Kennings and variability

Tarrin Wills

doi:10.1515/ejss-2020-2024

Kennings and variability

European Journal of Scandinavian Studies ◽

10.1515/ejss-2020-2024 ◽

2021 ◽

Vol 51 (1) ◽

pp. 11-25

Author(s):

Tarrin Wills

Keyword(s):

Structural Analysis ◽

Structural Framework ◽

Grammatical Variation

Abstract A casual examination of the skaldic corpus suggests that a very large proportion of kennings are unique, that is, the nouns that form a kenning are very unlikely to appear elsewhere as a kenning, even when grammatical variation is taken into account. This enormous productivity is due to the principle of variability and substitution in kennings. The phenomenon is discussed in Fidjestøl’s 1974 structural analysis of the kenning system and presented there as a reversal of the principle of linguistic economy. This paper investigates this phenomenon by quantitatively analysing the kenning corpus as recorded in the skaldic database, in order to identify matching kennings within the corpus. The results are broken down according to the complexity of the kennings in question and are then examined in relation to the structural framework of the kenning system. It is shown, firstly, that a relatively small number of kennings are repeated (10–12 % of kennings are repeated), but that there is a fairly high amount of repetition among simple kennings (at least 25 % of simple kennings are found elsewhere in the corpus), suggesting that the kenning system has quantitative similarities with other linguistic systems, albeit with a much higher level of variability.

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Structural analysis of the human SYCE2–TEX12 complex provides molecular insights into synaptonemal complex assembly

Open Biology ◽

10.1098/rsob.120099 ◽

2012 ◽

Vol 2 (7) ◽

pp. 120099 ◽

Cited By ~ 33

Author(s):

Owen R. Davies ◽

Joseph D. Maman ◽

Luca Pellegrini

Keyword(s):

Structural Analysis ◽

Synaptonemal Complex ◽

Recurrent Miscarriage ◽

Central Element ◽

Biological Data ◽

Structural Basis ◽

Structural Framework ◽

Chromosome Synapsis ◽

Heterotypic Interactions ◽

Physical Features

The successful completion of meiosis is essential for all sexually reproducing organisms. The synaptonemal complex (SC) is a large proteinaceous structure that holds together homologous chromosomes during meiosis, providing the structural framework for meiotic recombination and crossover formation. Errors in SC formation are associated with infertility, recurrent miscarriage and aneuploidy. The current lack of molecular information about the dynamic process of SC assembly severely restricts our understanding of its function in meiosis. Here, we provide the first biochemical and structural analysis of an SC protein component and propose a structural basis for its function in SC assembly. We show that human SC proteins SYCE2 and TEX12 form a highly stable, constitutive complex, and define the regions responsible for their homotypic and heterotypic interactions. Biophysical analysis reveals that the SYCE2–TEX12 complex is an equimolar hetero-octamer, formed from the association of an SYCE2 tetramer and two TEX12 dimers. Electron microscopy shows that biochemically reconstituted SYCE2–TEX12 complexes assemble spontaneously into filamentous structures that resemble the known physical features of the SC central element (CE). Our findings can be combined with existing biological data in a model of chromosome synapsis driven by growth of SYCE2–TEX12 higher-order structures within the CE of the SC.

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Expanding AHL Acylases Horizon - Insights From Structural Analysis of Choloylglycine Hydrolases From Shewanella lohica PV-4

10.1101/788646 ◽

2019 ◽

Author(s):

Pushparani D Philem ◽

Yashpal Yadav ◽

Avinash V Sunder ◽

Deepanjan Ghosh ◽

Asmita Prabhune ◽

...

Keyword(s):

Structural Analysis ◽

Active Site ◽

Acyl Chain ◽

Complex Structure ◽

Evolutionary Relationship ◽

Quorum Quenching ◽

Homoserine Lactone ◽

Signal Molecules ◽

Acyl Homoserine Lactone ◽

Structural Framework

AbstractAcyl homoserine lactone acylases are quorum quenching enzymes that degrade the Gram negative bacterial autoinducer N-acyl homoserine lactone (AHL) and belong to the Ntn-hydrolases superfamily of enzymes. Recent findings reported AHL acylase activity of pencillin V acylases (PVA) which, alongside bile salt hydrolases, are members of the cholyolglycine hydrolase (CGH) family of the Ntn-hydrolases superfamily. The present study reports the unique activity profile of two CGHs from a marine bacterium Shewanella loihica-PV4, designated here as SlCGH1 and SlCGH2, including the structural analysis of SlCGH1. Both the enzymes exhibit AHL acylase activity while unexpectedly being inactive on standard CGH substrates PenV and bile salts. SlCGH1 differs from known homotetrameric CGHs in being a homodimer displaying a reduced active site volume attributed to loop orientation, which subsequently directs the substrate specificity. Moreover a ligand bound complex structure revealed an unusual bent conformation of the saturated acyl chain bound to the active site and also predicts a single oxyanion hole forming residue during catalysis instead of the usual two residues. Phylogenetic analysis reveals SlCGH1 homologs cluster separate from reported CGHs and AHL acylases. On the whole, SlCGH1 could represent a functionally distinct new sub-class of CGH as an adaptation to the marine environment and its structure could provide the structural framework for understanding such a novel subclass. We also make a modest proposal of a probable evolutionary link between AHL acylases and β lactam acylases based on the overlap in activity and structural features.SignificanceCross-reactivity between AHL acylases and b lactam acylases has been recently identified giving us a vivid glimpse of a possible evolutionary relationship between the phenomena of quorum sensing and antibiotic resistance. We report here the first AHL acylase of the CGH structural framework. SlCGH1 from Shewanella loihica PV-4 is also the first report of a marine CGH with a unique activity and a new structural subclass of CGH family with AHL acylase activity. This finding highlights the vast diversity of AHL acylases and by extension quorum quenching enzymes as adaptation to different habitats. The results from this study also bolster the link between signal molecules and antibiotics, extending our understanding of the inadequately understood physiological roles of b-lactam acylases.

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A structural analysis of amyloid polymorphism in disease: clues for selective vulnerability?

10.1101/2021.03.01.433317 ◽

2021 ◽

Author(s):

Rob van der Kant ◽

Nikolaos Louros ◽

Joost Schymkowitz ◽

Frederic Rousseau

Keyword(s):

Structural Analysis ◽

Disease Progression ◽

Structural Model ◽

Selective Vulnerability ◽

Structural Framework ◽

The Cross ◽

Amyloid Structures

AbstractThe increasing amount of amyloid structures offers an opportunity to investigate the general principles determining amyloid stability and polymorphism in disease. We find that amyloid stability is dominated by about 30% of residues localized in few segments interspersed with regions that are often structurally frustrated in the cross-β conformation. These stable segments correspond to known aggregation-nucleating regions and constitute a cross-β structural framework that is shared among polymorphs. Alternative tertiary packing of these segments within the protofibril results in conformationally different but energetically similar polymorphs. This combination of a conserved structural framework along the axis and energetic ambiguity across the axis results in polymorphic plasticity that explains a number of fundamental amyloid properties, including fibril defects and brittleness but also the polymorphic instability of amyloids in simple aqueous buffers. Together these findings suggest a structural model for in vivo polymorphic bias and selective cellular vulnerability whereby (1) polymorphic bias is induced by particular templating interactions in susceptible cells, (2) once formed specific polymorphs are entropically primed to selectively bind similar targets in neighbouring cells, (3) conservation of polymorphic bias during pathological spreading implies the continued presence of similar templating interactions in successive susceptible cells and (4) absence of templating interactions relaxes polymorphic bias possibly allowing for the modification of cellular susceptibilities during disease progression by novel templating interactions.

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Structural analysis of the surface-layer protein of spirillum serpens by high-resolution electron microscopy

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100077268 ◽

1983 ◽

Vol 41 ◽

pp. 738-739

Author(s):

W. H. Wu ◽

R. M. Glaeser

Keyword(s):

Electron Microscopy ◽

Surface Layer ◽

Structural Analysis ◽

High Resolution ◽

Low Dose ◽

High Resolution Electron Microscopy ◽

Optical Diffraction ◽

Surface Layer Protein ◽

Morphological Unit ◽

Resolution Electron

Spirillum serpens possesses a surface layer protein which exhibits a regular hexagonal packing of the morphological subunits. A morphological model of the structure of the protein has been proposed at a resolution of about 25 Å, in which the morphological unit might be described as having the appearance of a flared-out, hollow cylinder with six ÅspokesÅ at the flared end. In order to understand the detailed association of the macromolecules, it is necessary to do a high resolution structural analysis. Large, single layered arrays of the surface layer protein have been obtained for this purpose by means of extensive heating in high CaCl2, a procedure derived from that of Buckmire and Murray. Low dose, low temperature electron microscopy has been applied to the large arrays.As a first step, the samples were negatively stained with neutralized phosphotungstic acid, and the specimens were imaged at 40,000 magnification by use of a high resolution cold stage on a JE0L 100B. Low dose images were recorded with exposures of 7-9 electrons/Å2. The micrographs obtained (Fig. 1) were examined by use of optical diffraction (Fig. 2) to tell what areas were especially well ordered.

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RNA polymerase: Preparation and structural analysis of helical polymers

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s042482010011091x ◽

1984 ◽

Vol 42 ◽

pp. 152-153

Author(s):

E. Loren Buhle ◽

Pamela Rew ◽

Ueli Aebi

Keyword(s):

Structural Analysis ◽

Rna Polymerase ◽

Molecular Level ◽

X Ray Diffraction ◽

Helical Polymers ◽

X Ray ◽

E Coli ◽

The Past ◽

Ordered Arrays ◽

Low Ionic Strength

While DNA-dependent RNA polymerase represents one of the key enzymes involved in transcription and ultimately in gene expression in procaryotic and eucaryotic cells, little progress has been made towards elucidation of its 3-D structure at the molecular level over the past few years. This is mainly because to date no 3-D crystals suitable for X-ray diffraction analysis have been obtained with this rather large (MW ~500 kd) multi-subunit (α2ββ'ζ). As an alternative, we have been trying to form ordered arrays of RNA polymerase from E. coli suitable for structural analysis in the electron microscope combined with image processing. Here we report about helical polymers induced from holoenzyme (α2ββ'ζ) at low ionic strength with 5-7 mM MnCl2 (see Fig. 1a). The presence of the ζ-subunit (MW 86 kd) is required to form these polymers, since the core enzyme (α2ββ') does fail to assemble into such structures under these conditions.

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Interpreting HVEM of muscle-cell impulse networks

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s042482010012103x ◽

1992 ◽

Vol 50 (1) ◽

pp. 126-127

Author(s):

Paul DeCosta ◽

Kyugon Cho ◽

Stephen Shemlon ◽

Heesung Jun ◽

Stanley M. Dunn

Keyword(s):

Structural Analysis ◽

Muscle Cell ◽

Electron Micrographs ◽

Relative Size ◽

Automatic Classification ◽

Nerve Fibers ◽

Analysis Algorithm ◽

Structural Networks

Introduction: The analysis and interpretation of electron micrographs of cells and tissues, often requires the accurate extraction of structural networks, which either provide immediate 2D or 3D information, or from which the desired information can be inferred. The images of these structures contain lines and/or curves whose orientation, lengths, and intersections characterize the overall network.Some examples exist of studies that have been done in the analysis of networks of natural structures. In, Sebok and Roemer determine the complexity of nerve structures in an EM formed slide. Here the number of nodes that exist in the image describes how dense nerve fibers are in a particular region of the skin. Hildith proposes a network structural analysis algorithm for the automatic classification of chromosome spreads (type, relative size and orientation).

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