncovalent interactions between protein and protein, protein and ligand, and protein and nucleic acids.
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    CHAPERONIN-MEDIATED PROTEIN FOLDING (2001)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 30 (2001), S. 245-269 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Molecular chaperones are required to assist folding of a subset of proteins in Escherichia coli. We describe a conceptual framework for understanding how the GroEL-GroES system assists misfolded proteins to reach their native states. The architecture of GroEL consists of double toroids stacked back-to-back. However, most of the fundamentals of the GroEL action can be described in terms of the single ring. A key idea in our framework is that, with coordinated ATP hydrolysis and GroES binding, GroEL participates actively by repeatedly unfolding the substrate protein (SP), provided that it is trapped in one of the misfolded states. We conjecture that the unfolding of SP becomes possible because a stretching force is transmitted to the SP when the GroEL particle undergoes allosteric transitions. Force-induced unfolding of the SP puts it on a higher free-energy point in the multidimensional energy landscape from which the SP can either reach the native conformation with some probability or be trapped in one of the competing basins of attraction (i.e., the SP undergoes kinetic partitioning). The model shows, in a natural way, that the time scales in the dynamics of the allosteric transitions are intimately coupled to folding rates of the SP. Several scenarios for chaperonin-assisted folding emerge depending on the interplay of the time scales governing the cycle. Further refinement of this framework may be necessary because single molecule experiments indicate that there is a great dispersion in the time scales governing the dynamics of the chaperonin cycle.
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    MY ROAD TO BIOPHYSICS: Picking Flowers on the Way to Photosynthesis (2002)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 31 (2002), S. 1-44 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
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    URL: http://dx.doi.org/10.1146/annurev.biophys.31.082901.134147
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    PROPERTIES AND BIOLOGICAL ACTIVITIES OF THIOREDOXINS (2001)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 30 (2001), S. 421-455 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract The mammalian thioredoxins are a family of small (approximately 12 kDa) redox proteins that undergo NADPH-dependent reduction by thioredoxin reductase and in turn reduce oxidized cysteine groups on proteins. The two main thioredoxins are thioredoxin-1, a cytosolic and nuclear form, and thioredoxin-2, a mitochondrial form. Thioredoxin-1 has been studied more. It performs many biological actions including the supply of reducing equivalents to thioredoxin peroxidases and ribonucleotide reductase, the regulation of transcription factor activity, and the regulation of enzyme activity by heterodimer formation. Thioredoxin-1 stimulates cell growth and is an inhibitor of apoptosis. Thioredoxins may play a role in a variety of human diseases including cancer. An increased level of thioredoxin-1 is found in many human tumors, where it is associated with aggressive tumor growth. Drugs are being developed that inhibit thioredoxin and that have antitumor activity.
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    NMR STUDIES OF LIPOPROTEIN STRUCTURE (2002)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 31 (2002), S. 177-206 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Early NMR structural studies of serum lipoproteins were based on 1H, 13C, 31P, and 2H studies of lipid components. From the early studies information on composition, lipid chain dynamics and order parameters, and monolayer organization resulted. More recently, selective or complete isotopic labeling techniques, combined with multidimensional NMR spectroscopy, have resulted in structural information of apoprotein fragments. Finally, use of heteronuclear three- and four-dimensional experiments have yielded solution structures and protein-lipid interactions of intact apolipoproteins C-I, C-II, and A-I.
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    THE LINKAGE BETWEEN PROTEIN FOLDING AND FUNCTIONAL COOPERATIVITY: Two Sides of the Same Coin? (2002)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 31 (2002), S. 235-256 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract During the course of their biological function, proteins undergo different types of structural rearrangements ranging from local to large-scale conformational changes. These changes are usually triggered by their interactions with small-molecular-weight ligands or other macromolecules. Because binding interactions occur at specific sites and involve only a small number of residues, a chain of cooperative interactions is necessary for the propagation of binding signals to distal locations within the protein structure. This process requires an uneven structural distribution of protein stability and cooperativity as revealed by NMR-detected hydrogen/deuterium exchange experiments under native conditions. The distribution of stabilizing interactions does not only provide the architectural foundation to the three-dimensional structure of a protein, but it also provides the required framework for functional cooperativity. In this review, the statistical thermodynamic linkage between protein stability, functional cooperativity, and ligand binding is discussed.
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    INTERPRETING THE EFFECTS OF SMALL UNCHARGED SOLUTES ON PROTEIN-FOLDING EQUILIBRIA (2001)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 30 (2001), S. 271-306 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Proteins are designed to function in environments crowded by cosolutes, but most studies of protein equilibria are conducted in dilute solution. While there is no doubt that crowding changes protein equilibria, interpretations of the changes remain controversial. This review combines experimental observations on the effect of small uncharged cosolutes (mostly sugars) on protein stability with a discussion of the thermodynamics of cosolute-induced nonideality and critical assessments of the most commonly applied interpretations. Despite the controversy surrounding the most appropriate manner for interpreting these effects of thermodynamic nonideality arising from the presence of small cosolutes, experimental advantage may still be taken of the ability of the cosolute effect to promote not only protein stabilization but also protein self-association and complex formation between dissimilar reactants. This phenomenon clearly has potential ramifications in the cell, where the crowded environment could well induce the same effects.
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    BINDING OF LIGANDS AND ACTIVATION OF TRANSCRIPTION BY NUCLEAR RECEPTORS (2001)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 30 (2001), S. 329-359 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Nuclear receptors (NRs) form a superfamily of ligand-inducible transcription factors composed of several domains. Recent structural studies focused on domain E, which harbors the ligand-binding site and the ligand-dependent transcription activation function AF-2. Structures of single representatives in an increasing number of various complexes as well as new structures of further NRs addressed issues such as discrimination of ligands, superagonism, isotype specificity, and partial agonism. Until today, one unique transcriptionally active form of domain E was determined; however, divergent tertiary structures of apo-forms and transcriptionally inactive forms are known. Thus, recent results link the transformation of NRs upon ligand binding to principles of protein folding. Furthermore, the ensemble of NR structures, including those of DNA-binding domains, provides one of the foundations for the understanding of interactions with transcription intermediary factors up to the characterization of the link between NR complexes and the basal transcriptional machinery at the structural level.
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    URL: http://dx.doi.org/10.1146/annurev.biophys.30.1.329
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    STRUCTURAL INSIGHTS INTO MICROTUBULE FUNCTION (2001)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 30 (2001), S. 397-420 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Microtubules are polymers that are essential for, among other functions, cell transport and cell division in all eukaryotes. The regulation of the microtubule system includes transcription of different tubulin isotypes, folding of alpha/beta-tubulin heterodimers, post-translation modification of tubulin, and nucleotide-based microtubule dynamics, as well as interaction with numerous microtubule-associated proteins that are themselves regulated. The result is the precise temporal and spatial pattern of microtubules that is observed throughout the cell cycle. The recent high-resolution analysis of the structure of tubulin and the microtubule has brought new insight to the study of microtubule function and regulation, as well as the mode of action of antimitotic drugs that disrupt normal microtubule behavior. The combination of structural, genetic, biochemical, and biophysical data should soon give us a fuller understanding of the exquisite details in the regulation of the microtubule cytoskeleton.
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    RIBOZYME STRUCTURES AND MECHANISMS (2001)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 30 (2001), S. 457-475 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract The past few years have seen exciting advances in understanding the structure and function of catalytic RNA. Crystal structures of several ribozymes have provided detailed insight into the folds of RNA molecules. Models of other biologically important RNAs have been constructed based on structural, phylogenetic, and biochemical data. However, many questions regarding the catalytic mechanisms of ribozymes remain. This review compares the structures and possible catalytic mechanisms of four small self-cleaving RNAs: the hammerhead, hairpin, hepatitis delta virus, and in vitro-selected lead-dependent ribozymes. The organization of these small catalysts is contrasted to that of larger ribozymes, such as the group I intron.
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    MAGNETIC RESONANCE STUDIES OF THE BACTERIORHODOPSIN PUMP CYCLE (2002)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 31 (2002), S. 73-95 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Active transport requires the alternation of substrate uptake and release with a switch in the access of the substrate binding site to the two sides of the membrane. Both the transfer and switch aspects of the photocycle have been subjects of magnetic resonance studies in bacteriorhodopsin. The results for ion transfer indicate that the Schiff base of the chromophore is hydrogen bonded before, during, and after its deprotonation. This suggests that the initial complex counterion of the Schiff base decomposes in such a way that the Schiff base carries its immediate hydrogen-bonding partner with it as it rotates during the first half of the photocycle. If so, bacteriorhodopsin acts as an inward-directed hydroxide pump rather than as an outward-directed proton pump. The studies of the access switch explore both protein-based and chromophore-based mechanisms. Combined with evidence from functional studies of mutants and other forms of spectroscopy, the results suggest that maintaining access to the extracellular side of the protein after photoisomerization involves twisting of the chromophore and that the decisive switch in access to the cytoplasmic side results from relaxation of the chromophore when the constraints on the Schiff base are released by decomposition of the complex counterion.
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    PIP2 AND PROTEINS: Interactions, Organization, and Information Flow (2002)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 31 (2002), S. 151-175 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract We review the physical properties of phosphatidylinositol 4,5-bisphosphate (PIP2) that determine both its specific interactions with protein domains of known structure and its nonspecific electrostatic sequestration by unstructured domains. Several investigators have postulated the existence of distinct pools of PIP2 within the cell to account for the myriad functions of this lipid. Recent experimental work indicates certain regions of the plasma membrane-membrane ruffles and nascent phagosomes-do indeed concentrate PIP2. We consider two mechanisms that could account for this phenomenon: local synthesis and electrostatic sequestration. We conclude by considering the hypothesis that proteins such as MARCKS bind a significant fraction of the PIP2 in a cell, helping to sequester it in lateral membrane domains, then release this lipid in response to local signals such as an increased concentration of Ca++/calmodulin or activation of protein kinase C.
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    STRUCTURAL AND THERMODYNAMIC CORRELATES OF T CELL SIGNALING (2002)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 31 (2002), S. 121-149 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract The first crystal structures of intact T cell receptors (TCRs) bound to class I peptide-MHC (pMHCs) antigens were determined in 1996. Since then, further structures of class I TCR/pMHC complexes have explored the degree of structural variability in the TCR-pMHC system and the structural basis for positive and negative selection. The recent determination of class II and allogeneic class I TCR/pMHC structures, as well as those of accessory molecules (e.g., CD3), has pushed our knowledge of TCR/pMHC interactions into new realms, shedding light on clinical pathologies, such as graft rejection and graft-versus-host disease. Furthermore, the determination of coreceptor structures lays the foundation for a more comprehensive structural description of the supramolecular TCR signaling events and those assemblies that arise in the immunological synapse. While these telling photodocumentaries of the TCR/pMHC interaction are composed mainly from static crystal structures, a full description of the biological snapshots in T cell signaling requires additional analytical methods that record the dynamics of the process. To this end, surface plasmon resonance (SPR), isothermal titration calorimetry (ITC), and ultracentrifugation (UC) have furnished both affinities and kinetics of the TCR/pMHC association. In the past year, structural, biochemical, and molecular biological data describing TCR/pMHC interactions have sublimely coalesced into a burgeoning well of understanding that promises to deliver further insights into T cell recognition. The coming years will, through a more intimate union of structural and kinetic data, allow many pressing questions to be addressed, such as how TCR/pMHC ligation is affected by coreceptor binding and what is the mechanism of TCR signaling in both early and late stages of T cell engagement with antigen-presenting cells.
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    THE alpha-HELIX AND THE ORGANIZATION AND GATING OF CHANNELS (2002)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 31 (2002), S. 207-233 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract The structures of an increasing number of channels and other alpha-helical membrane proteins have been determined recently, including the KcsA potassium channel, the MscL mechanosensitive channel, and the AQP1 and GlpF members of the aquaporin family. In this chapter, the orientation and packing characteristics of bilayer-spanning helices are surveyed in integral membrane proteins. In the case of channels, alpha-helices create the sealed barrier that separates the hydrocarbon region of the bilayer from the permeation pathway for solutes. The helices surrounding the permeation pathway tend to be rather steeply tilted relative to the membrane normal and are consistently arranged in a right-handed bundle. The helical framework further provides a supporting scaffold for nonmembrane-spanning structures associated with channel selectivity. Although structural details remain scarce, the conformational changes associated with gating transitions between closed and open states of channels are reviewed, emphasizing the potential roles of helix-helix interactions in this process.
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    PRINCIPLES AND BIOPHYSICAL APPLICATIONS OF LANTHANIDE-BASED PROBES (2002)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 31 (2002), S. 275-302 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Using luminescent lanthanides, instead of conventional fluorophores, as donor molecules in resonance energy transfer measurements offers many technical advantages and opens up a wide range of new applications. Advantages include farther measurable distances (~100 A) with greater accuracy, insensitivity to incomplete labeling, and the ability to use generic relatively large labels, when necessary. Applications highlighted include the study of ion channels in living cells, protein-protein interaction in cells, DNA-protein complexes, and high-throughput screening assays to measure peptide dimerization associated with DNA transcription factors and ligand-receptor interactions.
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    URL: http://dx.doi.org/10.1146/annurev.biophys.31.101101.140927
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    SINGLE-PARTICLE IMAGING OF MACROMOLECULES BY CRYO-ELECTRON MICROSCOPY (2002)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 31 (2002), S. 303-319 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Cryo-electron microscopy (cryo-EM) of biological molecules in single-particle (i.e., unordered, nonaggregated) form is a new approach to the study of molecular assemblies, which are often too large and flexible to be amenable to X-ray crystallography. New insights into biological function on the molecular level are expected from cryo-EM applied to the study of such complexes "trapped" at different stages of their conformational changes and dynamical interactions. Important molecular machines involved in the fundamental processes of transcription, mRNA splicing, and translation are examples for successful applications of the new technique, combined with structural knowledge gained by conventional techniques of structure determination, such as X-ray crystallography and NMR.
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    URL: http://dx.doi.org/10.1146/annurev.biophys.31.082901.134202
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    RHODOPSIN: Insights from Recent Structural Studies (2002)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 31 (2002), S. 443-484 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract The recent report of the crystal structure of rhodopsin provides insights concerning structure-activity relationships in visual pigments and related G protein-coupled receptors (GPCRs). The seven transmembrane helices of rhodopsin are interrupted or kinked at multiple sites. An extensive network of interhelical interactions stabilizes the ground state of the receptor. The ligand-binding pocket of rhodopsin is remarkably compact, and several chromophore-protein interactions were not predicted from mutagenesis or spectroscopic studies. The helix movement model of receptor activation, which likely applies to all GPCRs of the rhodopsin family, is supported by several structural elements that suggest how light-induced conformational changes in the ligand-binding pocket are transmitted to the cytoplasmic surface. The cytoplasmic domain of the receptor includes a helical domain extending from the seventh transmembrane segment parallel to the bilayer surface. The cytoplasmic surface appears to be approximately large enough to bind to the transducin heterotrimer in a one-to-one complex. The structural basis for several unique biophysical properties of rhodopsin, including its extremely low dark noise level and high quantum efficiency, can now be addressed using a combination of structural biology and various spectroscopic methods. Future high-resolution structural studies of rhodopsin and other GPCRs will form the basis to elucidate the detailed molecular mechanism of GPCR-mediated signal transduction.
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    CONFORMATIONAL REGULATION OF INTEGRIN STRUCTURE AND FUNCTION (2002)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 31 (2002), S. 485-516 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Integrins are a structurally elaborate family of heterodimers that mediate divalent cation-dependent cell adhesion in a wide range of biological contexts. The inserted (I) domain binds ligand in the subset of integrins in which it is present. Its structure has been determined in two alternative conformations, termed open and closed. In striking similarity to signaling G proteins, rearrangement of a Mg2+-binding site is linked to large conformational movements in distant backbone regions. Mutations have been used to stabilize either the closed or open structures. These show that the snapshots of the open conformation seen only in the presence of a ligand or a ligand mimetic represent a high-affinity, ligand-binding conformation, whereas those of the closed conformation correspond to a low-affinity conformation. The C-terminal alpha-helix moves 10 A down the side of the domain in the open conformation. Locking in the conformation of the preceding loop is sufficient to increase affinity for ligand 9000-fold. This C-terminal "bell-rope" provides a mechanism for linkage to conformational movements in other domains. The transition from the closed to open conformation has been implicated in fast (〈1 s) regulation of integrin affinity in response to activation signals from inside the cell. Recent integrin structures and functional studies reveal interactions between beta-propeller, I, and I-like domains in the headpiece, and a critical role for integrin EGF domains in the stalk region. These studies suggest that the headpiece of the integrin faces down toward the membrane in the inactive conformation and extends upward in a "switchblade"-like opening motion upon activation. These long-range structural rearrangements of the entire integrin molecule involving multiple interdomain contacts appear closely linked to conformational changes in the I domain, which result in increased affinity and competence for ligand binding.
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    OPTICAL SINGLE TRANSPORTER RECORDING: Transport Kinetics in Microarrays of Membrane Patches (2003)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 32 (2003), S. 47-67 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Optical single transporter recording (OSTR) is an emerging technique for the fluorescence microscopic measurement of transport kinetics in membrane patches. Membranes are attached to transparent microarrays of cylindrical test compartments (TCs) ~0.1-100 mum in diameter and ~10-100 mum in depth. Transport across membrane patches that may contain single transporters or transporter populations is recorded by confocal microscopy. By these means transport of proteins through single nuclear pore complexes has been recorded at rates of 〈1 translocation/s. In addition to the high sensitivity in terms of measurable transport rates OSTR features unprecedented spatial selectivity and parallel processing. This article reviews the conceptual basis of OSTR and its realization. Applications to nuclear transport are summarized. The further development of OSTR is discussed and its extension to a diversity of transporters, including translocases and ATP-binding cassette (ABC) pumps, projected.
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    STRUCTURE AND FUNCTION OF NATURAL KILLER CELL SURFACE RECEPTORS* (2003)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 32 (2003), S. 93-114 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Since mid-1990, with cloning and identification of several families of natural killer (NK) receptors, research on NK cells began to receive appreciable attention. Determination of structures of NK cell surface receptors and their ligand complexes led to a fast growth in our understanding of the activation and ligand recognition by these receptors as well as their function in innate immunity. Functionally, NK cell surface receptors are divided into two groups, the inhibitory and the activating receptors. Structurally, they belong to either the immunoglobulin (Ig)-like receptor superfamily or the C-type lectin-like receptor (CTLR) superfamily. Their ligands are either members of class I major histocompatibility complexes (MHC) or homologs of class I MHC molecules. The inhibitory form of NK receptors provides the protective immunity through recognizing class I MHC molecules with self-peptides on healthy host cells. The activating, or the noninhibitory, NK receptors mediate the killing of tumor or virally infected cells through their specific ligand recognition. The structures of activating and inhibitory NK cell surface receptors and their complexes with the ligands determined to date, including killer immunoglobulin-like receptors (KIRs) and their complexes with HLA molecules, CD94, Ly49A, and its complex with H-2Dd, and NKG2D receptors and their complexes with class I MHC homologs, are reviewed here.
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    THE POWER AND PROSPECTS OF FLUORESCENCE MICROSCOPIES AND SPECTROSCOPIES (2003)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 32 (2003), S. 161-182 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Recent years have witnessed a renaissance of fluorescence microscopy techniques and applications, from live-animal multiphoton confocal microscopy to single-molecule fluorescence spectroscopy and imaging in living cells. These achievements have been made possible not so much because of improvements in microscope design, but rather because of development of new detectors, accessible continuous wave and pulsed laser sources, sophisticated multiparameter analysis on one hand, and the development of new probes and labeling chemistries on the other. This review tracks the lineage of ideas and the evolution of thinking that have led to the actual developments, and presents a comprehensive overview of the field, with emphasis put on our laboratory's interest in single-molecule microscopy and spectroscopy.
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    NEW INSIGHT INTO SITE-SPECIFIC RECOMBINATION FROM FLP RECOMBINASE-DNA STRUCTURES (2003)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 32 (2003), S. 135-159 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract The lamba integrase, or tyrosine-based family of site-specific recombinases, plays an important role in a variety of biological processes by inserting, excising, and inverting DNA segments. Flp, encoded by the yeast 2-mum plasmid, is the best-characterized eukaryotic member of this family and is responsible for maintaining the copy number of this plasmid. Over the past several years, structural and biochemical studies have shed light on the details of a common catalytic scheme utilized by these enzymes with interesting variations under different biological contexts. The emergence of new Flp structures and solution data provides insights not only into its unique mechanism of active site assembly and activity regulation but also into the specific contributions of certain protein residues to catalysis.
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    X-RAY CRYSTALLOGRAPHIC ANALYSIS OF LIPID-PROTEIN INTERACTIONS IN THE BACTERIORHODOPSIN PURPLE MEMBRANE* (2003)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 32 (2003), S. 285-310 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract The past decade has witnessed increasingly detailed insights into the structural mechanism of the bacteriorhodopsin photocycle. Concurrently, there has been much progress within our knowledge pertaining to the lipids of the purple membrane, including the discovery of new lipids and the overall effort to localize and identify each lipid within the purple membrane. Therefore, there is a need to classify this information to generalize the findings. We discuss the properties and roles of haloarchaeal lipids and present the structural data as individual case studies. Lipid-protein interactions are discussed in the context of structure-function relationships. A brief discussion of the possibility that bacteriorhodopsin functions as a light-driven inward hydroxide pump rather than an outward proton pump is also presented.
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    URL: http://dx.doi.org/10.1146/annurev.biophys.32.110601.142516
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    THE CRYSTALLOGRAPHIC MODEL OF RHODOPSIN AND ITS USE IN STUDIES OF OTHER G PROTEIN-COUPLED RECEPTORS (2003)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 32 (2003), S. 375-397 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract G protein-coupled receptors (GPCRs) are integral membrane proteins that respond to environmental signals and initiate signal transduction pathways activating cellular processes. Rhodopsin is a GPCR found in rod cells in retina where it functions as a photopigment. Its molecular structure is known from cryo-electron microscopic and X-ray crystallographic studies, and this has reshaped many structure/function questions important in vision science. In addition, this first GPCR structure has provided a structural template for studies of other GPCRs, including many known drug targets. After presenting an overview of the major structural elements of rhodopsin, recent literature covering the use of the rhodopsin structure in analyzing other GPCRs will be summarized. Use of the rhodopsin structural model to understand the structure and function of other GPCRs provides strong evidence validating the structural model.
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    PROTEOME ANALYSIS BY MASS SPECTROMETRY* (2003)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 32 (2003), S. 399-424 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract The coupling of high-performance mass spectrometry instrumentation with highly efficient chromatographic and electrophoretic separations has enabled rapid qualitative and quantitative analysis of thousands of proteins from minute samples of biological materials. Here, we review recent progress in the development and application of mass spectrometry-based techniques for the qualitative and quantitative analysis of global proteome samples derived from whole cells, tissues, or organisms. Techniques such as multidimensional peptide and protein separations coupled with mass spectrometry, accurate mass measurement of peptides from global proteome digests, and mass spectrometric characterization of intact proteins hold great promise for characterization of highly complex protein mixtures. Advances in chemical tagging and isotope labeling techniques have enabled quantitative analysis of proteomes, and highly specific isolation strategies have been developed aimed at selective analysis of posttranslationally modified proteins.
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    RESIDUAL DIPOLAR COUPLINGS IN NMR STRUCTURE ANALYSIS*1 (2004)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 33 (2004), S. 387-413 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Residual dipolar couplings (RDCs) have recently emerged as a new tool in nuclear magnetic resonance (NMR) with which to study macromolecular structure and function in a solution environment. RDCs are complementary to the more conventional use of NOEs to provide structural information. While NOEs are local-distance restraints, RDCs provide long-range orientational information. RDCs are now widely utilized in structure calculations. Increasingly, they are being used in novel applications to address complex issues in structural biology such as the accurate determination of the global structure of oligonucleotides and the relative orientation of protein domains. This review briefly describes the theory and methods for obtaining RDCs and then describes the range of biological applications where RDCs have been used.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.33.110502.140306
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    MODEL SYSTEMS, LIPID RAFTS, AND CELL MEMBRANES1 (2004)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 33 (2004), S. 269-295 
    Details
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Views of how cell membranes are organized are presently changing. The lipid bilayer that constitutes these membranes is no longer understood to be a homogeneous fluid. Instead, lipid assemblies, termed rafts, have been introduced to provide fluid platforms that segregate membrane components and dynamically compartmentalize membranes. These assemblies are thought to be composed mainly of sphingolipids and cholesterol in the outer leaflet, somehow connected to domains of unknown composition in the inner leaflet. Specific classes of proteins are associated with the rafts. This review critically analyzes what is known of phase behavior and liquid-liquid immiscibility in model systems and compares these data with what is known of domain formation in cell membranes.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.32.110601.141803
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    SALMONELLA INTERACTIONS WITH HOST CELLS: Type III Secretion at Work (2001)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Cell and Developmental Biology 17 (2001), S. 53-86 
    Details
    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Abstract The bacterial pathogen Salmonella enterica has evolved a very sophisticated functional interface with its vertebrate hosts. At the center of this interface is a specialized organelle, the type III secretion system, that directs the translocation of bacterial proteins into the host cell. Salmonella spp. encode two such systems that deliver a remarkable array of bacterial proteins capable of modulating a variety of cellular functions, including actin cytoskeleton dynamics, nuclear responses, and endocytic trafficking. Many of these bacterial proteins operate by faithful mimicry of host proteins, in some cases representing the result of extensive molecular tinkering and convergent evolution. The coordinated action of these type III secreted proteins secures the replication and survival of the bacteria avoiding overt damage to the host. The study of this remarkable pathogen is not only illuminating general paradigms in microbial pathogenesis but is also providing valuable insight into host cell functions.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.cellbio.17.1.53
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    PATTERNING MECHANISMS CONTROLLING VERTEBRATE LIMB DEVELOPMENT (2001)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Cell and Developmental Biology 17 (2001), S. 87-132 
    Details
    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Abstract Vertebrate limb buds are embryonic structures for which much molecular and cellular data are known regarding the mechanisms that control pattern formation during development. Specialized regions of the developing limb bud, such as the zone of polarizing activity (ZPA), the apical ectodermal ridge (AER), and the non-ridge ectoderm, direct and coordinate the development of the limb bud along the anterior-posterior (AP), dorsal-ventral (DV), and proximal-distal (PD) axes, giving rise to a stereotyped pattern of elements well conserved among tetrapods. In recent years, specific gene functions have been shown to mediate the organizing and patterning activities of the ZPA, the AER, and the non-ridge ectoderm. The analysis of these gene functions has revealed the existence of complex interactions between signaling pathways operated by secreted factors of the HH, TGF-beta/BMP, WNT, and FGF superfamilies, which interact with many other genetic networks to control limb positioning, outgrowth, and patterning. The study of limb development has helped to establish paradigms for the analysis of pattern formation in many other embryonic structures and organs.
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    URL: http://dx.doi.org/10.1146/annurev.cellbio.17.1.87
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    IDENTIFICATION OF SELF THROUGH TWO-DIMENSIONAL CHEMISTRY AND SYNAPSES (2001)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Cell and Developmental Biology 17 (2001), S. 133-157 
    Details
    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Abstract Cells in the immune and nervous systems communicate through informational synapses. The two-dimensional chemistry underlying the process of synapse formation is beginning to be explored using fluorescence imaging and mechanical techniques. Early analysis of two-dimensional kinetic rates (kon and koff) and equilibrium constants (Kd) provides a number of biological insights. First, there are two regimes for adhesion-one disordered with slow kon and the other self-ordered with 104-fold faster kon. Despite huge variation in two-dimensional kon, the two-dimensional koff is like koff in solution, and two-dimensional koff is more closely related to intrinsic properties of the interaction than the two-dimensional kon. Thus difference in koff can be used to set signaling thresholds. Early signaling complexes are compartmentalized to generate synergistic signaling domains. Immune antigen receptor components have a role in neural synapse editing. This suggests significant parallels in informational synapse formation based on common two-dimensional chemistry and signaling strategies.
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    URL: http://dx.doi.org/10.1146/annurev.cellbio.17.1.133
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    POLARIZED CELL GROWTH IN HIGHER PLANTS (2001)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Cell and Developmental Biology 17 (2001), S. 159-187 
    Details
    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Abstract Pollen tubes and root hairs are highly elongated, cylindrically shaped cells whose polarized growth permits them to explore the environment for the benefit of the entire plant. Root hairs create an enormous surface area for the uptake of water and nutrients, whereas pollen tubes deliver the sperm cells to the ovule for fertilization. These cells grow exclusively at the apex and at prodigious rates (in excess of 200 nm/s for pollen tubes). Underlying this rapid growth are polarized ion gradients and fluxes, turnover of cytoskeletal elements (actin microfilaments), and exocytosis and endocytosis of membrane vesicles. Intracellular gradients of calcium and protons are spatially localized at the growing apex; inward fluxes of these ions are apically directed. These gradients and fluxes oscillate with the same frequency as the oscillations in growth rate but not with the same phase. Actin microfilaments, which together with myosin generate reverse fountain streaming, undergo rapid turnover in the apical domain, possibly being regulated by key actin-binding proteins, e.g., profilin, villin, and ADF/cofilin, in concert with the ion gradients. Exocytosis of vesicles at the apex, also dependent on the ion gradients, provides precursor material for the continuously expanding cell wall of the growing cell. Elucidation of the interactions and of the dynamics of these different components is providing unique insight into the mechanisms of polarized growth.
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    URL: http://dx.doi.org/10.1146/annurev.cellbio.17.1.159
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    BOUNDARIES IN DEVELOPMENT: Formation and Function (2001)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Cell and Developmental Biology 17 (2001), S. 189-214 
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    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Abstract Developing organisms may contain billions of cells destined to differentiate in numerous different ways. One strategy organisms use to simplify the orchestration of development is the separation of cell populations into distinct functional units. Our expanding knowledge of boundary formation and function in different systems is beginning to reveal general principles of this process. Fields of cells are subdivided by the interpretation of morphogen gradients, and these subdivisions are then maintained and refined by local cell-cell interactions. Sharp and stable separation between cell populations requires special mechanisms to keep cells segregated, which in many cases appear to involve the regulation of cell affinity. Once cell populations become distinct, specialized cells are often induced along the borders between them. These boundary cells can then influence the patterning of surrounding cells, which can result in progressively finer subdivisions of a tissue. Much has been learned about the signaling pathways that establish boundaries, but a key challenge for the future remains to elucidate the cellular and molecular mechanisms that actually keep cell populations separated.
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    URL: http://dx.doi.org/10.1146/annurev.cellbio.17.1.189
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    A CELL BIOLOGICAL PERSPECTIVE ON ALZHEIMER'S DISEASE (2002)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Cell and Developmental Biology 18 (2002), S. 25-51 
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    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Abstract The amyloid precursor protein and the proteases cleaving this protein are important players in the pathogenesis of Alzheimer's disease via the generation of the amyloid peptide. Physiologically, the amyloid precursor protein is implied in axonal vesicular trafficking and the proteases are implicated in developmentally important signaling pathways, most significantly those involving regulated intramembrane proteolysis or RIP. We discuss the cell biology behind the amyloid and tangle hypothesis for Alzheimer's disease, drawing on the many links to the fields of cell biology and developmental biology that have been established in the recent years.
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    URL: http://dx.doi.org/10.1146/annurev.cellbio.18.020402.142302
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    TYPE III PROTEIN SECRETION IN YERSINIA SPECIES (2002)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Cell and Developmental Biology 18 (2002), S. 107-133 
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    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Abstract The type III mechanism of protein secretion is a pathogenic strategy shared by a number of gram-negative pathogens of plants and animals that has evolved in order to inject virulence proteins into the cytosol of target eukaryotic cells. The pathogens of the Yersinia genus represent a model system where much progress has been made in understanding this secretion pathway. Herein, we review what has been recently learned in yersiniae about the various environmental signals that induce type III secretion, how the synthesis of secretion substrates is regulated, and how such a diverse group of proteins is recognized as a substrate for secretion.
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    URL: http://dx.doi.org/10.1146/annurev.cellbio.18.012502.105912
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    BREAK INS AND BREAK OUTS: Viral Interactions with the Cytoskeleton of Mammalian Cells (2002)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Cell and Developmental Biology 18 (2002), S. 135-161 
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    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Abstract The host cytoskeleton plays important roles in the entry, replication, and egress of viruses. An assortment of viruses hijack cellular motor proteins to move on microtubules toward the cell interior during the entry process; others reverse this transport during egress to move assembling virus particles toward the plasma membrane. Polymerization of actin filaments is sometimes used to propel viruses from cell to cell, while many viruses induce the destruction of select cytoskeletal filaments apparently to effect efficient egress. Indeed, the tactics used by any given virus to achieve its infectious life cycle are certain to involve multiple cytoskeletal interactions. Understanding these interactions, and their orchestration during viral infections, is providing unexpected insights into basic virology, viral pathogenesis, and the biology of the cytoskeleton.
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    URL: http://dx.doi.org/10.1146/annurev.cellbio.18.012502.105920
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    CHROMOSOME-MICROTUBULE INTERACTIONS DURING MITOSIS (2002)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Cell and Developmental Biology 18 (2002), S. 193-219 
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    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Abstract Spindle microtubules interact with mitotic chromosomes, binding to their kinetochores to generate forces that are important for accurate chromosome segregation. Motor enzymes localized both at kinetochores and spindle poles help to form the biologically significant attachments between spindle fibers and their cargo, but microtubule-associated proteins without motor activity contribute to these junctions in important ways. This review examines the molecules necessary for chromosome-microtubule interaction in a range of well-studied organisms, using biological diversity to identify the factors that are essential for organized chromosome movement. We conclude that microtubule dynamics and the proteins that control them are likely to be more important for mitosis than the current enthusiasm for motor enzymes would suggest.
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    URL: http://dx.doi.org/10.1146/annurev.cellbio.18.032002.132412
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    THE CHLAMYDIAL INCLUSION: Escape from the Endocytic Pathway1 (2002)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Cell and Developmental Biology 18 (2002), S. 221-245 
    Details
    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Abstract Chlamydiae, bacterial obligate intracellular pathogens, are the etiologic agents of several human diseases. A large part of the chlamydial intracellular survival strategy involves the formation of a unique organelle called the inclusion that provides a protected site within which they replicate. The chlamydial inclusion is effectively isolated from endocytic pathways but is fusogenic with a subset of exocytic vesicles that deliver sphingomyelin from the Golgi apparatus to the plasma membrane. A combination of host and parasite functions contribute to the biogenesis of this compartment. Establishment of the mature inclusion is accompanied by the insertion of multiple chlamydial proteins, suggesting that chlamydiae actively modify the inclusion to define its interactions with the eukaryotic host cell. Despite being sequestered within a membrane-bound vacuole, chlamydiae clearly communicate with and manipulate the host cell from within this privileged intracellular niche.
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    URL: http://dx.doi.org/10.1146/annurev.cellbio.18.012502.105845
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    MOLECULAR MECHANISMS OF EPITHELIAL MORPHOGENESIS (2002)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Cell and Developmental Biology 18 (2002), S. 463-493 
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    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Abstract Epithelial morphogenesis comprises the various processes by which epithelia contribute to organ formation and body shape. These complex and diverse events play a central role in animal development and regeneration. Recently, the characterization of some of the molecular mechanisms involved in epithelial morphogenesis has provided an abundance of new information on the role and regulation of the cytoskeleton, cell-cell adhesion, and cell-matrix adhesion in these processes. In this review, we discuss our current understanding of the molecular mechanisms driving cell shape changes, cell intercalation, fusion of epithelia, ingression, egression, and cell migration. Our discussion is mostly focused on results from Drosophila and mammalian tissue culture but also draws on the insights gained from other organisms.
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    URL: http://dx.doi.org/10.1146/annurev.cellbio.18.022602.131838
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    GOLGI ARCHITECTURE AND INHERITANCE (2002)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Cell and Developmental Biology 18 (2002), S. 379-420 
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    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Abstract Golgi inheritance proceeds via sequential biogenesis and partitioning phases. Although little is known about Golgi growth and replication (biogenesis), ultrastructural and fluorescence analyses have provided a detailed, though still controversial, perspective of Golgi partitioning during mitosis in mammalian cells. Partitioning requires the fragmentation of the juxtanuclear ribbon of interconnected Golgi stacks into a multitude of tubulovesicular clusters. This process is choreographed by a cohort of mitotic kinases and an inhibition of heterotypic and homotypic Golgi membrane-fusion events. Our model posits that accurate partitioning occurs early in mitosis by the equilibration of Golgi components on either side of the metaphase plate. Disseminated Golgi components then coalesce to regenerate Golgi stacks during telophase. Semi-intact cell and cell-free assays have accurately recreated these processes and allowed their molecular dissection. This review attempts to integrate recent findings to depict a more coherent, synthetic molecular picture of mitotic Golgi fragmentation and reassembly. Of particular importance is the emerging concept of a highly regulated and dynamic Golgi structural matrix or template that interfaces with cargo receptors, Golgi enzymes, Rab-GTPases, and SNAREs to tightly couple biosynthetic transport to Golgi architecture. This structural framework may be instructive for Golgi biogenesis and may encode sufficient information to ensure accurate Golgi inheritance, thereby helping to resolve some of the current discrepancies between different workers.
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    URL: http://dx.doi.org/10.1146/annurev.cellbio.18.030602.133733
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    CORTICAL NEURONAL MIGRATION MUTANTS SUGGEST SEPARATE BUT INTERSECTING PATHWAYS (2004)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Cell and Developmental Biology 20 (2004), S. 593-618 
    Details
    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: During brain development, neurons migrate great distances from proliferative zones to generate the cortical gray matter. A series of studies has identified genes that are critical for migration and targeting of neurons to specific brain regions. These genes encode three basic groups of proteins and produce three distinct phenotypes. The first group encodes cytoskeletal molecules and produces graded and dosage-dependent effects, with a significant amount of functional redundancy. This group also appears to play important roles during the initiation and ongoing progression of neuronal movement. The second group encodes signaling molecules for which homozygous mutations lead to an inverted cortex. In addition, this group is responsible for movement of neurons through anatomic boundaries to specific cortical layers. The third group encodes enzymatic regulators of glycosylation and appears to delineate where neuronal migration will arrest. There is significant cross-talk among these different groups of molecules, suggesting possible points of pathway convergence.
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    URL: http://dx.doi.org/10.1146/annurev.cellbio.20.082503.103047
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    FUNDAMENTALS OF PLANARIAN REGENERATION (2004)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Cell and Developmental Biology 20 (2004), S. 725-757 
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    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: The principles underlying regeneration in planarians have been explored for over 100 years through surgical manipulations and cellular observations. Planarian regeneration involves the generation of new tissue at the wound site via cell proliferation (blastema formation), and the remodeling of pre-existing tissues to restore symmetry and proportion (morphallaxis). Because blastemas do not replace all tissues following most types of injuries, both blastema formation and morphallaxis are needed for complete regeneration. Here we discuss a proliferative cell population, the neoblasts, that is central to the regenerative capacities of planarians. Neoblasts may be a totipotent stem-cell population capable of generating essentially every cell type in the adult animal, including themselves. The population properties of the neoblasts and their descendants still await careful elucidation. We identify the types of structures produced by blastemas on a variety of wound surfaces, the principles guiding the reorganization of pre-existing tissues, and the manner in which scale and cell number proportions between body regions are restored during regeneration.
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    URL: http://dx.doi.org/10.1146/annurev.cellbio.20.010403.095114
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    MEMBRANE TRAFFICKING IN PLANTS (2004)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Cell and Developmental Biology 20 (2004), S. 481-504 
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    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Plant membrane trafficking shares many features with other eukaryotic organisms, including the machinery for vesicle formation and fusion. However, the plant endomembrane system lacks an ER-Golgi intermediate compartment, has numerous Golgi stacks and several types of vacuoles, and forms a transient compartment during cell division. ER-Golgi trafficking involves bulk flow and efficient recycling of H/KDEL-bearing proteins. Sorting in the Golgi stacks separates bulk flow to the plasma membrane from receptor-mediated trafficking to the lytic vacuole. Cargo for the protein storage vacuole is delivered from the endoplasmic reticulum (ER), cis-Golgi, and trans-Golgi. Endocytosis includes recycling of plasma membrane proteins from early endosomes. Late endosomes appear identical with the multivesiculate prevacuolar compartment that lies on the Golgi-vacuole trafficking pathway. In dividing cells, homotypic fusion of Golgi-derived vesicles forms the cell plate, which expands laterally by targeted vesicle fusion at its margin, eventually fusing with the plasma membrane.
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    URL: http://dx.doi.org/10.1146/annurev.cellbio.20.082503.103057
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    DORSAL-VENTRAL PATTERNING AND NEURAL INDUCTION IN XENOPUS EMBRYOS (2004)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Cell and Developmental Biology 20 (2004), S. 285-308 
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    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: We review the current status of research in dorsal-ventral (D-V) patterning in vertebrates. Emphasis is placed on recent work on Xenopus, which provides a paradigm for vertebrate development based on a rich heritage of experimental embryology. D-V patterning starts much earlier than previously thought, under the influence of a dorsal nuclear -Catenin signal. At mid-blastula two signaling centers are present on the dorsal side: The prospective neuroectoderm expresses bone morphogenetic protein (BMP) antagonists, and the future dorsal endoderm secretes Nodal-related mesoderm-inducing factors. When dorsal mesoderm is formed at gastrula, a cocktail of growth factor antagonists is secreted by the Spemann organizer and further patterns the embryo. A ventral gastrula signaling center opposes the actions of the dorsal organizer, and another set of secreted antagonists is produced ventrally under the control of BMP4. The early dorsal -Catenin signal inhibits BMP expression at the transcriptional level and promotes expression of secreted BMP antagonists in the prospective central nervous system (CNS). In the absence of mesoderm, expression of Chordin and Noggin in ectoderm is required for anterior CNS formation. FGF (fibroblast growth factor) and IGF (insulin-like growth factor) signals are also potent neural inducers. Neural induction by anti-BMPs such as Chordin requires mitogen-activated protein kinase (MAPK) activation mediated by FGF and IGF. These multiple signals can be integrated at the level of Smad1. Phosphorylation by BMP receptor stimulates Smad1 transcriptional activity, whereas phosphorylation by MAPK has the opposite effect. Neural tissue is formed only at very low levels of activity of BMP-transducing Smads, which require the combination of both low BMP levels and high MAPK signals. Many of the molecular players that regulate D-V patterning via regulation of BMP signaling have been conserved between Drosophila and the vertebrates.
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    URL: http://dx.doi.org/10.1146/annurev.cellbio.20.011403.154124
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    NUCLEAR RECEPTORS IN MACROPHAGE BIOLOGY: At the Crossroads of Lipid Metabolism and Inflammation (2004)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Cell and Developmental Biology 20 (2004), S. 455-480 
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    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Macrophages are essential modulators of lipid metabolism and the innate immune system. Lipid and inflammatory pathways induced in activated macrophages are central to the pathogenesis of human diseases including atherosclerosis. Recent work has shown that expression of genes involved in lipid uptake and cholesterol efflux in macrophages is controlled by peroxisome proliferator-activated receptors (PPARs) and liver X receptors (LXRs). Other studies have implicated these same receptors in the modulation of macrophage inflammatory gene expression. Together, these observations position PPARs and LXRs at the crossroads of lipid metabolism and inflammation and suggest that these receptors may serve to integrate these pathways in the control of macrophage gene expression. In this review, we summarize recent work that has advanced our understanding of the roles of PPARs and LXRs in macrophage biology and discuss the implication of these results for cardiovascular physiology and disease.
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    URL: http://dx.doi.org/10.1146/annurev.cellbio.20.012103.134432
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    BI-DIRECTIONAL PROTEIN TRANSPORT BETWEEN THE ER AND GOLGI (2004)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Cell and Developmental Biology 20 (2004), S. 87-123 
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    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: The endoplasmic reticulum (ER) and the Golgi comprise the first two steps in protein secretion. Vesicular carriers mediate a continuous flux of proteins and lipids between these compartments, reflecting the transport of newly synthesized proteins out of the ER and the retrieval of escaped ER residents and vesicle machinery. Anterograde and retrograde transport is mediated by distinct sets of cytosolic coat proteins, the COPII and COPI coats, respectively, which act on the membrane to capture cargo proteins into nascent vesicles. We review the mechanisms that govern coat recruitment to the membrane, cargo capture into a transport vesicle, and accurate delivery to the target organelle.
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    URL: http://dx.doi.org/10.1146/annurev.cellbio.20.010403.105307
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    ASYMMETRIC CELL DIVISION IN C. ELEGANS: Cortical Polarity and Spindle Positioning (2004)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Cell and Developmental Biology 20 (2004), S. 427-453 
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    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: The one-cell Caenorhabditis elegans embryo divides asymmetrically into a larger and smaller blastomere, each with a different fate. How does such asymmetry arise? The sperm-supplied centrosome establishes an axis of polarity in the embryo that is transduced into the establishment of anterior and posterior cortical domains. These cortical domains define the polarity of the embryo, acting upstream of the PAR proteins. The PAR proteins, in turn, determine the subsequent segregation of fate determinants and the plane of cell division. We address how cortical asymmetry could be established, relying on data from C. elegans and other polarized cells, as well as from applicable models. We discuss how cortical polarity influences spindle position to accomplish an asymmetric division, presenting the current models of spindle orientation and anaphase spindle displacement. We focus on asymmetric cell division as a function of the actin and microtubule cytoskeletons, emphasizing the cell biology of polarity.
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    URL: http://dx.doi.org/10.1146/annurev.cellbio.19.111301.113823
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