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  • Wiley-Blackwell  (48,397)
  • American Institute of Physics  (31,801)
  • American Physical Society  (27,364)
  • Oxford University Press  (18,242)
  • 2020-2023  (43)
  • 1980-1984  (115,513)
  • 1940-1944  (10,248)
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  • 1
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    Natural Radioactivity of the Crystalline Basement Rocks of the Peloritani Mountains (North-Eastern Sicily, Italy): Measurements and Radiological Hazard (2021)
    Oxford University Press
    Details
    Publication Date: 2022-03-02
    Description: Crystalline rocks can produce dangerous radiation levels on the basis of their content in radioisotopes. Here, we report radiological data from 10 metamorphic and igneous rock samples collected from the crystalline basement of the Peloritani Mountains (southern Italy). In order to evaluate the radiological properties of these rocks, the gamma radiation and the radon emanation have been measured. Moreover, since some of these rocks are employed as building materials, we assess the potential hazard for population connected to their use. Gamma spectroscopy was used to measure the 226Ra, 232Th and 40K activity concentration, whereas the radon emanation was investigated by using a RAD 7 detector. The results show 226Ra, 232Th and 40K activity concentration values ranging from (17 ± 4) to (56 ± 8) Bq kg-1, (14 ± 3) to (77 ± 14) Bq kg-1 and (167 ± 84) to (1760 ± 242) Bq kg-1, respectively. Values of the annual effective dose equivalent outdoor range from 0.035 to 0.152 mSv y-1, whereas the gamma index is in the range of 0.22-0.98. The 222Rn emanation coefficient and the 222Rn surface exhalation rate vary from (0.63 ± 0.3) to (8.27 ± 1.6)% and from (0.12 ± 0.03) to (2.75 ± 0.17) Bq m-2 h-1, respectively. The indoor radon derived from the building use of these rocks induces an approximate contribution to the annual effective dose ranging from 8 to 176 μSv y-1. All the obtained results suggest that the crystalline rocks from the Peloritani Mountains are not harmful for the residential population, even though they induce annual effective doses due to terrestrial gamma radiation above the worldwide average values. Moreover, their use as building materials does not produce significant health hazards connected to the indoor radon exposure.
    Description: Published
    Description: 452–464
    Description: 6A. Geochimica per l'ambiente e geologia medica
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 2
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    3-D attenuation image of fluid storage and tectonic interactions across the Pollino fault network (2022)
    Oxford University Press
    Details
    Publication Date: 2022-03-07
    Description: The Pollino range is a region of slow deformation where earthquakes generally nucleate on low-angle normal faults. Recent studies have mapped fault structures and identified fluid related dynamics responsible for historical and recent seismicity in the area. Here, we apply the coda-normalization method at multiple frequencies and scales to image the 3-D P-wave attenuation (QP) properties of its slowly deforming fault network. The wide-scale average attenuation properties of the Pollino range are typical for a stable continental block, with a dependence of QP on frequency of Q−1 P = (0.0011   0.0008) f (0.36 0.32). Using only waveforms comprised in the area of seismic swarms, the dependence of attenuation on frequency increases [Q−1 P = (0.0373   0.0011) f (−0.59 0.01)], as expected when targeting seismically active faults. A shallow very-low-attenuation anomaly (max depth of 4–5 km) caps the seismicity recorded within the western cluster 1 of the Pollino seismic sequence (2012, maximum magnitude Mw = 5.1). High-attenuation volumes below this anomaly are likely related to fluid storage and comprise the western and northern portions of cluster 1 and the Mercure basin. These anomalies are constrained to the NW by a sharp low-attenuation interface, corresponding to the transition towards the eastern unit of the Apennine Platform under the Lauria mountains. The low-seismicity volume between cluster 1 and cluster 2 (maximum magnitude Mw = 4.3, east of the primary) shows diffuse low-to-average attenuation features. There is no clear indication of fluid-filled pathways between the two clusters resolvable at our resolution. In this volume, the attenuation values are anyway lower than in recognized low-attenuation blocks, like the Lauria Mountain and Pollino Range. As the volume develops in a region marked at surface by small-scale cross-faulting, it suggests no actual barrier between clusters, more likely a system of small locked fault patches that can break in the future. Our model loses resolution at depth, but it can still resolve a 5-to-15-km-deep high-attenuation anomaly that underlies the Castrovillari basin. This anomaly is an ideal deep source for the SE-to-NW migration of historical seismicity. Our novel deep structural maps support the hypothesis that the Pollino sequence has been caused by a mechanism of deep and lateral fluid-induced migration.
    Description: Natural Environment Research Council (NERC) Centre for Doctoral Training (CDT) in Oil and Gas. University of Aberdeen.
    Description: Published
    Description: 536–547
    Description: 4T. Sismicità dell'Italia
    Description: JCR Journal
    Keywords: body waves ; seismic attenuation ; seismic tomography ; 04.06. Seismology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 3
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    Genetic diversity and connectivity of southern right whales (Eubalaena australis) found in the Brazil and Chile-Peru wintering grounds and the South Georgia (Islas Georgias del Sur) feeding ground (2020)
    Oxford University Press
    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 Carroll, E. L., Ott, P. H., McMillan, L. F., Galletti Vernazzani, B., Neveceralova, P., Vermeulen, E., Gaggiotti, O. E., Andriolo, A., Baker, C. S., Bamford, C., Best, P., Cabrera, E., Calderan, S., Chirife, A., Fewster, R. M., Flores, P. A. C., Frasier, T., Freitas, T. R. O., Groch, K., Hulva, P., Kennedy, A., Leaper, R., Leslie, M. S., Moore, M., Oliveira, L., Seger, J., Stepien, E. N., Valenzuela, L. O., Zerbini, A., & Jackson, J. A. Genetic diversity and connectivity of southern right whales (Eubalaena australis) found in the Brazil and Chile-Peru wintering grounds and the South Georgia (Islas Georgias del Sur) feeding ground. Journal of Heredity, 111(3), (2020): 263-276, doi:10.1093/jhered/esaa010.
    Description: As species recover from exploitation, continued assessments of connectivity and population structure are warranted to provide information for conservation and management. This is particularly true in species with high dispersal capacity, such as migratory whales, where patterns of connectivity could change rapidly. Here we build on a previous long-term, large-scale collaboration on southern right whales (Eubalaena australis) to combine new (nnew) and published (npub) mitochondrial (mtDNA) and microsatellite genetic data from all major wintering grounds and, uniquely, the South Georgia (Islas Georgias del Sur: SG) feeding grounds. Specifically, we include data from Argentina (npub mtDNA/microsatellite = 208/46), Brazil (nnew mtDNA/microsatellite = 50/50), South Africa (nnew mtDNA/microsatellite = 66/77, npub mtDNA/microsatellite = 350/47), Chile–Peru (nnew mtDNA/microsatellite = 1/1), the Indo-Pacific (npub mtDNA/microsatellite = 769/126), and SG (npub mtDNA/microsatellite = 8/0, nnew mtDNA/microsatellite = 3/11) to investigate the position of previously unstudied habitats in the migratory network: Brazil, SG, and Chile–Peru. These new genetic data show connectivity between Brazil and Argentina, exemplified by weak genetic differentiation and the movement of 1 genetically identified individual between the South American grounds. The single sample from Chile–Peru had an mtDNA haplotype previously only observed in the Indo-Pacific and had a nuclear genotype that appeared admixed between the Indo-Pacific and South Atlantic, based on genetic clustering and assignment algorithms. The SG samples were clearly South Atlantic and were more similar to the South American than the South African wintering grounds. This study highlights how international collaborations are critical to provide context for emerging or recovering regions, like the SG feeding ground, as well as those that remain critically endangered, such as Chile–Peru.
    Description: This work was supported by the EU BEST 2.0 medium grant 1594 and UK DARWIN PLUS grant 057 and additional funding from the World Wildlife Fund GB107301. The collection of the Chile–Peru sample was supported by the Global Greengrants Fund and the Pacific Whale Foundation. The collection of the Brazilian samples was supported through grants by the Brazilian National Research Council to Paulo H. Ott (CNPq proc. n° 144064/98-7) and Paulo A.C. Flores (CNPq proc. n° 146609/1999-9) and with support from the World Wildlife Fund (WWF-Brazil). The collection of the South African samples was supported by the Global Greengrants Fund, the Pacific Whale Foundation and Charles University Grant Agency (1140217). E.L.C. was partially supported by a Rutherford Discovery Fellowship from the Royal Society of New Zealand. This study forms part of the Ecosystems component of the British Antarctic Survey Polar Sciences for Planet Earth Programme, funded by the Natural Environment Research Council.
    Keywords: population structure ; connectivity ; migration ; gene flow
    Repository Name: Woods Hole Open Access Server
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  • 4
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    Transfer learning: Improving neural network based prediction of earthquake ground shaking for an area with insufficient training data (2021)
    Oxford University Press
    Details
    Publication Date: 2022-03-16
    Description: This article has been accepted for publication in Geophysical Journal International ©: The Authors 2021. Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved. Uploaded in accordance with the publisher's self-archiving policy.
    Description: In a recent study (Jozinovi\'c et al, 2020) we showed that convolutional neural networks (CNNs) applied to network seismic traces can be used for rapid prediction of earthquake peak ground motion intensity measures (IMs) at distant stations using only recordings from stations near the epicenter. The predictions are made without any previous knowledge concerning the earthquake location and magnitude. This approach differs from the standard procedure adopted by earthquake early warning systems (EEWSs) that rely on location and magnitude information. In the previous study, we used 10 s, raw, multistation waveforms for the 2016 earthquake sequence in central Italy for 915 events (CI dataset). The CI dataset has a large number of spatially concentrated earthquakes and a dense station network. In this work, we applied the CNN model to an area around the VIRGO gravitational waves observatory sited near Pisa, Italy. In our initial application of the technique, we used a dataset consisting of 266 earthquakes recorded by 39 stations. We found that the CNN model trained using this smaller dataset performed worse compared to the results presented in the original study by Jozinovi\'c et al. (2020). To counter the lack of data, we adopted transfer learning (TL) using two approaches: first, by using a pre-trained model built on the CI dataset and, next, by using a pre-trained model built on a different (seismological) problem that has a larger dataset available for training. We show that the use of TL improves the results in terms of outliers, bias, and variability of the residuals between predicted and true IMs values. We also demonstrate that adding knowledge of station positions as an additional layer in the neural network improves the results. The possible use for EEW is demonstrated by the times for the warnings that would be received at the station PII.
    Description: RISE (Union's Horizon 2020 research and innovation programme, grant agreement No.821115)
    Description: Published
    Description: 704–718
    Description: 5T. Sismologia, geofisica e geologia per l'ingegneria sismica
    Description: JCR Journal
    Keywords: Physics - Geophysics; Physics - Geophysics ; machine learning ; ground motion prediction ; seismology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 5
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    Azimuthal anisotropy from Eikonal Tomography: example from ambient-noise measurements in the AlpArray network (2021)
    Oxford University Press
    Details
    Publication Date: 2021-12-24
    Description: This article has been accepted for publication in Geophysical Journal International ©: The Authors 2021. Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved. Uploaded in accordance with the publisher's self-archiving policy.
    Description: Ambient-noise records from the AlpArray network are used to measure Rayleigh wave phase velocities between more than 150,000 station pairs. From these, azimuthally anisotropic phase-velocity maps are obtained by applying the Eikonal tomography method. Several synthetic tests are shown to study the bias in the Ψ2 anisotropy. There are two main groups of bias, the first one caused by interference between refracted/reflected waves and the appearance of secondary wavefronts that affect the phase travel-time measurements. This bias can be reduced if the amplitude field can be estimated correctly. Another source of error is related to the incomplete reconstruction of the travel-time field that is only sparsely sampled due to the receiver locations. Both types of bias scale with the magnitude of the velocity heterogeneities. Most affected by the spurious Ψ2 anisotropy are areas inside and at the border of low-velocity zones. In the isotropic velocity distribution, most of the bias cancels out if the azimuthal coverage is good. Despite the lack of resolution in many parts of the surveyed area, we identify a number of anisotropic structures that are robust: in the central Alps, we find a layered anisotropic structure, arc-parallel at midcrustal depths and arc-perpendicular in the lower crust. In contrast, in the eastern Alps, the pattern is more consistently E-W oriented which we relate to the eastward extrusion. The northern Alpine forleand exhibits a preferential anisotropic orientation that is similar to SKS observations in the lowermost crust and uppermost mantle.
    Description: German Science Foundation (SPP-2017, Project Ha 2403/21-1); Swiss National Science Foundation SINERGIA Project CRSII2-154434/1 (Swiss-AlpArray); Progetto Pianeta Dinamico, finanziamento MUR-INGV, Task S2 – 2021
    Description: Published
    Description: 151–170
    Description: 1T. Struttura della Terra
    Description: JCR Journal
    Keywords: Seismic anisotropy ; Seismic interferometry ; Seismic tomography ; Wave propagation ; Continental tectonics: compressional ; 04.01. Earth Interior ; 04.06. Seismology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 6
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    The focal mechanism of the 7 September 1920, Mw 6.5 earthquake: insights into the seismotectonics of the Lunigiana–Garfagnana area, Tuscany, Italy (2021)
    Oxford University Press
    Details
    Publication Date: 2021-12-15
    Description: This article has been accepted for publication in Geophysical Journal International ©: The Authors 2022. Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved. Uploaded in accordance with the publisher's self-archiving policy.
    Description: To understand the seismotectonics and the seismic hazard of the study sector of the Northern Apennines (Italy), one of the most important earthquakes of magnitude Mw = 6.5 which struck the Lunigiana and Garfagnana areas (Tuscany) on 7 September 1920 should be studied. Given the early instrumental epoch of the event, neither geometric and kinematic information on the fault-source nor its fault-plane solution were available. Both areas were candidates for hosting the source fault and there was uncertainty between a normal fault with Apenninic direction or an anti-Apenninic strike-slip. We retrieved 11 focal parameters (including the fault-plane solution) of the 1920 earthquake. Only macroseismic intensity information (from 499 inhabited centres) through the KF-NGA inversion technique was used. This technique uses a Kinematic model of the earthquake source and speeds up the calculation by a Genetic Algorithm with Niching. The result is a pure dip-slip focal solution. The intrinsic ambiguities of the KF-NGA method (±180° on the rake angle; choice of the fault plane between the two nodal planes) were solved with field and seismotectonic evidence. The earthquake was generated by a normal fault (rake angle = 265° ± 8°) with an Apennine direction (114° ± 5°) and dipping 38° ± 6° towards SW. The likely candidate for hosting the source-fault in 1920 is the Compione-Comano fault that borders the NE edge of the Lunigiana graben. The KF-NGA algorithm proved to be invaluable for studying the kinematics of early instrumental earthquakes and allowed us to uniquely individuate, for the first time ever, the seismogenic source of the 1920 earthquake. Our findings have implications in hazard computation and seismotectonic contexts.
    Description: Published
    Description: 1465–1477
    Description: 4T. Sismicità dell'Italia
    Description: JCR Journal
    Keywords: Inverse theory ; Body waves ; Earthquake source observations ; Seismicity and tectonics ; Dynamics: seismotectonics ; Fractures, faults, and high strain deformation zones ; 04.06. Seismology
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  • 7
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    Intraplate Basalt Alkalinity Modulated by a Lithospheric Mantle Filter at the Dunedin Volcano (New Zealand) (2021)
    Oxford University Press
    Details
    Publication Date: 2021-12-22
    Description: Systematic variations in the crystal cargo and whole-rock isotopic compositions of mantle-derived basalts in the intraplate Dunedin Volcano (New Zealand) indicate the influence of a complex mantle-to-crust polybaric plumbing system. Basaltic rocks define a compositional spectrum from low-alkali basalts through mid-alkali basalts to high-alkali basalts. High-alkali basalts display clinopyroxene crystals with sector (hourglass) and oscillatory zoning (Mg#61–82) as well as Fe-rich green cores (Mg#43–69), whereas low-alkali basalts are characterized by clinopyroxenes with unzoned overgrowths (Mg#69–83) on resorbed mafic cores (Mg#78–88), coexisting with reversely zoned plagioclase crystals (An43–68 to An60–84 from core to rim). Complex magma dynamics are indicated by distinctive compositional variations in clinopyroxene phenocrysts, with Cr-rich zones (Mg#74–87) indicating continuous recharge by more mafic magmas. Crystallization of olivine, clinopyroxene and titanomagnetite occurred within a polybaric plumbing system extending from upper mantle to mid-crustal depths (485–1059 MPa and 1147–1286°C), whereas crystallization of plagioclase with subordinate clinopyroxene and titanomagnetite proceeded towards shallower crustal levels. The compositions of high-alkali basalts and mid-alkali basalts resemble those of ocean island basalts and are characterized by FOZO-HIMU isotopic signatures (87Sr/86Sri = 0.70277–0.70315, 143Nd/144Ndi = 0.51286–0.51294 and 206Pb/204Pb = 19.348–20.265), whereas low-alkali basalts have lower incompatible element abundances and isotopic compositions trending towards EMII (87Sr/86Sri = 0.70327–70397, 143Nd/144Ndi = 0.51282–0.51286 and 206Pb/204Pb = 19.278–19.793). High- and mid-alkali basalt magmas mostly crystallized in the lower crust, whereas low-alkali basalt magma recorded deeper upper mantle clinopyroxene crystallization before eruption. The variable alkaline character and isotope composition may result from interaction of low-alkaline melts derived from the asthenosphere with melts derived from lithospheric mantle, possibly initiated by asthenospheric melt percolation. The transition to more alkaline compositions was induced by variable degrees of melting of metasomatic lithologies in the lithospheric mantle, leading to eruption of predominantly small-volume, high-alkali magmas at the periphery of the volcano. Moreover, the lithosphere imposed a filtering effect on the alkalinity of these intraplate magmas. As a consequence, the eruption of low-alkali basalts with greater asthenospheric input was concentrated at the centre of the volcano, where the plumbing system was more developed.
    Description: Published
    Description: egab062
    Description: 2V. Struttura e sistema di alimentazione dei vulcani
    Description: 3V. Proprietà chimico-fisiche dei magmi e dei prodotti vulcanici
    Description: 4V. Processi pre-eruttivi
    Description: JCR Journal
    Keywords: alkali basalts ; Dunedin Volcano ; thermobarometry ; primary magma ; lithospheric mantle filter ; Igneous Petrology ; Thermobarometry ; Mantle melting and metasomatism ; Magmatic plumbing systems
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 8
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    Responses of benthic calcifying algae to ocean acidification differ between laboratory and field settings (2022)
    Oxford University Press
    Details
    Publication Date: 2022-06-24
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Page, H. N., Bahr, K. D., Cyronak, T., Jewett, E. B., Johnson, M. D., & McCoy, S. J. Responses of benthic calcifying algae to ocean acidification differ between laboratory and field settings. Ices Journal of Marine Science, 79(1), (2022): 1–11, https://doi.org/10.1093/icesjms/fsab232.
    Description: Accurately predicting the effects of ocean and coastal acidification on marine ecosystems requires understanding how responses scale from laboratory experiments to the natural world. Using benthic calcifying macroalgae as a model system, we performed a semi-quantitative synthesis to compare directional responses between laboratory experiments and field studies. Variability in ecological, spatial, and temporal scales across studies, and the disparity in the number of responses documented in laboratory and field settings, make direct comparisons difficult. Despite these differences, some responses, including community-level measurements, were consistent across laboratory and field studies. However, there were also mismatches in the directionality of many responses with more negative acidification impacts reported in laboratory experiments. Recommendations to improve our ability to scale responses include: (i) developing novel approaches to allow measurements of the same responses in laboratory and field settings, and (ii) researching understudied calcifying benthic macroalgal species and responses. Incorporating these guidelines into research programs will yield data more suitable for robust meta-analyses and will facilitate the development of ecosystem models that incorporate proper scaling of organismal responses to in situ acidification. This, in turn, will allow for more accurate predictions of future changes in ecosystem health and function in a rapidly changing natural climate.
    Description: We would like to thank the Ocean Carbon and Biogeochemistry Program for organizing the fourth U.S. Ocean Acidification Principal Investigators meeting, which is where this synthesis was conceived. HNP was a postdoctoral research fellow at Mote Marine Laboratory. MDJ is a postdoctoral scholar at Woods Hole Oceanographic Institution. SJM is a Norma J. Lang early career fellow of the Phycological Society of America.
    Repository Name: Woods Hole Open Access Server
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  • 9
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    Spectral elements numerical simulation of the 2009 L’Aquila earthquake on a detailed reconstructed domain (2022)
    Oxford University Press
    Details
    Publication Date: 2022-06-22
    Description: In this paper we simulate the earthquake that hit the city of L'Aquila on the 6th of April 2009 using SPEED (SPectral Elements in Elastodynamics with Discontinuous Galerkin), an open-source code able to simulate the propagation of seismic waves in complex three-dimensional (3D) domains. Our model includes an accurate 3D recon- struction of the Quaternary deposits, according to the most up-to-date data obtained from the Microzonation studies in Central Italy and a detailed model of the topography incorporated using a newly developed tool (May et al. 2021). The sensitivity of our results with respect to dfferent kinematic seismic sources is inves- tigated. The results obtained are in good agreement with the recordings at the available seismic stations at epicentral distances within a range of 20km. Finally, a blind source prediction scenario application shows a reasonably good agreement between simulations and recordings can be obtained by simulating stochastic rupture realizations with basic input data. These results, although limited to nine simulated scenarios, demonstrate that it is possible to obtain a satisfactory reconstruction of a ground shaking scenario employing a stochastic source constrained on a limited amount of ex-ante information. A similar approach can be used to model future and past earthquakes for which little or no information is typically available, with potential relevant implications for seismic risk assessment.
    Description: Published
    Description: 29–49
    Description: 3T. Fisica dei terremoti e Sorgente Sismica
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 10
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    Environmental effects and seismogenic source characterization of the December 2020 earthquake sequence near Petrinja, Croatia (2022)
    Oxford University Press
    Details
    Publication Date: 2022-06-22
    Description: This article has been accepted for publication in Geophysical Journal International ©: The Authors 2022. Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved. Uploaded in accordance with the publisher's self-archiving policy.
    Description: On 29 December 2020, a shallow earthquake of magnitude Mw 6.4 struck northern Croatia, near the town of Petrinja, more than 24 hours after a strong foreshock (Ml 5). We formed a reconnaissance team of European geologists and engineers, from Croatia, Slovenia, France, Italy and Greece, rapidly deployed in the field to map the evidence of coseismic environmental effects. In the epicentral area, we recognized surface deformation, such as tectonic breaks along the earthquake source at the surface, liquefaction features (scattered in the fluvial plains of Kupa, Glina and Sava rivers), and slope failures, both caused by strong motion. Thanks to this concerted, collective and meticulous work, we were able to document and map a clear and unambiguous coseismic surface rupture associated with the main shock. The surface rupture appears discontinuous, consisting of multi-kilometer en échelon right stepping sections, along a NW-SE striking fault that we call the Petrinja-Pokupsko Fault (PPKF). The observed deformation features, in terms of kinematics and trace alignments, are consistent with slip on a right lateral fault, in agreement with the focal solution of the main shock. We found mole tracks, displacement on faults affecting natural features (e. g. drainage channels), scarplets, and more frequently breaks of anthropogenic markers (roads, fences). The surface rupture is observed over a length of ∼13 km from end-to-end, with a maximum displacement of 38 cm, and an average displacement of ∼10 cm. Moreover, the liquefaction extends over an area of nearly 600 km² around the epicenter. Typology of liquefaction features include sand blows, lateral spreading phenomenon along the road and river embankments, as well as sand ejecta of different grain size and matrix. Development of large and long fissures along the fluvial landforms, current or ancient, with massive ejections of sediments is pervasive. These features are sometimes accompanied by small horizontal displacements. Finally, the environmental effects of the earthquake appear to be reasonably consistent with the usual scaling relationships, in particular the surface faulting. This rupture of the ground occurred on or near traces of a fault that shows clear evidence of Quaternary activity. Further and detailed studies will be carried out to characterize this source and related faults in terms of future large earthquakes potential, for their integration into seismic hazard models.
    Description: Published
    Description: 1394–1418
    Description: 2T. Deformazione crostale attiva
    Description: JCR Journal
    Keywords: Seismicity and tectonics ; Earthquake hazards ; Coseismic effects ; M6.4 Petrinja earthquake (Croatia)
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 11
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    Moho depths for Antarctica Region by the inversion of ground-based gravity data (2022)
    Oxford University Press
    Details
    Publication Date: 2022-09-01
    Description: In the last years the scientific literature has been enriched with new models of the Moho depth in the Antarctica Continent derived by the seismic reflection technique and refraction profiles, receiver functions and seismic surface waves, but also by gravimetric observations over the continent. In particular, the gravity satellite missions of the last two decades have provided data in this remote region of the Earth and have allowed the investigation of the crust properties. Meanwhile, other important contributions in this direction has been given by the fourth International Polar Year (IPY, 2007–2008) which started seismographic and geodetic networks of unprecedented duration and scale, including airborne gravimetry over largely unexplored Antarctic frontiers. In this study, a new model for the Antarctica Moho depths is proposed. This new estimation is based on no satellite gravity measures, thanks to the availability of the gravity database ANTGG2015, that collects gravity data from ground-base, airborne and shipborne campaigns. In this new estimate of the Moho depths the contribution of the gravity measures has been maximized reducing any correction of the gravity measures and avoiding constraints of the solution to seismological observations and to geological evidence. With this approach a pure gravimetric solution has been determined. The model obtained is pretty in agreement with other Moho models and thanks to the use of independent data it can be exploited also for cross-validating different Moho depths solutions.
    Description: Published
    Description: 1404–1420
    Description: 1T. Struttura della Terra
    Description: JCR Journal
    Keywords: Antarctica ; Moho ; Gravity inversion ; Collocation ; ANTGG2015
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 12
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    Distribution of oceanic crust in the Enderby Basin offshore East Antarctica (2022)
    Oxford University Press
    In:  EPIC3Geophysical Journal International, Oxford University Press, 231, pp. 1959-1981
    Details
    Publication Date: 2022-09-16
    Description: Seismic reflection and refraction data were collected in 2007 and 2012 to reveal the crustal fabric on a single long composite profile offshore Prydz Bay, East Antarctica. A P-wave velocity model provides insights on the crustal fabric, and a gravity-constrained density model is used to describe the crustal and mantle structure. The models show that a 230-km- wide continent–ocean transition separates stretched continental from oceanic crust along our profile. While the oceanic crust close to the continent–ocean boundary is just 3.5–5 km thick, its thickness increases northwards towards the Southern Kerguelen Plateau to 12 km. This change is accompanied by thickening of a lower crustal layer with high P-wave velocities of up to 7.5 km s–1, marking intrusive rocks emplaced beneath the mid-ocean ridge under increasing influence of the Kerguelen plume. Joint interpretations of our crustal model, seismic reflection data and magnetic data sets constrain the age and extent of oceanic crust in the research area. Oceanic crust is shown to continue to around 160 km farther south than has been interpreted in previous data, with profound implications for plate kinematic models of the region. Finally, by combining our findings with a regional magnetic data compilation and regional seismic reflection data we propose a larger extent of oceanic crust in the Enderby Basin than previously known.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
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  • 13
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    A phylogenomic approach to clarifying the relationship of Mesodinium within the Ciliophora: a case study in the complexity of mixed-species transcriptome analyses (2020)
    Oxford University Press
    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 Lasek-Nesselquist, E., & Johnson, M. D. A phylogenomic approach to clarifying the relationship of Mesodinium within the Ciliophora: a case study in the complexity of mixed-species transcriptome analyses. Genome Biology and Evolution, 11(11), (2019): 3218–3232, doi:10.1093/gbe/evz233.
    Description: Recent high-throughput sequencing endeavors have yielded multigene/protein phylogenies that confidently resolve several inter- and intra-class relationships within the phylum Ciliophora. We leverage the massive sequencing efforts from the Marine Microbial Eukaryote Transcriptome Sequencing Project, other SRA submissions, and available genome data with our own sequencing efforts to determine the phylogenetic position of Mesodinium and to generate the most taxonomically rich phylogenomic ciliate tree to date. Regardless of the data mining strategy, the multiprotein data set, or the molecular models of evolution employed, we consistently recovered the same well-supported relationships among ciliate classes, confirming many of the higher-level relationships previously identified. Mesodinium always formed a monophyletic group with members of the Litostomatea, with mixotrophic species of Mesodinium—M. rubrum, M. major, and M. chamaeleon—being more closely related to each other than to the heterotrophic member, M. pulex. The well-supported position of Mesodinium as sister to other litostomes contrasts with previous molecular analyses including those from phylogenomic studies that exploited the same transcriptomic databases. These topological discrepancies illustrate the need for caution when mining mixed-species transcriptomes and indicate that identifying ciliate sequences among prey contamination—particularly for Mesodinium species where expression from stolen prey nuclei appears to dominate—requires thorough and iterative vetting with phylogenies that incorporate sequences from a large outgroup of prey.
    Description: We thank David Beaudoin and Holly V. Moeller for their assistance in collecting cells and extracting RNA. We thank the Josephine Bay Paul Center for Comparative Molecular Biology and Evolution at the Marine Biological Laboratory for the generous use of their servers. This work was supported in part by a National Science Foundation grant to both authors (IOS 1354773).
    Keywords: Mesodinium ; Litostomatea ; ciliate phylogenomics ; mixed-species transcriptomes ; sequence contamination
    Repository Name: Woods Hole Open Access Server
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  • 14
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    Evolutionary transition between invertebrates and vertebrates via methylation reprogramming in embryogenesis (2020)
    Oxford University Press
    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 Xu, X., Li, G., Li, C., Zhang, J., Wang, Q., Simmons, D. K., Chen, X., Wijesena, N., Zhu, W., Wang, Z., Wang, Z., Ju, B., Ci, W., Lu, X., Yu, D., Wang, Q., Aluru, N., Oliveri, P., Zhang, Y. E., Martindale, M. Q., & Liu, J. Evolutionary transition between invertebrates and vertebrates via methylation reprogramming in embryogenesis. National Science Review, 6(5), (2019):993-1003, doi:10.1093/nsr/nwz064.
    Description: Major evolutionary transitions are enigmas, and the most notable enigma is between invertebrates and vertebrates, with numerous spectacular innovations. To search for the molecular connections involved, we asked whether global epigenetic changes may offer a clue by surveying the inheritance and reprogramming of parental DNA methylation across metazoans. We focused on gametes and early embryos, where the methylomes are known to evolve divergently between fish and mammals. Here, we find that methylome reprogramming during embryogenesis occurs neither in pre-bilaterians such as cnidarians nor in protostomes such as insects, but clearly presents in deuterostomes such as echinoderms and invertebrate chordates, and then becomes more evident in vertebrates. Functional association analysis suggests that DNA methylation reprogramming is associated with development, reproduction and adaptive immunity for vertebrates, but not for invertebrates. Interestingly, the single HOX cluster of invertebrates maintains unmethylated status in all stages examined. In contrast, the multiple HOX clusters show dramatic dynamics of DNA methylation during vertebrate embryogenesis. Notably, the methylation dynamics of HOX clusters are associated with their spatiotemporal expression in mammals. Our study reveals that DNA methylation reprogramming has evolved dramatically during animal evolution, especially after the evolutionary transitions from invertebrates to vertebrates, and then to mammals.
    Description: This work was supported by the National Key Research and Development Program of China (2018YFC1003303), the Strategic Priority Research Program of the CAS (XDB13040200), the National Natural Science Foundation of China (91519306, 31425015), the Youth Innovation Promotion Association of the CAS and the Key Research Program of Frontier Sciences, CAS (QYZDY-SSW-SMC016).
    Keywords: DNA methylation ; evolution ; development ; reprogramming
    Repository Name: Woods Hole Open Access Server
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  • 15
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    Spatially regulated editing of genetic information within a neuron (2020)
    Oxford University Press
    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 Vallecillo-Viejo, I. C., Liscovitch-Brauer, N., Diaz Quiroz, J. F., Montiel-Gonzalez, Maria F., Nemes, Sonya E., Rangan, K. J., Levinson, S. R., Eisenberg, E., & Rosenthal, J. J. C. Spatially regulated editing of genetic information within a neuron. Nucleic Acids Research, (2020): gkaa172, doi: 10.1093/nar/gkaa172.
    Description: In eukaryotic cells, with the exception of the specialized genomes of mitochondria and plastids, all genetic information is sequestered within the nucleus. This arrangement imposes constraints on how the information can be tailored for different cellular regions, particularly in cells with complex morphologies like neurons. Although messenger RNAs (mRNAs), and the proteins that they encode, can be differentially sorted between cellular regions, the information itself does not change. RNA editing by adenosine deamination can alter the genome’s blueprint by recoding mRNAs; however, this process too is thought to be restricted to the nucleus. In this work, we show that ADAR2 (adenosine deaminase that acts on RNA), an RNA editing enzyme, is expressed outside of the nucleus in squid neurons. Furthermore, purified axoplasm exhibits adenosine-to-inosine activity and can specifically edit adenosines in a known substrate. Finally, a transcriptome-wide analysis of RNA editing reveals that tens of thousands of editing sites (〉70% of all sites) are edited more extensively in the squid giant axon than in its cell bodies. These results indicate that within a neuron RNA editing can recode genetic information in a region-specific manner.
    Description: National Science Foundation (NSF) [IOS1557748 to J.R.]; United States–Israel Binational Science Foundation [BSF2013094 to J.R. and E.E.]; The Grass Foundation grant in support of the Doryteuthis pealeii Genome Project, and a gift by Mr. Edward Owens. Funding for open access charge: United States–Israel Binational Science Foundation [BSF2013094].
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  • 16
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    Flow-driven branching in a frangible porous medium (2020)
    American Physical Society
    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 Derr, N. J., Fronk, D. C., Weber, C. A., Mahadevan, A., Rycroft, C. H., & Mahadevan, L. Flow-driven branching in a frangible porous medium. Physical Review Letters, 125(15), (2020): 158002, doi:10.1103/PhysRevLett.125.158002.
    Description: Channel formation and branching is widely seen in physical systems where movement of fluid through a porous structure causes the spatiotemporal evolution of the medium. We provide a simple theoretical framework that embodies this feedback mechanism in a multiphase model for flow through a frangible porous medium with a dynamic permeability. Numerical simulations of the model show the emergence of branched networks whose topology is determined by the geometry of external flow forcing. This allows us to delineate the conditions under which splitting and/or coalescing branched network formation is favored, with potential implications for both understanding and controlling branching in soft frangible media.
    Description: N. D. was partially supported by the NSF-Simons Center for Mathematical and Statistical Analysis of Biology at Harvard, Grant No. 1764269, and the Harvard Quantitative Biology Initiative. C. H. R. and N. D. were partially supported by the National Science Foundation under Grant No. DMS-1753203. C. H. R. was partially supported by the Applied Mathematics Program of the U.S. DOE Office of Science Advanced Scientific Computing Research under Contract No. DE-AC02-05CH11231. L. M. was partially supported by the National Science Foundation under Grants No. DMR-2011754 and No. DMR-1922321.
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  • 17
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    A draft genome sequence of the elusive giant squid, Architeuthis dux (2020)
    Oxford University Press
    Details
    Publication Date: 2022-10-27
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in da Fonseca, R. R., Couto, A., Machado, A. M., Brejova, B., Albertin, C. B., Silva, F., Gardner, P., Baril, T., Hayward, A., Campos, A., Ribeiro, A. M., Barrio-Hernandez, I., Hoving, H. J., Tafur-Jimenez, R., Chu, C., Frazao, B., Petersen, B., Penaloza, F., Musacchia, F., Alexander, G. C., Osorio, H., Winkelmann, I., Simakov, O., Rasmussen, S., Rahman, M. Z., Pisani, D., Vinther, J., Jarvis, E., Zhang, G., Strugnell, J. M., Castro, L. F. C., Fedrigo, O., Patricio, M., Li, Q., Rocha, S., Antunes, A., Wu, Y., Ma, B., Sanges, R., Vinar, T., Blagoev, B., Sicheritz-Ponten, T., Nielsen, R., & Gilbert, M. T. P. A draft genome sequence of the elusive giant squid, Architeuthis dux. Gigascience, 9(1), (2020): giz152. doi: 10.1093/gigascience/giz152.
    Description: Background: The giant squid (Architeuthis dux; Steenstrup, 1857) is an enigmatic giant mollusc with a circumglobal distribution in the deep ocean, except in the high Arctic and Antarctic waters. The elusiveness of the species makes it difficult to study. Thus, having a genome assembled for this deep-sea–dwelling species will allow several pending evolutionary questions to be unlocked. Findings: We present a draft genome assembly that includes 200 Gb of Illumina reads, 4 Gb of Moleculo synthetic long reads, and 108 Gb of Chicago libraries, with a final size matching the estimated genome size of 2.7 Gb, and a scaffold N50 of 4.8 Mb. We also present an alternative assembly including 27 Gb raw reads generated using the Pacific Biosciences platform. In addition, we sequenced the proteome of the same individual and RNA from 3 different tissue types from 3 other species of squid (Onychoteuthis banksii, Dosidicus gigas, and Sthenoteuthis oualaniensis) to assist genome annotation. We annotated 33,406 protein-coding genes supported by evidence, and the genome completeness estimated by BUSCO reached 92%. Repetitive regions cover 49.17% of the genome. Conclusions: This annotated draft genome of A. dux provides a critical resource to investigate the unique traits of this species, including its gigantism and key adaptations to deep-sea environments.
    Description: R.R.F. thanks the Villum Fonden for grant VKR023446 (Villum Fonden Young Investigator Grant), the Portuguese Science Foundation (FCT) for grant PTDC/MAR/115347/2009; COMPETE-FCOMP-01-012; FEDER-015453, Marie Curie Actions (FP7-PEOPLE-2010-IEF, Proposal 272927), and the Danish National Research Foundation (DNRF96) for its funding of the Center for Macroecology, Evolution, and Climate. H.O. thanks the Rede Nacional de Espectrometria de Massa, ROTEIRO/0028/2013, ref. LISBOA-01-0145-FEDER-022125, supported by COMPETE and North Portugal Regional Operational Programme (Norte2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF). A.C. thanks FCT for project UID/Multi/04423/2019. M.P. acknowledges the support from the Wellcome Trust (grant number WT108749/Z/15/Z) and the European Molecular Biology Laboratory. M.P.T.G. thanks the Danish National Research Foundation for its funding of the Center for GeoGenetics (grant DNRF94) and Lundbeck Foundation for grant R52–5062 on Pathogen Palaeogenomics. S.R. was supported by the Novo Nordisk Foundation grant NNF14CC0001. A.H. is supported by a Biotechnology and Biological Sciences Research Council David Phillips Fellowship (fellowship reference: BB/N020146/1). T.B. is supported by the Biotechnology and Biological Sciences Research Council-funded South West Biosciences Doctoral Training Partnership (training grant reference BB/M009122/1). This work was partially funded by the Lundbeck Foundation (R52-A4895 to B.B.). H.J.T.H. was supported by the David and Lucile Packard Foundation, the Netherlands Organization for Scientific Research (#825.09.016), and currently by the Deutsche Forschungsgemeinschaft (DFG) under grant HO 5569/2-1 (Emmy Noether Junior Research Group). T.V. and B. Brejova were supported by grants from the Slovak grant agency VEGA (1/0684/16, 1/0458/18). F.S. was supported by a PhD grant (SFRH/BD/126560/2016) from FCT. A.A. was partly supported by the FCT project PTDC/CTA-AMB/31774/2017. C.C. and Y.W. are partly supported by grant IIS-1526415 from the US National Science Foundation. Computation for the work described in this article was partially supported by the DeiC National Life Science Supercomputer at DTU.
    Keywords: Cephalopod ; Invertebrate ; Genome assembly
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    TIAMMAt: leveraging biodiversity to revise protein domain models, evidence from innate immunity (2022)
    Oxford University Press
    Details
    Publication Date: 2022-10-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Tassia, M. G., David, K. T., Townsend, J. P., & Halanych, K. M. TIAMMAt: leveraging biodiversity to revise protein domain models, evidence from innate immunity. Molecular Biology and Evolution, 38(12), (2021): 5806–5818, https://doi.org/10.1093/molbev/msab258.
    Description: Sequence annotation is fundamental for studying the evolution of protein families, particularly when working with nonmodel species. Given the rapid, ever-increasing number of species receiving high-quality genome sequencing, accurate domain modeling that is representative of species diversity is crucial for understanding protein family sequence evolution and their inferred function(s). Here, we describe a bioinformatic tool called Taxon-Informed Adjustment of Markov Model Attributes (TIAMMAt) which revises domain profile hidden Markov models (HMMs) by incorporating homologous domain sequences from underrepresented and nonmodel species. Using innate immunity pathways as a case study, we show that revising profile HMM parameters to directly account for variation in homologs among underrepresented species provides valuable insight into the evolution of protein families. Following adjustment by TIAMMAt, domain profile HMMs exhibit changes in their per-site amino acid state emission probabilities and insertion/deletion probabilities while maintaining the overall structure of the consensus sequence. Our results show that domain revision can heavily impact evolutionary interpretations for some families (i.e., NLR’s NACHT domain), whereas impact on other domains (e.g., rel homology domain and interferon regulatory factor domains) is minimal due to high levels of sequence conservation across the sampled phylogenetic depth (i.e., Metazoa). Importantly, TIAMMAt revises target domain models to reflect homologous sequence variation using the taxonomic distribution under consideration by the user. TIAMMAt’s flexibility to revise any subset of the Pfam database using a user-defined taxonomic pool will make it a valuable tool for future protein evolution studies, particularly when incorporating (or focusing) on nonmodel species.
    Description: This work was supported by The National Science Foundation (Grant No. IOS—1755377 to K.M.H., Rita Graze, and Elizabeth Hiltbold Schwartz), and K.T.D. was supported by The National Science Foundation’s Graduate Research Fellowship Program.
    Keywords: Protein evolution ; Domain annotation ; Animal evolution ; Innate immunity
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  • 19
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    Adaptive proteome diversification by nonsynonymous A-to-I RNA editing in coleoid cephalopods (2022)
    Oxford University Press
    Details
    Publication Date: 2022-10-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Shoshan, Y., Liscovitch-Brauer, N., Rosenthal, J. J. C., & Eisenberg, E. Adaptive proteome diversification by nonsynonymous A-to-I RNA editing in coleoid cephalopods. Molecular Biology and Evolution, 38(9), (2021): 3775–3788, https://doi.org/10.1093/molbev/msab154.
    Description: RNA editing by the ADAR enzymes converts selected adenosines into inosines, biological mimics for guanosines. By doing so, it alters protein-coding sequences, resulting in novel protein products that diversify the proteome beyond its genomic blueprint. Recoding is exceptionally abundant in the neural tissues of coleoid cephalopods (octopuses, squids, and cuttlefishes), with an over-representation of nonsynonymous edits suggesting positive selection. However, the extent to which proteome diversification by recoding provides an adaptive advantage is not known. It was recently suggested that the role of evolutionarily conserved edits is to compensate for harmful genomic substitutions, and that there is no added value in having an editable codon as compared with a restoration of the preferred genomic allele. Here, we show that this hypothesis fails to explain the evolutionary dynamics of recoding sites in coleoids. Instead, our results indicate that a large fraction of the shared, strongly recoded, sites in coleoids have been selected for proteome diversification, meaning that the fitness of an editable A is higher than an uneditable A or a genomically encoded G.
    Description: This research was supported by a grants from the United States–Israel Binational Science Foundation (BSF), Jerusalem, Israel (BSF2017262 to J.J.C.R. and E.E.), the Israel Science Foundation (3371/20 to E.E.) and the National Science Foundation (IOS 1827509 and 1557748 to J.J.C.R).
    Keywords: RNA editing ; Adaptation ; Evolution
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  • 20
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    Interspecific differences in the flow regimes and drag of North Pacific skate egg cases (2022)
    Oxford University Press
    Details
    Publication Date: 2022-10-12
    Description: Author Posting. © The Author(s), 2022. This is the author's version of the work. It is posted here by permission of Oxford University Press for personal use, not for redistribution. The definitive version was published in Integrative & Comparative Biology 62(3), (2022): 805-816, https://doi.org/10.1093/icb/icac108.
    Description: Skates are a diverse group of dorso-ventrally compressed cartilaginous fish found primarily in high-latitude seas. These slow-growing oviparous fish deposit their fertilized eggs into cases, which then rest on the seafloor. Developing skates remain in their cases for 1–4 years after they are deposited, meaning the abiotic characteristics of the deposition sites, such as current and substrate type, must interact with the capsule in a way to promote long residency. Egg cases are morphologically variable and can be identified to species. Both the gross morphology and the microstructures of the egg case interact with substrate to determine how well a case stays in place on a current-swept seafloor. Our study investigated the egg case hydrodynamics of eight North Pacific skate species to understand how their morphology affects their ability to stay in place. We used a flume to measure maximum current velocity, or “break-away velocity,” each egg case could withstand before being swept off the substrate and a tilt table to measure the coefficient of static friction between each case and the substrate. We also used the programing software R to calculate theoretical drag on the egg cases of each species. For all flume trials, we found the morphology of egg cases and their orientation to flow to be significantly correlated with break-away velocity. In certain species, the morphology of the egg case was correlated with flow rate required to dislodge a case from the substrate in addition to the drag experienced in both the theoretical and flume experiments. These results effectively measure how well the egg cases of different species remain stationary in a similar habitat. Parsing out attachment biases and discrepancies in flow regimes of egg cases allows us to identify where we are likely to find other elusive species nursery sites. These results will aid predictive models for locating new nursery habitats and protective policies for avoiding the destruction of these nursery sites.
    Description: This work was supported by the NSF-REU and FHL Blinks-Beacon for funding JNE. And the Stephen and Ruth Wainwright Endowed Fellowship, BEACON and Hoag Awards, Robert T. Paine Experimental and Field Ecology Award, FHL Award, FHL Marine Science Fund, FHL Student Fund (Kohn), Patricia L. Dudley Endowment for funding KCH.
    Description: 2023-07-04
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  • 21
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    On the relationship between palaeomagnetic secular variation and excursions-records from MIS 8-ODP leg 172 (2021)
    Oxford University Press
    Details
    Publication Date: 2022-05-27
    Description: Author Posting. © Oxford University Press, 2021. This article is posted here by permission of [publisher] for personal use, not for redistribution. The definitive version was published in Lund, S., Acton, G., Clement, B., Okada, M., & Keigwin, L. On the relationship between palaeomagnetic secular variation and excursions-records from MIS 8-ODP leg 172. Geophysical Journal International, 225(2), (2021): 1129-1141, https://doi.org/10.1093/gji/ggaa564.
    Description: Palaeomagnetic secular variation (PSV) and excursion data obtained across MIS 8 (243–300 ka) from the western North Atlantic Ocean ODP (Ocean Drilling Program) sites 1060–1063 show composite high-resolution PSV records (both directions and relative palaeointensity) developed for each site and intercompared. Two methods of chronostratigraphy allow us to date these records. First, we used published results that compared the calcium carbonate records of ODP Leg 172 sediments and tuned them with Milankovich cyclicity. We also compared our palaeointensity records with the PISO-1500 global palaeointensity record that was dated with oxygen isotope stratigraphy. We prefer the PISO-1500 record to date our cores. Two excursions are preserved in our PSV records—Excursions 8α and 9α. Our revised age estimates for both excursions are 8α (236.7–239.8 ka) and 9α (283.7–286.9 ka). We have compared shipboard measurements of the two excursions with u-channel measurements of selected excursion intervals. Excursion 8α is interpreted as a ‘Class II’ excursion (local reversal) with in-phase inclination and declination changes; Excursion 9α is a ‘Class I’ excursion with 90° out-of-phase inclination and declination changes. Averaged directions (after removal of true excursional directions) and relative palaeointensity in 3 and 9 ka overlapping intervals show significant PSV directional variability over 104 yr timescales that is regionally correlatable among the four sites. A notable pattern of angular dispersion variability involves most time spent with low (∼10°) dispersion, with three shorter intervals of high (∼25°) dispersion. The relative palaeointensity variability also shows significant variability over 104 yr timescales with three notable intervals of low palaeointensity in all four records and a direct correspondence between the three low-palaeointensity intervals and the three intervals of high angular dispersion. The two magnetic field excursions occur in two of the three low-palaeointensity/high-dispersion intervals. This suggests that the geomagnetic field operates in two states between reversals, one with regular to high palaeointensity and low directional variability and one with low palaeointensity and significantly higher directional variability and excursions.
    Keywords: Geomagnetic excursions ; Palaeointensity ; Palaeomagnetic secular variation
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  • 22
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    Sensitivity of sand lance to shifting prey and hydrography indicates forthcoming change to the northeast US shelf forage fish complex (2022)
    Oxford University Press
    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 Suca, J. J., Wiley, D. N., Silva, T. L., Robuck, A. R., Richardson, D. E., Glancy, S. G., Clancey, E., Giandonato, T., Solow, A. R., Thompson, M. A., Hong, P., Baumann, H., Kaufman, L., & Llopiz, J. K. Sensitivity of sand lance to shifting prey and hydrography indicates forthcoming change to the northeast US shelf forage fish complex. Ices Journal of Marine Science, 78(3), (2021): 1023–1037, https://doi.org/10.1093/icesjms/fsaa251.
    Description: Northern sand lance (Ammodytes dubius) and Atlantic herring (Clupea harengus) represent the dominant lipid-rich forage fish species throughout the Northeast US shelf and are critical prey for numerous top predators. However, unlike Atlantic herring, there is little research on sand lance or information about drivers of their abundance. We use intra-annual measurements of sand lance diet, growth, and condition to explain annual variability in sand lance abundance on the Northeast US Shelf. Our observations indicate that northern sand lance feed, grow, and accumulate lipids in the late winter through summer, predominantly consuming the copepod Calanus finmarchicus. Sand lance then cease feeding, utilize lipids, and begin gonad development in the fall. We show that the abundance of C. finmarchicus influences sand lance parental condition and recruitment. Atlantic herring can mute this effect through intra-guild predation. Hydrography further impacts sand lance abundance as increases in warm slope water decrease overwinter survival of reproductive adults. The predicted changes to these drivers indicate that sand lance will no longer be able to fill the role of lipid-rich forage during times of low Atlantic herring abundance—changing the Northeast US shelf forage fish complex by the end of the century.
    Description: Research was funded by the Bureau of Ocean Energy Management (IA agreement M17PG0019; DNW, LK, HB, and JKL), including a subaward via the National Marine Sanctuary Foundation (18-11-B-203). Additional support came from the National Oceanic and Atmospheric Administration Woods Hole Sea Grant Program (NA18OAR4170104, Project No. R/O-57; JKL, HB, and DNW) and a National Science Foundation Long-term Ecological Research grant for the Northeast US Shelf Ecosystem (OCE 1655686; JKL). JJS was funded by the National Science Foundation Graduate Research Fellowship programme. ARR was funded by an NOAA Nancy Foster Scholarship.
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  • 23
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    An alternative method to evaluate earthquake detection from synthetic Wood–Anderson seismograms: an application in Italy (2022)
    Oxford University Press
    Details
    Publication Date: 2022-08-26
    Description: This article has been accepted for publication in Geophysical Journal International ©: The Authors 2022. Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved. Uploaded in accordance with the publisher's self-archiving policy.
    Description: Defining the regional variability of minimum magnitude for earthquake detection is crucial for planning seismic networks. Knowing the earthquake detection magnitude values is fundamental for the optimal location of new stations and to select the priority for reactivating the stations of a seismic network in case of a breakdown. In general, the assessment of earthquake detection is performed by analysing seismic noise with spectral or more sophisticated methods. Further, to simulate amplitude values at the recording sites, spectral methods require knowledge of several geophysical parameters including rock density, S-wave velocity, corner frequency, quality factor, site specific decay parameter and so on, as well as a velocity model for the Earth's interior. The simulation results are generally expressed in terms of Mw and therefore a further conversion must be done to obtain the values of local magnitude (ML), which is the parameter commonly used for moderate and small earthquakes in seismic catalogues. Here, the relationship utilized by a seismic network to determine ML is directly applied to obtain the expected amplitude [in mm, as if it were recorded by a Wood–Anderson (WA) seismometer] at the recording site, without any additional assumptions. The station detection estimates are obtained by simply considering the ratio of the expected amplitude with respect to the background noise, also measured in mm. The seismic noise level for the station is estimated starting from four waveforms (each signal lasting 1 min) sampled at various times of the day for a period of one week. The proposed method is tested on Italian seismic events occurring in 2019 by using the locations of 16.879 earthquakes recorded by 374 stations. The first results indicate that by evaluating the station noise level with 5-s windows, a representative sample of the variability in expected noise level is generated for every station, even if only 4 min of signal per day over a week of recordings is used. The method was applied to define the detection level of the Italian National Seismic Network (RSN). The RSN detection level represents a reference for the definition and application of guidelines in the field of monitoring of subsurface industrial activities in Italy. The proposed approach can be successfully applied to define the current performance of a local seismic network (managed by private companies) and to estimate the expected further improvements, requested to fulfil the guidelines with the installation of new seismic stations. This method has been tested in Italy and can be reproduced wherever the local magnitude ML, based on synthetic WA records, is used.
    Description: Published
    Description: 1283–1297
    Description: 4T. Sismicità dell'Italia
    Description: JCR Journal
    Keywords: Time-series analysis ; Earthquake ground motions ; Seismic noise ; Induced seismicity ; 04.06. Seismology ; 05.04. Instrumentation and techniques of general interest
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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    Preparing aquatic research for an extreme future: call for improved definitions and responsive, multidisciplinary approaches (2022)
    Oxford University Press
    Details
    Publication Date: 2022-08-19
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Aoki, L. R., Brisbin, M. M., Hounshell, A. G., Kincaid, D. W., Larson, E., Sansom, B. J., Shogren, A. J., Smith, R. S., & Sullivan-Stack, J. Preparing aquatic research for an extreme future: call for improved definitions and responsive, multidisciplinary approaches. Bioscience, 72(6), (2022): 508-520, https://doi.org/10.1093/biosci/biac020.
    Description: Extreme events have increased in frequency globally, with a simultaneous surge in scientific interest about their ecological responses, particularly in sensitive freshwater, coastal, and marine ecosystems. We synthesized observational studies of extreme events in these aquatic ecosystems, finding that many studies do not use consistent definitions of extreme events. Furthermore, many studies do not capture ecological responses across the full spatial scale of the events. In contrast, sampling often extends across longer temporal scales than the event itself, highlighting the usefulness of long-term monitoring. Many ecological studies of extreme events measure biological responses but exclude chemical and physical responses, underscoring the need for integrative and multidisciplinary approaches. To advance extreme event research, we suggest prioritizing pre- and postevent data collection, including leveraging long-term monitoring; making intersite and cross-scale comparisons; adopting novel empirical and statistical approaches; and developing funding streams to support flexible and responsive data collection.
    Repository Name: Woods Hole Open Access Server
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    Developmental exposure to domoic acid disrupts startle response behavior and circuitry in zebrafish (2021)
    Oxford University Press
    Details
    Publication Date: 2022-06-07
    Description: Author Posting. © The Author(s), 2021. This is the author's version of the work. It is posted here by permission of Oxford University Press for personal use, not for redistribution. The definitive version was published in Toxicological Sciences 182(20), (2021): 310-326, https://doi.org/10.1093/toxsci/kfab066.
    Description: Harmful algal blooms produce potent neurotoxins that accumulate in seafood and are hazardous to human health. Developmental exposure to the harmful algal bloom toxin, domoic acid (DomA), has behavioral consequences well into adulthood, but the cellular and molecular mechanisms of DomA developmental neurotoxicity are largely unknown. To assess these, we exposed zebrafish embryos to DomA during the previously identified window of susceptibility and used the well-known startle response circuit as a tool to identify specific neuronal components that are targeted by exposure to DomA. Exposure to DomA reduced startle responsiveness to both auditory/vibrational and electrical stimuli, and even at the highest stimulus intensities tested, led to a dramatic reduction of one type of startle (short-latency c-starts). Furthermore, DomA-exposed larvae had altered kinematics for both types of startle responses tested, exhibiting shallower bend angles and slower maximal angular velocities. Using vital dye staining, immunolabeling, and live imaging of transgenic lines, we determined that although the sensory inputs were intact, the reticulospinal neurons required for short-latency c-starts were absent in most DomA-exposed larvae. Furthermore, axon tracing revealed that DomA-treated larvae also showed significantly reduced primary motor neuron axon collaterals. Overall, these results show that developmental exposure to DomA targets large reticulospinal neurons and motor neuron axon collaterals, resulting in measurable deficits in startle behavior. They further provide a framework for using the startle response circuit to identify specific neural populations disrupted by toxins or toxicants and to link these disruptions to functional consequences for neural circuit function and behavior.
    Description: This research was supported by a WHOI Von Damm and Ocean Ridge Initiative Fellowships to J.M.P. and the Woods Hole Center for Oceans and Human Health (NIH: P01ES021923 and P01ES028938; NSF: OCE-1314642 and OCE-1840381).
    Description: 2022-06-07
    Keywords: domoic acid ; harmful algal blooms ; harmful algal bloom toxins ; developmental toxicity ; startle response ; escape response ; startle circuit
    Repository Name: Woods Hole Open Access Server
    Type: Preprint
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  • 26
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    Advancing an interdisciplinary framework to study seed dispersal ecology (2020)
    Oxford University Press
    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 Beckman, N. G., Asian, C. E., Rogers, H. S., Kogan, O., Bronstein, J. L., Bullock, J. M., Hartig, F., HilleRisLambers, J., Zhou, Y., Zurell, D., Brodie, J. F., Bruna, E. M., Cantrell, R. S., Decker, R. R., Efiom, E., Fricke, E. C., Gurski, K., Hastings, A., Johnson, J. S., Loiselle, B. A., Miriti, M. N., Neubert, M. G., Pejchar, L., Poulsen, J. R., Pufal, G., Razafindratsima, O. H., Sandor, M. E., Shea, K., Schreiber, S., Schupp, E. W., Snell, R. S., Strickland, C., & Zambrano, J. Advancing an interdisciplinary framework to study seed dispersal ecology. Aob Plants, 12(2), (2020): plz048, doi:10.1093/aobpla/plz048.
    Description: Although dispersal is generally viewed as a crucial determinant for the fitness of any organism, our understanding of its role in the persistence and spread of plant populations remains incomplete. Generalizing and predicting dispersal processes are challenging due to context dependence of seed dispersal, environmental heterogeneity and interdependent processes occurring over multiple spatial and temporal scales. Current population models often use simple phenomenological descriptions of dispersal processes, limiting their ability to examine the role of population persistence and spread, especially under global change. To move seed dispersal ecology forward, we need to evaluate the impact of any single seed dispersal event within the full spatial and temporal context of a plant’s life history and environmental variability that ultimately influences a population’s ability to persist and spread. In this perspective, we provide guidance on integrating empirical and theoretical approaches that account for the context dependency of seed dispersal to improve our ability to generalize and predict the consequences of dispersal, and its anthropogenic alteration, across systems. We synthesize suitable theoretical frameworks for this work and discuss concepts, approaches and available data from diverse subdisciplines to help operationalize concepts, highlight recent breakthroughs across research areas and discuss ongoing challenges and open questions. We address knowledge gaps in the movement ecology of seeds and the integration of dispersal and demography that could benefit from such a synthesis. With an interdisciplinary perspective, we will be able to better understand how global change will impact seed dispersal processes, and potential cascading effects on plant population persistence, spread and biodiversity.
    Description: Ideas for this manuscript initiated during the Seed Dispersal Workshop held in May 2016 at the Socio-Environmental Synthesis Center in Annapolis, MD and supported by the US National Science Foundation Grant DEB-1548194 to N.G.B. and the National Socio-Environmental Synthesis Center under the US National Science Foundation Grant DBI-1052875. D.Z. received funding from the Swiss National Science Foundation (SNF, grant: PZ00P3_168136/1) and from the German Science Foundation (DFG, grant: ZU 361/1-1).
    Keywords: Analytical models ; demography ; global change ; individual-based models ; long-distance seed dispersal ; population models ; seed dispersal
    Repository Name: Woods Hole Open Access Server
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  • 27
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    Not all nitrogen is created equal: differential effects of nitrate and ammonium enrichment in coastal wetlands (2021)
    Oxford University Press
    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 Bowen, J. L., Giblin, A. E., Murphy, A. E., Bulseco, A. N., Deegan, L. A., Johnson, D. S., Nelson, J. A., Mozdzer, T. J., & Sullivan, H. L. Not all nitrogen is created equal: differential effects of nitrate and ammonium enrichment in coastal wetlands. Bioscience, 70(12), (2020): 1108-1119, doi:10.1093/biosci/biaa140.
    Description: Excess reactive nitrogen (N) flows from agricultural, suburban, and urban systems to coasts, where it causes eutrophication. Coastal wetlands take up some of this N, thereby ameliorating the impacts on nearshore waters. Although the consequences of N on coastal wetlands have been extensively studied, the effect of the specific form of N is not often considered. Both oxidized N forms (nitrate, NO3−) and reduced forms (ammonium, NH4+) can relieve nutrient limitation and increase primary production. However, unlike NH4+, NO3− can also be used as an electron acceptor for microbial respiration. We present results demonstrating that, in salt marshes, microbes use NO3− to support organic matter decomposition and primary production is less stimulated than when enriched with reduced N. Understanding how different forms of N mediate the balance between primary production and decomposition is essential for managing coastal wetlands as N enrichment and sea level rise continue to assail our coasts.
    Description: This work was supported by the following funding sources: National Science Foundation (NSF) grant no. DEB 1902712 to LAD, JLB, DSJ, and TJM; NSF grant no. DEB 1902695 to AEG; NSF grant no. DEB 1902704 to JAN; NSF grant no. DEB 1354214 to TJM; NSF grant no. DEB 1350491 to JLB; NSF grant no. OCE 1637630 to AEG and LAD; and additional funding from the Dorr Foundation, the Department of the Interior Northeast Climate Science Center (grant no. DOI G12AC00001), and a Bullard Fellowship (Harvard University) to LAD and from the National Academies of Science, Medicine, and Engineering Gulf Research Program to JAN. Resources purchased with funds from the NSF Biological Field Stations and Marine Laboratories program (grant no. DBI 1722553, to Northeastern University) were used to generate the data for the manuscript. Initial conversations on the effects of nutrient enrichment in marshes with Scott Warren and Bruce Peterson were critical in informing the work described in the manuscript. Sam Kelsey and Jane Tucker contributed to much of the N cycling biogeochemistry; Caitlin Bauer, Frankie Leach, Paige Weber, Emily Geoghegan and Sophie Drew assisted with field work; and Joe Vineis assisted with metagenomic analysis. This is contribution 3941 from the Virginia Institute of Marine Science. The data were compiled from multiple published sources. Links to published data can be found here: https://pie-lter.ecosystems.mbl.edu/data. The sequence data used to derive figure 6 are publicly available on the MG-RAST website under project number mgp84173.
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    Conserved and unique transcriptional features of pharyngeal arches in the skate (Leucoraja erinacea) and evolution of the jaw (2021)
    Oxford University Press
    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 Hirschberger, C., Sleight, V. A., Criswell, K. E., Clark, S. J., & Gillis, J. A. Conserved and unique transcriptional features of pharyngeal arches in the skate (Leucoraja erinacea) and evolution of the jaw. Molecular Biology and Evolution, (2021): msab123, https://doi.org/10.1093/molbev/msab123
    Description: The origin of the jaw is a long-standing problem in vertebrate evolutionary biology. Classical hypotheses of serial homology propose that the upper and lower jaw evolved through modifications of dorsal and ventral gill arch skeletal elements, respectively. If the jaw and gill arches are derived members of a primitive branchial series, we predict that they would share common developmental patterning mechanisms. Using candidate and RNAseq/differential gene expression analyses, we find broad conservation of dorsoventral patterning mechanisms within the developing mandibular, hyoid and gill arches of a cartilaginous fish, the skate (Leucoraja erinacea). Shared features include expression of genes encoding members of the ventralising BMP and endothelin signalling pathways and their effectors, the joint markers nkx3.2 and gdf5 and pro-chondrogenic transcription factor barx1, and the dorsal territory marker pou3f3. Additionally, we find that mesenchymal expression of eya1/six1 is an ancestral feature of the mandibular arch of jawed vertebrates, while differences in notch signalling distinguish the mandibular and gill arches in skate. Comparative transcriptomic analyses of mandibular and gill arch tissues reveal additional genes differentially expressed along the dorsoventral axis of the pharyngeal arches, including scamp5 as a novel marker of the dorsal mandibular arch, as well as distinct transcriptional features of mandibular and gill arch muscle progenitors and developing gill buds. Taken together, our findings reveal conserved patterning mechanisms in the pharyngeal arches of jawed vertebrates, consistent with serial homology of their skeletal derivatives, as well as unique transcriptional features that may underpin distinct jaw and gill arch morphologies.
    Description: This work was supported by a Biotechnology and Biological Sciences Research Council Doctoral Training Partnership studentship to CH, by a Wolfson College Junior Research Fellowship and MBL Whitman Early Career Fellowship to VAS, and by a Royal Society University Research Fellowship (UF130182 and URF\R\191007), Royal Society Research Grant (RG140377) and University of Cambridge Sir Isaac Newton Trust Grant (14.23z) to JAG.
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    Environmental drivers and trends in forage fish occupancy of the Northeast US shelf (2022)
    Oxford University Press
    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 Suca, J. J., Deroba, J. J., Richardson, D. E., Ji, R., & Llopiz, J. K. Environmental drivers and trends in forage fish occupancy of the Northeast US shelf. Ices Journal of Marine Science, 78(10), (2021): 3687–3708, https://doi.org/10.1093/icesjms/fsab214.
    Description: The Northeast US shelf ecosystem is undergoing unprecedented changes due to long-term warming trends and shifts in regional hydrography leading to changes in community composition. However, it remains uncertain how shelf occupancy by the region's dominant, offshore small pelagic fishes, also known as forage fishes, has changed throughout the late 20th and early 21st centuries. Here, we use species distribution models to estimate the change in shelf occupancy, mean weighted latitude, and mean weighted depth of six forage fishes on the Northeast US shelf, and whether those trends were linked to coincident hydrographic conditions. Our results suggest that observed shelf occupancy is increasing or unchanging for most species in both spring and fall, linked both to gear shifts and increasing bottom temperature and salinity. Exceptions include decreases to observed shelf occupancy by sand lance and decreases to Atlantic herring's inferred habitat suitability in the fall. Our work shows that changes in shelf occupancy and inferred habitat suitability have varying coherence, indicating complex mechanisms behind observed shelf occupancy for many species. Future work and management can use these results to better isolate the aspects of forage fish life histories that are important for determining their occupancy of the Northeast US shelf.
    Description: Funding came from the National Oceanic and Atmospheric Administration Woods Hole Sea Grant Program (NA18OAR4170104, Project number R/O-57; RJ and JKL) and a National Science Foundation Long-term Ecological Research grant for the Northeast US Shelf Ecosystem (OCE1655686; RJ and JKL). JJS was funded by the National Science Foundation Graduate Research Fellowship program.
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    The challenges of detecting and attributing ocean acidification impacts on marine ecosystems (2021)
    Oxford University Press
    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 Doo, S. S., Kealoha, A., Andersson, A., Cohen, A. L., Hicks, T. L., Johnson, Z., I., Long, M. H., McElhany, P., Mollica, N., Shamberger, K. E. F., Silbiger, N. J., Takeshita, Y., & Busch, D. S. The challenges of detecting and attributing ocean acidification impacts on marine ecosystems. ICES Journal of Marine Science, 77(7-8), (2020): 2411-2422, https://doi.org/10.1093/icesjms/fsaa094.
    Description: A substantial body of research now exists demonstrating sensitivities of marine organisms to ocean acidification (OA) in laboratory settings. However, corresponding in situ observations of marine species or ecosystem changes that can be unequivocally attributed to anthropogenic OA are limited. Challenges remain in detecting and attributing OA effects in nature, in part because multiple environmental changes are co-occurring with OA, all of which have the potential to influence marine ecosystem responses. Furthermore, the change in ocean pH since the industrial revolution is small relative to the natural variability within many systems, making it difficult to detect, and in some cases, has yet to cross physiological thresholds. The small number of studies that clearly document OA impacts in nature cannot be interpreted as a lack of larger-scale attributable impacts at the present time or in the future but highlights the need for innovative research approaches and analyses. We summarize the general findings in four relatively well-studied marine groups (seagrasses, pteropods, oysters, and coral reefs) and integrate overarching themes to highlight the challenges involved in detecting and attributing the effects of OA in natural environments. We then discuss four potential strategies to better evaluate and attribute OA impacts on species and ecosystems. First, we highlight the need for work quantifying the anthropogenic input of CO2 in coastal and open-ocean waters to understand how this increase in CO2 interacts with other physical and chemical factors to drive organismal conditions. Second, understanding OA-induced changes in population-level demography, potentially increased sensitivities in certain life stages, and how these effects scale to ecosystem-level processes (e.g. community metabolism) will improve our ability to attribute impacts to OA among co-varying parameters. Third, there is a great need to understand the potential modulation of OA impacts through the interplay of ecology and evolution (eco–evo dynamics). Lastly, further research efforts designed to detect, quantify, and project the effects of OA on marine organisms and ecosystems utilizing a comparative approach with long-term data sets will also provide critical information for informing the management of marine ecosystems.
    Description: SSD was funded by NSF OCE (grant # 1415268). DSB and PM were supported by the NOAA Ocean Acidification Program and Northwest Fisheries Science Center, MHL was supported by NSF OCE (grant # 1633951), ZIJ was supported by NSF OCE (grant # 1416665) and DOE EERE (grant #DE-EE008518), NJS was supported by NSF OCE (grant # 1924281), ALC was supported by NSF OCE (grant # 1737311), and AA was supported by NSF OCE (grant # 1416518). KEFS, AK, and TLH were supported by Texas A&M University. This is CSUN Marine Biology contribution (# 306).
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    PCB126 exposure revealed alterations in m6A RNA modifications in transcripts associated with AHR activation (2020)
    Oxford University Press
    Details
    Publication Date: 2022-05-26
    Description: Author Posting. © The Author(s), 2020. This is the author's version of the work. It is posted here by permission of Oxford University Press for personal use, not for redistribution. The definitive version was published in Toxicological Sciences (2020): kfaa158, doi:10.1093/toxsci/kfaa158.
    Description: Chemical modifications of proteins, DNA, and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests the RNA modifications (epitranscriptomics) have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6-methyladenosine (m6A). In a subset of mRNAs, m6A sites are preferentially enriched near stop codons, in 3′ UTRs, and within exons, suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes, it is important to understand the effects of exposure on this important layer of gene regulation. Hence, the objective of this study was to characterize the acute effects of developmental exposure to PCB126, an environmentally relevant dioxin-like PCB, on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for 6 h starting from 72 h post fertilization and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing (MeRIP-seq). Our analysis revealed 117 and 217 m6A peaks in the DMSO and PCB126 samples (false discovery rate 5%), respectively. The majority of the peaks were preferentially located around the 3′ UTR and stop codons. Statistical analysis revealed 15 m6A marked transcripts to be differentially methylated by PCB126 exposure. These include transcripts that are known to be activated by AHR agonists (eg, ahrra, tiparp, nfe2l2b) as well as others that are important for normal development (vgf, cebpd, sned1). These results suggest that environmental chemicals such as dioxin-like PCBs could affect developmental gene expression patterns by altering m6A levels. Further studies are necessary to understand the functional consequences of exposure-associated alterations in m6A levels.
    Description: National Institute of Health National Institute of Environmental Health Sciences Outstanding New Environmental Scientist (NIH R01ES024915 to N.A.); Woods Hole Center for Oceans and Human Health [National Institutes of Health (NIH) (Grant P01ES028938); National Science Foundation (Grant OCE-1840381) to M. E. Hahn, J. J. Stegeman, N.A., and S.K.].
    Description: 2021-10-16
    Keywords: dioxin-like PCBs ; development ; zebrafish ; epitranscriptomics ; m6A ; MeRIP
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    Concerning P450 evolution: structural analyses support bacterial origin of sterol 14α-demethylases (2020)
    Oxford University Press
    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 Lamb, D. C., Hargrove, T. Y., Zhao, B., Wawrzak, Z., Goldstone, J. V., Nes, W. D., Kelly, S. L., Waterman, M. R., Stegeman, J. J., & Lepesheva, G. I. Concerning P450 evolution: structural analyses support bacterial origin of sterol 14α-demethylases. Molecular Biology and Evolution, (2020): msaa260, doi:10.1093/molbev/msaa260.
    Description: Sterol biosynthesis, primarily associated with eukaryotic kingdoms of life, occurs as an abbreviated pathway in the bacterium Methylococcus capsulatus. Sterol 14α-demethylation is an essential step in this pathway and is catalyzed by cytochrome P450 51 (CYP51). In M. capsulatus, the enzyme consists of the P450 domain naturally fused to a ferredoxin domain at the C-terminus (CYP51fx). The structure of M. capsulatus CYP51fx was solved to 2.7 Å resolution and is the first structure of a bacterial sterol biosynthetic enzyme. The structure contained one P450 molecule per asymmetric unit with no electron density seen for ferredoxin. We connect this with the requirement of P450 substrate binding in order to activate productive ferredoxin binding. Further, the structure of the P450 domain with bound detergent (which replaced the substrate upon crystallization) was solved to 2.4 Å resolution. Comparison of these two structures to the CYP51s from human, fungi, and protozoa reveals strict conservation of the overall protein architecture. However, the structure of an “orphan” P450 from nonsterol-producing Mycobacterium tuberculosis that also has CYP51 activity reveals marked differences, suggesting that loss of function in vivo might have led to alterations in the structural constraints. Our results are consistent with the idea that eukaryotic and bacterial CYP51s evolved from a common cenancestor and that early eukaryotes may have recruited CYP51 from a bacterial source. The idea is supported by bioinformatic analysis, revealing the presence of CYP51 genes in 〉1,000 bacteria from nine different phyla, 〉50 of them being natural CYP51fx fusion proteins.
    Description: The study was supported by National Institutes of Health (Grant No. R01 GM067871 to G.I.L.) and by a UK-USA Fulbright Scholarship and the Royal Society (to D.C.L.).
    Keywords: sterol biosynthesis ; evolution ; cytochrome P450 ; CYP51 redox partner ; crystallography
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    Identifying the distribution of Atlantic cod spawning using multiple fixed and glider-mounted acoustic technologies (2020)
    Oxford University Press
    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 Zemeckis, D. R., Dean, M. J., DeAngelis, A. I., Van Parijs, S. M., Hoffman, W. S., Baumgartner, M. F., Hatch, L. T., Cadrin, S. X., & McGuire, C. H. Identifying the distribution of Atlantic cod spawning using multiple fixed and glider-mounted acoustic technologies. ICES Journal of Marine Science, 76(6), (2019): 1610-1625, doi: 10.1093/icesjms/fsz064.
    Description: Effective fishery management measures to protect fish spawning aggregations require reliable information on the spatio-temporal distribution of spawning. Spawning closures have been part of a suite of fishery management actions to rebuild the Gulf of Maine stock of Atlantic cod (Gadus morhua), but difficulties remain with managing rebuilding. The objective of this study was to identify the spatial and temporal distribution of cod spawning during winter in Massachusetts Bay to improve our understanding of cod spawning dynamics and inform fisheries management. Spawning was investigated in collaboration with commercial fishermen during three winter spawning seasons (October 2013–March 2016) using acoustic telemetry and passive acoustic monitoring equipment deployed in fixed-station arrays and mounted on mobile autonomous gliders. Tagged cod exhibited spawning site fidelity and spawning primarily occurred from early November through January with a mid-December peak and some inter-annual variability. The spatial distribution of spawning was generally consistent among years with multiple hotspots in areas 〉50 m depth. Current closures encompass most of spawning, but important areas are recommended for potential modifications. Utilizing multiple complementary technologies and deployment strategies in collaboration with commercial fishermen enabled a comprehensive description of spawning and provides a valuable model for future studies.
    Description: Year 1 was jointly funded by The Nature Conservancy and Massachusetts Division of Marine Fisheries. The remainder of this research was funded through the 2013–2014 NOAA Saltonstall Kennedy grant program (Award No. NA14NMF4270027) with additional support from the Nature Conservancy and Cabot Family Charitable Foundation.
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    Physical modeling and validation of porpoises' directional emission via hybrid metamaterials (2020)
    Oxford University Press
    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 Dong, E., Zhang, Y., Song, Z., Zhang, T., Cai, C., & Fang, N. X. Physical modeling and validation of porpoises' directional emission via hybrid metamaterials. National Science Review, 6(5), (2019): 921-928, doi:10.1093/nsr/nwz085.
    Description: In wave physics and engineering, directional emission sets a fundamental limitation on conventional simple sources as their sizes should be sufficiently larger than their wavelength. Artificial metamaterial and animal biosonar both show potential in overcoming this limitation. Existing metamaterials arranged in periodic microstructures face great challenges in realizing complex and multiphase biosonar structures. Here, we proposed a physical directional emission model to bridge the gap between porpoises’ biosonar and artificial metamaterial. Inspired by the anatomical and physical properties of the porpoise's biosonar transmission system, we fabricated a hybrid metamaterial system composed of multiple composite structures. We validated that the hybrid metamaterial significantly increased directivity and main lobe energy over a broad bandwidth both numerically and experimentally. The device displayed efficiency in detecting underwater target and suppressing false target jamming. The metamaterial-based physical model may be helpful to achieve the physical mechanisms of porpoise biosonar detection and has diverse applications in underwater acoustic sensing, ultrasound scanning, and medical ultrasonography.
    Description: E.D., Y.Z., Z.S., T.Z. and C.C. acknowledge the financial support in part by the National Key Research and Development Program of China (2018YFC1407504), the National Natural Science Foundation of China (41676023, 41276040 and 41422604). N.X.F. acknowledges the support from the MIT Energy Initiative grant. Z.S. thanks the China Scholarship Council for the financial support of his oversea study in Woods Hole Oceanographic Institution.
    Keywords: porpoise's physical model ; metamaterials ; biosonar ; directional emission
    Repository Name: Woods Hole Open Access Server
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  • 35
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    Mantle upwelling beneath the South China Sea and links to surrounding subduction systems (2020)
    Oxford University Press
    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 Lin, J., Xu, Y., Sun, Z., & Zhou, Z. Mantle upwelling beneath the South China Sea and links to surrounding subduction systems. National Science Review, 6(5), (2019): 877-881, doi:10.1093/nsr/nwz123.
    Description: The evolution of the South China Sea (SCS) is directly linked to the complex subduction systems of the surrounding Pacific, Philippine Sea and Indo-Australian Plates (Fig. 1a). Major advances in the last several years are providing new insights into the SCS-mantle dynamics, through regional seismic imaging of the upper mantle [1,2], unprecedented IODP drilling expeditions (349/367/368/368X) [3–5] that obtained the oceanic basement basalt samples for the first time, geochemical analyses of the SCS-mantle source compositions [6–8] and geodynamic modeling [9,10]. Furthermore, new geological mapping, seismic imaging [11,12] and IODP drilling [13,14] have revealed evidence for significantly greater magma production at the northern SCS rifted margin, in comparison to the magma-poor end-member of the Atlantic rifted margins. This paper provides a new perspective of the SCS-mantle dynamics inspired by new observations and geodynamic modeling. We first highlight new geophysical evidence for a broad region of low-seismic-velocity anomalies in the upper mantle beneath the northern SCS, abundant magmatism during continental breakup and post-seafloor spreading, and geochemical evidence for recycled oceanic components beneath the SCS. We then present new models of layered flows in the mantle beneath the SCS, revealing two modes of plate- and subduction-driven mantle upwelling, including (i) narrow centers of mantle upwelling at shallow depths induced by divergent plate motion at seafloor-spreading centers and (ii) broad zones of mantle upwelling as a result of subduction-induced mantle-return flows at greater depths. These new observations and geodynamic studies suggest strong links between mantle upwelling beneath the SCS and surrounding subducting plates.
    Description: This work was supported by the National Natural Science Foundation of China (41890813, 91628301, U1606401, 41976066, 91858207 and 41706056), the Chinese Academy of Sciences (Y4SL021001, QYZDY-SSW-DQC005 and 133244KYSB20180029), the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou, GML2019ZD0205), the National Key R&D Program of China (2018YFC0309800 and 2018YFC0310100), the State Oceanic Administration (GASI-GEOGE-02) and China Ocean Mineral Resources R&D Association (DY135-S2–1-04).
    Repository Name: Woods Hole Open Access Server
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  • 36
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    The role of magmatism in the thinning and breakup of the South China Sea continental margin: Special Topic: the South China Sea Ocean Drilling (2020)
    Oxford University Press
    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 Sun, Z., Lin, J., Qiu, N., Jian, Z., Wang, P., Pang, X., Zheng, J., & Zhu, B. The role of magmatism in the thinning and breakup of the South China Sea continental margin: Special Topic: the South China Sea Ocean Drilling. National Science Review, 6(5), (2019): 871-876, doi:10.1093/nsr/nwz116.
    Description: Magmatism plays a key role in the process of continental margin breakup and ocean formation. Even in the extremely magma-poor Iberia and Newfoundland margin, studies of field outcrops have shown that syn-rift magmatism had participated in rifting from a very early stage and contributed directly to the rifting process. The final transition from exhumed continental mantle to the ocean formation is also triggered by the accumulation and eruption of magma [1]. Therefore, Atlantic-type passive continental margins are classified into two end-members: magma-poor (non-volcanic) and magma-rich (volcanic). The differences between them lie in whether a large amount of intrusive and extrusive magmatism from the mantle plume/hotspot is involved in the syn-rift and breakup stages. A magma-rich margin [2] should include the following characteristics: (i) a high-velocity lower crust (HVLC) caused by syn-rift mafic magma underplating; (ii) continental crust intruded by abundant sills and dikes; (iii) a large volume of seaward-dipping reflectors (SDRs) caused by flood basalt eruption or tuffs. All other margins are classified as magma-poor margins.
    Description: We thank the research team project of Guangdong Natural Science Foundation (2017A030312002), IODP-China and South China Sea Deep Project (91628301) and K.C. Wong Education Foundation (GJTD-2018-13) for providing support for the research. This research was also supported by the China National Science and Technology Major Project (2016ZX05026–003), the joint foundation of the National Natural Science Foundation of China and Guangdong province (U1301233), as well as the National Natural Science Foundation of China (41576070 and 41890813).
    Repository Name: Woods Hole Open Access Server
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  • 37
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    Auxotrophic interactions: A stabilizing attribute of aquatic microbial communities? (2020)
    Oxford University Press
    Details
    Publication Date: 2022-10-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Johnson, W. M., Alexander, H., Bier, R. L., Miller, D. R., Muscarella, M. E., Pitz, K. J., & Smith, H. Auxotrophic interactions: A stabilizing attribute of aquatic microbial communities? FEMS Microbiology Ecology, (2020): fiaa115, doi: 10.1093/femsec/fiaa115.
    Description: Auxotrophy, or an organism's requirement for an exogenous source of an organic molecule, is widespread throughout species and ecosystems. Auxotrophy can result in obligate interactions between organisms, influencing ecosystem structure and community composition. We explore how auxotrophy-induced interactions between aquatic microorganisms affect microbial community structure and stability. While some studies have documented auxotrophy in aquatic microorganisms, these studies are not widespread, and we therefore do not know the full extent of auxotrophic interactions in aquatic environments. Current theoretical and experimental work suggests that auxotrophy links microbial community members through a complex web of metabolic dependencies. We discuss the proposed ways in which auxotrophy may enhance or undermine the stability of aquatic microbial communities, highlighting areas where our limited understanding of these interactions prevents us from being able to predict the ecological implications of auxotrophy. Finally, we examine an example of auxotrophy in harmful algal blooms to place this often theoretical discussion in a field context where auxotrophy may have implications for the development and robustness of algal bloom communities. We seek to draw attention to the relationship between auxotrophy and community stability in an effort to encourage further field and theoretical work that explores the underlying principles of microbial interactions.
    Description: This work was supported by the National Science Foundation [OCE-1356192].
    Keywords: Auxotrophy ; Microbial community stability ; Microbial interactions ; Aquatic
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  • 38
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    Characterizing the culturable surface microbiomes of diverse marine animals (2021)
    Oxford University Press
    Details
    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Keller, A. G., Apprill, A., Lebaron, P., Robbins, J., Romano, T. A., Overton, E., Rong, Y., Yuan, R., Pollara, S., & Whalen, K. E. Characterizing the culturable surface microbiomes of diverse marine animals. FEMS Microbiology Ecology, 97(4), (2021): fiab040, https://doi.org/10.1093/femsec/fiab040.
    Description: Biofilm-forming bacteria have the potential to contribute to the health, physiology, behavior and ecology of the host and serve as its first line of defense against adverse conditions in the environment. While metabarcoding and metagenomic information furthers our understanding of microbiome composition, fewer studies use cultured samples to study the diverse interactions among the host and its microbiome, as cultured representatives are often lacking. This study examines the surface microbiomes cultured from three shallow-water coral species and two whale species. These unique marine animals place strong selective pressures on their microbial symbionts and contain members under similar environmental and anthropogenic stress. We developed an intense cultivation procedure, utilizing a suite of culture conditions targeting a rich assortment of biofilm-forming microorganisms. We identified 592 microbial isolates contained within 15 bacterial orders representing 50 bacterial genera, and two fungal species. Culturable bacteria from coral and whale samples paralleled taxonomic groups identified in culture-independent surveys, including 29% of all bacterial genera identified in the Megaptera novaeangliae skin microbiome through culture-independent methods. This microbial repository provides raw material and biological input for more nuanced studies which can explore how members of the microbiome both shape their micro-niche and impact host fitness.
    Description: Funding was provided by the National Science Foundation (Biological Oceanography) award #1657808 and National Institutes of Health grants 1R21-AI119311–01 to K. E. Whalen, as well as funding from the Koshland Integrated Natural Science Center and Green Fund at Haverford College. This constitutes scientific manuscript #298 from the Sea Research Foundation.
    Keywords: Bacteria ; SSU rRNA ; Coral ; Whale ; Microbiome ; Skin
    Repository Name: Woods Hole Open Access Server
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  • 39
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    The South China Sea is not a mini-Atlantic: plate-edge rifting vs intra-plate rifting (2020)
    Oxford University Press
    Details
    Publication Date: 2022-10-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Wang, P., Huang, C., Lin, J., Jian, Z., Sun, Z., & Zhao, M. The South China Sea is not a mini-Atlantic: plate-edge rifting vs intra-plate rifting. National Science Review, 6(5), (2019): 902-913, doi:10.1093/nsr/nwz135.
    Description: The South China Sea, as ‘a non-volcanic passive margin basin’ in the Pacific, has often been considered as a small-scale analogue of the Atlantic. The recent ocean drilling in the northern South China Sea margin found, however, that the Iberian model of non-volcanic rifted margin from the Atlantic does not apply to the South China Sea. In this paper, we review a variety of rifted basins and propose to discriminate two types of rifting basins: plate-edge type such as the South China Sea and intra-plate type like the Atlantic. They not only differ from each other in structure, formation process, lifespan and geographic size, but also occur at different stages of the Wilson cycle. The intra-plate rifting occurred in the Mesozoic and gave rise to large oceans, whereas the plate-edge rifting took place mainly in the mid-Cenozoic, with three-quarters of the basins concentrated in the Western Pacific. As a member of the Western Pacific system of marginal seas, the South China Sea should be studied not in isolation on its origin and evolution, but in a systematic context to include also its neighboring counterparts.
    Description: This work was supported by the National Natural Science Foundation of China as a part of the ‘South China Sea Deep’ Project (91128000).
    Keywords: Rifting ; Marginal basin ; Passive margin ; South China Sea ; Western Pacific ; Subduction
    Repository Name: Woods Hole Open Access Server
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  • 40
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    Relative relocation of earthquakes without a predefined velocity model: an example from a peculiar seismic cluster on Katla volcano's south-flank (Iceland) (2022)
    Oxford University Press
    Details
    Publication Date: 2022-10-28
    Description: Relative relocation methods are commonly used to precisely relocate earthquake clusters consisting of similar waveforms. Repeating waveforms are often recorded at volcanoes, where, however, the crust structure is expected to contain strong heterogeneities and therefore the 1D velocity model assumption that is made in most location strategies is not likely to describe reality. A peculiar cluster of repeating low-frequency seismic events was recorded on the south flank of Katla volcano (Iceland) from 2011. As the hypocentres are located at the rim of the glacier, the seismicity may be due to volcanic or glacial processes. Information on the size and shape of the cluster may help constraining the source process. The extreme similarity of waveforms points to a very small spatial distribution of hypocentres. In order to extract meaningful information about size and shape of the cluster, we minimize uncertainty by optimizing the cross-correlation measurements and relative-relocation process. With a synthetic test we determine the best parameters for differential-time measurements and estimate their uncertainties, specifically for each waveform. We design a relocation strategy to work without a predefined velocity model, by formulating and inverting the problem to seek changes in both location and slowness, thus accounting for azimuth, take-off angles and velocity deviations from a 1D model. We solve the inversion explicitly in order to propagate data errors through the calculation. With this approach we are able to resolve a source volume few tens of meters wide on horizontal directions and around 100 meters in depth. There is no suggestion that the hypocentres lie on a single fault plane and the depth distribution indicates that their source is unlikely to be related to glacial processes as the ice thickness is not expected to exceed few tens of meters in the source area.
    Description: Published
    Description: 1244–1257
    Description: 5T. Sismologia, geofisica e geologia per l'ingegneria sismica
    Description: JCR Journal
    Keywords: Physics - Geophysics; Physics - Geophysics
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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    Estimating genotypic richness and proportion of identical multi-locus genotypes in aquatic microalgal populations (2022)
    Oxford University Press
    Details
    Publication Date: 2022-11-10
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Sassenhagen, I., Erdner, D., Lougheed, B., Richlen, M., & SjÖqvist, C. Estimating genotypic richness and proportion of identical multi-locus genotypes in aquatic microalgal populations. Journal of Plankton Research, 44(4), (2022): 559-572, https://doi.org/10.1093/plankt/fbac034.
    Description: The majority of microalgal species reproduce asexually, yet population genetic studies rarely find identical multi-locus genotypes (MLG) in microalgal blooms. Instead, population genetic studies identify large genotypic diversity in most microalgal species. This paradox of frequent asexual reproduction but low number of identical genotypes hampers interpretations of microalgal genotypic diversity. We present a computer model for estimating, for the first time, the number of distinct MLGs by simulating microalgal population composition after defined exponential growth periods. The simulations highlighted the effects of initial genotypic diversity, sample size and intraspecific differences in growth rates on the probability of isolating identical genotypes. We estimated the genotypic richness for five natural microalgal species with available high-resolution population genetic data and monitoring-based growth rates, indicating 500 000 to 2 000 000 distinct genotypes for species with few observed clonal replicates (〈5%). Furthermore, our simulations indicated high variability in genotypic richness over time and among microalgal species. Genotypic richness was also strongly impacted by intraspecific variability in growth rates. The probability of finding identical MLGs and sampling a representative fraction of genotypes decreased noticeably with smaller sample sizes, challenging the detection of differences in genotypic diversity with typical isolate numbers in the field.
    Description: This work was supported by the Olle Engkvist foundation [200-0564 to I.S.]; the Swedish Research Council (Vetenskapsrådet) [2018-04992 to B.C.L.]; the Academy of Finland [321609 to C.S.]; the National Science Foundation [NSF OCE-1841811 to D.L.E. and M.L.R.]; and the National Institute of Environmental Health [NIEHS P01ES028949 to M.L.R.].
    Repository Name: Woods Hole Open Access Server
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  • 42
    Electronic Resource
    Electronic Resource
    Reversion of the B to A transition of DNA induced by specific interaction with the oligopeptide distamycin A (1980)
    New York : Wiley-Blackwell
    Biopolymers 19 (1980), S. 823-831 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The effect of the DNA-binding oligopeptide distamycin A on the B to A transition of DNA in ethanol/water solutions has been studied by means of CD. (The overbars indicate that it does not matter which particular form of the corresponding families is considered.) The results show that increasing the concentration of distamycin A reverses the A conformation (in 82% ethanol) to the B conformation due to its strong binding and stabilization of the latter. In accordance with previous data for pure aqueous solutions, a site size of 3.5 base pairs is obtained from the studies in water/ethanolic solutions. From the data on the B to A transition in the presence of distamycin A, we estimated the length of the cooperativity ν0 = 10 base pairs.The results demonstrate that the oligopeptide systems of distamycin, as well as those of netropsin, are effective stabilizers of the DNA B-conformation.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1980.360190408
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  • 43
    Electronic Resource
    Electronic Resource
    NMR evidence for a type I β-turn in (Pro2)-tetrapeptides and interdependence of cis:Trans isomerism, ring flexibility, and backbone conformation (1980)
    New York : Wiley-Blackwell
    Biopolymers 19 (1980), S. 781-804 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Tetrapeptides with proline in position 2, asparagine or leucine in position 3, and glycine in positions 1 and 4, with end groups free or blocked on the N-terminal side, were studied in their various ionic states in 2H2O and in Me2SO-d6 by 1H- and 13C-nmr. In order to clarify or refine some details, successive substitutions of the residues in these peptides with amino acids enriched to 85% in 13C, or to 85% 13C plus 97% 2H were carried out. The 1H and 13C chemical shifts as well as the 1H-1H, 13C-13C, and 13C-1H coupling constants and the signal intensities show strong similarity of behavior between the tetrapeptides of asparagine and leucine. The main conformational characteristics are (1) the almost total stabilization of the trans conformer in the type I β-turn structure when the peptide is in the zwitterion state dissolved in Me2SO. This is deduced from the 3JC3αH-N3H and the 3JC2′-H3α coupling constants, which both furnish a dihedral angle of φ3 = -90°, and from the positive value of the temperature coefficient of the glycine-4 amide protons, which suggests a type 4 → 1 hydrogen bond; (2) the evolution of cis and trans isomer fractions which change with the ionic state of the peptides in Me2SO, whereas they remain constant in aqueous solution; and (3) the conformation of the pyrrolidine ring as it follows the variations in cis:trans isomer populations together with the side-chain rotamer fractions of the residue in position 3. In the β-turn conformation the isomer cis is less abundant and the pyrrolidine ring is more flexible; this explains the perfect accommodation of the proline residue in position 2 of a bend. The interdependence of these phenomena where interactive forces play a predominant role underlines the importance of cooperative effects in the molecule. The results also suggest that the cis isomer of proline can adapt itself just as well as the trans isomer to position 2 of a type I β-turn.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1980.360190406
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  • 44
    Electronic Resource
    Electronic Resource
    Transport properties of particles with segmental flexibility. II. Decay of fluorescence polarization anisotropy from hinged macromolecules (1980)
    New York : Wiley-Blackwell
    Biopolymers 19 (1980), S. 913-930 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: An algorithm is presented for the Monte Carlo simulation of the decay of fluorescence polarization from segmentally flexible molecules. Based on the random walk model of Brownian motion, the treatment explicitly follows the stochastic changes in the diffusion coefficients as the molecule bends. It includes the effects of a linear restoring force opposing the bending and the effects of hydrodynamic coupling between the translational, rotational, and bending motions. One application is presented: the simulation of anisotropy decay curves for hinged rods. A variety of decay curves are obtained, including single- and multiexponential behavior, and the following conclusions are reached: (1) increasing the flexibility is usually, but not always, accompanied by a more rapid rate of depolarization; (2) reducing the size of the fluorescent subunit will usually, but not always, increase the rate of depolarization; and (3) the complex interplay between the effects of molecular shape, relative sizes of the subunits, restoring force, and orientation of the transition dipoles renders it unlikely that any simple method can be used to interpret anisotrophy data without simulation. In particular, it is not possible to determine the extent of bending by fitting the data with the two-exponential approximation used by some investigators in the past.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1980.360190414
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  • 45
    Electronic Resource
    Electronic Resource
    13C-nmr spectroscopy of red algal galactans (1980)
    New York : Wiley-Blackwell
    Biopolymers 19 (1980), S. 977-990 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: 13C-nmr spectra of red seaweed galactans, belonging to the agar and carrageenan groups or having the “intermediate” type of structure, were interpreted on the basis of 13C-nmr spectra of model compounds. Signal assignments have been made for most of the known extreme structures of such galactans. 13C-nmr spectroscopy was shown to be a rapid and convenient method of structural analysis, which permits one to determine the type of galactan structure, the absolute configurations of its constituents (galactose and 3,6-anhydrogalactose), and the positions of the sulfate and O-methyl groups in a polysaccharide molecule.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1980.360190504
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  • 46
    Electronic Resource
    Electronic Resource
    Dielectric changes in hyaluronate solutions at microwave frequencies as a function of concentration, system pH, and temperature (1980)
    New York : Wiley-Blackwell
    Biopolymers 19 (1980), S. 931-944 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The dielectric response of human umbilical cord hyaluronic acid in various environments has been studied at microwave frquencies using a resonant microwave cavity as a probe. Both the real and imaginary parts of complex dielectric constant and the loss tangent for hyaluronate solutions are obtained by utilizing equations for perturbation of a resonant cavity. Dielectric changes at room temperature have been observed in aqueous solutions of hyaluronic acid as a function of concentration ranging from 0 to 350 mg/ml. The data indicate the existence of ordered phases in hyaluronate solutions at selective concentrations, that is, exhibiting lyotropic-type transitions. Hyaluronate solutions at 1.5 and 3 mg/ml concentrations have been studied at various pH in the range of 6-8 and at constant ionic strength 0.1. A temperature-dependent transition in hyaluronate solution of 120 mg/ml concentration has been observed at physiological temperature. It is shown that this temperature-dependent behavior can be related to the orientational polarizability term in the Debye theory of polar molecules in liquids.
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1980.360190415
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  • 47
    Electronic Resource
    Electronic Resource
    A quantitative test of Zimm's model for the rotor-speed-department sedimentation of linear DNA molecules (1980)
    New York : Wiley-Blackwell
    Biopolymers 19 (1980), S. 945-964 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In 1974, Zimm described a theory which predicts that the sedimentation coefficient of high-molecular-weight DNA will decrease as the rotor speed of measurement increases. In 1979, this theory was revised, and the new formula predicts speed-dependence effects that are substantially smaller than the predictions of the original version. This report describes the results of subjecting both the original and the revised versions of the theory to quantitative tests using a well-defined sucrose-gradient system and a DNA of known molecular weight (T4c DNA). T4c bacteriophage is a mutant, whose DNA contains the unmodified base cytosine, instead of the glucosylated hydroxymethylcytosine characteristic of the T-even bacteriophages, and has a molecular weight of 115 ± 3 × 106. The DNA of the wild-type phage (T4D+) was also used in some experiments.In addition to the quantitative tests, the experiments test for an effect first observed by Rubenstein and Leighton, which showed that the sedimentation coefficient measured for T2 DNA depended on the composition of the centrifuge tube used for the measurement (tube composition effect). It can be inferred from this observation that an interaction occurs between particle and tube wall during sedimentation, and this leads to a reduction in sedimentation velocity independent of the reduction in S described by Zimm's theory.The results show that in the range of 25,000-50,000 rpm, the original but theoretically incorrect form of the theory quite accurately describes the sedimentation behavior of both T4c and T4D+ DNA, although T4D+ was a special case in some respects. The revised (corrected) form of the theory predicts much less of a speed-dependence effect than that actually observed. The discrepancy between corrected theory and observation suggests that other factors (perhaps arising from the use of the swinging bucket rotor geometry) are causing the additional observed reduction in S20,w. However, the experiments show that the tube composition effect does not seem to be one of these.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1980.360190502
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  • 48
    Electronic Resource
    Electronic Resource
    Proton NMR study of the interaction of cis-dichloro-diamine-platinum(II) with poly(I) and poly(I)·poly(C) (1980)
    New York : Wiley-Blackwell
    Biopolymers 19 (1980), S. 1299-1309 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The fixation of cis (NH3)2Cl2Pt(II) to poly(I)·poly(C) leads to the formation of two complexed species. One involves coordination to a single base (accounting for about 70% of the total platinum bound over the rb range 0.07-0.25) and the other to two bases which are not adjacent to each other but may be on the same strand and separated by a loop. Reaction of the platinum compound with poly(I) gives in addition to the above two species a minor one (about 15%, independent of rb over the range 0.05-0.30) in which the platinum is bound to two adjacent bases. The availability of such coordination reduces the dominance of the 1:1 species, which, however, remains the major one (ca. 55%).
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1980.360190706
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  • 49
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    Electronic Resource
    Heavy-atom effects associated with methylmercury (II) binding to rabbit glyceraldehyde-3-phosphate dehydrogenase (1980)
    New York : Wiley-Blackwell
    Biopolymers 19 (1980), S. 1329-1344 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The complex of CH3Hg(II) with the accessible cysteines of glyceraldehyde-3-phosphate dehydrogenase (GAPD, EC 1.2.1.12) from rabbit muscle has been studied by phosphorescence and optically detected magnetic resonance (ODMR) spectroscopy. The wavelength dependence of the phosphorescence decay kinetics has also been measured. Comparison of CH3Hg(II)-GAPD with GAPD by these methods shows that a specific optically resolved tryptophan site of GAPD is perturbed by the interaction with a nearby mercury atom. The perturbation on the luminescence and ODMR properties is typical of an external heavy-atom effect. Based on the x-ray diffraction structure of the lobster enzyme, it is proposed that the heavy-atom effect results from the interaction of tryptophan-310 with CH3Hg(II) bound to cysteine-281 in the rabbit muscle enzyme.
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    Interaction of spermine with different forms of DNA. A conformational study (1980)
    New York : Wiley-Blackwell
    Biopolymers 19 (1980), S. 1415-1434 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The energy of interaction of a spermine molecule with the A- and B-forms of DNA has been calculated, assuming that the molecule of spermine is fixed in the narrow groove of the DNA helix with the formation of hydrogen bonds between the amino groups of spermine and the phosphate groups of DNA. The atom-atom potentials method was used. Optimal structures for the A-DNA-spermine and B-DNA-spermine complexes are suggested. It is shown that, in agreement with the experimental data, the interaction of the spermine molecule with the A-DNA is energetically more favorable than that with the B-DNA. Two main factors are responsible for this: (1) the distance between neighboring phosphates of the chain in A-DNA (which is about 1 Å less than that in B-DNA) corresponds better to the distance between the amino groups of the propyl part of spermine; and (2) the orientation of phosphate groups in A-DNA inside the groove is preferable for complex formation with spermine to the outside groove arrangement of the phosphates in B-DNA. These conclusions are further confirmed by the calculations for DNA-propane diamine complexes.
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    Crystal and molecular structure of isoleucinomycin, cyclo[-(D-Ile-Lac-Ile-D-Hyi)3-](C60H102N6O18) (1980)
    New York : Wiley-Blackwell
    Biopolymers 19 (1980), S. 1517-1534 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The crystal structure of a synthetic analog of valinomycin, cyclo[-(D-Ile-Lac-Ile-D-Hyi)3-] (C60H102N6O18), has been determined by x-ray diffraction procedures. The crystals are orthorhombic, space group P212121, with cell parameters a = 11.516, b = 15.705, c = 39.310 Å, and Z = 4. The atomic coordinates for the C, N, O atoms were refined in the anisotropic thermal motion approximation and for the H atoms in the isotropic approximation. Values of standard (R) and weighted (Rw) reliability factors after refinement are 0.073 and 0.056, respectively. The structure is completely asymmetric. The cyclic molecular backbone is stabilized by six intramolecular hydrogen bonds N—H…O=C, five bonds being of the 4→1 type and one being of the 5→1 type. The side chains are located on the molecular periphery. The conformational state of isoleucinomycin in the crystal is intermediate between the corresponding crystalline states of valinomycin and meso-valinomycin. The observed conformation suggests that complexation could proceed via entry of the ion at the face possessing the L-Lac residues, the less crowded face.
    Additional Material: 5 Ill.
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    Conformational analysis of the milk oligosaccharides (1980)
    New York : Wiley-Blackwell
    Biopolymers 19 (1980), S. 1555-1566 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Possible conformations of lacto-N-tetraose, lacto-N-neotetraose, related disaccharides, and other milk oligosaccharides have been studied by an energy-minimization procedure using empirical potential functions. Lacto-N-tetraose favors a “curved” conformation, while lacto-N-neotetraose favors an approximately “straight” conformation. These two conformations differ mainly in the position of the terminal galactose residue with respect to the rest of the molecule. This difference explains the greater strength of lacto-N-neotetraose compared with lacto-N-tetraose in its ability to inhibit the cross-reaction of blood group P1 fractions with Type XIV pneumococcal antipolysaccharide. Although the favored conformation of lacto-N-tetraose (inactive) agrees with the model proposed by the earlier workers, that for lacto-N-neotetraose (active) differs. The favored conformations for the disaccharides galactose-β(1-4)-N-acetylglucosamine, galactose-β(1-3)-N-acetylglucosamine, and lactose are similar in overall shape, differing only in the nature and orientation of the side groups. This explains their nearly equal inhibitory activity. These theoretical models also explain the increased activity of lacto-N-fucopentaose I over that of lacto-N-tetraose and the relative activities of the substituted lactoses. The present studies suggest that it is the overall shape of the molecule which is important for activity, rather than the terminal β(1-4)-linked galactose residue alone.
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    Influence of methanol on the rotational diffusion of poly(L-lysine) in the helix-coil transition (1980)
    New York : Wiley-Blackwell
    Biopolymers 19 (1980), S. 1571-1585 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: 13C spin-lattice relaxation times of poly(L-lysine) have been obtained at 67.9 MHz in aqueous solution and in a mixed solvent (40% methanol/60% water). A concomitant determination of the conformation by CD permits the correlation of conformation and rotational diffusion of the polymer. The dependence on pH of the spin-lattice relaxation times of the 13Cα and the side-chain carbon resonances reflects the diffusional motion in the random-coil conformation, in the helix-coil transition, and in the conformation of the α-helix. In the mixed solvent the reorientational correlation time of the Cα-Hα vector increases from τ = 0.37 nsec (random coil) to τ = 12.0 nsec (α-helix). In aqueous solution the correlation time of this vector increases from τ = 0.33 nsec (random coil) to τ ≫ 11 nsec. The reorientation rates of the side-chain methylene groups in the two solvents are markedly different. The reorientation of all methylene groups is reduced in the mixed solvent.
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    Solid-state conformation of copolymers of β-benzyl-L-aspartate with L-alanine, L-leucine, L-valine, γ-benzyl-L-glutamate, or ∊-carbobenzoxy-L-lysine (1980)
    New York : Wiley-Blackwell
    Biopolymers 19 (1980), S. 1603-1615 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The solid-state conformation of copolymers of β-benzyl-L-aspartate [L-Asp(OBzl)] with L-leucine (L-Leu), L-alanine (L-Ala), L-valine (L-Val), γ-benzyl-L-glutamate [L-Glu(OBzl)], or ∊-carbobenzoxy-L-lysine (Cbz-L-Lys) has been studied by ir spectroscopy and circular dichroism (CD). The ir spectra in the region of the amide I and II bands and in the region of 700-250 cm-1 have been determined. The results from the ir studies are in good agreement with data obtained by CD experiments. Incorporation of the amino acid residues mentioned above into poly[L-Asp(OBzl)] induces a change from the left-handed into the right-handed α-helix. This conformational change for the poly[L-Asp(OBzl)] copolymers was observed in the following composition ranges: L-Leu, 0-15 mol %; L-Ala, 0-32 mol %; L-Val, 0-8 mol %; L-Glu(OBzl), 3-10 mol %; and Cbz-L-Lys, 0-9 mol %.
    Additional Material: 7 Ill.
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    Physical aging of dry elastin (1980)
    New York : Wiley-Blackwell
    Biopolymers 19 (1980), S. 1667-1673 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Dry purified ligamentum nuchae elastin has been investigated for physical aging. The samples were quenched from a temperature (197°C) close to the softening point to a number of measuring temperatures ranging from -20 to +180°C. At each temperature, the small-strain torsional creep properties were determined at a number of elapsed intervals after the quench. Aging effects were found over the whole temperature range, and the creep and aging behavior of elastin turned out to be very similar to that of synthetic polymers.
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    DNA backbone conformation in cis-syn pyrimidine[]pyrimidine cyclobutane dimersPresented at the American Society of Biological Chemists and Biophysical Society Meeting, June 1-5, 1980, New Orleans, Louisiana [(1980) Fed. Proc. 39, 1879]. (1980)
    New York : Wiley-Blackwell
    Biopolymers 19 (1980), S. 1695-1701 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
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    Toroidal elastic supercoiling of DNA (1980)
    New York : Wiley-Blackwell
    Biopolymers 19 (1980), S. 1705-1713 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Notes: Covalently closed circular DNA can exist in different configurations known as circular, toroidal, and interwound. Changes among these forms can be made in several ways, including the insertion of dye molecules between adjacent base pairs, which tends to untwist the double-helical structure. The aim of this paper is to discuss these configurations, and the changes among them, in the context of classical elastomechanics. The concepts of twisting, linkage and writhing are explained. Simple experiments on a twisted linear-elastic rod are described, and it is shown that although the circular and interwound forms may be modeled in this way, the toroidal form does not occur, being mechanically unstable. Theoretical energy calculations by Levitt on bent and twisted DNA show that DNA exhibits a particular kind of nonlinear elasticity in which there is an unusual coupling between bending and twisting. The aim of the paper is to show qualitatively that this special kind of elasticity can stabilize the toroidal form of closed circular DNA.
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    Physicochemical investigation of k-carrageenan in the random state (1980)
    New York : Wiley-Blackwell
    Biopolymers 19 (1980), S. 1357-1374 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Light-scattering, viscosity, and sedimentation experiments on aqueous solutions of k-carrageenan show that this sulfated polygalactose is an expanded flexible random coil. This expansion is due to long-range interactions that are predominantly electrostatic. Extrapolation of viscosity data to infinite ionic strength provided values for the intrinsic viscosity which were subjected to the Stockmayer-Fixman analysis, giving a value for the Mark-Houwink coefficient under theta-conditions, Kθ, of 0.27. The characteristic ratio, C∞, under these conditions is 7.8, and the conformation factor σ is 2. In a solution of 0.118 ionic strength, where a Mark-Houwink exponent aη of 0.86 is found, the radii of gyration calculated from viscosity data are lower than those found from the angular dependence of scattered light. On the other hand, the radius of gyration found from the sedimentation rate agrees well with the light-scattering radius. The relations between molecular parameters are corrected for the poly-dispersity of the sample.
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    An interaction of albumin with hyaluronic acid and chondroitin sulfate: A study of affinity chromatography and circular dichroism (1980)
    New York : Wiley-Blackwell
    Biopolymers 19 (1980), S. 1407-1414 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 4 Ill.
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    Masthead (1980)
    New York : Wiley-Blackwell
    Biopolymers 19 (1980) 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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    The translational friction of toroids (1980)
    New York : Wiley-Blackwell
    Biopolymers 19 (1980), S. 1475-1489 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: An approximate analytic expression for the translational friction coefficient of a toroid modeled as a continuous shell of frictional elements is derived using the Kirkwood approximation. The accuracy of this expression was determined by comparing the friction coefficients predicted by it to those predicted by extrapolated shell-model calculations using the modified Oseen tensor. To show that these calculations do indeed yield the correct friction coefficients, actual translational friction coefficients were determined by observing settling rates of macroscopic model rings or toroids in a high-viscosity silicone fluid. Our conclusion is that the approximate expression yields friction coefficients that are about 1.5-3% low for finite rings. For thin rings, a comparison is also made with the exact result of Yamakawa and Yamaki [J. Chem. Phys. 57, 1572 (1972); 58, 2049 (1973)] for the translational friction of plane polygonal rings. This comparison shows that the approximate expression yields results which are low by 2-3% unless the rings are extremely thin, in which case the error is larger. In the limit of an infinitely thin ring the approximate expression reduces to the Kirkwood result [J. Polym. Sci. 12, 1 (1954)], which is low by 8.3%. We discuss briefly how this work may be useful in determining the structure of DNA compacted by various solvent-electrolyte systems and polyamines.
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    Dynamic light scattering studies of internal motions in DNA. II. Clean viral DNAs (1980)
    New York : Wiley-Blackwell
    Biopolymers 19 (1980), S. 1451-1474 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: Internal Brownian motions of clean φ29 and λ-DNAs have been studied using photon-correlation techniques at both visible (λ0 = 632.8 nm) and uv (λ0 = 363.8 nm) wavelengths. The present dynamic light scattering data, which extend to K2 = 19 × 1010 cm-2, can in every case be satisfactorily simulated by a Rouse-Zimm model polymer with an appropriate choice of the three model parameters. The effects of pH, salt concentration, single-strand breaks, and molecular weight on those model parameters have also been investigated. Intact clean DNAs exhibit surprisingly little variation with pH from 7.85 to 10.25, with salt concentration from 0.01 NaCl to 5.4M NH4Cl, or with molecular weight or GC content. The single-strand breaks have no effect at pH 9.46, but produce dramatic changes in the model parameters at pH 10.0 and 10.25, indicating the introduction of titratable joints at those pHs. The failure of either single-strand breaks or a large change in GC content to alter the model parameters in the neutral pH range is a strong indication that local denaturation is not required for those flexions and torsions that dominate the relaxation of fluctuations in the scattered light. The Langevin relaxation time for the slowest internal mode of a particular Rouse-Zimm model derived from the dynamic light scattering data is compared with pertinent literature data extrapolated to the same molecular weight. The present algorithm for determining model parameters from the light-scattering Dapp vs K2 curve actually yields a Langevin time in fairly good agreement with the literature value. For unknown reasons the light-scattering D0 values generally exceed those obtained from the molecular weight and sedimentation coefficient by about 20%.
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    Ultraviolet Raman spectroscopy of polyribouridylic acid: Excitation profile of the hypochromism induced by order-disorder transition (1980)
    New York : Wiley-Blackwell
    Biopolymers 19 (1980), S. 1507-1515 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: Raman spectra of polyribouridylic acid excited in the uv region, from 363 to 290 nm, are reported. The conformational changes of the polymer from random coil to ordered structure with stacked bases at high and low temperature, respectively, are reflected by important changes in the Raman line intensities; this Raman hypochromism is itself a function of the excitation wavelength - its profile has been determined and shows negative values in the region of 290 nm (near resonance), i.e., hypochromism becomes hyperchromism. Thus the knowledge of the hypochromism excitation profile is important in following order-disorder transition of a polymer using resonance Raman spectroscopy. Theoretical attempts are proposed for explanation, involving not only the relative variations of the molar extinction coefficient on the order-disorder transition of the polymer, but also the damping factors of the vibronic levels. The theoretical curve is found to fit adequately the experimental data over the excitation range, using only the frequency of the O-O transition of uracil and a vibronic linewidth of 2200 cm-1.
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    Interaction of poly(α-L-glutamic acid) and sodium poly(α-L-glutamate) with solvent components in water-2-chloroethanol mixtures (1980)
    New York : Wiley-Blackwell
    Biopolymers 19 (1980), S. 2177-2190 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: The preferential interaction of sodium poly(α-L-glutamate) and poly(α-L-glutamic acid) with the solvent components in water/2-chloroethanol mixtures has been determined using density-increment measurements. The degree of preferential interaction was deduced from the density increments at constant molality of 2-chloroethanol and at constant chemical potential of 2-chloroethanol. Sodium poly(α-L-glutamate) and poly(α-L-glutamic acid) are both preferentially hydrated in the whole range of solvent composition. A dehydration process occurs during the 2-chloroethanol-induced coil-to-helix transition of sodium poly(α-L-glutamate). This dehydration process was attributed to the release of some moles of water from the neighborhood of the peptide bond during the nucleation of the helix. After the conformational transition, sodium poly(α-L-glutamate) is solvated by one 2-chloroethanol molecule. The location of water and 2-chloroethanol molecules in the different parts of the residue (more polar and less polar portions) is also discussed.
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    Effects of pD on ring-stacking interactions between dinucleoside phosphates and tryptamine (1980)
    New York : Wiley-Blackwell
    Biopolymers 19 (1980), S. 2223-2245 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: Complex formation between tryptamine and mononucleotides and dinucleoside phosphates containing adenine and/or cytosine has been studied at five pD's ranging from 1.1 to 7.4 by proton magnetic resonance spectroscopy. Chemical shifts of base ring protons and the ribose anomeric proton in the nucleotides and indole ring protons in tryptamine were monitored and their changes with pD and intermolecular interactions interpreted qualitatively. Stacked complexes were found to exist at all pD's in the range studied. Complex geometries differ depending on pD. An electrostatic interaction between the tryptamine amino group and the nucleotide phosphate group contributes to complex formation above pD 4 but is not strong enough to shift the dinucleoside phosphate equilibrium towards the unstacked conformer.
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    Rǒle des electrons π des fonctions amide et ester dans les peptides et depsipeptides (1981)
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 169-185 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Notes: The IR data for the R1 CO-O-CHR2-CO-NHR3 derivatives are interpreted in terms of a H…π interaction involving the N—H bond and the π orbitals of the ester function and giving rise to a high ν(C=O) frequency and a low ν frequency. The resulting molecular conformation corresponds to the angular values φ # -90°, ψ # 0°. The H…π interaction in MeCO-L-Lac-NHMe is highly destabilized by water and aprotic solvents but is retained in methanol. Considering the high ν(C=O) ester or amide frequency of the middle function in β-folded depsipeptide or peptide sequences, it may be supposed that the residue indexed i + 2 in β turns experiences a H…π interaction which has a stabilizing effect on β turns. Some examples concerning valinomycin and some model compounds are discussed.
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    Masthead (1981)
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    Biopolymers 20 (1981) 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
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    Polyelectrolyte contribution to the persistence length of DNA (1981)
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 251-268 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Notes: The difference between the theories of Manning, on the one hand, and of Odijk and Skolnick and Fixman, on the other, for the polyelectrolyte contribution to the persistence length of DNA is shown to arise entirely from a subtle geometrical error in the theory of Manning. The corrected theory of Manning predicts a negligible polyelectrolyte contribution in 1.0M NaCl and only 33 Å in 0.01M NaCl, thus giving a change in total persistence length by a factor of only 1.07 over that range, in agreement with Odijk. Pertinent data in the literature indicate that the persistence length must change by a factor of ≤ 1.6 between 1.0 and 0.01M NaCl, and very likely by less than a factor of 1.4. Evidently, the intrinsic rigidity of the uncharged double-strand filament dominates the bending rigidity at NaCl concentrations above 0.01M.
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    Conformational studies of peptides: Crystal and molecular structures of L-3,4-dehydroproline and its t-butoxycarbonyl and acetyl amide derivatives (1981)
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 283-302 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The crystal structures of L-3,4-dehydroproline, t-butoxycarbonyl-L-3,4-dehydroproline amide, and acetyl-L-3,4-dehydroproline amide have been determined. L-3,4-Dehydroproline is orthorhombic with a = 16.756, b = 5.870, c = 5.275 Å, and Z = 4; t-butoxycarbonyl-L-3,4-dehydroproline amide is orthorhombic with a = 6.448, b = 8.602, c = 21.710 Å, and Z = 4; acetyl-L-3,4-dehydroproline amide is monoclinic with a = 4.788, b = 10.880, c = 7.785 Å, β = 105.25°, and Z = 2. The final R value for the L-3,4-dehydroproline is 0.046 based on 529 reflections; for t-butoxycarbonyl-L-3,4-dehydroproline amide, 0.050 based on 792 reflections; and for acetyl-L-3,4-dehydroproline amide, 0.058 based on 632 reflections. The structures clearly establish that the free amino acid exists in the zwitterionic form in the crystalline state. The molecular conformations of the t-Boc and acetyl derivatives consist of two planes: one involving the primary amide and the other the remaining atoms of the molecule. The acetyl-L-3,4-dehydroproline amide contains a tertiary amide bond in the cis conformation. To the best of our knowledge, this is the first example of a cis bond in an acetyl derivative of an amino acid or peptide. At variance with the previously reported proline amides, which present φ and ψ values corresponding to those of a right-handed α-helical conformation (conformation A), the t-Boc and acetyl derivatives both have φ and ψ values corresponding to a collagenlike conformation (conformation F).
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    Physical properties of type i collagen in solution: Structure of α-Chains and β- and γ-components and two-component mixtures (1981)
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 359-371 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The structure of thermally denatured Type I collagen has been studied using laser light scattering. The results indicate that the diffusion coefficients of α-chains and β- and γ-components are 1.550 ± 0.08 × 10-7, 1.000 ± 0.05 × 10-7, and 0.835 ± 0.04 × 10-7 cm2/sec, respectively, at temperatures between 20 and 40°C. It is concluded from diffusion data that these species have hydrodynamic radii of about 13.8 nm (α-chain), 21.5 nm (β-component), and 25.7 nm (γ-component), consistent with previous studies of thermal denaturation by light scattering. It is also concluded, based on volume calculations, that a large volume increase occurs when the triple helix unfolds. Homodyne correlation functions for two component mixtures of α-chains and β-and γ-components appeared to decay exponentially. In all but one case discussed the correlation function could be fitted with a single component having a translational diffusion coefficient which was an intensity weighted average of the diffusion coefficient of each component present.
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    Theoretical π-π* circular dichroic spectra of helical poly(glycine) and poly(L-alanine) as functions of backbone torsion angles (1981)
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 387-397 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Circular dichroic spectra and oscillator strengths of the π-π transition near 190 nm are calculated for helical (Gly)6 and (Ala)6 at 30° intervals of the backbone torsion angles (φ,ψ) over the range -180° ≤ φ ≤ -60°, -60° ≤ ψ ≤ 180°, using the partially dispersive normal mode treatment of the dipole interaction model. Polarizabilities of atoms and the NC′O group are those determined semiempirically in previous studies. Calculations for (Ala)6 at (φ,ψ) angles corresponding to the α-helix, the poly(Pro) II helix, a collagen single helix, a poly-(MeAla) helix, and single β-helices are found to agree well with most of the available experimental data.
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    Interaction of the antimalarial drug fluoroquine with DNA, tRNA, and poly(A): 19F-NMR chemical-shift and relaxation, optical absorption, and fluorescence studies (1981)
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 435-449 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The interaction of the fluorinated antimalarial drug fluoroquine [7-fluoro-4-(diethyl-amino-1-methylbutylamino)quinoline] with DNA, tRNA, and poly(A) has been investigated by optical absorption, fluorescence, and 19F-nmr chemical-shift and relaxation methods. Optical absorption and fluorescence experiments indicate that fluoroquine binds to nucleic acids in a similar manner to that of its well-known analog chloroquine. At low drug-to-base pair ratios, binding of both drugs appears to be random. Fluoroquine and chloroquine also elevate the melting temperature (Tm) of DNA to a comparable extent. Binding of fluoroquine to DNA, tRNA, or poly(A) results in a downfield shift of about 1.5 ppm for the 19F-nmr resonance. The chemical shift of free fluoroquine depends on the isotopic composition of the solvent (D2O vs H2O). The solvent isotope shift is virtually eliminated by fluoroquine binding to any one of the nucleic acids. 19F-nmr relaxation experiments were carried out to measure the spin-lattice relaxation time (T1), 19F{1H} nuclear Overhauser effect (NOE), off-resonance intensity ratio (R), off-resonance rotating-frame spin-lattice relaxation time (T1ρoff), and linewidth for fluoroquine in the nucleic acid complexes. By accounting for intramolecular proton-fluorine dipolar and chemical-shift anisotropy contributions to the fluorine relaxation, all of the relaxation parameters for the fluoroquine-DNA complex can be well described by a motional model incorporating long-range DNA bending on the order of a microsecond and an internal motion of the drug on the order of a nanosecond. Selective NOE experiments indicate that the fluorine in the drug is near the ribose protons in the RNA complexes, but not in the DNA complex. Details of the binding evidently differ for the two types of nucleic acids. This study provides the foundation for an investigation of fluoroquine in intact cells.
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    Conformational energy studies on N-methylated analogs of thyrotropin releasing hormone, enkephalin, and luteinizing hormone-releasing hormone (1980)
    New York : Wiley-Blackwell
    Biopolymers 19 (1980), S. 1943-1973 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Empirical conformational energy calculations have been carried out for N-methyl derivatives of alanine and phenylalanine dipeptide models and N-methyl-substituted active analogs of three biologically active peptides, namely thyrotropin-releasing hormone (TRH), enkephalin (ENK), and luteinizing hormone-releasing hormone (LHRH). The isoenergetic contour maps and the local dipeptide minima obtained, when the peptide bond (ω) preceding the N-methylated residue is in the trans configuration show that (1) N-methylation constricts the conformational freedom of both the ith and (i + 1)th residues; (2), the lowest energy position for both residues occurs around φ = -135° ± 5° and ψ = 75° ± 5°, and (3) the αL conformational state is the second lowest energy state for the (i + 1)th residue, whereas for the ith residue the C5 (extended) conformation is second lowest in energy. When the peptide bond (ωi) is in the cis configuration the ith residue is energetically forbidden in the range φ = 0° to 180° and ψ = -180° to +180°. Conformations of low energy for ωi = 0° are found to be similar to those obtained for the trans peptide bond. In all the model systems (irrespective of cis or trans), the αR conformational state is energetically very high. Significant deviations from planarity are found for the peptide bond when the amide hydrogen is replaced by a methyl group. Two low-energy conformers are found for [(N-Me)His2]TRH. These conformers differ only in the φ and ψ values at the (N-Me)His2 residue. Among the different low-energy conformers found for each of the ENK analogs [D-Ala2,(N-Me)Phe4, Met5]ENK amide and [D-Ala2,(N-Me)Met5]ENK amide, one low-energy conformer was found to be common for both analogs with respect to the side-chain orientations. The stability of the low-energy structures is discussed in the light of the activity of other analogs. Two low-energy conformers were found for [(N-Me)Leu7]LHRH. These conformations differ in the types of bend around the positions 6 and 7 of LHRH. One bend type is eliminated when the active analog [D-Ala6,(M-Me)Leu7]LHRH is considered.
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    Interactions of molecules with nucleic acids. III. Steric and electrostatic energy contours for the principal intercalation sites, prerequisites for binding, and the exclusion of essential metabolites from intercalation (1980)
    New York : Wiley-Blackwell
    Biopolymers 19 (1980), S. 2067-2089 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Based on steric and electrostatic considerations, the prerequisites for binding to DNA via the intercalation mechanism are proposed. Steric contour energy curves are presented to demonstrate the region inaccessible to an intercalant. They are calculated with a 6-n (n = 14) potential. This method is a soft potential analog of an excluded-volume approach. Electrostatic contours on the steric surface illustrate the relatively positive and negative regions of the binding site. The principal intercalation sites, predicted to fit into B-DNA via a tetramer-duplex unit, and the unconstrained dimer-duplex units, obtained in crystal structures, are examined. These contours illustrate the requirements of size, conformation, and net atomic charges necessary for intercalation and optimum binding. Based on the limited space available for intercalation by the presence of the backbone and the maximum base-pair separation of 8.25 Å, an Essential Metabolite Exclusion Hypothesis is presented.
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    Hydrodynamic behavior and molecular conformation of poly(L-lysine HBr) in carbonate buffer solution (1981)
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 345-357 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In carbonate buffer at pH 10.5, a transparent solution of poly(L-lysine HBr) was obtained up to fairly high concentration of 3 g/dl at room temperature. The hydrodynamic behavior of the solution has been studied by sedimentation analyses and viscosity measurements. A dimer form for high concentrations and a monomer form for low concentrations were inferred. The dimer and monomer forms were assigned to a β-structure and α-helix, respectively, based on the CD and optical rotary dispersion spectra. Using CD spectroscopy, a reversible transition between α-helix and β-structure was observed as a function of either poly(L-lysine HBr) concentration or temperature. An aggregated form which was assigned to the antiparallel pleated sheet appeared at 50°C on the basis of its ir spectrum.
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    Stability and geometry of hydrogen-bonded complexes of peptides (1981)
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 707-718 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Observations of induced circular dichroism (CD) bands in chloroform solution demonstrate the formation of specific, asymmetric complexes of the aromatic ligands 2-pyridone and 2,6-dichlorobenzoic acid with cyclic dipeptides of the general formula cyclo(L-Pro-X). The induced CD changes sign with the configuration of X due to subtle influences of the side chain on the geometry of the complex. Computations of interaction energies suggest that a plausible model for the complex of an aromatic ligand with the -CONH- of the cis secondary amide is a nearly planar arrangement of six heavy atoms in a ring containing two hydrogen bonds. The observed CD is matched by that computed for a tilt of the aromatic ligand toward the side chain of X. Binding constants were determined from the induced CD as a function of ligand concentration. For dichlorobenzoic acid these are about 450m-1 for the secondary amide and 50m-1 for the tertiary amide. For pyridone the binding constant is about 45m-1 for either the secondary or tertiary amide. For comparison self-dimerization constants determined by vapor-pressure osmometry in chloroform solution at 25°C are 870, 350, 50, and 20m-1 for pyridone, benzoic acid, dichlorobenzoic acid, and cyclo(L-Pro-Gly), respectively.
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    Proton and phosphorus nmr investigation of the conformational states of acid polyadenylic double helix (1981)
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 803-816 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Proton and phosphorus nmr have been used to investigate the double-helical structures of polyriboadenylic acid [poly(A)] formed in acidic solutions (pH 〈 6). The results obtained at low pH (∼4.5) are consistent with the model for the acid poly(A) double helix proposed by Rich [Rich, A., Davies, D. R., Crick, F. H. C. & Watson, J. D. (1961) J. Mol. Biol. 3, 71-86]. Other models that have been proposed are inconsistent with the nmr data. The nmr measurements have also been used to examine the conformation of poly(A) helix in the half-protonated state. Although the base-stacking arrangement of this state is similar to that observed in the more extensively protonated low-pH state, the phosphate backbone conformation is different from that found in either the neutral or low-pH structures.
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    The chiroptical properties of proteins. II. Near-ultraviolet circular dichroism of lysozymeTaken in part from the Ph.D. dissertation of W. J. G. (1980)
    New York : Wiley-Blackwell
    Biopolymers 19 (1980), S. 2191-2208 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A study of the near-uv CD spectrum of lysozyme was carried out in the presence and absence of the inhibitor tri-N-acetylglucosamine, and theoretical chiroptical calculations based on the tetragonal crystal structure of the enzyme and the enzyme-inhibitor complex were performed. The results of these calculations indicate that the near-uv CD spectrum of lysozyme can be adequately explained in terms of negative rotatory strengths arising from the tryptophan 1La (293-300 nm) and the disulfide n-σ* bands (250 rm), and positive rotatory strength contributions from the tryptophan 1Lb bands (291 nm) and the tyrosine 1Lb bands (275 nm). Contributions to the rotatory strength of each band were approximated in terms of specific interactions between chromophores. It was found that the rotatory strength of most of the near-uv transitions arises primarily from coupling interactions involving other side-chain chromophores and amide groups which are in close proximity. Changes which are observed in the lysozyme CD spectrum on binding of tri-N-acetylglucosamine may be explained in terms of changes in the rotatory strength which result from interactions of the 1La transitions of the active-site tryptophans with the acetamide groups of the inhibitor. The reasonable agreement which is found between the experimental and calculated rotatory strengths implies that the crystal conformation of lysozyme must resemble the solution conformation.
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    Masthead (1981)
    New York : Wiley-Blackwell
    Biopolymers 20 (1981) 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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    URL: http://dx.doi.org/10.1002/bip.1981.360200101
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    Effect of some organic cosolvents on the reaction of hemoglobin with oxygen (1981)
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 39-51 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We studied the effects of some organic cosolvents (monohydric alcohols and amides) on the reaction of hemoglobin with oxygen. We present evidence showing that our data can be analyzed within the framework of the Monod-Wyman-Changeux model and that the main effect of cosolvents is to alter the T ⇄ R conformational equilibrium of hemoglobin, without significantly affecting the intrinsic oxygen dissociation constants. Following a previously described phenomenological approach, the overall effects have been separated into effects related to the variation of the bulk dielectric constant of the solvent and effects not related to the variation of this constant.
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    XII. Conformational studies of histidine-containing peptides in solution (1981)
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 65-88 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The spectroscopic properties (uv, CD, nmr) of histidine, glycylhistidine, histidylglycine, glycylhistidylglycine have been investigated in water and methanol in the temperature range 200-320 K in order to obtain information about their conformational equilibria. This analysis has been carried out for the different ionic forms of the compounds, in order to evaluate the influence of the ionization state of the carboxyl, histidyl, and amino groups on the rotamer distribution of the histidyl side chain (as evaluated from proton nmr analysis) and on the overall molecule (as judged from CD spectra). On the basis of certain approximations and from the temperature dependence of the proton nmr resonance, the thermodynamic parameters (ΔH° and ΔS°) characterizing the conformational equilibrium of the hystidyl side chain have been evaluated for the different structures and ionization states. Relatively large entropy differences between the rotamers are obtained in some cases. The data of the sidechain rotamer population, as determined by nmr, have been analytically correlated with the CD data, and in the case of hystidine and histidylglycine in basic solution, first-approximation values for the ellipticity of the single conformers have been evaluated. Finally, in the example of glycylhistidine and histidylglycine in basic solution, it is shown how the data obtained from the different experimental approaches (nmr and CD), as well as from theoretical energy calculations, converge to characterize the most stable conformation in solution.
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    Laser light-scattering analysis of the dimerization of transfer ribonucleic acids with complementary anticodons (1981)
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 155-168 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Photon-correlation spectroscopy is a powerful technique for measuring the translational diffusion coefficient of particles and macromolecules in solution. In the study described here, this technique was used to analyze a specific dimerization process involving the association of two tRNA molecules through complementary anticodons. The tRNAs used in the analysis were E. coli tRNA2Glu and yeast tRNAPhe. The experimental data on the concentration dependence of the observed diffusion constants are shown to agree well with theoretical predictions. From these data, the equilibrium constant of the association reaction was determined for dimers formed over a wide range of temperatures and in several different solution conditions. In solutions of 0.1M ionic strength at 22°C, the equilibrium constants vary from 1 × 105M-1 in the absence of magnesium to 1.5 × 106M-1 in 10 mM Mg+2. The enthalpy and entropy changes for dimer formation in the absence and presence, 5 and 10 mM, of magnesium have been obtained from the temperature dependence of the equilibrium constant. The results show that both ΔH and ΔS contribute to the free energy of binding and that their relative contributions are similar for each solution condition evaluated.
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    Dependence of DNA conformation on the concentration of salt (1981)
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 231-235 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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    URL: http://dx.doi.org/10.1002/bip.1981.360200116
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    Vibrational circular dichroism of poly(γ-benzyl-L-glutamate) (1981)
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 237-240 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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    Low-frequency modes in the raman spectrum of DNA (1981)
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 243-247 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 4 Ill.
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    Quantum-mechanical study of model molecules in relation to collagen structure. II. (Gly-Phe-Pro) and (Gly-Pro-Phe) repeating units (1981)
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 269-282 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A conformational quantum-mechanical study of (Gly-Phe-Pro) and (Gly-Pro-Phe) repeating tripeptide sequences has been carried out with the PCILO method. Using appropriate molecules as a model, we investigated the conformational possibilities of each in situ residue. Computations have been done taking into account the two typical pyrrolidine ring puckering and the most favorable orientations of the phenylalanyl side chain. Major conclusions drawn from this study are that the phenylalanyl can be accommodated at both second and third positions in the sequence without preventing the formation of triple-helix conformation. However, the analogy observed between the rotational possibilities around the second residue of Gly-Pro-Pro and Gly-Phe-Pro indicates that phenylalanyl in the second position favors the triple-helix formation.
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    Neutron-scattering studies of the structure of chromatin core particles in solution (1981)
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 327-343 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The structure of the nucleosome core particle in solution has been studied by neutron scattering using the full-contrast variation technique, which reduces the experimental spectra to three fundamental scatter functions holding information on shape and structure. Systematic calculations of the fundamental scatter functions expected from proposed core-particle models have been compared with the observed functions and show that the neutron-scattering criteria severely restrict the number of models which can be valid for the structure in solution. The best model for the core particle in solution has a hydrophobic histone core about which 1.7 ± 0.1 turns of DNA are wrapped at a pitch between 3.0 and 3.5 nm. This core contains most of the histone and has an average thickness of 4 nm and diameter 6.4-7.5 nm. While solution scattering is not able to specify uniquely the actual shape of the core to high resolution, all models which are possible for the shape of the core to a resolution justified by the data have been considered. It is clear that cylindrical or wedge shapes compatible with the above dimensions are valid structures. A hole probably penetrates the histone core, but the data do not allow a diameter greater than 1 nm. Available evidence suggests that about a quarter of the total histone is outside the core.
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    Relationship between proton-proton nmr coupling constants and substituent electronegativities. III. Conformational analysis of proline rings in solution using a generalized Karplus equation (1981)
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 1211-1245 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The relationship between published vicinal proton-proton coupling constants and the pseudorotation properties of the pyrrolidine ring in L-proline, 4-hydroxy-L-proline, 4-fluoro-L-proline, and several linear and cyclic model proline peptides is investigated. Compared to earlier studies, several important improvements are incorporated: (1) a new empirical generalization of the classical Karplus equation is utilized, which allows a valid correction for the effects of electronegativity and orientation of substitutents on 3JHH; (2) an empirical correlation between proton-proton torsion angles and the pseudorotational parameters P and τm is derived; and (3) the best fit of the conformational parameters to the experimental coupling constants is obtained by means of a computerized iterative least-squares procedure. Two pseudorotation ranges were considered, classified as type N (χ2 positive sign) and type S (χ2 negative sign). The conformational equilibrium is fully described in terms of four geometrical parameters (PN, τN, PS, τS) and the equilibrium constant K. The present results indicate that, in general, the geometrical properties found in x-ray studies of proline and hydroxyproline residues are well preserved in solution. Several novel features are encountered, however. It is demonstrated that the proline ring occurs in a practically 1:1 conformational equilibrium between well-defined N- and S-type forms. Introduction of an amide group at the C-terminal end has no observable effect on this equilibrium, but the formation of a peptide bond at the imino nitrogen site results in a pronounced, but not exclusive, preference for an S-type form which is roughly 1.1 kcal/mol more stable than its N-type counterpart. The hydroxyproline ring system in neutral or acidic medium displays a pure N-type state, but N-acetylation results in the appearance of a minor (S-type) conformation. Cyclic proline dipeptides similarly exist in a biased conformational equilibrium. The major form (77-88%) corresponds to the N-type conformer observed in the solid state; the minor S-form has not been observed before. In contrast, cyclic hydroxyproline dipeptides display complete conformational purity. Ranges of endocyclic torsion angles deduced for the various classes of pyrrolidine derivatives in solution are presented. Each torsion appears confined to a surprisingly narrow range, comprising about 4°-8° in most cases. In all, the proline ring is far less “floppy” than hitherto assumed.
    Additional Material: 5 Ill.
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    Thermodynamics and equilibrium sedimentation analysis of the close approach of DNA molecules and a molecular ordering transition (1981)
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 1305-1328 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Measurement of the equilibrium distribution of persistence length fragments of DNA in high concentration in the ultracentrifuge shows that the reduced osmotic pressure rises much faster than linearly. From analysis of the data in terms of the Zimm cluster integral we infer that the net interactions between helices are purely repulsive at all distances. A theoretical equation of state derived from scaled particle theory with one adjustable parameter is in excellent agreement with the experimental data so long as the salt concentration is not excessively low. The parameter represents the hard-core radius in a simplified approximation to the potential function for the electrostatic repulsion between helices. Its value depends on the salt concentration, and it shrinks at high salt to a radius in close agreement with direct structural estimates. At a particular value of the osmotic pressure that is only slightly salt dependent, the solution undergoes a reversible transition to a denser, turbid, optically anisotropic phase. The relation between DNA volume fraction, including the electrostatic radius, at the transition point and the effective asymmetry of the molecules as a function of salt is in approximate correspondence with various theoretical treatments. However, the experimental function extrapolates to the correct limit for spherical particles. The work needed to bring DNA to a high concentration is estimated. The results suggest that the phase transition is first order.
    Additional Material: 7 Ill.
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    URL: http://dx.doi.org/10.1002/bip.1981.360200615
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  • 90
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    Quantitative test of Record's theory for proton-induced lowering of DNA melting temperature (1981)
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 2121-2136 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: This report presents a quantitative test of the ability of the counterion condensation theory to describe the proton-induced lowering of DNA melting temperature. From a general approach of Record et al. [Record, M. T., Anderson, C. F. & Lohman, T. H. (1978) Q. Rev. Biophys. 11, 103-178], we have obtained an expression that may be computer-fitted to the experimental data by numerical minimization of χ2. To do this, in addition to the assumptions made by Record et al., it was necessary to suppose that the interchange between protons and sodium is independent of pH and, due to the absence of data, take the enthalpies of protonation as thermally independent over the experimental temperature range. The dependences of the enthalpy of denaturation at neutral pH on sodium concentration and on G + C content were taken from literature. In the fitting process we have used 250 melting temperatures obtained at different pH and sodium concentrations for various natural DNAs. The theoretical expression gives a good quantitative description of the G + C and sodium concentration influences on the phenomenon but is only qualitative with respect to the dependence of dT/d log[Na+] on the pH. The adjusted pK values for the bases in denatured DNA agree with those for isolated deoxynucleosides. Interchange between sodium and protons is found to be less than 1:1. Calculated protonation enthalpies are ill-defined because of their low numerical influence. In short, it appears that the theory gives a good description of most of the aspects of the phenomenon even if it has some shortcomings, perhaps due to the great number of assumptions.
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    URL: http://dx.doi.org/10.1002/bip.1981.360201007
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  • 91
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    Effects of some organic cosolvents on the functional properties of hemoglobin: Kinetics of O2 displacement by CO (1981)
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 2137-2142 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We studied the kinetics of replacement of O2 by CO in hemoglobin in the presence and absence of organic cosolvents (methanol, ethanol, iso-propanol, n-propanol, formamide, acetamide, N-methyl-formamide) and at 10 and 25°C. Quantitative analysis of the results indicates that these cosolvents do not affect the intrinsic binding constants of ligands to the heme when hemoglobin is in the R conformation. The present results confirm the previously reported suggestion that the effects of the above cosolvents on the oxygen affinity of hemoglobin are related to effects on the T ⇄ R conformational equilibrium.
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    URL: http://dx.doi.org/10.1002/bip.1981.360201008
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    Influence of the telopeptides on type I collagen fibrillogenesis (1981)
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 2195-2202 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Preparations have been made of acid-soluble collagens whose telopeptides have suffered different levels of proteolytic attack. The collagens with more intact telopeptides form fibrils more rapidly than those with degraded telopeptides. In addition, we have shown that a high molecular weight aggregate rich in the carboxyterminal CNBr peptide, α1CB6, can be found in cyanogen bromide digests of fibrils formed from intact collagen. A similar aggregate is found in CNBr digests of native tendons. The aggregate formed in fibrils assembled in vitro can be stabilized by reduction, and its generation is strongly dependent on the presence of intact telopeptides. The latter point is the most objective evidence that to reproduce the characteristics of native fibrils in vitro, the collagen telopeptides must be preserved from proteolysis.
    Additional Material: 2 Ill.
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    URL: http://dx.doi.org/10.1002/bip.1981.360201012
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    Free-sliding ligands: An alternative model of DNA-protein interactions (1981)
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 2225-2241 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We present an alternative to the common lattice model for nonspecific DNA-protein interactions by using ligands that translate freely along the polynucleotide instead of binding to distinct lattice sites along the polynucleotide chain. The general model we present corresponds to a one-dimensional continuum gas and is referred to as the “continuum model” to distinguish it from the general lattice model. Explicit expressions are obtained for the binding isotherm equation for two version of the continuum model, including the effects of binding-site exclusion and attractions between bound ligands. Theoretical results are compared to those obtained from the McGhee-von Hippel (1974) analysis of the lattice model with cooperative interactions between ligands occupying more than one lattice site. Practical applications of the continuum model are illustrated by analyzing (i) the noncooperative binding to single-stranded DNA by RNase (Jensen and von Hippel, 1976), and (ii) the highly cooperative binding to poly(rA) by a proteolyzed fragment of the gene 32 protein of phage T4 (Lonberg et al., 1981).
    Additional Material: 3 Ill.
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    URL: http://dx.doi.org/10.1002/bip.1981.360201015
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  • 94
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    Simulations of the solvent structure for macromolecules. II. Structure of water solvating Na+-B-DNA at 300 K and a model for conformational transitions induced by solvent variations (1981)
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 2427-2483 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The structure of water and its interaction energy with a fragment of B-DNA composed of 12 base pairs and of the corresponding 24 sugar and 22 phosphate units and Na+ ions (one at each phosphate group) are analyzed using Monte Carlo simulations. The sample of water molecules, at the simulated temperature of 300 K, is composed of 447 water molecules. The results are discussed either in terms of statistical analyses over the 2,000,000 simulated conformations (after equilibration) or with reference to an “average configuration.” Comparison is made to a simulation previously presented for the same system but without counterions. Isotherm at different relative humidity, hydration, and reactivity scales for different sites, the hydration number at each site, the structure of intraphosphate and interphosphate hydrogen-bonded filaments of water are reported and discussed. The stabilization of the B-conformation induced by the solvent with counterion (“ion-induced compression effect”) is analyzed on the base of the above findings. A preliminary model to predict conformational transition in DNA is presented. The analyses reported are very detailed to allow refined interpretations of spectroscopic (infrared, Raman, and nmr) and scattering (x-ray and neutron beam) data on DNA insolution.
    Additional Material: 21 Ill.
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    URL: http://dx.doi.org/10.1002/bip.1981.360201111
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    Condensed states of nucleic acids. III. Ψ(+) and Ψ(-) Conformational transitions of DNA induced by ethanol and saltPaper II of this series is S.-M. Cheng and S. C. Mohr (1975) Biopolymers 14, 663-674. Portions of this work were presented at the XIth International Congress of Biochemistry, Toronto, Canada, July 1979. (1981)
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 2533-2552 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The conformational response of calf thymus DNA to solvent conditions altered by varying amounts of ethanol and NaCl has been monitored by circular dichroism (CD). These measurements, which extend over a much greater range of conditions than previously examined, reveal (above critical concentrations of ethanol and salt) a condensed form of the macro-molecule with unusually large positive ellipticity in the 250-300-nm region [the Ψ(+) state]. Mere increase in NaCl concentration at constant 35% (v/v) concentration of ethanol suffices to convert such Ψ(+) samples - via a series of intermediate forms with CD spectra resembling those of A-DNA, then B-DNA - into Ψ(-) states having anomalously large negative ellipticity similar to the well-known Ψ(-) forms produced by above-critical concentrations of poly-(ethylene oxide) and salt. These ethanol/salt-induced transitions are all completely reversible and can occur without formation of any visible precipitates. We suggest that they represent predominantly tertiary structural changes of B-form DNA molecules analogous to the changes which occur in several other systems where Ψ(+) ⇌ Ψ(-) interconversion has been reported. A “skein-of-yarn” model for the condensed tertiary (and quaternary, i.e., aggregated) state of the DNA affords one possible explanation for the inversions of ellipticity in all these cases. Such a model accords well with the accepted description of cholesteric liquid crystals.
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    URL: http://dx.doi.org/10.1002/bip.1981.360201205
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    Reduced sedimentation equilibrium time by two-step initial loading (1982)
    New York : Wiley-Blackwell
    Biopolymers 21 (1982), S. 17-24 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Computer simulation shows that the time required to attain near sedimentation equilbrium is dramatically reduced by a two-step initial loading in which a macromolecular solution at low or zero concentration is layered above one at a higher concentration. To achieve the minimum time requires a good estimate of the molecular weight, but at least a 50% reduction in time can be achieved if the molecular weight of the macromolecule is known only within a factor of 2. Numerical solutions to the differential equation of the ultracentrifuge are calculated using the finite element method. An efficient Gaussian elimination algorithm can be used to minimize calculation time and computer storage requirements.
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    URL: http://dx.doi.org/10.1002/bip.360210103
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    Fluorescent-labeled crosslinks in collagen: Pyrenebutyrylhydrazine (1982)
    New York : Wiley-Blackwell
    Biopolymers 21 (1982), S. 79-88 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The aldehydes present in acid-soluble type I collagen react with pyrenebutyrylhydrazine to form various types of complexes under different reaction conditions. These complexes exhibit one or more of three different pyrene fluorescence bands: monomer, excimer, and aggregate fluorescence. Collagen, whose aldehydes have been reduced with NaBH4, does not react with this fluorescent hydrazine, confirming that the hydrazine reacts specifically with aldehyde groups to form hydrazones. The absence of a reaction with pepsin-treated collagen also shows that the fluorescent labels are primarily in the nonhelical terminal telopeptides. Upon dialysis, the pyrene label bound to a saturated aldehyde in an α-chain is lost; whereas that bound to an unsaturated aldehyde remains on the protein. The pyrene monomer fluorescence in the β-chain of old collagen is stronger than that of young collagen. The formation of the pyrene excimer fluorescence implies the proximity of two pyrene molecules, probably attached to two adjacent aldehydes. Upon changing from acidic to neutral pH, both excimer and aggregate fluorescence bands disappear within a few seconds, revealing a very rapid alteration at the telopeptides.
    Additional Material: 6 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360210107
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    A stereospecific complex of poly(I) with ammonium ion (1982)
    New York : Wiley-Blackwell
    Biopolymers 21 (1982), S. 147-157 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We describe conditions which lead to complete helix formation of poly(I) in the presence of NH4+. Binding of NH4+ is shown to be specific in the presence of Li+, which does not by itself support helix formation under these conditions. The NH4+-poly(I) complex is characterized by uv, CD, and ir spectroscopy. The CD spectrum is strikingly different from those of the Na+ or K+ complexes, the first extremum being changed from negative for the metal ions to positive for NH4+. A stereospecific model is proposed for the NH4+-poly(I) helix in which the N of NH4+ is located on the axis of the four-stranded helix, midway between planar tetramers formed by the bases. The model is consistent with the tetrahedral symmetry of NH4+, the requirement for four acceptable hydrogen bonds, the observed stability of the helix, and the accepted geometry of the backbone.
    Additional Material: 8 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360210112
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    The δ-function counterion condensate around a line charge derived from the Fuoss, Katchalsky, and Lifson polyelectrolyte theory (1982)
    New York : Wiley-Blackwell
    Biopolymers 21 (1982), S. 159-167 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: It has recently been proven that the counterion condensate around an isolated line charge in an electrolyte, as characterized by nonlinear Poisson-Boltzmann theory, is an encapsulating δ-function. Here the identical result is shown to hold in the framework of the polyelectrolyte theory of Fuoss, Katchalsky, and Lifson. The proof fully exploits analytic solutions to the differential equation which are not available for the nonlinear, cylindrical Poisson-Boltzmann equation.
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    URL: http://dx.doi.org/10.1002/bip.360210113
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    Interactions of DNA with divalent metal ions. II. Proton relaxation enhancement studies (1982)
    New York : Wiley-Blackwell
    Biopolymers 21 (1982), S. 203-218 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The extent and modes of binding of the divalent metal ions Mn2+ and Co2+ to DNA and the effects of salt on the binding have been studied by measurements of the effects of these paramagnetic metal ions on the longitudinal and transverse relaxation rates of the protons of the solvent water molecules, a technique that is sensitive to overall binding. The number of water molecules coordinated to the DNA-bound Mn2+ and Co2+ is found to be between five and six, and the electron spin relaxation times and the electron-nuclear hyperfine constants associated with Mn2+ and Co2+ are little or not affected by the binding. These observations indicate little disturbance of the hydration sphere of Mn2+ and Co2+ upon binding to DNA. An average 2-3-fold reduction in the exchange rate of the water of hydration of the bound metal ions and an order-of-magnitude increase in their rotational correlation time are attributed to hydrogen-bond formation with the DNA. The binding constants of Mn2+ to DNA, at metal concentrations approaching zero, are found to be inversely proportional to the second power of the salt concentration, in agreement with the predictions of Manning's polyelectrolyte theory. A remarkable quantitative agreement with the polyelectrolyte theory is also obtained for the anticooperativity in the binding of Mn2+ to DNA, although the experimental results can be well accounted for by another simple electrostatic model. The various modes of binding of divalent metal ions to DNA are discussed.
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    URL: http://dx.doi.org/10.1002/bip.360210116
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