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  • Articles  (28,516)
  • Nature Publishing Group  (19,876)
  • Blackwell Publishing Ltd  (4,825)
  • Oxford University Press  (3,815)
  • American Institute of Physics (AIP)
  • 2020-2023  (45)
  • 1955-1959  (28,471)
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  • 1
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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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  • 2
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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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  • 3
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    The impact of faulting complexity and type on earthquake rupture dynamics (2022)
    Nature Publishing Group
    Details
    Publication Date: 2022-10-31
    Description: The statistical properties of seismicity are known to be affected by several factors such as the rheological parameters of rocks. We analysed the earthquake double-couple as a function of the faulting type. Here we show that it impacts the moment tensors of earthquakes: thrust- faulting events are characterized by higher double-couple components with respect to strike- slip- and normal-faulting earthquakes. Our results are coherent with the stress dependence of the scaling exponent of the Gutenberg-Richter law, which is anticorrelated to the double- couple. We suggest that the structural and tectonic control of seismicity may have its origin in the complexity of the seismogenic source marked by the width of the cataclastic damage zone and by the slip of different fault planes during the same seismic event; the sharper and concentrated the slip as along faults, the higher the double-couple. This phenomenon may introduce bias in magnitude estimation, with possible impact on seismic forecasting.
    Description: Published
    Description: 258
    Description: 2T. Deformazione crostale attiva
    Description: JCR Journal
    Keywords: double couple ; damage zone ; different fault type ; seismicity ; tectonics ; fault type ; seismicity ; 04.06. Seismology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 4
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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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  • 5
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    Arctic glaciers record wavier circumpolar winds (2022)
    Nature Publishing Group
    In:  EPIC3Nature Climate Change, Nature Publishing Group, 12(3), pp. 249-255
    Details
    Publication Date: 2022-06-20
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
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  • 6
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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.
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  • 7
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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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  • 8
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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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  • 9
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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
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  • 10
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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
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  • 11
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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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  • 12
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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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  • 13
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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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  • 14
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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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  • 15
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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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  • 16
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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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  • 17
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    Non-syntrophic methanogenic hydrocarbon degradation by an archaeal species (2022)
    Nature Publishing Group
    In:  EPIC3Nature, Nature Publishing Group, 601(7892), pp. 257-262
    Details
    Publication Date: 2022-08-11
    Description: The methanogenic degradation of oil hydrocarbons can proceed through syntrophic partnerships of hydrocarbon-degrading bacteria and methanogenic archaea1,2,3. However, recent culture-independent studies have suggested that the archaeon ‘Candidatus Methanoliparum’ alone can combine the degradation of long-chain alkanes with methanogenesis4,5. Here we cultured Ca. Methanoliparum from a subsurface oil reservoir. Molecular analyses revealed that Ca. Methanoliparum contains and overexpresses genes encoding alkyl-coenzyme M reductases and methyl-coenzyme M reductases, the marker genes for archaeal multicarbon alkane and methane metabolism. Incubation experiments with different substrates and mass spectrometric detection of coenzyme-M-bound intermediates confirm that Ca. Methanoliparum thrives not only on a variety of long-chain alkanes, but also on n-alkylcyclohexanes and n-alkylbenzenes with long n-alkyl (C≥13) moieties. By contrast, short-chain alkanes (such as ethane to octane) or aromatics with short alkyl chains (C≤12) were not consumed. The wide distribution of Ca. Methanoliparum4,5,6 in oil-rich environments indicates that this alkylotrophic methanogen may have a crucial role in the transformation of hydrocarbons into methane.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , NonPeerReviewed
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  • 18
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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.
    Repository Name: Woods Hole Open Access Server
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  • 19
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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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  • 20
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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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  • 21
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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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  • 22
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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
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 23
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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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  • 24
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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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  • 25
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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
    Repository Name: Woods Hole Open Access Server
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  • 26
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    Small sinking particles control anammox rates in the Peruvian oxygen minimum zone (2021)
    Nature Publishing Group
    In:  EPIC3Nature Communications, Nature Publishing Group, 12(1), pp. 1-12
    Details
    Publication Date: 2022-08-15
    Description: Anaerobic oxidation of ammonium (anammox) in oxygen minimum zones (OMZs) is a major pathway of oceanic nitrogen loss. Ammonium released from sinking particles has been suggested to fuel this process. During cruises to the Peruvian OMZ in April–June 2017 we found that anammox rates are strongly correlated with the volume of small particles (128–512 µm), even though anammox bacteria were not directly associated with particles. This suggests that the relationship between anammox rates and particles is related to the ammonium released from particles by remineralization. To investigate this, ammonium release from particles was modelled and theoretical encounters of free-living anammox bacteria with ammonium in the particle boundary layer were calculated. These results indicated that small sinking particles could be responsible for ~75% of ammonium release in anoxic waters and that free-living anammox bacteria frequently encounter ammonium in the vicinity of smaller particles. This indicates a so far underestimated role of abundant, slow-sinking small particles in controlling oceanic nutrient budgets, and furthermore implies that observations of the volume of small particles could be used to estimate N-loss across large areas.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , NonPeerReviewed
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  • 27
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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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  • 28
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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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  • 29
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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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  • 30
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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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  • 31
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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
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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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    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
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  • 34
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    Return to rapid ice loss in Greenland and record loss in 2019 detected by the GRACE-FO satellites (2020)
    Nature Publishing Group
    In:  EPIC3Communications Earth & Environment, Nature Publishing Group, 1(1), pp. 1-8
    Details
    Publication Date: 2022-06-20
    Description: Between 2003-2016, the Greenland ice sheet (GrIS) was one of the largest contributors to sea level rise, as it lost about 255 Gt of ice per year. This mass loss slowed in 2017 and 2018 to about 100 Gt yr−1. Here we examine further changes in rate of GrIS mass loss, by analyzing data from the GRACE-FO (Gravity Recovery and Climate Experiment – Follow On) satellite mission, launched in May 2018. Using simulations with regional climate models we show that the mass losses observed in 2017 and 2018 by the GRACE and GRACE-FO missions are lower than in any other two year period between 2003 and 2019, the combined period of the two missions. We find that this reduced ice loss results from two anomalous cold summers in western Greenland, compounded by snow-rich autumn and winter conditions in the east. For 2019, GRACE-FO reveals a return to high melt rates leading to a mass loss of 223 ± 12 Gt month−1 during the month of July alone, and a record annual mass loss of 532 ± 58 Gt yr−1.
    Repository Name: EPIC Alfred Wegener Institut
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  • 35
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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
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  • 36
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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
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  • 37
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    Spatially regulated editing of genetic information within a neuron (2020)
    Oxford University Press
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    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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    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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  • 39
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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
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  • 40
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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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  • 41
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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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  • 42
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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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  • 43
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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
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  • 44
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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).
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  • 45
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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).
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  • 46
    Electronic Resource
    Electronic Resource
    New Colorless Eugleninae (1959)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 6 (1959), S. 0 
    Details
    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: SYNOPSIS. Ten new species of colorless Eugleninae are described. One of them is the type of a new genus (Calycimonas physaloides nov. gen. nov. sp.). Especially remarkable forms are: Astasia acus, a species related to the green Euglena acus but without chromatophores and stigma and considerably smaller; Astasia edax, a species with animal-like nutrition and peculiar ecological adaptations; Petalomonas striata, a form which is not spirally but transversely striated; and finally Hyalophacus caecus, which was observed already by Klebs and Pochmann but was not sufficiently described. The new genus Calycimonas (ex fam. Peranemacearum) is related to Tropidoscyphus on the one hand (nearly the same shape as e.g. Tr. octocostatus, but possessing only a single flagellum) and to Petalomonas on the other hand (mode of nutrition and of swimming, formation of the reservoir, rigidity: however in transverse section not flattened).The Astasiae with zootrophic nutrition are collected in a new subgenus Astasiae devorantes or Phytophaga which comprises besides A. edax three species already described by Skuja.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1550-7408.1959.tb04371.x
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  • 47
    Electronic Resource
    Electronic Resource
    Malayan Protozoa 2. Hepatozoon Miller (Sporozoa : Coccidia), with an unusual host record for H. canis (James) (1959)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 6 (1959), S. 0 
    Details
    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: SYNOPSIS. H. canis (James) is reported from three of 36 stray dogs at Singapore and one of 34 palm civets (Paradoxurus hermaphroditus Pallas) from Jeram, Selangor. H. muris (Balfour) was found at Singapore in 10 of 61 examples of Rattus norvegicus (Erxleben) and five of 23 of R. rattus diardi (Jentinck), and is also recorded from six of 139 examples of R. r. jarak (Bonhote) from Pulau Jarak, Straits of Malacca. Neutrophils of P. hermaphroditus containing gametocytes of H. canis exhibit pronounced karyorrhexis, while most of the parasites themselves show signs of pyknosis.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1550-7408.1959.tb04375.x
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  • 48
    Electronic Resource
    Electronic Resource
    Mating Types and their Determination in Stylonychia putrina (1959)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 6 (1959), S. 0 
    Details
    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: SYNOPSIS. A total of 155 clones of Stylonychia putrina collected in nature were tested for mating type. Two sexually isolated varieties were found among them: Variety I with 12 mating types and Var. II with 11. Five of the clones isolated in the laboratory belonged to 3 additional mating types of Var. I making a total of 15 mating types in this variety.Crosses were made among 6 of the mating types of Var. I, and 114 clones of progeny were raised and tested for mating type. No simple genetic explanation of the results was evident.An abnormal type of conjugation with fusion of the conjugants and subsequent fission was studied. Both parental mating types sometimes segregated during the first two fissions of a fused animal. Mating type determination in the progeny of the fused animals seemed to parallel that of the progeny of the normal conjugants in that in both cases certain mating types tended to be dominant over others.
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  • 49
    Electronic Resource
    Electronic Resource
    Addendum to: Effects of metabolic inhibitors on pigments of Euglena. (1959)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 6 (1959), S. 0 
    Details
    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1550-7408.1959.tb04376.x
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  • 50
    Electronic Resource
    Electronic Resource
    Cytochemical Evidence for Urease Activity in Tetrahymena (1959)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 6 (1959), S. 0 
    Details
    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: SYNOPSIS. The cytochemical procedure of Sen was used to demonstrate urease activity in Tetrahymena pyriformis S.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1550-7408.1959.tb04379.x
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  • 51
    Electronic Resource
    Electronic Resource
    The Susceptibility of the Higher Primates to Piroplasms (1959)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 6 (1959), S. 0 
    Details
    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: SYNOPSIS. The chimpanzee is shown to behave like man to infection with Babesia divergens or bovis: the intact animal is totally resistant, whereas the splenectomized animal develops a fulminating infection accompanied by blackwater. The splenectomized rhesus monkey reacts in the same way also, but splenectomized rabbits are insusceptible. In the chimpanzee the typical accolé position of the “divergens” organisms (as seen in cattle) is absent, but occurs in the rhesus. It is suggested that latent piroplasmosis in man may exist on a large scale in rural populations in infected localities.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1550-7408.1959.tb04383.x
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  • 52
    Electronic Resource
    Electronic Resource
    Immobilizing Antigens of Tetrahymena pyriformis (1959)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 6 (1959), S. 0 
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    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: SYNOPSIS. Studies cf 3 conjugating strains of Tetrahymena pyriformis grown in a bacterized medium indicated the presence of a system of alternative immobilizing surface antigens. Each strain was found to have the potential for the expression of 3 serologically unrelated antigens. These consisted of a “high temperature” antigen (expressed in the range of 20–35d̀C), a “low temperature” antigen (exhibited in cultures at 10d̀), and an antigen induced by growth in the presence of the above-mentioned “high temperature” antiserum. Normally, by the immobilization reaction, only one of these antigens could be detected as present on any one organism at any given time. The “high temperature” antigens of two of the strains were serclogically related while that of the 3rd strain did not cross-react with antisera to the other two. The “low temperature” antigens of the 3 strains were serologically related as were the antigens induced by growth in antiserum.Studies of inbred hybrids of two of the strains indicated a potential for still more alternative antigens as well as for the spontaneous expression of the antigen which in the parental strains could only be induced to appear by the presence of the specific antiserum.Study of the 3 strains in axenic medium indicated the existence of a more complex system and the possibility that two or more immobilizing antigens may be present simultaneously.
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    URL: http://dx.doi.org/10.1111/j.1550-7408.1959.tb04359.x
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    The Invasion of the Cecal Mucosa by Eimeria tenella sporozoites and their Transport by Macrophages (1959)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 6 (1959), S. 0 
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    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: SYNOPSIS. The establishment of Eimeria tenella sporozoites in the cecal mucosa of the chicken is described. The invasion process was similar to that reported for E. necatrix by Van Doorninck and Becker. Sporozoites were found to pass through the surface epithelium of the cecal mucosa into the lamina propria. Within the lamina propria the sporozoites were engulfed by macrophages and transported to the cells of the glands of Lieberkühn. Development of the sporozoites ensues within the gland epithelium.
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    URL: http://dx.doi.org/10.1111/j.1550-7408.1959.tb04364.x
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    Sexual Isolation in Pandorina morum (1959)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 6 (1959), S. 0 
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    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: SYNOPSIS. The morphology of the vegetative phase and the sexual process in Pandorina morum have been studied in detail under controlled laboratory conditions. A number of strains from various areas of the United States, all essentially indistinguishable on morphological grounds, were analyzed for sexual compatibility. Forty-seven heterothallic clones were found to represent 15 separate pairs of mating types, or a minimum of 15 syngens (sensu Sonneborn, 1957). Two clones proved to be homothallic. Nine additional clones, which were not observed to mate with any strain, can be classified only after further collecting. The separate heterothallic pairs of mating types are sexually isolated by factors acting at the stage of gamete production; incompatible mating types produce no gametes when they are mixed together. The geographical distribution of the sets of mating types is very incompletely defined as yet, but they are not strictly endemic forms. Thirty heterothallic strains, representing each of the 15 sexually isolated sets of mating types of Pandorina morum, have been deposited with the Culture Collection of Algae maintained at Indiana University, Bloomington, Indiana, U.S.A.
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    The Relation of the Stage of the Population Growth Curve to the Survival of Tritrichomonas foetus upon Freezing in the Presence of Glycerol (1959)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 6 (1959), S. 0 
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    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: SYNOPSIS. When grown in CPLM medium or in a similar medium containing glucose instead of maltose as its sugar, Tritrichomonas foetus, Strain O, was much more sensitive to injury when frozen to -21d̀ C. in the presence. of 1 m glycerol during the initial and logarithmic phases of its population growth curve than at its peak and for some time thereafter. In 7 experiments in which the population peak occurred an average of 28.1 hours after inoculation, the average culture age at which the protozoa first survived freezing was 20.3 hours, at which time the population had reached 52.6% of its peak. The optimum culture age for survival after 1 day of freezing averaged 37.7 hours at which time the population averaged 75.6% of its peak. The optimum culture age for survival after 7 to 15 days of freezing averaged 32.3 hours, at which time the population averaged 82.7% of its peak. Better survival upon freezing was obtained in those experiments in which the population peak was reached relatively rapidly.
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    URL: http://dx.doi.org/10.1111/j.1550-7408.1959.tb03936.x
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    Macronuclear Changes in a Strain of Blepharisma undulans during the Divisional Cycle (1959)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 6 (1959), S. 0 
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    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: SYNOPSIS. Specimens of Blepharisma undulans were transferred from young clone cultures to a rotocompressor with 3 mm3 of culture medium. The organisms were slightly compressed and photographed at various intervals with dark field illumination. The sequence of macronuclear and cytoplasmic changes was compared with similarly followed Feulgen preparations.The cycle falls into several phases: (1) an interphase (12–24 hr.) in which the organism increases in size while cytoplasmic and macronuclear appearances remain unchanged. During this phase, the macronucleus consists of 3 to 5 nodes of various sizes connected by strands. (2) a pre-condensation phase (1 hr.) in which a new posterior peristome and cytopyge appear without visible macronuclear change. (3) a condensation phase (10–20 min.) in which the macronuclear nodes coalesce into a round mass without dissolution of the central nodes or strands. (4) a postcondensation phase (1 hr.) characterized by: (a) elongation of the condensed macronucleus into a rod-like shape followed by typical nodal formation; or (b) elongation of the condensed macronucleus into a form resembling the letter “J”, followed by nodal formation, and resulting in a double row of nodes in one daughter and a single row in the other. Separation occurs at this time, initiating the new interphase. The development of the j-form macronucleus. the lack of obliteration of the central nodes, and the characteristic interphase condition distinguish this strain of B. undulans from others described elsewhere.
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    Observations sur Quelques Ciliés Astomes des Oligochètes du lac d'Ohrid (Yougoslavie). I. Famille des Radiophryinae. (1959)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 6 (1959), S. 0 
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    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: SYNOPSIS. Six species of astomatous Infusoria, 4 new, are described from the alimentary tract of Oligochaeta from Ochrida Lake. Two belong to Ochridanus, characterized by a cytoskeleton whose “V”-shaped basal piece bears on its branches two articulated hooks brought together by a skeletal blade. This genus found in Ochridanous Tubificidae represents the counterpart of Anthonyella in the Lumbriculidae of Lake Baïkal. The presence of Ochridanus in these worms concurs with the almost complete absence of representatives of Radiophrya of which we have found but one species. A species of Metaradiophrya, a genus unknown to date from the Lumbricidae, was noticed in Glossoscolecidae. The different species of Ochridanus, Anthonyella, Metaradiophrya, and Radiophrya compose a very homogeneous group of Radiophryinae. The study of the ciliary rows and the cytoskeleton of 2 species of Juxtaradiophrya, parasitic in the Lumbriculidae of Ochrida, shows that, in the morphology of these ciliates, as well as in the same forms from Lake Baïkal, many transition characteristics exist between the Radiophryinae and Hoplitophryinae or Mesnilellinae. These 3 sub-families, with their undeniable genetic kinship give coherence to the family Hoplitophryidae.
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    Enzyme Systems of Stylonychia pustulata. II. Miscellaneous Systems (Hydrases, Hydrolases, and Dehydrogenases) (1959)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 6 (1959), S. 0 
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    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: SYNOPSIS. Histochemical techniques were used to demonstrate the intracellular distribution of some hydrases, hydrolases, oxidases, and dehydrogenases in Stylonychia pustulata. The hydrase, aconitase, was confined to the mitochondria. Zymohexase activity occurred in the cytoplasm and probably in the mitochondria. The hydrolases, acid and alkaline phosphatases, lipase, and urease, were localized in the mitochondria. Lactic and glutamic dehydrogenases were confined to the mitochondria. Peroxidase and glycerophosphate dehydrogenase were absent.
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    URL: http://dx.doi.org/10.1111/j.1550-7408.1959.tb03933.x
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    Observations on Eimeria raillieti in the “Slow-worm”, Anguis fragilis (Reptilia, Anguidae) (1959)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 6 (1959), S. 0 
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    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: SYNOPSIS. The oocysts, sporulation process, and endogenous stages of Eimeria raillieti (Léger, 1899) Galli-Valerio, 1930 from the slow-worm, Anguis fragilis, in England are described. The oocysts average 18 × 15 μ. Schizonts, microgametocytes and macrogametocytes were found in the ileum, and macro-gametocytes alone in the duodenum.
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    URL: http://dx.doi.org/10.1111/j.1550-7408.1959.tb04384.x
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    Studies in Marine Biology. IV. On the Role of Algal Cells in the Tissues of Marine Invertebrates (1959)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 6 (1959), S. 0 
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    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: SYNOPSIS. Zooxanthellae in pure culture, exposed to continuous light, release free O2 in amounts varying with time and cell number. Zooxanthellae exposed to alternate light and dark produce essentially as much O2 as in continuous light. Those in continuous dark do not yield free O2; rather, they draw from the medium's residual O2.Both the anemone Condylactis and the scyphozoan Cassiopeia are markedly phototactic. Kept in total darkness, both species show a dramatic numerical diminution in zooxanthellae. During 24 days of darkness, the mean total number of zooxanthellae in the individual Condylactis body was reduced from 26 million to ∼ 1 million. Specimens so bleached lost phototaxis.It is suggested that each species of zooxanthella host animal has its own specific light needs, which it caters to in various ways: (a) early selection of position, as with planulae or other freely motile larval forms; (b) gross body movement or posturing, as with anemones, medusae, and worms; (c) possession of light-filtering pigments, as with colored corals and molluscs; (d) possession of light-concentrating devices, as with tridacnids; (e) possession of highly contractile and differentially light-absorbing tissues, as with most coelenterates and some molluscs.Susceptibility of marine invertebrates to zooxanthellae infection may be related to the known paucity of nitrates and phosphates in tropical seas, a situation possibly inducing the free-swimming gymnodinioid forms to enter animal tissues where catabolic products are available to them. Zooxanthellae are reported from sessile marine invertebrates taken at depths of 100–116 fathoms.
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    Atoxoplasma Garnham, 1950, as a synonym for Lankesterella Labbé, 1899. Its life cycle in the English sparrow (Passer domesticus domesticus, Linn.) (1959)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 6 (1959), S. 0 
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    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: SYNOPSIS. All of 99 adult English house-sparrows, examined in the St. Albans area of Hertfordshire, England, were found to be infected with the organism previously defined by Garnham (1950) as Atoxoplasma. Young birds were found to become infected while still in the nests and as early as 6 days after hatching; there was no evidence to suggest that the parasite was transmitted through the egg. Within a few weeks of leaving the nests, all of 150 fledgling sparrows examined were heavily infected and several trapped birds died from massive infections.All stages of schizogony were found in the lymphoid-macrophage cells of the spleen, bone marrow and liver of these birds; later, as the schizogonic cycle abated, gametocytes developed in similar cells of the liver, lungs and kidney. These gametocytes are of the Eimeria type: the zygote nucleus divides to produce an asporous and polyzoic oocyst containing a large number of sporozoites, and after the rupture of the oocyst these sporozoites invade the lymphocytes and monocytes of the peripheral blood.Transmission of the parasite in the sparrow is thought to take place after the ingestion of infected mites (Dermanyssus gallinae) by the young birds in the nests: unchanged sporozoites were found in smears of these mites that had been fed on infected sparrows. Transmission experiments were impossible due to the complete lack of clean sparrows.The taxonomic status of Atoxoplasma is discussed. The type of life cycle and the production of asporous, polyzoic oocysts indicate inclusion of this parasite in the Order Coccidiida, Family Eimeriidae, Sub-Family Cryptosporidiinae Hoare, 1933. After comparison of the two genera, the author concludes that Atoxoplasma must be regarded as a synonym for Lankesterella. Some previously described species of Atoxoplasma are, therefore, transferred to the genus Lankesterella.The name Lankesterella garnhami nov. sp., is proposed for the parasite in the English sparrow (Passer domesticus domesticus), and Lankesterella serini nov. sp., for that in the canary (Serinus canarius).
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    URL: http://dx.doi.org/10.1111/j.1550-7408.1959.tb04385.x
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    Effects of Some Metabolic Inhibitors on the Pigments of Euglena gracilis in an Acidic Medium (1959)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 6 (1959), S. 0 
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    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: SYNOPSIS. Darkness and O2-lack promote formation of a pheophytin-like pigment from chlorophyll in Euglena gracilis in an acidic medium. Dinitrophenol (DNP) produces similar but more drastic pigment alterations in aerated and illuminated cells. The extent of pigment decay was dependent on DNP concentration and external pH. Since volume expansion and inhibition of the contractile vacuole were also noted, it is suggested that pheophytin formation is secondary to hydrogen ion influx from the external medium. Major structural alterations of the chloroplast accompanied the pigment changes.Pentachlorophenol, iodoacetamide, Na fluoride, and Na azide produced similar pigment changes. Malonic acid and fluoroacetate were ineffective under the conditions described. However, in the dark, cells treated with fluoroacetate formed pheophytin rapidly. These effects are discussed in relation to the maintenance of intracellular [H+].
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    A Comparative Biochemical Study of Two Species of Ochromonas (1959)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 6 (1959), S. 0 
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    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: SYNOPSIS. The heterotrophic, phototrophic, and phagotrophic nutrition of the chrysomonad flagellates Ochromonas malhamensis and O. danica were compared. Unlike O. malhamensis, O. danica, which is much richer in chloroplast pigments, grew readily photoautotrophically in a substrate-free medium in 5% CO2. Utilization of bound biotin in bacterial (Thiobacillus) bodies served to demonstrate phagotrophy in both flagellates. This nutritional versatility suggests that this group of flagellates will be exceptionally valuable for studying the evolutionary steps connecting photoautotrophy, heterotrophy, and phagotrophy.
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    Requirement of Trichomonads for Unidentified Growth Factors, Saturated and Unsaturated Fatty Acids (1959)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 6 (1959), S. 0 
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    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: SYNOPSIS. In a synthetic medium containing 57 compounds, including cholesterol, Trichomonas gallinae and T. gallinarum require 3 factors for growth and acid fermentation of maltose: (1) factor R, found in the protein contaminating some samples of ribonucleic acid, and in other isolated proteins such as conalbumin, γ-globulin, and bovine albumin fraction V; (2) factor T, found in Trypticase and in the same isolated proteins, but with activity at 4 times the dose required for factor-R activity, may be a large peptide containing proline; (3) factor S, found in serum, was replaceable by a saturated and an unsaturated fatty acid, each inactive alone. Only C14 through C18 saturated fatty acids were active over a range of 0.058 to 2.34 μm per tube in the presence of oleic acid, while C18 through C22 unsaturated fatty acids were active in the same range with palmitic acid as the supplement. The unsaturated fatty acids were toxic at the largest dose. All fatty acids were not equally active. Surface-active agents containing mixtures of fatty acids also replaced serum. A 4th factor, found in serum, stimulates the rate of growth as shown by cell counts at 3 days of incubation. T. gallinarum, T. foetus, and a trichomonad from a pig's nose responded to the same supplements when grown on another synthetic medium.
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    Some Physiological Characteristics of the Mating Types and Varieties of Tetrahymena pyriformis (1959)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 6 (1959), S. 0 
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    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: SYNOPSIS. Differences in temperature-tolerance, generation time, nutritional requirements, osmoresistance, pigment production, and sensitivity to high hydrogen or hydroxyl ion concentration have been observed among varieties, and among mating types within varieties of Tetrahymena pyriformis. The usefulness of these differences to taxonomists and geneticists is discussed.The nutrition of a temperature-tolerant strain, mating type II, variety 1, was given special attention and a chemicallydefined medium devised to support rapid growth at 35d̀ C. At 40d̀, growth in this medium failed, but was good in a crude medium. Temperature factors are suggested. Permeability of this ciliate, as inferred by utilization of nucleotides, was high.
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    Vegetative Mutants and Clonal Senility in Tetrahymena (1959)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 6 (1959), S. 0 
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    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: SYNOPSIS. Eight strains of Tetrahymena pyriformis were examined in multiple daily isolation series over ∼ 800 generations. Dead and defective lineages appeared in all clones. In 7, the defective sub-lines appeared at a constant characteristic rate; the 8th showed an increasing rate of production of two defects. A breeding analysis of certain persistent morphological and growth rate variants suggests that the variations derive from macronuclear alterations. The relationship between these cellular changes and “senility” in metazoa and other protozoa is discussed.
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    Further Nutritional Requirements of Paramecium aurelia (1959)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 6 (1959), S. 0 
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    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: SYNOPSIS. An acetone-insoluble yeast fraction required for axenic growth of P. aurelia, stock 51, variety 4, sensitive, after fractionation contained at least 3 essential components: (1) one soluble in perchloric acid and completely replaceable by a mixture of ribosides or ribotides; (2) one inactivated after digestion with trypsin, chymotrypsin or papain. Proteose-Peptone restored activity to this preparation, which suggests a peptide requirement; and (3) one not yet characterized.As for the purine and pyrimidines, these combinations, in decreasing order of activity, supported growth: guanosine + cytidine, guanosine + uridine, guanylic acid + cytidylic acid, and guanylic acid + uridylic acid. Each combination was maximally effective when the molar purine: pyrimidine ratio was ∼ 0.4. On a molar basis, the minimal riboside combinations were ∼ 1.3 × more active than the ribotides.Sparing of the purine and pyrimidine requirement was also investigated. In the presence of limiting amounts of guanylic acid, the following compounds, in decreasing order of activity, had sparing activity: deoxyguanosine, inosine, xanthosine, adenylic acid, and guanine. Adenine, adenosine, and deoxyadenosine were inhibitory under the test conditions. The requirement for cytidylic acid was spared by deoxycytidine, uridine, uridylic acid, deoxyuridine, thymidine, thymine, and uracil, in descending order.
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    A Quarter Century Exploring Tetrahymena (1959)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 6 (1959), S. 0 
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    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: SYNOPSIS. In reviewing 25 years of work on Tetrahymena, the author describes early difficulties experienced by himself and others in developing a chemically-defined medium and in defining the taxonomy of T. pyriformis. With identification of its essential requirements, a variety of nutritional studies revealed the close resemblance between the metabolic pathways of this ciliate and those of the chick and rat. This suggested studies on the effects of gamma radiation and the effect of antibiotics.Attention then turned to the puzzle of the absence of conjugation in all strains of T. pyriformis then maintained in laboratories. The observation that these strains were all amicronucleate led to the discovery of mating types (with D. F. Gruchy). This brought up the problem of what constitutes a species and how it might be solved in T. pyriformis where clearly defined groups are set off from other similar groups (varieties) by a breeding barrier.Another problem is whether a life cycle exists in this ciliate and if so, the role amicronucleate strains play in this cycle.The origin and obvious evolutionary success of these “genetically dead” strains are other problems that are considered.The search for nutritional markers for genetic experiments inspired large-scale collections, including some from tropical habitats. Strains were found which differed in serine and pyridoxine requirements. Genetic analysis was hindered by the high lethality following conjugation, unsatisfactory mating behavior in some clones, and the complete absence of autogamy, the latter making it difficult to obtain homozygous clones. The use of x-radiation yielded haploid individuals; when these were mated with diploid clones the resulting haploid progeny proved that the genes controlling mating type and pyridoxine synthesis resided in the micronucleus.Genetic analysis of the serine and pyridoxine mutants supports the idea that T. pyriformis is more of an outbreeder than an inbreeder. Left for the future is an extension of our knowledge of the breeding system of T. pyriformis and ultimately to examine critically the factors responsible for the success of this ubiquitous ciliate.
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    Program and abstracts of the 11th Annual Meeting of the Society of Protozoologists, Pennsylvania State University, University Park, Pennsylvania, 31 August-3 September, 1959. (1959)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 6 (1959), S. 0 
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    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
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    URL: http://dx.doi.org/10.1111/j.1550-7408.1959.tb04386.x
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    Respiration of Colpoda cucullus During Active Life and Encystment (1959)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 6 (1959), S. 0 
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    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: SYNOPSIS. During encystment of Colpoda cucullus (O. F. Müller) the respiratory rate decreases from about 11.3 × 10-5μl. O2/hr. (mean value for active form) to about 1.3 × 10-5μl./hr. (mean for unstable cyst); the process takes about 24 hrs. At the same time the activity of the contractile vacuole is stopped, but there is no correlation in time between the two processes: when respiration is inhibited by 1/2–2/3 the vacuolar activity is hardly changed. The respiration of unstable cysts remains approximately constant at least for 4 weeks. Experiments with methylene blue suggest that inhibition of respiration at encystment may be due to inhibition of terminal oxidase.
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    Serial Passage of Trypanosoma lewisi in the Heterologous Mouse Host. I. Development in Calorically-restricted Hosts. (1959)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 6 (1959), S. 0 
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    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: SYNOPSIS. Two isolates (“A” and “B”) of Trypanosoma lewisi from the same rat stock source were serially transferred in calorically-restricted mice supplemented daily with normal rat serum. The “A” strain was transferred consecutively through 300 mice over a period of more than 3 years and was voluntarily discontinued. The “B” strain died out spontaneously after 43 consecutive passages in mice. The developmental histories of these 2 isolates were analyzed and compared with respect to duration of the parasitemic period, interval to the next subsequent passage in mice, day of death of each host animal, proportion of host animals that died, intensity of parasitemia in mouse tail blood, interval required for development of the observed maximal parasitemia, and duration of maximal parasitemia.“A” appeared to have become progressively adapted to the mouse as judged by a decrease in parasitemic period with successive transfer associated with a progressive increase in trypanosome population, and declines in the interval required for development of the observed maximal parasitemia and in the duration of this maximal response. There did not appear to be any correlation of the percentage of animals that died with any other factor. The “B” strain did not appear to have adapted itself to mice as judged by the foregoing criteria.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1550-7408.1959.tb04374.x
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    Cytology of an Indian Race of Blepharisma undulans (Stein) (1959)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 6 (1959), S. 0 
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    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: SYNOPSIS. The Indian race of Blepharisma undulans described in this paper measures 150 μ in length. The macronucleus consists of 5–7 nodes, all of equal size. During binary fission, condensation of macronucleus is followed by its elongation and a thinning of the middle region which breaks with the division of the animal. It later attains the typical vegetative form.During conjugation 7 or 8 micronuclei pass through the first pregamic division, 5 to 7 through the second pregamic division and one product of the second division takes part in the third division. The rest degenerate. At the same time, the macronucleus also starts degenerating. After the synkaryon has divided twice, the conjugating pairs separate. Of the 4 products, 3 become macronuclear anlagen and one, micronuclear anlage.The micronuclei divide asynchronously both during binary fission and during conjugation. There is apparently considerable diversity in the structure and behaviour of the macronucleus and micronuclei in the different races of Blepharisma undulans.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1550-7408.1959.tb04380.x
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  • 73
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    Bacterial Ingestion by the Rumen Ciliates Entodinium and Diplodinium (1959)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 6 (1959), S. 0 
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    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: SYNOPSIS. In cattle fed a high-starch diet, species of Entodinium and Diplodinium ingested associated ruminal bacteria. Stained preparations of diluted rumen contents showed Entodinium caudatum, E. minimum, E. dubardi, (syn. E. simplex), E. longinucleatum, E. bursa, E. nanellum, E. exiguum, and E. vorax contained gram-positive diplococci. Starch grains with adherent gram-positive diplococci were observed within Entodinium spp. Diplodinium ecaudatum forma ecaudatum, D. ecaudatum forma caudatum, D. neglectum and an unidentified species of Diplodinium also ingested ruminal diplococci. Bacteria were isolated from mixed species of Entodinium by washing and culturing the protozoa in a starch feed-extract agar medium. The strains isolated from the ciliates were gram-positive diplococci, 0.8 times 1–1.5 μm, which attached themselves to starch granules and were able to digest the starch. Conclusive evidence of bacterial ingestion by the oligotrichs was obtained by providing the bacterial cultures to Entodinium species (E. dubardi and E. minimum) which had been starved 24 hr. Gram-stained preparations showed the ciliates readily ingested the bacteria. The amylolytic cocci utilized by Entodinium spp. were identified as Streptococcus bovis.
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    URL: http://dx.doi.org/10.1111/j.1550-7408.1959.tb04361.x
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  • 74
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    Lankesterella corvi n. sp., a Blood Parasite of the English Rook, Corvus f. frugilegus L. (1959)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 6 (1959), S. 0 
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    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: SYNOPSIS. Lankesterella corvi n. sp. (Coccidia, Eimeriidae, Cryptosporidiinae) is described from the rook, Corvus f. frugilegus L. in England. It was found in 36 of 196 fledged rooks less than 1-year old, but not in 25 nestlings or 38 adults. It was not found in 71 jackdaws (C. monedula spermologus) or in 110 other birds of 16 species.Mature sporozoites were found in the erythrocytes and occasionally in other blood cells. They were 6.2 times 2.5 μ, with a central, band-like nucleus, and cytoplasm which failed to stain with Giemsa's stain. Gametogonic and sporogonic stages, found in the bone-marrow of one bird, resembled corresponding stages of Eimeria.A fledgling rook was infected experimentally by inoculation of a blood and tissue suspension from an infected bird. Sporozoites appeared in its blood 4 days after inoculation. They appeared to increase slightly in size and their cytoplasm lost its initial affinity for Giemsa's stain during the next few days. Engorged mites (Ornithonyssus sylviarum) from the experimentally infected rock contained unchanged sporozoites but no developmental stages of the parasite. A canary could not be infected by intraperitoneal inoculation and feeding of such mites.
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    URL: http://dx.doi.org/10.1111/j.1550-7408.1959.tb04363.x
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    An Illustrated Key to the Higher Groups of the Ciliated Protozoa, with Definition of Terms (1959)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 6 (1959), S. 0 
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    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: SYNOPSIS. A dichotomous, analytical key is offered for use in recognition and differentiation of the 26 orders and suborders belonging to the two subclasses of the single class Ciliata of the subphylum CILIOPHORA. The basic terminology employed in these brief characterizations, usable in systematic studies of ciliates in general, is defined first, and a plea is made for a more uniform vocabulary, especially in reference to structures which are without doubt homologous throughout the several higher ciliate taxa. Particular emphasis is placed on the all-important features in the oral area; many of these are figured as well as being described in words.Both the key and the definitions are essentially the first to be offered since Kahl's monographic work on the ciliates published in 1930–1935. They are demanded by the great accumulation of new pertinent data in the protozoclogical literature of the past 25 years.
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    URL: http://dx.doi.org/10.1111/j.1550-7408.1959.tb04368.x
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    An Electron-Microscope Study of the Cytology of the Protozoan Peranema trichophorum (1959)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 6 (1959), S. 0 
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    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: SYNOPSIS. The flagellate, Peranema trichophorum, has been studied in the electron microscope by thin-sectioning techniques. The flagella have the fibrillar pattern typical of cilia and flagella, but accessory structures including tapered, intraflagellar rods, striated, layered material on the outside of the membrane, and mastigonemes are present. In the near basal region of the flagellum, there is a swelling of the shaft which is correlated with the absence of the two central flagellar fibrils. The basal portion of the intraflagellar material is structurally and locationally similar to the basal parts of the flagellar fibril bundle; this similarity suggests that the two structures originated from similar precursors and that two kinetosomes comprise the light microscopist's blepharoplast in this organism.The ridged pellicle is composed of 3 membranes, only two of which follow the contour of the ridges. Several filaments 21 mμ in diameter are localized under the low point of each ridge, and a single, larger fibril which has a periodic structure is often located beneath the high point of each ridge.The cytostome and structures associated with it are described and discussed in relation to food taking. The pharyngeal rods are cross-connected and each is composed of numerous tubular elements surrounded by a denser, homogeneous layer. A system of membranes is attached to the rods and extends anteriorly.The nucleus contains two large nucleoli, numerous rod-shaped, membrane-limited bodies which appear similar in structure to bacteria, and a smaller granular component.Other organelles are briefly described including mitochondria, Golgi bodies, vacuoles, and endoplasmic reticulum.
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    URL: http://dx.doi.org/10.1111/j.1550-7408.1959.tb03935.x
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    Studies on the Fine Structure of a Gregarine Parasitic in the Gut of the Grasshopper, melanoplus differentialis (1959)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 6 (1959), S. 0 
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    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: SYNOPSIS. Materials within the endoplasm of both the protomerite and deutomerite may be displaced and stratified by ultracentrifugation. Animals are not killed by this treatment, and in time a redistribution of stratified materials may occur. The electron microscope reveals numerous ultramicroscopic folds in the surface envelope which is composed of 3 membranes; the outer and middle cover the surface of the folds while the inner one continues as a smooth membrane over the ectoplasm. The contact surfaces of animals in syzygy do not show the small folds to be interlocked; instead, they are in fold-to-fold contact. Numerous relatively dense bodies which appear to be filamentous are sometimes observed immediately underneath or within the middle or inner membrane. Within the ectoplasm is an ultramicroscopic net-like fibrillar structure much denser than the surrounding cytoplasm. This system of fibrils is composed of anastomosing elements varying from ∼ 50 to 200 Å in diameter. Certain of the larger fibrils are directly attached to the surface envelope at positions between the folds. A second filamentous structure within the ectoplasm appears to be tubular. Elements of this system also appear to join and penetrate the surface envelope by means of pores.A large amount of gelatinous secretion forms at the surface of the sporont; as it glides forward a trail of mucous is left behind. The actual mechanism involved in the gliding movement was unobserved, but evidence is lacking to support the view that the gliding movement is engendered by posteriorly directed “jets” of mucus.
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    URL: http://dx.doi.org/10.1111/j.1550-7408.1959.tb03940.x
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    Axenizing Vorticella convallaria (1959)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 6 (1959), S. 0 
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    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: SYNOPSIS. Vorticellas were subjected to achromycin, polymyxin, and mixtures of penicillin-streptomycin to remove bacterial contaminants. Although achromycin and polymyxin were most effective in controlling bacteria isolated from vorticella cultures, they proved too toxic for practical use. However, certain dilutions of penicillin-streptomycin were tolerated by vorticellas and, therefore, were incorporated into the axenizing procedure. Yeasts did not yield to the antibiotics and had to be removed by washing and dilution. Sterile vorticellas were finally obtained by transfer of groups of individuals through 6 washes. One of these, the 4th, lasted 8 hours and contained diluted penicillin-streptomycin.
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    Mitosis in the Rhizopod Lesquereusia spiralis (1959)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 6 (1959), S. 0 
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    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: SYNOPSIS. The interphase nucleus of Lesquereusia spiralis, a testate rhizopod, 20–25 μ in diameter, contains 40–50 endosomes and a diffuse granular reticulum. Onset of nuclear division is marked by a cessation of pseudopod activity. Prophase changes include increase in size of the nucleus, disappearance of the endosomes except the peripheral ones, formation of 175–200 chromosomes from the reticulum, and the appearance of spindle fibers. By the end of prophase a well formed equatorial plate is present. The metaphase nucleus is slightly smaller and elongated; the chromosomes remain distinct. In anaphase the nucleus continues to elongate along the polar axis; the chromosomes apparently split lengthwise and polar caps appear. The nucleus elongates further so that by telophase it has become hour-glass shaped. The spindle fibers are now twisted. Separation of the nuclei takes place in the neck region. The nuclear membrane is unbroken during the process and peripheral endosomes are present at all stages. Total time for mitosis averages 45 minutes.
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    URL: http://dx.doi.org/10.1111/j.1550-7408.1959.tb03949.x
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    Some Gregarines from Crustaceans taken near Bombay, India (1959)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 6 (1959), S. 0 
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    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: SYNOPSIS. Three gregarines are described from the digestive tracts of marine crustacea from Bombay, India. These are Carcinoecetes etisi n.sp. from Etisus laevimanus, C. matutae n.sp. from Matuta lunaris, and Caridohabitans setnai n.gen., n.sp. from Peneus semisulcatus. Various life history stages are reported.
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    URL: http://dx.doi.org/10.1111/j.1550-7408.1959.tb03919.x
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    Le Cortex de la Vacuole Contractile et son Ultrastructure chez les Ciliés (1959)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 6 (1959), S. 0 
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    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: SYNOPSIS. In various ciliates the contractile vacuole is a permanent organelle, delimited by a differentiated cortex.The cortex is made up of a dense reticulum of anastomosing tubules limited by a smooth membrane, and vesicles. This “spongiome” can be considered as a localized and specialized condensation of the endoplasmic reticulum.
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    URL: http://dx.doi.org/10.1111/j.1550-7408.1959.tb03923.x
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    Flagellate Parasites of the Fly, Phaenicia sericata (Meigen) (1959)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 6 (1959), S. 0 
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    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: SYNOPSIS. Two species of flagellate parasites, Herpetomonas muscarum (Leidy 1856) Kent 1881 and Crithidia luciliae (Strickland 1911) have been isolated in pure culture from the fly, Phaenicia sericata. Laboratory-reared Musca domestica were infected with each of the species. These two species have often been confused, the latter being regarded as “cysts” of the former. H. muscarum is long and slender and occurs actively swimming in the midgut of the host. C. luciliae is short and truncate and occurs mainly in the hindgut where it is often attached to the gut wall. C. luciliae grows readily and abundantly in culture and outgrows H. muscarum in mixed cultures. Attempts to infect Aedes aegypti and Culex pipiens with C. luciliae failed while control feedings of these mosquitoes with Crithidia fasciculata produced infections.
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    URL: http://dx.doi.org/10.1111/j.1550-7408.1959.tb03927.x
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    Studies on Amebo-flagellates, I. The General Morphology and Mastigonts of Trimastigamoeba philippinensis Whitmore 1911 (1959)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 6 (1959), S. 0 
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    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: SYNOPSIS. Trimastigamoeba philippinensis Whitmore 1911 from Florida was cultured in the laboratory at 22 to 25° C. on a modified Bunting's agar medium overlaid or not with Neff's ameba-saline. Studies of its general morphology, transition from ameboid to flagellate phase and vice versa, encystment, and excystment were made. In general, Whitmore's observations are confirmed, except for his conclusions concerning the number of flagella and whether or not there is a rhizoplast. The flagellate phase has two mastigonts, each composed of a pair of flagella attached to a basal granule (blepharoplast). Intermediate stages in the development of the mastigonts may have caused Whitmore to decide that a tri-flagellar phase was the usual condition. The two mastigonts are not at any time attached to one another, nor to the nucleus, nor is there any evidence of a rhizoplast or rhizostyle. In the flagellate phase the bases of the mastigonts are closely surrounded by an anterior, gullet-like invagination, posterior to which the blepharoplasts rest adjacent to the nucleus. The four flagella extend 20 to 25 μ beyond the anterior limit of the pocket. Detailed descriptions of the morphologies of the ameboid and flagellate phases are given to supplement the morphology described by Whitmore. Possible affinities to other amebo-flagellates are discussed. It is concluded that the organism is generically and specifically distinct; and while its name is erroneously descriptive of its flagellate phase, it is taxonomically valid.
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    URL: http://dx.doi.org/10.1111/j.1550-7408.1959.tb03929.x
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    Mating Types in Euplotes eurystomus (1959)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 6 (1959), S. 0 
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    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: SYNOPSIS. The organism used in the experiments fits Pierson's satisfactory description for Euplotes eurystomus. The mating behavior of 90 stocks of E. eurystomus collected from west Japan was studied. Mating occurs only after a decline in nutritive conditions. When the stocks were mixed together, two at a time, in all possible combinations, mating took place in all the mixtures. Mating occurs in the evening or the morning after mixing. An agglutinative reaction does not precede mating; but before pair formation, characteristic pre-pairing behavior is observed. Selfing is found in all the stocks, usually after the log-phase of the growth curve. Culture fluids from various cultures have no detectable capacity to induce selfing, but some of them can suppress selfing. The latter occurs only in specific combinations. Controls mixed with distilled water instead of culture fluid always contain selfers. From the results of such experiments, it is possible to classify the stocks into 9 types, so that stocks of the same type have the same character with respect to suppression of selfing. The culture fluid from type II suppresses selfing only in animals of type I, type IV acts only on type III, VI on V, VIII on VII, and VII on both V and VI. The reciprocal actions also occur, i.e., fluid from I suppresses selfing of type II, etc. The origin of the two mating members of a conjugating pair was traced by making mixtures of normal animals of one type with morphologically abnormal animals of another type. The latter have a distinct swelling at the left margin of the body. Such mixtures (I × II, V × VI and VII × VIII) yield conjugating pairs of normal mated with abnormal animals, i.e. cross-conjugating pairs, in 86–94% of the animals. Mixtures of type VI with VII yield a smaller percentage (48%) of cross-conjugating pairs. Mixtures of two cultures belonging to the same type, (II × II, VI × VI and VIII × VIII), in which selfing is not suppressed, yield 42–50% conjugating pairs of normal with normal, (selfing of the normal culture), and 32–45% conjugating pairs of abnormal with abnormal, (selfing in the abnormal culture). Mixtures of two cultures belonging to diverse types in which selfing is not suppressed (I × V, I × VIII, II × III, II × VII, II × IX, III × V, III × VI, III × VIII, IV × VI and VI × IX), yield 36–48% conjugating pairs (selfing) of normal with normal, and 26–50% conjugating pairs (selfing) of abnormal with abnormal. Interbreeding between two types thus normally occurs only when culture fluid of each type inhibits selfing by animals of the other type. These two types, which interbreed freely, may be considered as complementary mating types. The mating types of E. eurystomus thus fall into 5 varieties so that each one (except the fifth) has two complementary mating types. The mating types are numbered I and II in variety 1, III and IV in variety 2, V and VI in variety 3, VII and VIII in variety 4, and only IX in variety 5. Intervarietal mating does not occur in many combinations, but exceptionally it occurs between types V and VII, and between VI and VII. These hybrids become senile and finally die.
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    Simple Methods for Purifying Balantidia (1959)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 6 (1959), S. 0 
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    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: SYNOPSIS. Two methods for purifying balantidia are described. The first one may be applied to cultures which are not thriving when it is desirable to keep the purified ciliates without loss in number. Another method may be used for bulk material such as intestinal contents containing these ciliates.
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    Babesia tachyglossi n. sp. from the Echidna Tachyglossus aculeatus (1959)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 6 (1959), S. 0 
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    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: SYNOPSIS. A piroplasm occurring in the erythrocytes of 38 of 42 echidnas (Tachyglossus aculeatus) has been described and named Babesia tachyglossi.
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    URL: http://dx.doi.org/10.1111/j.1550-7408.1959.tb04377.x
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    The Cultivation of Some Trypanosomes from Urodeles (1959)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 6 (1959), S. 0 
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    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: SYNOPSIS. Identical cultural forms of Trypanosoma granulosae occur in NNN agar, Diamonds SNB-9 agar and Proteosepeptone blood agar. The inclusion of penicillin G sulfate and streptomycin had no effect upon the cultures. The first cultural forms to appear (24 hours) were long, slender crithidia which divided to produce short slender crithidia. The latter were the only forms encountered until the 18th day when rosettes, composed of 3–10 short, slender crithidia were found. Following the production of metacyclic trypanosomes (24th day) the culture rapidly died. Transfer of metacyclic trypanosomes and rosettes did not extend the length of culture life. T. diemyctyli is also unaffected by antibiotics and shows similar growth in all media used. Division in this species begins 50–96 hours after inoculation with the production, from the blood stream form, of two unequal, plump crithidia. These divide twice to form slender crithidia; the latter rapidly divide, but do not separate, and yield rosettes with a maximum number of 60 individuals. As the slender crithidia leave the rosette each either remains in the same form or transforms to a plump, pear shaped individual. Secondary rosettes are then formed from the latter. Metacyclic trypanosomes appear, in small numbers, after the 14th day.
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    On the Parasitic Protozoa of Liberia. V. Coccidia of Liberian Rodents. (1959)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 6 (1959), S. 0 
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    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: SYNOPSIS. In a survey of coccidia of rodents from Harbel, Libera, the following species of Eimeria were found and described: E. musculoidei n. sp. from Mus (Leggada) musculoides; E. separata Becker & Hall, 1931 from Rattus (Dephomys) defua (new host record); E. praomysis n. sp. from Rattus (Praomys) tullbergi rostratus; E. dasymysis n. sp. from Dasymys incomptus rufulus; E. lemniscomysis n. sp. from Lemniscomys striatus striatus; and E. lophuromysis n. sp., E. sikapusii n. sp., E. liberiensis n. sp., E. harbelensis n. sp., E. africana n. sp., and E. kruidenieri n. sp. from Lophuromys sikapusi sikapusi.
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    URL: http://dx.doi.org/10.1111/j.1550-7408.1959.tb04360.x
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    Comparative Morphology of Four Genera of Trypanosomatidae (1959)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 6 (1959), S. 0 
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    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: SYNOPSIS. The morphology of 4 genera of the family Trypanosomatidae has been studied with particular reference to the contractile vacuole, reservoir, flagellum, undulating membrane, kinetoplast, and nucleus. Both the contractile vacuole and reservoir have been found in all species examined. Four morphological types of culture forms are described with special reference to these structures: (1), the Crithidia fasciculata type which is short and membraneless with a rounded posterior end, truncate anterior end and a well developed reservoir; (2) the Herpetomonas muscarum type with no undulating membrane, a truncate posterior end, a rounded anterior end and a reservoir which varies in length from about 1/6 of the length of the body to the full length of the body; (3) the Leishmania type with no undulating membrane, a pointed posterior end, an asymmetrical anterior end and a short reservoir which remains constant in size; and (4), the short-membraned type exemplified by Trypanosoma cruzi, with a pointed posterior end, a short reservoir near the middle of the body and the flagellum attached to the body along a portion of its length. This last form is derived from the blood stream morphology as exemplified by Trypanosoma lewisi in the rat by a shifting of the kinetoplast, flagellum, reservoir and contractile vacuole along the surface of the body from a position posterior to a position anterior to the nucleus.
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  • 90
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    Electronic Resource
    Ultraviolet Inactivation and Photoreactivation of Chloroplast Development in Euglena Without Cell Death (1959)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 6 (1959), S. 0 
    Details
    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: SYNOPSIS. Exposure to non-lethal doses of ultraviolet completely inactivates chloroplast development and chlorophyll synthesis in Euglena gracilis var. bacillaris and in the Z strain. Treatment with visible light immediately following UV reverses the inactivation completely. The presence of chloroplasts is not necessary for this inactivation since similar results are obtained with light-grown cells (containing chloroplasts) and dark-grown cells (lacking chloroplasts).
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1550-7408.1959.tb04367.x
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  • 91
    Electronic Resource
    Electronic Resource
    Attempts to Transfer Drug-resistance of Trypanosomes in vivo (1959)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 6 (1959), S. 0 
    Details
    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: SYNOPSIS. Strains of Trypanosoma rhodesiense resistant to atoxyl and to antrypol respectively were allowed to multiply in the blood of mice and were also maintained for some hours in the gut of tsetse flies. They failed to acquire cross-resistance as shown by tests with the respective drugs given singly and in combination to infected mice.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1550-7408.1959.tb03937.x
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  • 92
    Electronic Resource
    Electronic Resource
    Effects of pH and Viscosity on Surface Membranes in Paramecium multimicronucleatum (1959)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 6 (1959), S. 0 
    Details
    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: SYNOPSIS. Paramecium multimicronucleatum was grown in a buffered desiccated lettuce medium maintained at pH 7.5, with Aerobacter aerogenes the main bacterial source. The maximum expansion in length and width was at pH 6.0; the minimum expansion in length and width at pH 8.5. The paramecia were usually stouter at pH levels 〈 7.0 except at pH 5.5 and generally more slender 〉 pH 7.0.The pH of the medium affected the size of food vacuoles as indicated by the fact that the maximum food vacuolar diameter was at pH 6.0, the minimum at 7.0.The fastest and greatest expansion of food vacuole diam. was at a relative viscosity of 8; the minimum food vacuolar diam. was in controls (without gum arabic) having a viscosity of 1.3.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1550-7408.1959.tb03941.x
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  • 93
    Electronic Resource
    Electronic Resource
    Trypanosoma granulosae n. sp. from the newt, Taricha granulosa twittyi (1959)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 6 (1959), S. 0 
    Details
    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: SYNOPSIS. Trypanosoma granulosae n. sp. was found in the salamander, Taricha granulosa twittyi, from Dutch Bill Creek, Sonoma County, California. This polymorphic trypanosome has an anterior nucleus containing a definite endosome. The kinetoplast is rod-shaped and never contained within a vacuole. Myonemes are occasionally seen in slender individuals.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1550-7408.1959.tb03944.x
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  • 94
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    Electronic Resource
    Abnormal Infraciliatures of Balantidium coli and B. caviae (?) and Some Morphological Observations on These Species (1959)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 6 (1959), S. 0 
    Details
    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: SYNOPSIS. Balantidium coli was cultured for 4 months in Dobell-Laidlaw's medium. About 10 specimens of monsters were found in the preparations (Chatton-Lwoff silver impregnation technique). One individual showed a tendency to polystomy. One doublet of Balantidium caviae (?) in preparations treated by the same technique was found in a population from a guinea pig.The monsters of Balantidium coli are either single distomic individuals or doublets (homopolar or heteropolar).The infraciliature of the monsters shows different degrees of deviation from the normal pattern. No reorganization field during the formation of additional cytostomes was observed, which agrees with the data on normal stomatogenesis. This process is very similar in both normal specimens and monsters and is characterized by the arrangement of radiating kineties surrounding the anlage of the cytostome and, evidently, by invagination of this area which later forms the peristome. The fate of single monsters and that of homopelar doublets is unknown. The heteropolar monsters are considered non-viable because the arrangement of the kineties in both presumptive daughters contradicts the rule of desmodexy (Chatton-Lwoff).The occurrence of the monsters in cultures may possibly be explained by the action of acriflavine which is mutagenic for Escherichia coli, or by gentian-violet which inhibits fission of sea urchin eggs.This paper apparently constitutes the first presentation of anomalies of the infraciliature in parasitic ciliates.In addition the exact arrangement of the kineties and kinetosomes at the posterior pole of Balantidium coli is described.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1550-7408.1959.tb03928.x
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  • 95
    Electronic Resource
    Electronic Resource
    Immunizing Action of a Nonpathogenic Strain of Histomonas against Blackhead in Turkeys (1959)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 6 (1959), S. 0 
    Details
    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: SYNOPSIS. A nonpathogenic strain of Histomonas was used in an attempt to immunize young turkeys against blackhead. Rectal inoculation of several thousand nonpathogenic histomonads on 2 or 3 consecutive days afforded considerable protection against modest rectal challenges with pathogenic histomonads 3 to 6 weeks later, but was much less effective against pathogenic histomonads introduced by feeding eggs of Heterakis gallinae. It is believed that an immune barrier limited to the surface of the cecal mucosa was established, and that the larvae of the cecal worms often penetrated this barrier before liberating their histomonads, thus permitting blackhead to develop. Immunization by the introduction of nonpathogenic histomonads with Heterakis eggs was not satisfactory. Apparently, the nonpathogenic organisms introduced in this way were too few to assure formation of an intact barrier.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1550-7408.1959.tb03948.x
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  • 96
    Electronic Resource
    Electronic Resource
    Nutritional Effects of Nucleic Acids and Nucleic Acid Components on Cultures of the Suctorian Podophrya collini (1959)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 6 (1959), S. 0 
    Details
    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: SYNOPSIS. Podophrya collini was fed homozygous killer Paramecium aurelia (containing kappa particles DNA). The rate of giant formation in the suctorian population was then determined; controls were fed homozygous sensitive P. aurelia. No difference in the rate of giant formation was observed; the DNA contribution by the kappa particles was not enough to induce a higher rate of giant formation. Cultures of P. collini containing only animals of known uniform age were then fed controlled numbers of Tetrahymena pyriformis or sensitive P. aurelia after these ciliates had been pretreated with guanylic acid, 8-azaguanine, commercial DNA or DNA isolated from Tetrahymena. Giant formation was increased after guanylic acid pretreatment, reduced after the 8-azaguanine pretreatment, and unaffected after DNA pretreatment over a 5-day test period. The changes in rate of giant formation are clearly caused by pretreatment agents. These agents reach the suctorian's metabolism via the food ciliates' food vacuoles before they are altered in the food vacuole.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1550-7408.1959.tb03951.x
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  • 97
    Electronic Resource
    Electronic Resource
    Carbon Nutrition and Metabolism of Polytomella caeca (1959)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 6 (1959), S. 0 
    Details
    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: SYNOPSIS. Polytomella caeca utilizes as sole carbon sources in chemically defined media: acetate, propionate, butyrate, valerate, pyruvate, succinate, ethyl, butyl, amyl, and hexyl alcohols. Glyceraldehyde and α-ketoglutarate sustain very small populations. Caproate, caprylate, fumarate, malate, propyl, heptyl, and octyl alcohols and the iso-compounds iso-butyrate, iso-butyl and iso-hexyl alcohols are inadequate.Acetate is not assimilated 〈pH 5.0, propionate and butyrate 〈pH 6.0, and valerate 〈pH 7.0. Optimum for utilization of succinate is pH 3.0, for pyruvate pH 4.0, utilized also at pH 2.0 Fatty acids are utilized dissociated; succinate and pyruvate are utilized undissociated. Alcohols are assimilated throughout pH 4.0–7.4, except hexanol at pH 7.4. Alcohol availability is proportional to molecular length-1.pH after growth of fatty acid media is 8.4 ± 0.4; stable in pH 2.0 pyruvate and pH 3.0 succinate media; 3.5 ± 0.3 in alcohol media with initial pH 〈6.0. Longer alcohols cause less pH decrease during growth.Acetate concentrations 〈0.2% do not support maximum populations; concentrations of 0.2–1.0% do. pH after growth increases in these media to pH 8.5 with maximum populations.Malate, fumarate, α-ketoglutarate, and lactate seem not to penetrate the cell, but are metabolized by homogenates. Methylene blue reduction by homogenates indicates the presence of lactic, malic, succinic and α-ketoglutaric dehydrogenases, fumarase and glutamic transaminase. Extracts contain Embden-Meyerhof phosphate esters, ATP, and ADP.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1550-7408.1959.tb03921.x
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  • 98
    Electronic Resource
    Electronic Resource
    Resistance of Calves to Reinfection with Eimeria bovis (1959)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 6 (1959), S. 0 
    Details
    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: SYNOPSIS. An immunity to reinfection with E. bovis was demonstrated in 3 experiments involving 60 calves. This immunity develops rapidly, as indicated by resistance to a challenge given 14 days after the immunizing inoculation. In 3 groups of 3 to 6 young calves each, immunity was still present to a moderate degree 2 to 3 months after inoculation; in one group of 5 animals about a year old there was apparently a high degree of immunity about 7 months after the last inoculation. In one experiment an immunizing inoculum of 10,000 oöcysts did not produce as much immunity as 50,000 oöcysts. In 2 experiments there appeared to be little difference in the immunity produced by a single inoculation of 50,000 as compared with 100,000 oöcysts, but inoculation with 100,000 oöcysts, resulted in substantially longer and more severe illness than 50,000 oöcysts. There appeared to be no appreciable difference in clinical symptoms or development of immunity between calves given a single immunizing inoculum and those given the same number of oöcysts in 5 equal inocula on successive days. Treatment with sulfamethazine and sulfamerazine (Merameth) 13 to 15 days after inoculation alleviated the clinical symptoms of coccidiosis without interfering appreciably with the development of immunity. In one experiment with 7 calves, no beneficial effect was noted from 1 or 2 transfusions of 500 ml. of plasma and leucocytes from immune calves into 4 calves 1 and 12 days or 11 days after a challenge inoculation.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1550-7408.1959.tb03926.x
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  • 99
    Electronic Resource
    Electronic Resource
    The Effect of Lowered Temperatures of the Host on the Reproductive Activity of Plasmodium cathemerium (1959)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 6 (1959), S. 0 
    Details
    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: SYNOPSIS. Experiments were carried out to determine if the course of infection with Plasmodium cathemerium was changed when the temperature of incubation of the duck embryo host was lowered. At 30° C. the infection developed more slowly and never reached the peak seen in infected embryos incubated at 37° C. If infected embryos at 30° were returned to 37° C. the resultant parasitemia developed similarly to that usually seen in this host at the latter temperature. Studies of the periodic behavior of the parasite at 30° C. and 38° C. revealed no differences in the time of segmentation. Merozoite counts were unchanged. The reduced parasitemia in embryos at 30° C. may result from reduced ability of the parasite to penetrate new host cells.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1550-7408.1959.tb03931.x
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  • 100
    Electronic Resource
    Electronic Resource
    Nuclear Division in Pelomyxa illinoisensis Kudo (1959)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 6 (1959), S. 0 
    Details
    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: SYNOPSIS. Pelomyxa illinoisensis exhibits several phenomena of an interesting and uncommon nature, such as the presence of polar granules and the appearance of chromosomes through most of the resting and dividing stages of the nucleus. For these reasons and because of the importance of the nucleus as a stable characteristic in the taxonomy of amoebae, this study of the nucleus and nuclear division was undertaken.Culture methods were the same as those used for P. carolinensis. Best fixatives for nuclei were Carnoy, Flemming, 10% formalin, Duboscq-Brazil, Schaudinn and 2% osmium tetroxide. The body shape of P. illinoisensis in nuclear division is correlated with the stage of nuclear division and resembles the same stages in Amoeba proteus and P. carolinensis, with the exception of a ragged appearance of the cytoplasm of organisms containing prophase nuclei and the halo-like appearance of the pseudopods in those containing metaphase nuclei. The condensation of resting nuclei when subjected to acidified methyl green, reported by Kudo (18), occurred with all fixatives used with the exception of 10% formalin and 2% osmium tetroxide. The metaphase nuclei have a disk of polar granules on either side of the equatorial plate with fibers running from them to the chromosomes. The nature of these granules is unknown. Similarities and differences between P. illinoisensis and P. carolinensis are discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1550-7408.1959.tb04378.x
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