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  • Wiley-Blackwell  (51,683)
  • Springer Nature  (47,666)
  • Annual Reviews
  • Periodicals Archive Online (PAO)
  • 2020-2023  (37)
  • 1995-1999  (88,644)
  • 1945-1949  (25,035)
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  • 1
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    Resource partitioning of phytoplankton metabolites that support bacterial heterotrophy (2020)
    Springer Nature
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Ferrer-González, F. X., Widner, B., Holderman, N. R., Glushka, J., Edison, A. S., Kujawinski, E. B., & Moran, M. A. Resource partitioning of phytoplankton metabolites that support bacterial heterotrophy. ISME Journal, (2020), doi:10.1038/s41396-020-00811-y.
    Description: The communities of bacteria that assemble around marine microphytoplankton are predictably dominated by Rhodobacterales, Flavobacteriales, and families within the Gammaproteobacteria. Yet whether this consistent ecological pattern reflects the result of resource-based niche partitioning or resource competition requires better knowledge of the metabolites linking microbial autotrophs and heterotrophs in the surface ocean. We characterized molecules targeted for uptake by three heterotrophic bacteria individually co-cultured with a marine diatom using two strategies that vetted the exometabolite pool for biological relevance by means of bacterial activity assays: expression of diagnostic genes and net drawdown of exometabolites, the latter detected with mass spectrometry and nuclear magnetic resonance using novel sample preparation approaches. Of the more than 36 organic molecules with evidence of bacterial uptake, 53% contained nitrogen (including nucleosides and amino acids), 11% were organic sulfur compounds (including dihydroxypropanesulfonate and dimethysulfoniopropionate), and 28% were components of polysaccharides (including chrysolaminarin, chitin, and alginate). Overlap in phytoplankton-derived metabolite use by bacteria in the absence of competition was low, and only guanosine, proline, and N-acetyl-d-glucosamine were predicted to be used by all three. Exometabolite uptake pattern points to a key role for ecological resource partitioning in the assembly marine bacterial communities transforming recent photosynthate.
    Description: This work was supported by grants from the Gordon and Betty Moore Foundation (5503) and the National Science Foundation (IOS-1656311) to MAM, ASE, and EBK, and by the Simons Foundation grant 542391 to MAM within the Principles of Microbial Ecosystems (PriME) Collaborative.
    Repository Name: Woods Hole Open Access Server
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  • 2
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    Exploring Employee Perceptions towards Smart Working during the COVID-19 Pandemic: a Comparative Analysis of Two Italian Public Research Organizations (2021)
    Springer Nature
    Details
    Publication Date: 2022-03-16
    Description: Of all the socio-economic changes caused by the Covid-19 pandemic, the disruption to workforce organizations will probably leave the largest indelible mark. The way work will be organized in the future will be closely linked to the experience of work-ing under the same institution’s response to the pandemic. This paper aims to fill the gap in knowledge about smart working (SW) in public organizations, with a focus on the experience of the employees of two Italian research organizations, CNR and INGV. Analysing primary data, it explored and assessed how SW had been experi-enced following the implementation of governmental measures aimed at limiting the spread of COVID-19
    Description: Published
    Description: 815–833
    Description: 2TM. Divulgazione Scientifica
    Description: JCR Journal
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  • 3
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    Combining audio and visual displays to highlight temporal and spatial seismic patterns (2021)
    Springer Nature
    Details
    Publication Date: 2022-03-16
    Description: Data visualization, and to a lesser extent data sonification, are classic tools to the scientific community. However, these two approaches are very rarely combined, although they are highly complementary: our visual system is good at recognizing spatial patterns, whereas our auditory system is better tuned for temporal patterns. In this article, data representation methods are proposed that combine visualization, sonification, and spatial audio techniques, in order to optimize the user’s perception of spatial and temporal patterns in a single display, to increase the feeling of immersion, and to take advantage of multimodal integration mechanisms. Three seismic data sets are used to illustrate the methods, covering different physical phenomena, time scales, spatial distributions, and spatio-temporal dynamics. The methods are adapted to the specificities of each data set, and to the amount of information that the designer wants to display. This leads to further developments, namely the use of audification with two time scales, the switch from pure audification to time-modulated noise, and the switch from pure audification to sonic icons. First user feedback from live demonstrations indicates that the methods presented in this article seem to enhance the perception of spatio-temporal patterns, which is a key parameter to the understanding of seismically active systems, and a step towards apprehending the processes that drive this activity.
    Description: Published
    Description: 125–142
    Description: 7T. Variazioni delle caratteristiche crostali e "precursori"
    Description: JCR Journal
    Keywords: 04.06. Seismology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 4
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    Deep water inflow slowed offshore expansion of the West Antarctic Ice Sheet at the Eocene-Oligocene transition (2022)
    Springer Nature
    In:  EPIC3Nature Communications Earth & Environment, Springer Nature, 3(1)
    Details
    Publication Date: 2022-02-21
    Description: The stability of the West Antarctic Ice Sheet is threatened by the incursion of warm Circumpolar Deepwater which flows southwards via cross-shelf troughs towards the coast there melting ice shelves. However, the onset of this oceanic forcing on the development and evolution of the West Antarctic Ice Sheet remains poorly understood. Here, we use single- and multichannel seismic reflection profiles to investigate the architecture of a sediment body on the shelf of the Amundsen Sea Embayment. We estimate the formation age of this sediment body to be around the Eocene-Oligocene Transition and find that it possesses the geometry and depositional pattern of a plastered sediment drift. We suggest this indicates a southward inflow of deep water which probably supplied heat and, thus, prevented West Antarctic Ice Sheet advance beyond the coast at this time. We conclude that the West Antarctic Ice Sheet has likely experienced a strong oceanic influence on its dynamics since its initial formation.
    Repository Name: EPIC Alfred Wegener Institut
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  • 5
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    Short-term clustering modeling of seismicity in Eastern Aegean Sea (Greece): a retrospective forecast test of the 2017 Mw = 6.4 Lesvos, 2017 Mw = 6.6 Kos and 2020 Mw = 7.0 Samos earthquake sequences (2021)
    Springer Nature
    Details
    Publication Date: 2021-11-03
    Description: Short-term earthquake clustering properties in the Eastern Aegean Sea (Greece) area investigated through the application of an epidemic type stochastic model (Epidemic Type Earthquake Sequence; ETES). The computations are performed in an earthquake catalog covering the period 2008 to 2020 and including 2332 events with a completeness threshold of Mc = 3.1 and separated into two subcatalogs. The first subcatalog is employed for the learning period, which is between 2008/01/01 and 2016/12/31 (N = 1197 earthquakes), and used for the model’s parameters estimation. The second subcatalog from 2017/01/01 to 2020/11/10 (1135 earthquakes), in which the sequences of 2017 Mw = 6.4 Lesvos, 2017 Mw = 6.6 Kos and 2020 Mw = 7.0 Samos main shocks are included, and used for a retrospective forecast testing based on the constructed model. The estimated model parameters imply a swarm like behavior, indicating the ability of earthquakes of small to moderate magnitude above Mc to produce their own offsprings, along with the stronger earthquakes. The retrospective evaluation of the model is examined in the three aftershock sequences, where lack of foreshocks resulted in low predictability of the mainshocks, with estimated daily probabilities around 10– 5. Immediately after the mainshocks occurrence the model adjusts with notable resemblance between the expected and observed aftershock rates, particularly for earthquakes with M ≥ 3.5.
    Description: Published
    Description: 1085–1099
    Description: 6T. Studi di pericolosità sismica e da maremoto
    Description: JCR Journal
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  • 6
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    Simulation of non-stationary stochastic ground motions based on recent Italian earthquakes (2021)
    Springer Nature
    Details
    Publication Date: 2021-11-29
    Description: This work presents an up-to-date model for the simulation of non-stationary ground motions, including several novelties compared to the original study of Sabetta and Pugliese (Bull Seism Soc Am 86:337–352, 1996). The selection of the input motion in the framework of earthquake engineering has become progressively more important with the growing use of nonlinear dynamic analyses. Regardless of the increasing availability of large strong motion databases, ground motion records are not always available for a given earthquake scenario and site condition, requiring the adoption of simulated time series. Among the different techniques for the generation of ground motion records, we focused on the methods based on stochastic simulations, considering the time- frequency decomposition of the seismic ground motion. We updated the non-stationary stochastic model initially developed in Sabetta and Pugliese (Bull Seism Soc Am 86:337–352, 1996) and later modified by Pousse et al. (Bull Seism Soc Am 96:2103–2117, 2006) and Laurendeau et al. (Nonstationary stochastic simulation of strong ground-motion time histories: application to the Japanese database. 15 WCEE Lisbon, 2012). The model is based on the S-transform that implicitly considers both the amplitude and frequency modulation. The four model parameters required for the simulation are: Arias intensity, significant duration, central frequency, and frequency bandwidth. They were obtained from an empirical ground motion model calibrated using the accelerometric records included in the updated Italian strong-motion database ITACA. The simulated accelerograms show a good match with the ground motion model prediction of several amplitude and frequency measures, such as Arias intensity, peak acceleration, peak velocity, Fourier spectra, and response spectra.
    Description: Published
    Description: 3287–3315
    Description: 5T. Sismologia, geofisica e geologia per l'ingegneria sismica
    Description: JCR Journal
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  • 7
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    Insights on the Italian Seismic Network from location uncertainties (2021)
    Springer Nature
    Details
    Publication Date: 2021-12-01
    Description: Probabilistic earthquake locations provide confidence intervals for the hypocentre solutions such as errors encountered in the position, the origin time, and in magnitude. If the relationship of the parameters relative to the local arrangement of the seismic network is considered, such as the node distance, the number of stations, the seismic gap, and the quality of phase readings), the uncertainties can then provide insights on the location capability of the network. In this paper, we collect the earthquake data recorded from the Italian Seismic Network for a time span of 5 years. The data pertain to three different catalogues according to the progressive refinement phases of the location procedure: automatic location, revised location, and published location. By means of spatial analysis,we assess the distribution of the location-related and network-related estimators across the study area. These estimators are subsequently combined to assess the existence of spatial correlations at a local scale. The results indicate that the Italian network is generally able to provide robust locations at the national scale and for smaller earthquakes, and the elongated shape of Italy (and of its network) does not cause systematic bias in the locations. However, we highlight the existence of subregions in which the performance of the network is weaker. At present, a unique 2D, 3-layer velocity model is used for the earthquake location procedure, and this could represent the main limitation for the improvement of the locations. Therefore, the assessment of locally optimized velocity models is the priority for the homogenization and the improvement of the Italian Seismic Network performance.
    Description: Published
    Description: 1061–1076
    Description: 1IT. Reti di monitoraggio e sorveglianza
    Description: JCR Journal
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  • 8
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    New trenching results along the İznik segment of the central strand of the North Anatolian Fault (Turkey): an integration with preexisting data (2021)
    Springer Nature
    Details
    Publication Date: 2021-12-06
    Description: This paper provides a new contribution to the construction of the complex and fragmentary mosaic of the Late Holocene earthquakes history of the İznik segment of the central strand of the North Anatolian Fault (CNAF) in Turkey. The CNAF clearly displays lower dextral slip rates with respect to the northern strand however, surface rupturing and large damaging earthquakes (M 〉 7) occurred in the past, leaving clear signatures in the built and natural environments. The association of these historical events to specific earthquake sources (e.g., Gemlik, İznik, or Geyve fault segments) is still a matter of debate. We excavated two trenches across the İznik fault trace near Mustafali, a village about 10 km WSW of İznik where the morphological fault scarp was visible although modified by agricultural activities. Radiocarbon and TL dating on samples collected from the trenches show that the displaced deposits are very recent and span the past 2 millennia at most. Evidence for four surface faulting events was found in the Mustafali trenches. The integration of these results with historical data and previous paleoseismological data yields an updated Late Holocene history of surface-rupturing earthquakes along the İznik Fault in 1855, 740 (715), 362, and 121 CE. Evidence for the large M7 + historical earthquake dated 1419 CE generally attributed to this fault, was not found at any trench site along the İznik fault nor in the subaqueous record. This unfit between paleoseismological, stratigraphic, and historical data highlights one more time the urge for extensive paleoseismological trenching and offshore campaigns because of the high potential to solve the uncertainties on the seismogenic history (age, earthquake location, extent of the rupture and size) of this portion of NAFZ and especially on the attribution of historical earthquakes to the causative fault.
    Description: Published
    Description: 115–128
    Description: 2T. Deformazione crostale attiva
    Description: N/A or not JCR
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 9
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    Checking the site categorization criteria and amplification factors of the 2021 draft of Eurocode 8 Part 1–1 (2021)
    Springer Nature
    Details
    Publication Date: 2021-11-29
    Description: In this paper the site categorization criteria and the corresponding site amplification factors proposed in the 2021 draft of Part 1 of Eurocode 8 (2021-draft, CEN/TC250/SC8 Working Draft N1017) are first introduced and compared with the current version of Eurocode 8, as well as with site amplification factors from recent empirical ground motion prediction equations. Afterwards, these values are checked by two approaches. First, a wide dataset of strong motion records is built, where recording stations are classified according to 2021-draft, and the spectral amplifications are empirically estimated computing the site-to-site residuals from regional and global ground motion models for reference rock conditions. Second, a comprehensive parametric numerical study of one-dimensional (1D) site amplification is carried out, based on randomly generated shear-wave velocity profiles, classified according to the new criteria. A reasonably good agreement is found by both approaches. The most relevant discrepancies occur for the shallow soft soil conditions (soil category E) that, owing to the complex interaction of shear wave velocity, soil deposit thickness and frequency range of the excitation, show the largest scatter both in terms of records and of 1D numerical simulations. Furthermore, 1D numerical simulations for soft soil conditions tend to provide lower site amplification factors than 2021-draft, as well as lower than the corresponding site-to-site residuals from records, because of higher impact of non-linear (NL) site effects in the simulations. A site-specific study on NL effects at three KiK-net stations with a significantly large amount of high-intensity recorded ground motions gives support to the 2021-draft NL reduction factors, although the very limited number of recording stations allowing such analysis prevents deriving more general implications. In the presence of such controversial arguments, it is reasonable that a standard should adopt a prudent solution, with a limited reduction of the site amplification factors to account for NL soil response, while leaving the possibility to carry out site-specific estimations of such factors when sufficient information is available to model the ground strain dependency of local soil properties.
    Description: Published
    Description: 4199–4234
    Description: 5T. Sismologia, geofisica e geologia per l'ingegneria sismica
    Description: JCR Journal
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  • 10
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    Exceedance of design actions in epicentral areas: insights from the ShakeMap envelopes for the 2016–2017 central Italy sequence (2021)
    Springer Nature
    Details
    Publication Date: 2021-11-29
    Description: ShakeMap is the tool to evaluate the ground motion effect of earthquakes in vast areas. It is useful to delimit the zones where the shaking is expected to have been most significant, for civil defense rapid response. From the earthquake engineering point of view, it can be used to infer the seismic actions on the built environment to calibrate vulnerability models or to define the reconstruction policies based on observed damage vs shaking. In the case of long-lasting seismic sequences, it can be useful to develop ShakeMap envelopes, that is, maps of the largest ground intensity among those from the ShakeMap of (selected) events of a seismic sequence, to delimit areas where the effects of the whole sequence have been of structural engineering relevance. This study introduces ShakeMap envelopes and discusses them for the central Italy 2016–2017 seismic sequence. The specific goals of the study are: (i) to compare the envelopes and the ShakeMap of the main events of the sequence to make the case for sequence-based maps; (ii) to quantify the exceedance of design seismic actions based on the envelopes; (iii) to make envelopes available for further studies and the reconstruction planning; (iv) to gather insights on the (repeated) exceedance of design seismic actions at some sites. Results, which include considerations of uncertainty in ShakeMap, show that the sequence caused exceedance of design hazard in thousands of square kilometers. The most relevant effects of the sequence are, as expected, due to the mainshock, yet seismic actions larger than those enforced by the code for structural design are found also around the epicenters of the smaller magnitude events. At some locations, the succession of ground-shaking that has excited structures, provides insights on structural damage accumulation that has likely taken place; something that is not accounted for explicitly in modern seismic design. The envelopes developed are available as supplemental material.
    Description: Published
    Description: 5391–5414
    Description: 5T. Sismologia, geofisica e geologia per l'ingegneria sismica
    Description: JCR Journal
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  • 11
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    Automatic inspection and analysis of digital waveform images by means of convolutional neural networks (2021)
    Springer Nature
    Details
    Publication Date: 2021-12-13
    Description: Analyzing seismic data to get information about earthquakes has always been a major task for seismologists and, more in general, for geophysicists. Recently, thanks to the technological development of observation systems, more and more data are available to perform such tasks. However, this data “grow up” makes “human possibility” of data processing more complex in terms of required efforts and time demanding. That is why new technological approaches such as artificial intelligence are becoming very popular and more and more exploited. In this paper, we explore the possibility of interpreting seismic waveform segments by means of pre-trained deep learning. More specifically, we apply convolutional networks to seismological waveforms recorded at local or regional distances without any pre-elaboration or filtering. We show that such an approach can be very successful in determining if an earthquake is “included” in the seismic wave image and in estimating the distance between the earthquake epicenter and the recording station.
    Description: Published
    Description: 1347–1359
    Description: 1T. Struttura della Terra
    Description: 3T. Fisica dei terremoti e Sorgente Sismica
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 12
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    Midlatitude climatology of the ionospheric equivalent slab thickness over two solar cycles (2021)
    Springer Nature
    Details
    Publication Date: 2021-10-25
    Description: Themain climatological features of the ionospheric equivalent slab thickness (τ ) for the Northern hemispheremidlatitudes are analyzed. F2-layer peak electron density values recorded at three midlatitude ionospheric stations (Chilton 51.5° N, 0.6° W, U.K.; Roquetes 40.8° N, 0.5° E, Spain;Wallops Island 37.9° N, 75.5°W, USA) and vertical total electron content values from colocated ground-based Global Navigation Satellite System receivers are used to calculate a dataset of τ values for the last two solar cycles, considering only magnetically quiet periods. Results are presented both as grids of binned medians and as boxplots as a function of local time and month of the year, for different solar activity levels. Corresponding trends are first compared to those output by the midlatitude empirical model developed by Fox et al. (Radio Sci 26:429–438, 1991) and then discussed in the light of what is known so far. From this investigation, the strong need to implement an improved empirical model of τ has emerged. Both Space Weather and Space Geodesy applications might benefit from such model. Therefore, both the dataset and the methodology described in the paper represent a first fundamental step aimed at implementing an empirical climatological model of the ionospheric equivalent slab thickness. The study highlighted also that at midlatitudes τ shows the following main patterns: daytime values considerably smaller than nighttime ones (except in summer); well-defined maxima at solar terminator hours; a greater dispersion during nighttime and solar terminator hours; no clear and evident solar activity dependence.
    Description: Published
    Description: 124
    Description: 2A. Fisica dell'alta atmosfera
    Description: JCR Journal
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  • 13
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    Fracturing and healing of basaltic magmas during explosive volcanic eruptions (2021)
    Springer Nature
    Details
    Publication Date: 2021-11-26
    Description: The eruption of basaltic magmas dominates explosive volcanism on Earth and other planets within the Solar System. The mechanism through which continuous magma fragments into volcanic particles is central in governing eruption dynamics and the ensuing hazards. However, the mechanism of fragmentation of basaltic magmas is still disputed, with both viscous and brittle mechanisms having been proposed. Here we carry out textural analysis of the products of ten eruptions from seven volcanoes by scanning electron microscopy. We find broken crystals surrounded by intact glass that testify to the brittle fragmentation of basaltic magmas during explosive activity worldwide. We then replicated the natural textures of broken crystals in laboratory experiments where variably crystallized basaltic melt was fragmented by rapid deformation. The experiments reveal that crystals are broken by the propagation of a network of fractures through magma, and that afterwards the fractures heal by viscous flow of the melt. Fracturing and healing affect gas mobility, stress distribution, and bubble and crystal size distributions in magma. Our results challenge the idea that the grain size distribution of basaltic eruption products reflects the density of fractures that initially fragmented the magma and ultimately indicate that brittle fracturing and viscous healing of magma may underlie basaltic explosive eruptions globally.
    Description: Published
    Description: 248–254
    Description: 4V. Processi pre-eruttivi
    Description: 5V. Processi eruttivi e post-eruttivi
    Description: JCR Journal
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  • 14
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    Catching the Main Ethiopian Rift evolving towards plate divergence (2022)
    Springer Nature
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    Publication Date: 2022-02-11
    Description: Magmatism accompanies rifting along divergent plate boundaries, although its role before continental breakup remains poorly understood. For example, the magma-assisted Northern Main Ethiopian Rift (NMER) lacks current volcanism and clear tectono-magmatic relationships with its contiguous rift portions. Here we define its magmatic behaviour, identifying the most recent eruptive fissures (EF) whose aphyric basalts have a higher Ti content than those of older monogenetic scoria cones (MSC), which are porphyritic and plagioclase-dominated. Despite these differences, calculations highlight a similar parental melt for EF and MSC products, suggesting only a different evolutionary history after melt generation. While MSC magmas underwent a further step of storage at intermediate crustal levels, EF magmas rose directly from the base of the crust without contamination, even below older polygenetic volcanoes, suggesting rapid propagation of transcrustal dikes across solidified magma chambers. Whether this recent condition in the NMER is stable or transient, it indicates a transition from central polygenetic to linear fissure volcanism, indicative of increased tensile conditions and volcanism directly fed from the base of the crust, suggesting transition towards mature rifting.
    Description: Published
    Description: 21821
    Description: 2V. Struttura e sistema di alimentazione dei vulcani
    Description: JCR Journal
    Keywords: 04.08. Volcanology
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  • 15
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    Neapolitan volcanoes (2021)
    Springer Nature
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    Publication Date: 2021-12-24
    Description: This book serves as a guide to discovering the most interesting volcano sites in Italy. Accompanied by some extraordinary contemporary images of active Neapolitan volcanoes, it explains the main volcanic processes that have been shaping the landscape of the Campania region and influencing human settlements in this area since Greek and Roman times and that have prompted leading international scientists to visit and study this natural volcanology laboratory. While volcanology is the central topic, the book also addresses other aspects related to the area’s volcanism and is divided into three sections: 1) Neapolitan volcanic activity and processes (with a general introduction to volcanology and its development around Naples together with descriptions of the landscape and the main sites worth visiting); 2) Volcanoes and their interactions with local human settlements since the Bronze Age, recent population growth and the transformation of the territory; 3) The risks posed by Neapolitan Volcanoes, their recent activity and the problem of forecasting any future eruption.
    Description: Published
    Description: 2TM. Divulgazione Scientifica
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 16
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    Northern Hemisphere drought risk in a warming climate (2021)
    Springer Nature
    In:  EPIC3npj Climate and Atmospheric Science, Springer Nature, 4(1), ISSN: 2397-3722
    Details
    Publication Date: 2022-02-15
    Repository Name: EPIC Alfred Wegener Institut
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  • 17
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    Environmental stability and phenotypic plasticity benefit the cold-water coral Desmophyllum dianthus in an acidified fjord (2022)
    Springer Nature
    In:  EPIC3Communications Biology, Springer Nature, 5(683)
    Details
    Publication Date: 2022-07-13
    Description: The stratified Chilean Comau Fjord sustains a dense population of the cold-water coral (CWC) Desmophyllum dianthus in aragonite supersaturated shallow and aragonite under- saturated deep water. This provides a rare opportunity to evaluate CWC fitness trade-offs in response to physico-chemical drivers and their variability. Here, we combined year-long reciprocal transplantation experiments along natural oceanographic gradients with an in situ assessment of CWC fitness. Following transplantation, corals acclimated fast to the novel environment with no discernible difference between native and novel (i.e. cross-transplanted) corals, demonstrating high phenotypic plasticity. Surprisingly, corals exposed to lowest ara- gonite saturation (Ωarag 〈 1) and temperature (T 〈 12.0 °C), but stable environmental condi- tions, at the deep station grew fastest and expressed the fittest phenotype. We found an inverse relationship between CWC fitness and environmental variability and propose to consider the high frequency fluctuations of abiotic and biotic factors to better predict the future of CWCs in a changing ocean.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , NonPeerReviewed
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  • 18
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    Mid-Pliocene El Niño/Southern Oscillation suppressed by Pacific intertropical convergence zone shift (2022)
    Springer Nature
    In:  EPIC3Nature Geoscience, Springer Nature, ISSN: 1752-0908
    Details
    Publication Date: 2022-08-16
    Description: The El Niño/Southern Oscillation (ENSO), the dominant driver of year-to-year climate variability in the equatorial Pacific Ocean, impacts climate pattern across the globe. However, the response of the ENSO system to past and potential future temperature increases is not fully understood. Here we investigate ENSO variability in the warmer climate of the mid-Pliocene (~3.0–3.3 Ma), when surface temperatures were ~2–3 °C above modern values, in a large ensemble of climate models—the Pliocene Model Intercomparison Project. We show that the ensemble consistently suggests a weakening of ENSO variability, with a mean reduction of 25% (±16%). We further show that shifts in the equatorial Pacific mean state cannot fully explain these changes. Instead, ENSO was suppressed by a series of off-equatorial processes triggered by a northward displacement of the Pacific intertropical convergence zone: weakened convective feedback and intensified Southern Hemisphere circulation, which inhibit various processes that initiate ENSO. The connection between the climatological intertropical convergence zone position and ENSO we find in the past is expected to operate in our warming world with important ramifications for ENSO variability.
    Repository Name: EPIC Alfred Wegener Institut
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    Stable aerobic and anaerobic coexistence in anoxic marine zones (2020)
    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 Zakem, E. J., Mahadevan, A., Lauderdale, J. M., & Follows, M. J. Stable aerobic and anaerobic coexistence in anoxic marine zones. ISME Journal, 14, (2019): 288–301, doi: 10.1038/s41396-019-0523-8.
    Description: Mechanistic description of the transition from aerobic to anaerobic metabolism is necessary for diagnostic and predictive modeling of fixed nitrogen loss in anoxic marine zones (AMZs). In a metabolic model where diverse oxygen- and nitrogen-cycling microbial metabolisms are described by underlying redox chemical reactions, we predict a transition from strictly aerobic to predominantly anaerobic regimes as the outcome of ecological interactions along an oxygen gradient, obviating the need for prescribed critical oxygen concentrations. Competing aerobic and anaerobic metabolisms can coexist in anoxic conditions whether these metabolisms represent obligate or facultative populations. In the coexistence regime, relative rates of aerobic and anaerobic activity are determined by the ratio of oxygen to electron donor supply. The model simulates key characteristics of AMZs, such as the accumulation of nitrite and the sustainability of anammox at higher oxygen concentrations than denitrification, and articulates how microbial biomass concentrations relate to associated water column transformation rates as a function of redox stoichiometry and energetics. Incorporating the metabolic model into an idealized two-dimensional ocean circulation results in a simulated AMZ, in which a secondary chlorophyll maximum emerges from oxygen-limited grazing, and where vertical mixing and dispersal in the oxycline also contribute to metabolic co-occurrence. The modeling approach is mechanistic yet computationally economical and suitable for global change applications.
    Description: We are grateful for the thorough and thoughtful comments of two anonymous reviewers. We also thank Andrew Babbin for helpful comments. EJZ was supported by the Simons Foundation (Postdoctoral Fellowship in Marine Microbial Ecology). AM was supported by the Office of Naval Research (ONR #N000-14-15-1-2555). JML was supported by U.S. National Science Foundation (NSF #OCE-1259388). MJF was supported by the Gordon and Betty Moore Foundation (GBMF #3778) and the Simons Foundation: the Simons Collaboration on Ocean Processes and Ecology (SCOPE #329108) and the Simons Collaboration on Computational Biogeochemical Modeling of Marine Ecosystems (CBIOMES #549931).
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    Comparative proteomics of related symbiotic mussel species reveals high variability of host-symbiont interactions (2020)
    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 Ponnudurai, R., Heiden, S. E., Sayavedra, L., Hinzke, T., Kleiner, M., Hentschker, C., Felbeck, H., Sievert, S. M., Schlüter, R., Becher, D., Schweder, T., & Markert, S. Comparative proteomics of related symbiotic mussel species reveals high variability of host-symbiont interactions. ISME Journal, 14, (2019): 649–656, doi: 10.1038/s41396-019-0517-6.
    Description: Deep-sea Bathymodiolus mussels and their chemoautotrophic symbionts are well-studied representatives of mutualistic host–microbe associations. However, how host–symbiont interactions vary on the molecular level between related host and symbiont species remains unclear. Therefore, we compared the host and symbiont metaproteomes of Pacific B. thermophilus, hosting a thiotrophic symbiont, and Atlantic B. azoricus, containing two symbionts, a thiotroph and a methanotroph. We identified common strategies of metabolic support between hosts and symbionts, such as the oxidation of sulfide by the host, which provides a thiosulfate reservoir for the thiotrophic symbionts, and a cycling mechanism that could supply the host with symbiont-derived amino acids. However, expression levels of these processes differed substantially between both symbioses. Backed up by genomic comparisons, our results furthermore revealed an exceptionally large repertoire of attachment-related proteins in the B. thermophilus symbiont. These findings imply that host–microbe interactions can be quite variable, even between closely related systems.
    Description: Thanks to captain, crew, and pilots of the research vessels Atlantis (ROV Jason cruise AT26–10 in 2014) and Meteor (cruise M82–3 in 2010). We thank Jana Matulla, Sebastian Grund, and Annette Meuche for excellent technical assistance during sample preparation, MS measurements in the Orbitrap Classic, and TEM imaging preparation, respectively. We appreciate Nikolaus Leisch’s help with TEM image interpretation, Inna Sokolova’s advice on bivalve physiology, and Marie Zühlke’s support during manuscript revision. RP was supported by the EU-funded Marie Curie Initial Training Network ‘Symbiomics’ (project no. 264774) and by a fellowship of the Institute of Marine Biotechnology e.V. TH was supported by the German Research Foundation DFG (grant MA 6346/2–1 to SM). The Atlantis cruise was funded by a grant of the US National Science Foundation’s Dimensions of Biodiversity program to SMS (OCE-1136727).
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  • 21
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    Coordinated transformation of the gut microbiome and lipidome of bowhead whales provides novel insights into digestion (2020)
    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 Miller, C. A., Holm, H. C., Horstmann, L., George, J. C., Fredricks, H. F., Van Mooy, B. A. S., & Apprill, A. Coordinated transformation of the gut microbiome and lipidome of bowhead whales provides novel insights into digestion. ISME Journal, 14, (2019): 688-701, doi: 10.1038/s41396-019-0549-y.
    Description: Whale digestion plays an integral role in many ocean ecosystems. By digesting enormous quantities of lipid-rich prey, whales support their energy intensive lifestyle, but also excrete nutrients important to ocean biogeochemical cycles. Nevertheless, whale digestion is poorly understood. Gastrointestinal microorganisms play a significant role in vertebrate digestion, but few studies have examined them in whales. To investigate digestion of lipids, and the potential contribution of microbes to lipid digestion in whales, we characterized lipid composition (lipidomes) and bacterial communities (microbiotas) in 126 digesta samples collected throughout the gastrointestinal tracts of 38 bowhead whales (Balaena mysticetus) harvested by Alaskan Eskimos. Lipidomes and microbiotas were strongly correlated throughout the gastrointestinal tract. Lipidomes and microbiotas were most variable in the small intestine and most similar in the large intestine, where microbiota richness was greatest. Our results suggest digestion of wax esters, the primary lipids in B. mysticetus prey representing more than 80% of total dietary lipids, occurred in the mid- to distal small intestine and was correlated with specific microorganisms. Because wax esters are difficult to digest by other marine vertebrates and constitute a large reservoir of carbon in the ocean, our results further elucidate the essential roles that whales and their gastrointestinal microbiotas play in the biogeochemical cycling of carbon and nutrients in high-latitude seas.
    Description: Devonshire Foundation (to CAM), Marine Mammal Center, Woods Hole Oceanographic Institution (WHOI; to CAM), WHOI Ocean Life Institute (to AA and CAM), Dalio Foundation’s Dalio Ocean Initiative (now ‘OceanX’) (to AA), National Science Foundation (OCE-1756254 and OPP-1543328 to BASVM). Samples were collected under Department of Commerce National Oceanic and Atmospheric Administration National Marine Fisheries Service permit numbers 17350-00, 17350-01, and 17350-02 to North Slope Borough Department of Wildlife Management.
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  • 22
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    Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters (2020)
    Springer Nature
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Gazitua, M. C., Vik, D. R., Roux, S., Gregory, A. C., Bolduc, B., Widner, B., Mulholland, M. R., Hallam, S. J., Ulloa, O., & Sullivan, M. B. Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters. Isme Journal, (2020), doi:10.1038/s41396-020-00825-6.
    Description: Viruses play an important role in the ecology and biogeochemistry of marine ecosystems. Beyond mortality and gene transfer, viruses can reprogram microbial metabolism during infection by expressing auxiliary metabolic genes (AMGs) involved in photosynthesis, central carbon metabolism, and nutrient cycling. While previous studies have focused on AMG diversity in the sunlit and dark ocean, less is known about the role of viruses in shaping metabolic networks along redox gradients associated with marine oxygen minimum zones (OMZs). Here, we analyzed relatively quantitative viral metagenomic datasets that profiled the oxygen gradient across Eastern Tropical South Pacific (ETSP) OMZ waters, assessing whether OMZ viruses might impact nitrogen (N) cycling via AMGs. Identified viral genomes encoded six N-cycle AMGs associated with denitrification, nitrification, assimilatory nitrate reduction, and nitrite transport. The majority of these AMGs (80%) were identified in T4-like Myoviridae phages, predicted to infect Cyanobacteria and Proteobacteria, or in unclassified archaeal viruses predicted to infect Thaumarchaeota. Four AMGs were exclusive to anoxic waters and had distributions that paralleled homologous microbial genes. Together, these findings suggest viruses modulate N-cycling processes within the ETSP OMZ and may contribute to nitrogen loss throughout the global oceans thus providing a baseline for their inclusion in the ecosystem and geochemical models.
    Description: We thank Sullivan Lab members and Heather Maughan for comments on the paper, Bess Ward for her contribution in the N-cycle context of our story, Kurt Hanselmann for his assistance in the calculations of the Gibbs-free energies, and the scientific party and crew of the R/V Atlantis (grant OCE-1356056 to MRM) for the sampling opportunity and support at sea. This work was funded in part by awards from the Agouron Institute to OU and MBS, a Gordon and Betty Moore Foundation Investigator Award (#3790) and NSF Biological Oceanography Awards (#1536989 and #1829831) to MBS, and the Millennium Science Initiative (grant ICN12_019-IMO) to OU. The work conducted by the U.S. Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S. Department of Energy under contract no. DE-AC02-05CH11231.
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    Discovery and quantification of anaerobic nitrogen metabolisms among oxygenated tropical Cuban stony corals (2021)
    Springer Nature
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Babbin, A. R., Tamasi, T., Dumit, D., Weber, L., Rodríguez, M. V. I., Schwartz, S. L., Armenteros, M., Wankel, S. D., & Apprill, A. Discovery and quantification of anaerobic nitrogen metabolisms among oxygenated tropical Cuban stony corals. ISME Journal, (2020), doi:10.1038/s41396-020-00845-2.
    Description: Coral reef health depends on an intricate relationship among the coral animal, photosynthetic algae, and a complex microbial community. The holobiont can impact the nutrient balance of their hosts amid an otherwise oligotrophic environment, including by cycling physiologically important nitrogen compounds. Here we use 15N-tracer experiments to produce the first simultaneous measurements of ammonium oxidation, nitrate reduction, and nitrous oxide (N2O) production among five iconic species of reef-building corals (Acropora palmata, Diploria labyrinthiformis, Orbicella faveolata, Porites astreoides, and Porites porites) in the highly protected Jardines de la Reina reefs of Cuba. Nitrate reduction is present in most species, but ammonium oxidation is low potentially due to photoinhibition and assimilatory competition. Coral-associated rates of N2O production indicate a widespread potential for denitrification, especially among D. labyrinthiformis, at rates of ~1 nmol cm−2 d−1. In contrast, A. palmata displays minimal active nitrogen metabolism. Enhanced rates of nitrate reduction and N2O production are observed coincident with dark net respiration periods. Genomes of bacterial cultures isolated from multiple coral species confirm that microorganisms with the ability to respire nitrate anaerobically to either dinitrogen gas or ammonium exist within the holobiont. This confirmation of anaerobic nitrogen metabolisms by coral-associated microorganisms sheds new light on coral and reef productivity.
    Description: Research was conducted in the Gardens of the Queen, Cuba in accordance with the requirements of the Republic of Cuba, conducted under permit NV2370 and NV2568 issued by the Ministerio de Relaciones Exteriores. We gratefully acknowledge funding for this research by MIT Sea Grant award #2018-DOH-49-LEV, Simons Foundation award #622065, and MIT ESI seed funding to ARB, the MIT Montrym, Ferry, and mTerra Seed Grant Funds, and the generous contributions by Dr Bruce L. Heflinger.
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    Time-series transcriptomics from cold, oxic subseafloor crustal fluids reveals a motile, mixotrophic microbial community (2021)
    Springer Nature
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Seyler, L. M., Trembath-Reichert, E., Tully, B. J., & Huber, J. A. Time-series transcriptomics from cold, oxic subseafloor crustal fluids reveals a motile, mixotrophic microbial community. Isme Journal, (2020), doi:10.1038/s41396-020-00843-4.
    Description: The oceanic crustal aquifer is one of the largest habitable volumes on Earth, and it harbors a reservoir of microbial life that influences global-scale biogeochemical cycles. Here, we use time series metagenomic and metatranscriptomic data from a low-temperature, ridge flank environment representative of the majority of global hydrothermal fluid circulation in the ocean to reconstruct microbial metabolic potential, transcript abundance, and community dynamics. We also present metagenome-assembled genomes from recently collected fluids that are furthest removed from drilling disturbances. Our results suggest that the microbial community in the North Pond aquifer plays an important role in the oxidation of organic carbon within the crust. This community is motile and metabolically flexible, with the ability to use both autotrophic and organotrophic pathways, as well as function under low oxygen conditions by using alternative electron acceptors such as nitrate and thiosulfate. Anaerobic processes are most abundant in subseafloor horizons deepest in the aquifer, furthest from connectivity with the deep ocean, and there was little overlap in the active microbial populations between sampling horizons. This work highlights the heterogeneity of microbial life in the subseafloor aquifer and provides new insights into biogeochemical cycling in ocean crust.
    Description: The Gordon and Betty Moore Foundation sponsored most of the observatory components at North Pond through grant GBMF1609. This work was supported by NSF OCE-1062006, OCE-1745589 and OCE-1635208 to J.A.H. E.T.R. was supported by a NASA Postdoctoral Fellowship with the NASA Astrobiology Institute and a L’Oréal USA For Women in Science Fellowship. The Center for Dark Energy Biosphere Investigations (C-DEBI OCE-0939564) also supported the participation of J.A.H. and B.T. This is C-DEBI contribution number 548.
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    Modeling the morphodynamics of coastal responses to extreme events: what shape are we in? (2022)
    Annual Reviews
    Details
    Publication Date: 2022-10-27
    Description: This paper is not subject to U.S. copyright. The definitive version was published in Sherwood, C. R., van Dongeren, A., Doyle, J., Hegermiller, C. A., Hsu, T.-J., Kalra, T. S., Olabarrieta, M., Penko, A. M., Rafati, Y., Roelvink, D., van der Lugt, M., Veeramony, J., & Warner, J. C. Modeling the morphodynamics of coastal responses to extreme events: what shape are we in? Annual Review of Marine Science, 14, (2022): 457–492, https://doi.org/10.1146/annurev-marine-032221-090215.
    Description: This review focuses on recent advances in process-based numerical models of the impact of extreme storms on sandy coasts. Driven by larger-scale models of meteorology and hydrodynamics, these models simulate morphodynamics across the Sallenger storm-impact scale, including swash,collision, overwash, and inundation. Models are becoming both wider (as more processes are added) and deeper (as detailed physics replaces earlier parameterizations). Algorithms for wave-induced flows and sediment transport under shoaling waves are among the recent developments. Community and open-source models have become the norm. Observations of initial conditions (topography, land cover, and sediment characteristics) have become more detailed, and improvements in tropical cyclone and wave models provide forcing (winds, waves, surge, and upland flow) that is better resolved and more accurate, yielding commensurate improvements in model skill. We foresee that future storm-impact models will increasingly resolve individual waves, apply data assimilation, and be used in ensemble modeling modes to predict uncertainties.
    Description: All authors except D.R. were partially supported by the IFMSIP project, funded by US Office of Naval Research grant PE 0601153N under contracts N00014-17-1-2459 (Deltares), N00014-18-1-2785 (University of Delaware), N0001419WX00733 (US Naval Research Laboratory, Monterey), N0001418WX01447 (US Naval Research Laboratory, Stennis Space Center), and N0001418IP00016 (US Geological Survey). C.R.S., C.A.H., T.S.K., and J.C.W. were supported by the US Geological Survey Coastal/Marine Hazards and Resources Program. A.v.D. and M.v.d.L. were supported by the Deltares Strategic Research project Quantifying Flood Hazards and Impacts. M.O. acknowledges support from National Science Foundation project OCE-1554892.
    Keywords: Coastal morphodynamics ; Extreme storms ; Coastal modeling ; Sandy coasts ; Waves ; Sediment transport
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    Quantifying the effects of hydrogen on carbon assimilation in a seafloor microbial community associated with ultramafic rocks (2021)
    Springer Nature
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Coskun, O. K., Vuillemin, A., Schubotz, F., Klein, F., Sichel, S. E., Eisenreich, W., & Orsi, W. D. Quantifying the effects of hydrogen on carbon assimilation in a seafloor microbial community associated with ultramafic rocks. Isme Journal. (2021), https://doi.org/10.1038/s41396-021-01066-x.
    Description: Thermodynamic models predict that H2 is energetically favorable for seafloor microbial life, but how H2 affects anabolic processes in seafloor-associated communities is poorly understood. Here, we used quantitative 13C DNA stable isotope probing (qSIP) to quantify the effect of H2 on carbon assimilation by microbial taxa synthesizing 13C-labeled DNA that are associated with partially serpentinized peridotite rocks from the equatorial Mid-Atlantic Ridge. The rock-hosted seafloor community was an order of magnitude more diverse compared to the seawater community directly above the rocks. With added H2, peridotite-associated taxa increased assimilation of 13C-bicarbonate and 13C-acetate into 16S rRNA genes of operational taxonomic units by 146% (±29%) and 55% (±34%), respectively, which correlated with enrichment of H2-oxidizing NiFe-hydrogenases encoded in peridotite-associated metagenomes. The effect of H2 on anabolism was phylogenetically organized, with taxa affiliated with Atribacteria, Nitrospira, and Thaumarchaeota exhibiting the most significant increases in 13C-substrate assimilation in the presence of H2. In SIP incubations with added H2, an order of magnitude higher number of peridotite rock-associated taxa assimilated 13C-bicarbonate, 13C-acetate, and 13C-formate compared to taxa that were not associated with peridotites. Collectively, these findings indicate that the unique geochemical nature of the peridotite-hosted ecosystem has selected for H2-metabolizing, rock-associated taxa that can increase anabolism under high H2 concentrations. Because ultramafic rocks are widespread in slow-, and ultraslow-spreading oceanic lithosphere, continental margins, and subduction zones where H2 is formed in copious amounts, the link between H2 and carbon assimilation demonstrated here may be widespread within these geological settings.
    Description: This work was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)—Project-ID 364653263—TRR 235 to WDO and WE, and under Germany’s Excellence Strategy—EXC 2077-390741603. The work was also supported by the Dalio Explore Fund and LMU Mentoring Program. Open Access funding enabled and organized by Projekt DEAL.
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    Sea ice surface temperatures from helicopter-borne thermal infrared imaging during the MOSAiC expedition (2022)
    Springer Nature
    In:  EPIC3Scientific Data, Springer Nature, 9(1), ISSN: 2052-4463
    Details
    Publication Date: 2022-06-27
    Description: The sea ice surface temperature is important to understand the Arctic winter heat budget. We conducted 35 helicopter flights with an infrared camera in winter 2019/2020 during the Multidisciplinary Drifting Observatory for the Study of Arctic Climate (MOSAiC) expedition. The flights were performed from a local, 5 to 10 km scale up to a regional, 20 to 40 km scale. The infrared camera recorded thermal infrared brightness temperatures, which we converted to surface temperatures. More than 150000 images from all flights can be investigated individually. As an advanced data product, we created surface temperature maps for every flight with a 1 m resolution. We corrected image gradients, applied an ice drift correction, georeferenced all pixels, and corrected the surface temperature by its natural temporal drift, which results in time-fixed surface temperature maps for a consistent analysis of one flight. The temporal and spatial variability of sea ice characteristics is an important contribution to an increased understanding of the Arctic heat budget and, in particular, for the validation of satellite products.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , NonPeerReviewed
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    Diversity and origins of bacterial and archaeal viruses on sinking particles reaching the abyssal ocean (2022)
    Springer Nature
    Details
    Publication Date: 2022-06-14
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Luo, E., Leu, A. O., Eppley, J. M., Karl, D. M., & DeLong, E. F. Diversity and origins of bacterial and archaeal viruses on sinking particles reaching the abyssal ocean. ISME Journal, 16, : 1627–1635, https://doi.org/10.1038/s41396-022-01202-1.
    Description: Sinking particles and particle-associated microbes influence global biogeochemistry through particulate matter export from the surface to the deep ocean. Despite ongoing studies of particle-associated microbes, viruses in these habitats remain largely unexplored. Whether, where, and which viruses might contribute to particle production and export remain open to investigation. In this study, we analyzed 857 virus population genomes associated with sinking particles collected over three years in sediment traps moored at 4000 m in the North Pacific Subtropical Gyre. Particle-associated viruses here were linked to cellular hosts through matches to bacterial and archaeal metagenome-assembled genome (MAG)-encoded prophages or CRISPR spacers, identifying novel viruses infecting presumptive deep-sea bacteria such as Colwellia, Moritella, and Shewanella. We also identified lytic viruses whose abundances correlated with particulate carbon flux and/or were exported from the photic to abyssal ocean, including cyanophages. Our data are consistent with some of the predicted outcomes of the viral shuttle hypothesis, and further suggest that viral lysis of both autotrophic and heterotrophic prokaryotes may play a role in carbon export. Our analyses revealed the diversity and origins of prevalent viruses found on deep-sea sinking particles and identified prospective viral groups for future investigation into processes that govern particle export in the open ocean.
    Description: This project is funded by grants from the Simons Foundation (#329108 to EFD and DMK, #721223 to EFD, and #721252 to DMK) and the Gordon and Betty Moore Foundation (GBMF3777 to EFD and GBMF3794 to DMK). Partial support for EL was provided by the Natural Sciences and Engineering Research Council of Canada (PGSD3-487490-2016).
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    Intracellular nitrate storage by diatoms can be an important nitrogen pool in freshwater and marine ecosystems (2022)
    Springer Nature
    In:  EPIC3Communications Earth & Environment, Springer Nature, 3(1), ISSN: 2662-4435
    Details
    Publication Date: 2022-07-06
    Description: Identifying and quantifying nitrogen pools is essential for understanding the nitrogen cycle in aquatic ecosystems. The ubiquitous diatoms represent an overlooked nitrate pool as they can accumulate nitrate intracellularly and utilize it for nitrogen assimilation, dissipation of excess photosynthetic energy, and Dissimilatory Nitrate Reduction to Ammonium (DNRA). Here, we document the global co-occurrence of diatoms and intracellular nitrate in phototrophic microbial communities in freshwater (n = 69), coastal (n = 44), and open marine (n = 4) habitats. Diatom abundance and total intracellular nitrate contents in water columns, sediments, microbial mats, and epilithic biofilms were highly significantly correlated. In contrast, diatom community composition had only a marginal influence on total intracellular nitrate contents. Nitrate concentrations inside diatom cells exceeded ambient nitrate concentrations ∼100–4000-fold. The collective intracellular nitrate pool of the diatom community accounted for 〈1% of total nitrate in pelagic habitats and 65–95% in benthic habitats. Accordingly, nitrate-storing diatoms are emerging as significant contributors to benthic nitrogen cycling, in particular through Dissimilatory Nitrate Reduction to Ammonium activity under anoxic conditions.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , NonPeerReviewed , info:eu-repo/semantics/article
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    Physiological dynamics of chemosynthetic symbionts in hydrothermal vent snails (2020)
    Springer Nature
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Breusing, C., Mitchell, J., Delaney, J., Sylva, S. P., Seewald, J. S., Girguis, P. R., & Beinart, R. A. Physiological dynamics of chemosynthetic symbionts in hydrothermal vent snails. Isme Journal, (2020), doi:10.1038/s41396-020-0707-2.
    Description: Symbioses between invertebrate animals and chemosynthetic bacteria form the basis of hydrothermal vent ecosystems worldwide. In the Lau Basin, deep-sea vent snails of the genus Alviniconcha associate with either Gammaproteobacteria (A. kojimai, A. strummeri) or Campylobacteria (A. boucheti) that use sulfide and/or hydrogen as energy sources. While the A. boucheti host–symbiont combination (holobiont) dominates at vents with higher concentrations of sulfide and hydrogen, the A. kojimai and A. strummeri holobionts are more abundant at sites with lower concentrations of these reductants. We posit that adaptive differences in symbiont physiology and gene regulation might influence the observed niche partitioning between host taxa. To test this hypothesis, we used high-pressure respirometers to measure symbiont metabolic rates and examine changes in gene expression among holobionts exposed to in situ concentrations of hydrogen (H2: ~25 µM) or hydrogen sulfide (H2S: ~120 µM). The campylobacterial symbiont exhibited the lowest rate of H2S oxidation but the highest rate of H2 oxidation, with fewer transcriptional changes and less carbon fixation relative to the gammaproteobacterial symbionts under each experimental condition. These data reveal potential physiological adaptations among symbiont types, which may account for the observed net differences in metabolic activity and contribute to the observed niche segregation among holobionts.
    Description: We thank the Schmidt Ocean Institute, the crew of the R/V Falkor and the pilots of the ROV ROPOS for facilitating the sample collections and shipboard experiments, and the Broad Institute Microbial ‘Omics Core for preparing and sequencing the transcriptomic libraries. This material is based in part upon work supported by the National Science Foundation under Grant Numbers NSF OCE-1536653 (to PRG), OCE-1536331 (to RAB and JSS), OCE-1819530 and OCE-1736932 (to RAB).
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    Degradation of biological macromolecules supports uncultured microbial populations in Guaymas Basin hydrothermal sediments (2021)
    Springer Nature
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Castro, S. P., Borton, M. A., Regan, K., de Angelis, I. H., Wrighton, K. C., Teske, A. P., Strous, M., & Ruff, S. E. Degradation of biological macromolecules supports uncultured microbial populations in Guaymas Basin hydrothermal sediments. Isme Journal. (2021), https://doi.org/10.1038/s41396-021-01026-5.
    Description: Hydrothermal sediments contain large numbers of uncultured heterotrophic microbial lineages. Here, we amended Guaymas Basin sediments with proteins, polysaccharides, nucleic acids or lipids under different redox conditions and cultivated heterotrophic thermophiles with the genomic potential for macromolecule degradation. We reconstructed 20 metagenome-assembled genomes (MAGs) of uncultured lineages affiliating with known archaeal and bacterial phyla, including endospore-forming Bacilli and candidate phylum Marinisomatota. One Marinisomatota MAG had 35 different glycoside hydrolases often in multiple copies, seven extracellular CAZymes, six polysaccharide lyases, and multiple sugar transporters. This population has the potential to degrade a broad spectrum of polysaccharides including chitin, cellulose, pectin, alginate, chondroitin, and carrageenan. We also describe thermophiles affiliating with the genera Thermosyntropha, Thermovirga, and Kosmotoga with the capability to make a living on nucleic acids, lipids, or multiple macromolecule classes, respectively. Several populations seemed to lack extracellular enzyme machinery and thus likely scavenged oligo- or monomers (e.g., MAGs affiliating with Archaeoglobus) or metabolic products like hydrogen (e.g., MAGs affiliating with Thermodesulfobacterium or Desulforudaceae). The growth of methanogens or the production of methane was not observed in any condition, indicating that the tested macromolecules are not degraded into substrates for methanogenesis in hydrothermal sediments. We provide new insights into the niches, and genomes of microorganisms that actively degrade abundant necromass macromolecules under oxic, sulfate-reducing, and fermentative thermophilic conditions. These findings improve our understanding of the carbon flow across trophic levels and indicate how primary produced biomass sustains complex and productive ecosystems.
    Description: We are grateful to the captain and crew of the R/V Atlantis AT37-06 as well as the crew of the human occupied vehicle Alvin for their tireless support. Sampling at Guaymas Basin was supported by NSF (OCE-1357238).
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    Viral elements and their potential influence on microbial processes along the permanently stratified Cariaco Basin redoxcline (2020)
    Springer Nature
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Mara, P., Vik, D., Pachiadaki, M. G., Suter, E. A., Poulos, B., Taylor, G. T., Sullivan, M. B., & Edgcomb, V. P. Viral elements and their potential influence on microbial processes along the permanently stratified Cariaco Basin redoxcline. ISME Journal, (2020), doi:10.1038/s41396-020-00739-3.
    Description: Little is known about viruses in oxygen-deficient water columns (ODWCs). In surface ocean waters, viruses are known to act as gene vectors among susceptible hosts. Some of these genes may have metabolic functions and are thus termed auxiliary metabolic genes (AMGs). AMGs introduced to new hosts by viruses can enhance viral replication and/or potentially affect biogeochemical cycles by modulating key microbial pathways. Here we identify 748 viral populations that cluster into 94 genera along a vertical geochemical gradient in the Cariaco Basin, a permanently stratified and euxinic ocean basin. The viral communities in this ODWC appear to be relatively novel as 80 of these viral genera contained no reference viral sequences, likely due to the isolation and unique features of this system. We identify viral elements that encode AMGs implicated in distinctive processes, such as sulfur cycling, acetate fermentation, signal transduction, [Fe–S] formation, and N-glycosylation. These AMG-encoding viruses include two putative Mu-like viruses, and viral-like regions that may constitute degraded prophages that have been modified by transposable elements. Our results provide an insight into the ecological and biogeochemical impact of viruses oxygen-depleted and euxinic habitats.
    Description: This work was supported by the National Science Foundation grant OCE-1336082 to VPE, OCE-1335436 to GTT, OCE-1536989, a Moore Foundation Award (#3790) to MBS, and WHOI subaward A101259 to MP. The sequencing conducted by the U.S. Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S. Department of Energy under contract no. DE-AC02-05CH11231.
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    Sediment dynamics of a divergent bay-marsh complex (2020)
    Springer Nature
    Details
    Publication Date: 2022-05-26
    Description: Author Posting. © Springer Nature , 2020. This article is posted here by permission of Springer Nature for personal use, not for redistribution. The definitive version was published in Nowacki, D. J., & Ganju, N. K. Sediment dynamics of a divergent bay-marsh complex. Estuaries and Coasts, (2020), doi:10.1007/s12237-020-00855-5.
    Description: Bay–marsh systems, composed of an embayment surrounded by fringing marsh incised by tidal channels, are widely distributed coastal environments. External sediment availability, marsh-edge erosion, and sea-level rise acting on such bay–marsh complexes may drive diverse sediment-flux regimes. These factors reinforce the ephemeral and dynamic nature of fringing marshes: material released by marsh-edge erosion becomes part of a bay–marsh exchange that fuels the geomorphic evolution of the coupled system. The dynamics of this sediment exchange determine the balance among seaward export, deposition on the embayment seabed, flux into tidal channels, and import to the marsh platform. In this work, we investigate the sediment dynamics of a transgressive bay–marsh complex and link them to larger-scale considerations of its geomorphic trajectory. Grand Bay, Alabama/Mississippi, is a shallow microtidal embayment surrounded by salt marshes with lateral erosion rates of up to 5 m year−1. We collected 6 months of oceanographic data at four moorings within Grand Bay and its tidal channels to assess hydrographic conditions and net sediment-flux patterns and augmented the observations with numerical modeling. The observations imply a divergent sedimentary system in which a majority of the suspended sediment is exported seaward, while a smaller fraction is imported landward via tidal channels, assisting in vertical marsh-plain accumulation, maintenance of channel and intertidal-flat morphologies, and landward transgression. These results describe a dynamic system that is responsive to episodic atmospheric forcing in the absence of a strong tidal signal and the presence of severe lateral marsh loss.
    Description: We thank the staff of the Grand Bay NERR for their role in facilitating fieldwork within Grand Bay. Jonathan Pitchford, also of the Grand Bay NERR, provided the SET data. Giulio Mariotti and an anonymous reviewer are acknowledged for their helpful comments.
    Keywords: Salt marsh ; Geomorphic trajectory ; Sediment flux
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    Metabolic versatility of the nitrite-oxidizing bacterium Nitrospira marina and its proteomic response to oxygen-limited conditions (2021)
    Springer Nature
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Bayer, B., Saito, M. A., McIlvin, M. R., Lucker, S., Moran, D. M., Lankiewicz, T. S., Dupont, C. L., & Santoro, A. E. (2020). Metabolic versatility of the nitrite-oxidizing bacterium Nitrospira marina and its proteomic response to oxygen-limited conditions. Isme Journal, doi:10.1038/s41396-020-00828-3.
    Description: The genus Nitrospira is the most widespread group of nitrite-oxidizing bacteria and thrives in diverse natural and engineered ecosystems. Nitrospira marina Nb-295T was isolated from the ocean over 30 years ago; however, its genome has not yet been analyzed. Here, we investigated the metabolic potential of N. marina based on its complete genome sequence and performed physiological experiments to test genome-derived hypotheses. Our data confirm that N. marina benefits from additions of undefined organic carbon substrates, has adaptations to resist oxidative, osmotic, and UV light-induced stress and low dissolved pCO2, and requires exogenous vitamin B12. In addition, N. marina is able to grow chemoorganotrophically on formate, and is thus not an obligate chemolithoautotroph. We further investigated the proteomic response of N. marina to low (∼5.6 µM) O2 concentrations. The abundance of a potentially more efficient CO2-fixing pyruvate:ferredoxin oxidoreductase (POR) complex and a high-affinity cbb3-type terminal oxidase increased under O2 limitation, suggesting a role in sustaining nitrite oxidation-driven autotrophy. This putatively more O2-sensitive POR complex might be protected from oxidative damage by Cu/Zn-binding superoxide dismutase, which also increased in abundance under low O2 conditions. Furthermore, the upregulation of proteins involved in alternative energy metabolisms, including Group 3b [NiFe] hydrogenase and formate dehydrogenase, indicate a high metabolic versatility to survive conditions unfavorable for aerobic nitrite oxidation. In summary, the genome and proteome of the first marine Nitrospira isolate identifies adaptations to life in the oxic ocean and provides insights into the metabolic diversity and niche differentiation of NOB in marine environments.
    Description: We thank John B. Waterbury and Frederica Valois for providing the culture of Nitrospira marina Nb-295T and for continued advice about cultivation. The N. marina genome was sequenced as part of US Department of Energy Joint Genome Institute Community Sequencing Project 1337 to CLD, AES, and MAS in collaboration with the user community. We thank Claus Pelikan for bioinformatic assistance. This research was supported by a Simons Foundation Early Career Investigator in Marine Microbiology and Evolution Award (345889) and US National Science Foundation (NSF) award OCE-1924512 to AES. Proteomics analysis was supported by NSF awards OCE-1924554 and OCE-1850719, and NIH award R01GM135709 to MAS. BB was supported by the Austrian Science Fund (FWF) Project Number: J4426-B (“The influence of nitrifiers on the oceanic carbon cycle”), SL by the Netherlands Organization for Scientific Research (NWO) grant 016.Vidi.189.050, and CLD by NSF award OCE-125999.
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    Energy threshold changes in volcanic activity at Mt. Etna (Italy) inferred from volcanic tremor (2022)
    Springer Nature
    Details
    Publication Date: 2022-10-28
    Description: From the 2010s on, pattern classification has proven an effective method for flagging alerts of volcano unrest before eruptive activity at Mt. Etna, Italy. The analysis has been applied online to volcanic tremor data, and has supported the surveillance activity of the volcano that provides timely information to Civil Protection and other authorities. However, after declaring an alert, no one knows how long the volcano unrest will last and if a climactic eruptive activity will actually begin. These are critical aspects when considering the effects of a prolonged state of alert. An example of longstanding unrest is related to the Christmas Eve eruption in 2018, which was heralded by several months of almost continuous Strombolian activity. Here, we discuss the usage of thresholds to detect conditions leading to paroxysmal activity, and the challenges associated with defining such thresholds, leveraging a dataset of 52 episodes of lava fountains occurring in 2021. We were able to identify conservative settings regarding the thresholds, allowing for an early warning of impending paroxysm in almost all cases (circa 85% for the first 4 months in 2021, and over 90% for the whole year). The chosen thresholds also proved useful to predict that a paroxysmal activity was about to end. Such information provides reliable numbers for volcanologists for their assessments, based on visual information, which may not be available in bad weather or cloudy conditions.
    Description: Project IMPACT (A multidisciplinary Insight on the kinematics and dynamics of Magmatic Processes at Mt. Etna Aimed at identifying preCursor phenomena and developing early warning sysTems). IMPACT belongs to the Progetti Dipartimentali INGV [DIP7], https://progetti.ingv.it/index.php/it/progetti-dipartimentali/vulcani/impact#informazioni-sul-progetto.
    Description: Published
    Description: 17895
    Description: 4V. Processi pre-eruttivi
    Description: JCR Journal
    Keywords: Volcanic tremor ; Volcano monitoring ; Pattern recognition ; Self Organizing maps ; Fuzzy clustering ; Mt. Etna ; 04.06. Seismology ; 04.08. Volcanology ; 05.01. Computational geophysics
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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    Evidence for late glacial oceanic carbon redistribution and discharge from the Pacific Southern Ocean (2022)
    Springer Nature
    In:  EPIC3Nature Communications, Springer Nature, 13, 12 p., ISSN: 2041-1723
    Details
    Publication Date: 2022-11-14
    Description: Southern Ocean deep-water circulation plays an important role in the global carbon cycle. On geological time-scales, upwelling along the Chilean continental margin likely contributed to the deglacial atmospheric carbon dioxide rise, but little quantitative evidence exists of carbon storage. Here, we use a new X-ray Micro-Computer-Tomography method to assess foraminiferal test dissolution as proxy for paleo-carbonate ion concentrations [CO3^2−]. Our subantarctic Southeast Pacific sediment core depth transect shows significant deep-water [CO3^2−] variations during the Last Glacial Maximum and Deglaciation (10 – 22 ka BP). We provide evidence for an increase in [CO3^2−] during the early deglacial period (15-19 ka BP), followed by a ca. 40 µmol kg^-1 reduction in Lower Circumpolar Deepwater (CDW). This decreased Pacific to Atlantic export of low-carbon CDW contributed to significantly lowered carbon storage within the Southern Ocean, highlighting the importance of a dynamic Pacific–Southern Ocean deep-water reconfiguration for shaping late-glacial oceanic carbon storage, and subsequent deglacial oceanic-atmospheric CO2 transfer.
    Repository Name: EPIC Alfred Wegener Institut
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    Southern Ocean biogenic blooms freezing-in Oligocene colder climates (2022)
    Springer Nature
    In:  EPIC3Nature Communications, Springer Nature, 13(1), pp. 1-10, ISSN: 2041-1723
    Details
    Publication Date: 2022-11-24
    Description: 〈jats:title〉Abstract〈/jats:title〉〈jats:p〉Crossing a key atmospheric CO〈jats:sub〉2〈/jats:sub〉 threshold triggered a fundamental global climate reorganisation ~34 million years ago (Ma) establishing permanent Antarctic ice sheets. Curiously, a more dramatic CO〈jats:sub〉2〈/jats:sub〉 decline (~800–400 ppm by the Early Oligocene(~27 Ma)), postdates initial ice sheet expansion but the mechanisms driving this later, rapid drop in atmospheric carbon during the early Oligocene remains elusive and controversial. Here we use marine seismic reflection and borehole data to reveal an unprecedented accumulation of early Oligocene strata (up to 2.2 km thick over 1500 × 500 km) with a major biogenic component in the Australian Southern Ocean. High-resolution ocean simulations demonstrate that a tectonically-driven, one-off reorganisation of ocean currents, caused a unique period where current instability coincided with high nutrient input from the Antarctic continent. This unrepeated and short-lived environment favoured extreme bioproductivity and enhanced sediment burial. The size and rapid accumulation of this sediment package potentially holds ~1.067 × 10〈jats:sup〉15〈/jats:sup〉 kg of the ‘missing carbon’ sequestered during the decline from an Eocene high CO〈jats:sub〉2〈/jats:sub〉-world to a mid-Oligocene medium CO〈jats:sub〉2〈/jats:sub〉-world, highlighting the exceptional role of the Southern Ocean in modulating long-term climate.〈/jats:p〉
    Repository Name: EPIC Alfred Wegener Institut
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  • 38
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    NMR Spectroscopic Studies of Paramagnetic Proteins: Iron-Sulfur Proteins (1995)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 24 (1995), S. 209-237 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.bb.24.060195.001233
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    Applications of Parallel Computing to Biological Problems (1995)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 24 (1995), S. 239-267 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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    The Cystine-Knot Growth-Factor Superfamily (1995)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 24 (1995), S. 269-292 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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    Structure and Function of DNA Methyltransferases (1995)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 24 (1995), S. 293-318 
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    Nucleic Acid Hybridization: Triplex Stability and Energetics (1995)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 24 (1995), S. 319-350 
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    ISSN: 1056-8700
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    Membrane-Structure Studies Using X-Ray Standing Waves (1995)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 24 (1995), S. 351-377 
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    Exceptionally Stable Nucleic Acid Hairpins (1995)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 24 (1995), S. 379-404 
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    Fluorescent Protein Biosensors: Measurement of Molecular Dynamics in Living Cells (1995)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 24 (1995), S. 405-434 
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    ISSN: 1056-8700
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    Site-Directed Mutagenesis with an Expanded Genetic Code (1995)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 24 (1995), S. 435-462 
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    ISSN: 1056-8700
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    Complexes of the Minor Groove of DNA (1995)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 24 (1995), S. 463-493 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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    Compact Intermediate States in Protein Folding (1995)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 24 (1995), S. 495-522 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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    Molecular and Structural Basis of Target Recognition by Calmodulin (1995)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 24 (1995), S. 85-116 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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    Gating-Spring Models of Mechanoelectrical Transduction by Hair Cells of the Internal Ear (1995)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 24 (1995), S. 59-83 
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    ISSN: 1056-8700
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    Mass Spectrometry of Nucleic Acids: The Promise of Matrix-Assisted Laser Desorption-Ionization (MALDI) Mass Spectrometry (1995)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 24 (1995), S. 117-140 
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    ISSN: 1056-8700
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    Thermodynamics of Partly Folded Intermediates in Proteins (1995)
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    Annual Review of Biophysics and Biomolecular Structure 24 (1995), S. 141-165 
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    URL: http://dx.doi.org/10.1146/annurev.bb.24.060195.001041
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    Site-Specific Dynamics in DNA: Theory (1995)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 24 (1995), S. 523-549 
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    Using Self-Assembled Monolayers to Understand the Interactions of Man-made Surfaces with Proteins and Cells (1996)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 25 (1996), S. 55-78 
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    Bridging the Protein Sequence-Structure Gap by Structure Predictions (1996)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 25 (1996), S. 113-136 
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    Use of 19F NMR to Probe Protein Structure and Conformational Changes (1996)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 25 (1996), S. 163-195 
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    Engineering the Gramicidin Channel (1996)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 25 (1996), S. 231-258 
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    Electron Paramagnetic Resonance and Nuclear Magnetic Resonance Studies of Class I Ribonucleotide Reductase (1996)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 25 (1996), S. 259-286 
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    Antibodies as Tools to Study the Structure of Membrane Proteins: The Case of the Nicotinic Acetylcholine Receptor (1996)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 25 (1996), S. 197-229 
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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.bb.25.060196.001213
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    Activating Mutations of Rhodopsin and Other G Protein-Coupled Receptors (1996)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 25 (1996), S. 287-314 
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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.bb.25.060196.001443
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    Computational Studies of Protein Folding (1996)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 25 (1996), S. 315-342 
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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.bb.25.060196.001531
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    Modeling DNA in Aqueous Solutions: Theoretical and Computer Simulation Studies on the Ion Atmosphere of DNA (1996)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 25 (1996), S. 367-394 
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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.bb.25.060196.002055
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    Lipoxygenases: Structural Principles and Spectroscopy (1996)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 25 (1996), S. 431-459 
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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.bb.25.060196.002243
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    Visualizing Protein-Nucleic Acid Interactions on a Large Scale with the Scanning Force Microscope (1996)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 25 (1996), S. 395-429 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.bb.25.060196.002143
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    WHATEVER HAPPENED TO THE FUN? An Autobiographical Investigation (1997)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 26 (1997), S. 1-25 
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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.26.1.1
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    STRUCTURAL AND MECHANISTIC DETERMINANTS OF AFFINITY AND SPECIFICITY OF LIGANDS DISCOVERED OR ENGINEERED BY PHAGE DISPLAY (1997)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 26 (1997), S. 27-45 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract The scope and utility of phage display is reviewed with emphasis on medical applications and structure-based ligand and drug design, from literature mostly after 1994. General principles by which phage-displayed peptides achieve affinity and selectivity for targets are described, along with selected structural or mechanistic studies of the binding of peptides or proteins discovered or engineered by phage display. Such engineered proteins whose wild-type or mutant crystal or 2D-NMR structures yield insight about the basis for enhanced affinity or altered specificity include antibodies, zinc fingers, human growth hormone, protein A, and atrial natriuretic peptide. Structures of complexes of de novo phage-discovered peptide ligands with targets such as the Src SH3 domain, streptavidin, and erythropoietin receptor reveal the structural basis for receptor-peptide recognition in these systems.
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    HISTONE STRUCTURE AND THE ORGANIZATION OF THE NUCLEOSOME (1997)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 26 (1997), S. 83-112 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Chromatin structure is now believed to be dynamic and intimately related with cellular processes such as transcription. Over the past few years, high-resolution structures for the histones have become available. These structures and their implications for nucleosome organization are reviewed here.
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    HIERARCHY AND DYNAMICS OF RNA FOLDING (1997)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 26 (1997), S. 113-137 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract The evidence showing that the self-assembly of complex RNAs occurs in discrete transitions, each relating to the folding of sub-systems of increasing size and complexity starting from a state with most of the secondary structure, is reviewed. The reciprocal influence of the concentration of magnesium ions and nucleotide mutations on tertiary structure is analyzed. Several observations demonstrate that detrimental mutations can be rescued by high magnesium concentrations, while stabilizing mutations lead to a lesser dependence on magnesium ion concentration. Recent data point to the central controlling and monitoring roles of RNA-binding proteins that can bind to the different folding stages, either before full establishment of the secondary structure or at the molten globule state before the cooperative transition to the final three-dimensional structure.
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    FLEXIBILITY OF RNA (1997)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 26 (1997), S. 139-156 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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    Notes: Abstract One of the fundamental properties of the RNA helix is its intrinsic resistance to bend- or twist-deformations. Results of a variety of physical measurements point to a persistence length of 700-800 A for double-stranded RNA in the presence of magnesium cations, approximately 1.5-2.0-fold larger than the corresponding value for DNA. Although helix flexibility represents an important, quantifiable measure of the forces of interaction within the helix, it must also be considered in describing conformational variation of nonhelix elements (e.g. internal loops, branches), since the latter always reflect the properties of the flanking helices; that is, such elements are never completely rigid. For one important element of tertiary structure, namely, the core of yeast tRNAPhe, the above consideration has led to the conclusion that the core is not substantially more flexible than an equivalent length of pure helix.
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    STRUCTURAL PERSPECTIVES OF PHOSPHOLAMBAN, A HELICAL TRANSMEMBRANE PENTAMER (1997)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 26 (1997), S. 157-179 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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    Notes: Abstract Phospholamban is a 52-amino-acid protein that assembles into a pentamer in sarcoplasmic reticulum membranes. The protein has a role in the regulation of the resident calcium ATPase through an inhibitory association that can be reversed by phosphorylation. The phosphorylation of phospholamban is initiated by beta-adrenergic stimulation, identifying phospholamban as an important component in the stimulation of cardiac activity by beta-agonists. It is this role of phospholamban that has motivated studies in recent decades. There is evidence that phospholamban may also function as a Ca2+-selective ion channel. The structural properties of phospholamban have been studied by mutagenesis, modeling, and spectroscopy, resulting in a new view of the organization of this key molecule in membranes.
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    BIOMOLECULAR DYNAMICS AT LONG TIMESTEPS:Bridging the Timescale Gap Between Simulation and Experimentation (1997)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 26 (1997), S. 181-222 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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    Notes: Abstract Innovative algorithms have been developed during the past decade for simulating Newtonian physics for macromolecules. A major goal is alleviation of the severe requirement that the integration timestep be small enough to resolve the fastest components of the motion and thus guarantee numerical stability. This timestep problem is challenging if strictly faster methods with the same all-atom resolution at small timesteps are sought. Mathematical techniques that have worked well in other multiple-timescale contexts-where the fast motions are rapidly decaying or largely decoupled from others-have not been as successful for biomolecules, where vibrational coupling is strong. This review examines general issues that limit the timestep and describes available methods (constrained, reduced-variable, implicit, symplecttic, multiple-timestep, and normal-mode-based schemes). A section compares results of selected integrators for a model dipeptide, assessing physical and numerical performance. Included is our dual timestep method LN, which relies on an approximate linearization of the equations of motion every Deltat interval (5 fs or less), the solution of which is obtained by explicit integration at the inner timestep Deltatau (e.g., 0.5 fs). LN is computationally competitive, providing 4-5 speedup factors, and results are in good agreement, in comparison to 0.5 fs trajectories. These collective algorithmic efforts help fill the gap between the time range that can be simulated and the timespans of major biological interest (milliseconds and longer). Still, only a hierarchy of models and methods, along with experimentational improvements, will ultimately give theoretical modeling the status of partner with experiment.
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    MOLECULAR MECHANISM OF PHOTOSIGNALING BY ARCHAEAL SENSORY RHODOPSINS (1997)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 26 (1997), S. 223-258 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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    Notes: Abstract Two sensory rhodopsins (SRI and SRII) mediate color-sensitive phototaxis responses in halobacteria. These seven-helix receptor proteins, structurally and functionally similar to animal visual pigments, couple retinal photoisomerization to receptor activation and are complexed with membrane-embedded transducer proteins (HtrI and HtrII) that modulate a cytoplasmic phosphorylation cascade controlling the flagellar motor. The Htr proteins resemble the chemotaxis transducers from Escherichia coli. The SR-Htr signaling complexes allow studies of the biophysical chemistry of signal generation and relay, from the photobiophysics of initial excitation of the receptors to the final output at the level of the flagellar motor switch, revealing fundamental principles of sensory transduction and more broadly the nature of dynamic interactions between membrane proteins. We review here recent advances that have led to new insights into the molecular mechanism of signaling by these membrane complexes.
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    MODULAR PEPTIDE RECOGNITION DOMAINS IN EUKARYOTIC SIGNALING (1997)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 26 (1997), S. 259-288 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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    Notes: Abstract A characteristic feature of cellular signal transduction pathways in eukaryotes is the separation of catalysis from target recognition. Several modular domains that recognize short peptide sequences and target signaling proteins to these sequences have been identified. The structural bases of the specificities of recognition by SH2, SH3, and PTB domains have been elucidated by X-ray crystallography and NMR, and these results are reviewed here. In addition, the mechanism of cooperative interactions between these domains is discussed.
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    LESSONS FROM ZINC-BINDING PEPTIDES (1997)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 26 (1997), S. 357-371 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Zinc-finger domains are small metal-binding modules that are found in a wide range of gene regulatory proteins. Peptides corresponding to these domains have provided valuable model systems for examining a number of biophysical parameters entirely unrelated to their nucleic acid binding properties. These include the chemical basis for metal-ion affinity and selectivity, thermodynamic properties related to hydrophobic packing and beta-sheet propensities, and constraints on the generation of ligand-binding and potential catalytic sites. These studies have laid the foundation for applications such as the generation of optically detected zinc probes and the design of metal-binding peptides and proteins with desired spectroscopic and chemical properties.
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    NANOSECOND TIME-RESOLVED SPECTROSCOPY OF BIOMOLECULAR PROCESSES (1997)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 26 (1997), S. 327-355 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Over the past two decades, nanosecond absorption and vibrational spectroscopies have developed into powerful tools for monitoring the secondary, tertiary, and quaternary structural relaxations of biological macromolecules under near-physiological conditions of solvent and temperature. Observed through such methods, the dynamic response of a biomolecule to photoinitiated excursions from equilibrium can reveal valuable information about the structure-function relationship, information beyond that obtained from the static structures provided by X-ray crystallography, nuclear magnetic resonance spectroscopy, and other steady-state methods. Most recently, the development of ultra-sensitive polarization techniques for absorption spectroscopy has greatly enhanced the amount of time-resolved structural information that can be obtained from the broadened electronic spectra of biomolecules. This review examines nanosecond absorption, vibrational, and polarized absorption methods, and their applications to protein function and folding, emphasizing the complementary nature of information obtained from electronic and vibrational spectra measured on the nanosecond time scale.
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    EUKARYOTIC TRANSCRIPTION FACTOR-DNA COMPLEXES (1997)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 26 (1997), S. 289-325 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Eukaryotes have three distinct RNA polymerases that catalyze transcription of nuclear genes. RNA polymerase II is responsible for transcribing nuclear genes encoding the messenger RNAs and several small nuclear RNAs. Like RNA polymerases I and III, polymerase II cannot recognize its target promoter directly and initiate transcription without accessory factors. Instead, this large multisubunit enzyme relies on general transcription factors and transcriptional activators and coactivators to regulate transcription from class II promoters. X-ray crystallography and nuclear magnetic resonance spectroscopy have been used to study complexes of general transcription factors and transcriptional activators with their specific DNA targets. This work has provided important structural insights into transcription initiation by polymerase II and the more general problem of DNA sequence recognition.
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    CALCIUM IN CLOSE QUARTERS:Microdomain Feedback in Excitation-Contraction Coupling and Other Cell Biological Phenomena (1997)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 26 (1997), S. 47-82 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Researchers have made good progress in unraveling the molecular mechanisms of excitation-contraction (EC) coupling in striated muscle. Despite this progress, paradoxes abound. In skeletal muscle, the existence of a mechanical coupling between membrane charge movement and activation of sarcoplasmic reticulum (SR) release channels is essentially established, but the contribution of Ca2+-induced Ca2+ release (CICR) to the transient and steady-state components of Ca2+ release remains controversial. In cardiac muscle, the role of CICR as the primary mechanism of EC coupling is well established, but the stability and tight coupling between membrane Ca2+ current and release are paradoxical. Answers may lie in microdomain issues, and in the examination of discrete elementary release events, although quantitative treatments are needed. This review explores the theoretical and experimental methods used and the observations made in the study of microdomain Ca2+.
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    SINGLE-PARTICLE TRACKING:Applications to Membrane Dynamics (1997)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 26 (1997), S. 373-399 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Measurements of trajectories of individual proteins or lipids in the plasma membrane of cells show a variety of types of motion. Brownian motion is observed, but many of the particles undergo non-Brownian motion, including directed motion, confined motion, and anomalous diffusion. The variety of motion leads to significant effects on the kinetics of reactions among membrane-bound species and requires a revision of existing views of membrane structure and dynamics.
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    ADVANCED EPR SPECTROSCOPY ON ELECTRON TRANSFER PROCESSES IN PHOTOSYNTHESIS AND BIOMIMETIC MODEL SYSTEMS (1997)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 26 (1997), S. 495-540 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract This review focuses on the recent advances in EPR spectroscopy as they are applied both to photoinduced electron transfer in the photosynthetic apparatus and to biomimetic systems. The review deals with time-resolved direct-detection cw and pulsed EPR and ENDOR methods, both at conventional bands [X-(9.5 GHz), K-(24 GHz), and Q-(35 GHz)] and at high frequency bands (W-band, 95 GHz, and even highter frequency bands). EPR studies on photosynthetic and model systems in their doublet, triplet and radical pair states are surveyed, including their static and dynamic properties. Applications of time-resolved EPR in studying photoinduced electron and energy transfer in isotropic and anisotropic environments, and the concepts of electron spin polarization and magnetic field effects in photochemical reactions are also reviewed.
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    USE OF SURFACE PLASMON RESONANCE TO PROBE THE EQUILIBRIUM AND DYNAMIC ASPECTS OF INTERACTIONS BETWEEN BIOLOGICAL MACROMOLECULES1 (1997)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 26 (1997), S. 541-566 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Surface plasmon resonance biosensors have become increasingly popular for the qualitative and quantitative characterization of the specific binding of a mobile reactant to a binding partner immobilized on the sensor surface. This article reviews the use of this new technique to measure the binding affinities and the kinetic constants of reversible interactions between biological macromolecules. Immobilization techniques, the most commonly employed experimental strategies, and various analytical approaches are summarized. In recent years, several sources of potential artifacts have been identified: immobilization of the binding partner, steric hindrance of binding to adjacent binding sites at the sensor surface, and finite rate of mass transport of the mobile reactant to the sensor surface. Described here is the influence of these artifacts on the measured binding kinetics and equilibria, together with suggested control experiments.
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    PROTEIN FOLDS IN THE ALL-beta AND ALL-alpha CLASSES (1997)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 26 (1997), S. 597-627 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Analysis of the structures in the Protein Databank, released in June 1996, shows that the number of different protein folds, i.e. the number of different arrangements of major secondary structures and/or chain topologies, is 327. Of these folds, approximately 25% belong to the all-alpha class, 20% belong to the all-beta class, 30% belong to the alpha/beta class, and 25% belong to the alpha + beta class. We describe the types of folds now known for the all-beta and all-alpha classes, emphasizing those that have been discovered recently. Detailed theories for the physical determinants of the structures of most of these folds now exist, and these are reviewed.
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    SIGNALING COMPLEXES:Biophysical Constraints on Intracellular Communication (1998)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 27 (1998), S. 59-75 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract This review surveys the kinds of protein complex that participate in cell communication and identifies, where possible, general principles by which they form and act. It also advances the notion that biophysical constraints imposed by macromolecular crowding and diffusion have had a controlling influence on the evolution of cell signaling pathways. Complexes associated with the bacterial aspartate receptor, with eucaryotic tyrosine kinase receptors, with T-cell receptors, and with focal contacts are examined together with proteins that serve as adaptors, anchors, and scaffolds for signaling complexes. The importance of diffusion in controlling the numbers and locations of signaling complexes is discussed, as is the special role played by membranes in signaling pathways.
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    STRUCTURE, DYNAMICS, AND FUNCTION OF CHROMATIN IN VITRO (1998)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 27 (1998), S. 285-327 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract The substrates for the essential biological processes of transcription, replication, recombination, DNA repair, and cell division are not naked DNA; rather, they are protein-DNA complexes known as chromatin, in one or another stage of a hierarchical series of compactions. These are exciting times for students of chromatin. New studies provide incontrovertible evidence linking chromatin structure to function. Exceptional progress has been made in studies of the structure of chromatin subunits. Surprising new dynamic properties have been discovered. And, much progress has been made in dissecting the functional roles of specific chromatin proteins and domains. This review focuses on in vitro studies of chromatin structure, dynamics, and function.
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    INHIBITORS OF HIV-1 PROTEASE: A Major Success of Structure-Assisted Drug Design1 (1998)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 27 (1998), S. 249-284 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Retroviral protease (PR) from the human immunodeficiency virus type 1 (HIV-1) was identified over a decade ago as a potential target for structure-based drug design. This effort was very successful. Four drugs are already approved, and others are undergoing clinical trials. The techniques utilized in this remarkable example of structure-assisted drug design included crystallography, NMR, computational studies, and advanced chemical synthesis. The development of these drugs is discussed in detail. Other approaches to designing HIV-1 PR inhibitors, based on the concepts of symmetry and on the replacement of a water molecule that had been found tetrahedrally coordinated between the enzyme and the inhibitors, are also discussed. The emergence of drug-induced mutations of HIV-1 PR leads to rapid loss of potency of the existing drugs and to the need to continue the development process. The structural basis of drug resistance and the ways of overcoming this phenomenon are mentioned.
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    SIMULATION OF PROKARYOTIC GENETIC CIRCUITS (1998)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 27 (1998), S. 199-224 
    Details
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Biochemical and genetic approaches have identified the molecular mechanisms of many genetic reactions, particularly in bacteria. Now a comparably detailed understanding is needed of how groupings of genes and related protein reactions interact to orchestrate cellular functions over the cell cycle, to implement preprogrammed cellular development, or to dynamically change a cell's processes and structures in response to environmental signals. Simulations using realistic, molecular-level models of genetic mechanisms and of signal transduction networks are needed to analyze dynamic behavior of multigene systems, to predict behavior of mutant circuits, and to identify the design principles applicable to design of genetic regulatory circuits. When the underlying design rules for regulatory circuits are understood, it will be far easier to recognize common circuit motifs, to identify functions of individual proteins in regulation, and to redesign circuits for altered functions.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.27.1.199
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    CYTOCHROME C OXIDASE: Structure and Spectroscopy (1998)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 27 (1998), S. 329-356 
    Details
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Cytochrome c oxidase, the terminal enzyme of the respiratory chains of mitochondria and aerobic bacteria, catalyzes electron transfer from cytochrome c to molecular oxygen, reducing the latter to water. Electron transfer is coupled to proton translocation across the membrane, resulting in a proton and charge gradient that is then employed by the F0F1-ATPase to synthesize ATP. Over the last years, substantial progress has been made in our understanding of the structure and function of this enzyme. Spectroscopic techniques such as EPR, absorbance and resonance Raman spectroscopy, in combination with site-directed mutagenesis work, have been successfully applied to elucidate the nature of the cofactors and their ligands, to identify key residues involved in proton transfer, and to gain insight into the catalytic cycle and the structures of its intermediates. Recently, the crystal structures of a bacterial and a mitochondrial cytochrome c oxidase have been determined. In this review, we provide an overview of the crystal structures, summarize recent spectroscopic work, and combine structural and spectroscopic data in discussing mechanistic aspects of the enzyme. For the latter, we focus on the structure of the oxygen intermediates, proton-transfer pathways, and the much-debated issue of how electron transfer in the enzyme might be coupled to proton translocation.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.27.1.329
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    THE USE OF 2H, 13C, 15N MULTIDIMENSIONAL NMR GTO STUDY THE STRUCTURE AND DYNAMICS OF PROTEINS (1998)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 27 (1998), S. 357-406 
    Details
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract During the past thirty years, deuterium labeling has been used to improve the resolution and sensitivity of protein NMR spectra used in a wide variety of applications. Most recently, the combination of triple resonance experiments and 2H, 13C, 15N labeled samples has been critical to the solution structure determination of several proteins with molecular weights on the order of 30 kDa. Here we review the developments in isotopic labeling strategies, NMR pulse sequences, and structure-determination protocols that have facilitated this advance and hold promise for future NMR-based structural studies of even larger systems. As well, we detail recent progress in the use of solution 2H NMR methods to probe the dynamics of protein sidechains.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.27.1.357
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    CRYSTALLOGRAPHIC STRUCTURES OF THE HAMMERHEAD RIBOZYME: Relationship to Ribozyme Folding and Catalysis (1998)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 27 (1998), S. 475-502 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract The hammerhead ribozyme is a small catalytic RNA that cleaves a target phosphodiester bond in a reaction dependent on divalent metal ions. Crystal structures of the hammerhead reveal the tertiary fold of an enzymatic "ground state" of the molecule; however, they do not clarify the catalytic mechanism of the ribozyme, presumably because a significant conformational rearrangement is required to reach an enzymatic transition state. The structural domains seen in the hammerhead can be related to sequence or structural motifs in transfer and ribosomal RNAs, suggesting that they represent tertiary building blocks that will be found in large, complex RNAs.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.27.1.475
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    RAMAN SPECTROSCOPY OF PROTEIN AND NUCLEIC ACID ASSEMBLIES (1999)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 28 (1999), S. 1-27 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract The Raman spectrum of a protein or nucleic acid consists of numerous discrete bands representing molecular normal modes of vibration and serves as a sensitive and selective fingerprint of three-dimensional structure, intermolecular interactions, and dynamics. Recent improvements in instrumentation, coupled with innovative approaches in experimental design, dramatically increase the power and scope of the method, particularly for investigations of large supramolecular assemblies. Applications are considered that involve the use of (a) time-resolved Raman spectroscopy to elucidate assembly pathways in icosahedral viruses, (b) polarized Raman microspectroscopy to determine detailed structural parameters in filamentous viruses, (c) ultraviolet-resonance Raman spectroscopy to probe selective DNA and protein residues in nucleoprotein complexes, and (d) difference Raman methods to understand mechanisms of protein/DNA recognition in gene regulatory and chromosomal complexes.
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    URL: http://dx.doi.org/10.1146/annurev.biophys.28.1.1
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    PLECKSTRIN HOMOLOGY DOMAINS: A Common Fold with Diverse Functions (1998)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 27 (1998), S. 503-528 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Pleckstrin homology (PH) motifs are approximately 100 amino-acid residues long and have been identified in nearly 100 different eukaryotic proteins, many of which participate in cell signaling and cytoskeletal regulation. Despite minimal sequence homology, the three-dimensional structures are remarkably conserved. This review gives an overview of the PH domain architecture and examines the best-studied examples in an attempt to understand their function.
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    URL: http://dx.doi.org/10.1146/annurev.biophys.27.1.503
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    MULTIPROTEIN-DNA COMPLEXES IN TRANSCRIPTIONAL REGULATION (1999)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 28 (1999), S. 29-56 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Transcription in eukaryotes is frequently regulated by a mechanism termed combinatorial control, whereby several different proteins must bind DNA in concert to achieve appropriate regulation of the downstream gene. X-ray crystallographic studies of multiprotein complexes bound to DNA have been carried out to investigate the molecular determinants of complex assembly and DNA binding. This work has provided important insights into the specific protein-protein and protein-DNA interactions that govern the assembly of multiprotein regulatory complexes. The results of these studies are reviewed here, and the general insights into the mechanism of combinatorial gene regulation are discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.28.1.29
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    MODERN APPLICATIONS OF ANALYTICAL ULTRACENTRIFUGATION (1999)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 28 (1999), S. 75-100 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Analytical ultracentrifugation is a classical method of biochemistry and molecular biology. Because it is a primary technique, sedimentation can provide first-principle hydrodynamic and first-principle thermodynamic information for nearly any molecule, in a wide range of solvents and over a wide range of solute concentrations. For many questions, it is the technique of choice. This review stresses what information is available from analytical ultracentrifugation and how that information is being extracted and used in contemporary applications.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.28.1.75
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    NITROXIDE SPIN-SPIN INTERACTIONS: Applications to Protein Structure and Dynamics (1999)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 28 (1999), S. 129-153 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Measurement of the distance between two spin label probes in proteins permits the spatial orientation of elements of defined secondary structure. By using site-directed spin labeling, it is possible to determine multiple distance constraints and thereby build tertiary and quaternary structural models as well as measure the kinetics of structural changes. New analytical methods for determining interprobe distances and relative orientations for uniquely oriented spin labels have been developed using global analysis of multifrequency electron paramagnetic resonance data. New methods have also been developed for determining interprobe distances for randomly oriented spin labels. These methods are being applied to a wide range of structural problems, including peptides, soluble proteins, and membrane proteins, that are not readily characterized by other structural techniques.
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    URL: http://dx.doi.org/10.1146/annurev.biophys.28.1.129
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    MOLECULAR DYNAMICS SIMULATIONS OF BIOMOLECULES: Long-Range Electrostatic Effects (1999)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 28 (1999), S. 155-179 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Current computer simulations of biomolecules typically make use of classical molecular dynamics methods, as a very large number (tens to hundreds of thousands) of atoms are involved over timescales of many nanoseconds. The methodology for treating short-range bonded and van der Waals interactions has matured. However, long-range electrostatic interactions still represent a bottleneck in simulations. In this article, we introduce the basic issues for an accurate representation of the relevant electrostatic interactions. In spite of the huge computational time demanded by most biomolecular systems, it is no longer necessary to resort to uncontrolled approximations such as the use of cutoffs. In particular, we discuss the Ewald summation methods, the fast particle mesh methods, and the fast multipole methods. We also review recent efforts to understand the role of boundary conditions in systems with long-range interactions, and conclude with a short perspective on future trends.
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    URL: http://dx.doi.org/10.1146/annurev.biophys.28.1.155
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    DNA REPAIR MECHANISMS FOR THE RECOGNITION AND REMOVAL OF DAMAGED DNA BASES (1999)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 28 (1999), S. 101-128 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Recent structural and biochemical studies have begun to illuminate how cells solve the problems of recognizing and removing damaged DNA bases. Bases damaged by environmental, chemical, or enzymatic mechanisms must be efficiently found within a large excess of undamaged DNA. Structural studies suggest that a rapid damage-scanning mechanism probes for both conformational deviations and local deformability of the DNA base stack. At susceptible lesions, enzyme-induced conformational changes lead to direct interactions with specific damaged bases. The diverse array of damaged DNA bases are processed through a two-stage pathway in which damage-specific enzymes recognize and remove the base lesion, creating a common abasic site intermediate that is processed by damage-general repair enzymes to restore the correct DNA sequence.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.28.1.101
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    THE LYSOSOMAL CYSTEINE PROTEASES (1999)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 28 (1999), S. 181-204 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract A significant number of exciting papain-like cysteine protease structures have been determined by crystallographic methods over the last several years. This trove of data allows for an analysis of the structural features that empower these molecules as they efficiently carry out their specialized tasks. Although the structure of the paradigm for the family, papain, has been known for twenty years, recent efforts have reaped several structures of specialized mammalian enzymes. This review first covers the commonalities of architecture and purpose of the papain-like cysteine proteases. From that broad platform, each of the lysosomal enzymes for which there is an X-ray structure (or structures) is then examined to gain an understanding of what structural features are used to customize specificity and activity. Structure-based design of inhibitors to control pathological cysteine protease activity will also be addressed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.28.1.181
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    STRUCTURE AND CONFORMATION OF COMPLEX CARBOHYDRATES OF GLYCOPROTEINS, GLYCOLIPIDS, AND BACTERIAL POLYSACCHARIDES (1999)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 28 (1999), S. 269-293 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract For nuclear magnetic resonance determinations of the conformation of oligosaccharides in solution, simple molecular mechanics calculations and nuclear Overhauser enhancement measurements are adequate for small oligosaccharides that adopt single, relatively rigid conformations. Polysaccharides and larger or more flexible oligosaccharides generally require additional types of data, such as scalar and dipolar coupling constants, which are most conveniently measured in 13C-enriched samples. Nuclear magnetic resonance relaxation data provide information on the dynamics of oligosaccharides, which involves several different types of internal motion. Oligosaccharides complexed with lectins and antibodies have been successfully studied both by X-ray crystallography and by nuclear magnetic resonance spectroscopy. The complexes have been shown to be stabilized by a combination of polar hydrogen bonding interactions and van der Waals attractions. Although theoretical calculations of the conformation and stability of free oligosaccharides and of complexes with proteins can be carried out by molecular mechanics methods, the role of solvent water for these highly polar molecules continues to present computational problems.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.28.1.269
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    THE PROTEASOME (1999)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 28 (1999), S. 295-317 
    Details
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Proteasomes are large multisubunit proteases that are found in the cytosol, both free and attached to the endoplasmic reticulum, and in the nucleus of eukaryotic cells. Their ubiquitous presence and high abundance in these compartments reflects their central role in cellular protein turnover. Proteasomes recognize, unfold, and digest protein substrates that have been marked for degradation by the attachment of a ubiquitin moiety. Individual subcomplexes of the complete 26S proteasome are involved in these different tasks: The ATP-dependent 19S caps are believed to unfold substrates and feed them to the actual protease, the 20S proteasome. This core particle appears to be more ancient than the ubiquitin system. Both prokaryotic and archaebacterial ancestors have been identified. Crystal structures are now available for the E. coli proteasome homologue and the T. acidophilum and S. cerevisiae 20S proteasomes. All three enzymes are cylindrical particles that have their active sites on the inner walls of a large central cavity. They share the fold and a novel catalytic mechanism with an N-terminal nucleophilic threonine, which places them in the family of Ntn (N terminal nucleophile) hydrolases. Evolution has added complexity to the comparatively simple prokaryotic prototype. This minimal proteasome is a homododecamer made from two hexameric rings stacked head to head. Its heptameric version is the catalytic core of archaebacterial proteasomes, where it is sandwiched between two inactive antichambers that are made up from a different subunit. In eukaryotes, both subunits have diverged into seven different subunits each, which are present in the particle in unique locations such that a complex dimer is formed that has six active sites with three major specificities that can be attributed to individual subunits. Genetic, biochemical, and high-resolution electron microscopy data, but no crystal structures, are available for the 19S caps. A first step toward a mechanistic understanding of proteasome activation and regulation has been made with the elucidation of the X-ray structure of the alternative, mammalian proteasome activator PA28.
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    URL: http://dx.doi.org/10.1146/annurev.biophys.28.1.295
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    The Biology of Hematopoietic Stem Cells (1995)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Cell and Developmental Biology 11 (1995), S. 35-71 
    Details
    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.cb.11.110195.000343
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    Biological Atomic Force Microscopy: From Microns to Nanometers and Beyond (1995)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Cell and Developmental Biology 11 (1995), S. 241-265 
    Details
    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.cb.11.110195.001325
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