Early diagenesis of carbonate biocrystals : isomineralogical changes in aragonite coral skeletons

2004 ◽  
Vol 175 (2) ◽  
pp. 95-106 ◽  
Author(s):  
Christine Perrin

Abstract Early diagenetic changes occurring in aragonite coral skeletons were characterized at the micro- and ultra-structural scales in living and fossil scleractinian colonies, the latter of Pleistocene age. The skeleton of scleractinian corals, like all biomineralized structures, is a composite material formed by the intimate association of inorganic aragonite crystallites and organic matrices. In addition to its organo-mineral duality, the scleractinian skeleton is formed by the three-dimensional arrangement of two clearly distinct basic structural features, the centers of calcification and the fibers. The latter are typically characterized by a transverse micron-scale zonation revealing their incremental growth process. The size, geometry and three-dimensional arrangement of calcification centers and fibers are taxon-specific. The earliest diagenetic modifications of these skeletons have been clearly recognized in the older parts of living colonies. The first steps of diagenesis therefore take place only a few years after the skeleton had been secreted by the living polyps, and in the same environmental conditions. Comparisons with the uppermost living parts of the coral colonies clearly show that these first diagenetic changes are driven by the biological ultrastructural characteristics of these skeletons and are conditioned by the presence of organic envelopes interbedded with and surrounding aragonite crystallites. These first diagenetic processes induce the development of thin fringes of fibrous aragonite cements growing syntaxially on the aragonitic coral fibers, an alteration of the incremental zonation of coral fibers and also preferential diagenetic changes in the calcification centers, including dissolution of their minute internal crystals. Diagenetic patterns observed in Pleistocene coral colonies typically involve the same processes already recognized in the older skeletal parts of living colonies, suggesting that diagenesis occurs through continuous processes instead of clearly differentiated stages. Selective dissolution affects calcification centers and some growth increments of coral fibers. Alteration of the initial transverse zonation of coral fibers also occur through the development of micro-inclusions clearly seen in ultra-thin sections. Although usually thicker than those observed in the ancient skeletal parts of living colonies, syntaxial aragonite cements commonly occur in these fossil skeletons. These cements are often associated with gradual textural modifications of the underlying coral fibers, in particular the loss of the transverse micron-scale zonation. This suggests that the coral skeleton forming the substratum of diagenetic cements is progressively recrystallized in secondary aragonite. This recrystallization of coral aragonite begins at the external margin of the skeleton, just below the diagenetic cements and gradually moves towards the internal skeletal parts. Recrystallization takes place through concomitant fine-scale dissolution-precipitation processes and occurs with textural changes but no mineralogical change. The process of recrystallization is likely initiated by a biological degradation of organic skeletal matrices and can be also driven by thermodynamical constraints involving the lowering of surface free energies resulting from changes in crystal size. Alteration of skeletal organic matrix, textural changes in coral biocrystals through recrystallization and precipitation of secondary diagenetic aragonite may bias the original geochemical characteristics of coral skeletons. Although more work is needed to establish the influence of these early diagenetic processes on the geochemical signatures, it is already well known that the breakdown of organic skeletal envelopes and early recrystallization of shallow-water carbonates alter the stable isotopic composition. The widespread use of coral skeletons as environmental and climatic proxies makes strongly necessary a better understanding of these early diagenetic mechanisms and a precise characterization of the fine-scale diagenetic patterns of specimens for the optimization of geochemical interpretations. In particular, it cannot be assumed that an entire aragonitic composition can guarantee that there is no or slight diagenetic alteration.

2021 ◽  
Author(s):  
Clayton J Harry ◽  
Sonia M Messar ◽  
Erik J Ragsdale

Pristionchus pacificus is a nematode model for the developmental genetics of morphological polyphenism, especially at the level of individual cells. The polyphenism of P. pacificus includes an evolutionary novelty, moveable teeth, which have enabled predatory feeding in this species and others in its family (Diplogastridae). From transmission electron micrographs of serial thin sections through an adult hermaphrodite of P. pacificus, we three-dimensionally reconstructed the 73 epithelial cells of its face, mouth, and pharynx. We found that the epithelia that produce the predatory morphology of P. pacificus are identical to Caenorhabditis elegans in the number of cell classes and nuclei. However, differences in cell form, connectivity, and nucleus position correlate with gross morphological differences from C. elegans and outgroups. Moreover, we identified fine-structural features, especially in the anteriormost pharyngeal muscles, that underlie the conspicuous, left-right asymmetry that characterizes the P. pacificus feeding apparatus. Our reconstruction provides an anatomical map for studying the genetics of polyphenism, feeding behaviour, and the development of novel form in a satellite model to C. elegans.


Author(s):  
Robert Glaeser ◽  
Thomas Bauer ◽  
David Grano

In transmission electron microscopy, the 3-dimensional structure of an object is usually obtained in one of two ways. For objects which can be included in one specimen, as for example with elements included in freeze- dried whole mounts and examined with a high voltage microscope, stereo pairs can be obtained which exhibit the 3-D structure of the element. For objects which can not be included in one specimen, the 3-D shape is obtained by reconstruction from serial sections. However, without stereo imagery, only detail which remains constant within the thickness of the section can be used in the reconstruction; consequently, the choice is between a low resolution reconstruction using a few thick sections and a better resolution reconstruction using many thin sections, generally a tedious chore. This paper describes an approach to 3-D reconstruction which uses stereo images of serial thick sections to reconstruct an object including detail which changes within the depth of an individual thick section.


Author(s):  
S. Cusack ◽  
J.-C. Jésior

Three-dimensional reconstruction techniques using electron microscopy have been principally developed for application to 2-D arrays (i.e. monolayers) of biological molecules and symmetrical single particles (e.g. helical viruses). However many biological molecules that crystallise form multilayered microcrystals which are unsuitable for study by either the standard methods of 3-D reconstruction or, because of their size, by X-ray crystallography. The grid sectioning technique enables a number of different projections of such microcrystals to be obtained in well defined directions (e.g. parallel to crystal axes) and poses the problem of how best these projections can be used to reconstruct the packing and shape of the molecules forming the microcrystal.Given sufficient projections there may be enough information to do a crystallographic reconstruction in Fourier space. We however have considered the situation where only a limited number of projections are available, as for example in the case of catalase platelets where three orthogonal and two diagonal projections have been obtained (Fig. 1).


Author(s):  
R. P. Becker ◽  
J. J. Wolosewick ◽  
J. Ross-Stanton

Methodology has been introduced recently which allows transmission and scanning electron microscopy of cell fine structure in semi-thin sections unencumbered by an embedding medium. Images obtained from these “resinless” sections show a three-dimensional lattice of microtrabeculfee contiguous with cytoskeletal structures and membrane-bounded cell organelles. Visualization of these structures, especially of the matiiDra-nous components, can be facilitated by employing tannic acid in the fixation step and dessicator drying, as reported here.Albino rats were fixed by vascular perfusion with 2% glutaraldehyde or 1.5% depolymerized paraformaldehyde plus 2.5% glutaraldehyde in 0.1M sodium cacodylate (pH 7.4). Tissues were removed and minced in the fixative and stored overnight in fixative containing 4% tannic acid. The tissues were rinsed in buffer (0.2M cacodylate), exposed to 1% buffered osmium tetroxide, dehydrated in ethyl alcohol, and embedded in pure polyethylene glycol-6000 (PEG). Sections were cut on glass knives with a Sorvall MT-1 microtome and mounted onto poly-L-lysine, formvar-carbon coated grids while submerged in a solution of 95% ethanol containing 5% PEG.


Author(s):  
Jerome J. Paulin

Within the past decade it has become apparent that HVEM offers the biologist a means to explore the three-dimensional structure of cells and/or organelles. Stereo-imaging of thick sections (e.g. 0.25-10 μm) not only reveals anatomical features of cellular components, but also reduces errors of interpretation associated with overlap of structures seen in thick sections. Concomitant with stereo-imaging techniques conventional serial Sectioning methods developed with thin sections have been adopted to serial thick sections (≥ 0.25 μm). Three-dimensional reconstructions of the chondriome of several species of trypanosomatid flagellates have been made from tracings of mitochondrial profiles on cellulose acetate sheets. The sheets are flooded with acetone, gluing them together, and the model sawed from the composite and redrawn.The extensive mitochondrial reticulum can be seen in consecutive thick sections of (0.25 μm thick) Crithidia fasciculata (Figs. 1-2). Profiles of the mitochondrion are distinguishable from the anterior apex of the cell (small arrow, Fig. 1) to the posterior pole (small arrow, Fig. 2).


Author(s):  
Bert Ph. M. Menco ◽  
Ido F. Menco ◽  
Frans L.T. Verdonk

Previously we presented an extensive study of the distributions of intramembranous particles of structures in apical surfaces of nasal olfactory and respiratory epithelia of the Sprague-Dawley rat. For the same structures these distributions were compared in samples which were i) chemically fixed and cryo-protected with glycerol before cryo-fixation, after excision, and ii)ultra-rapidly frozen by means of the slam-freezing method. Since a three-dimensional presentation markedly improves visualization of structural features micrographs were presented as stereopairs. Two exposures were made by tiling the sample stage of the electron microscope 6° in either direction with an eucentric goniometer. The negatives (Agfa Pan 25 Professional) were reversed with Kodak Technical Pan Film 2415 developed in D76 1:1. The prints were made from these reversed negatives. As an example tight-junctional features of an olfactory supporting cell in a region where this cell conjoined with two other cells are presented (Fig. 1).


Author(s):  
Matthew J. Genge

Drawings, illustrations, and field sketches play an important role in Earth Science since they are used to record field observations, develop interpretations, and communicate results in reports and scientific publications. Drawing geology in the field furthermore facilitates observation and maximizes the value of fieldwork. Every geologist, whether a student, academic, professional, or amateur enthusiast, will benefit from the ability to draw geological features accurately. This book describes how and what to draw in geology. Essential drawing techniques, together with practical advice in creating high quality diagrams, are described the opening chapters. How to draw different types of geology, including faults, folds, metamorphic rocks, sedimentary rocks, igneous rocks, and fossils, are the subjects of separate chapters, and include descriptions of what are the important features to draw and describe. Different types of sketch, such as drawings of three-dimensional outcrops, landscapes, thin-sections, and hand-specimens of rocks, crystals, and minerals, are discussed. The methods used to create technical diagrams such as geological maps and cross-sections are also covered. Finally, modern techniques in the acquisition and recording of field data, including photogrammetry and aerial surveys, and digital methods of illustration, are the subject of the final chapter of the book. Throughout, worked examples of field sketches and illustrations are provided as well as descriptions of the common mistakes to be avoided.


mSphere ◽  
2019 ◽  
Vol 4 (3) ◽  
Author(s):  
Emily G. Sweeney ◽  
Andrew Nishida ◽  
Alexandra Weston ◽  
Maria S. Bañuelos ◽  
Kristin Potter ◽  
...  

ABSTRACTBacteria are often found living in aggregated multicellular communities known as biofilms. Biofilms are three-dimensional structures that confer distinct physical and biological properties to the collective of cells living within them. We used agent-based modeling to explore whether local cellular interactions were sufficient to give rise to global structural features of biofilms. Specifically, we asked whether chemorepulsion from a self-produced quorum-sensing molecule, autoinducer-2 (AI-2), was sufficient to recapitulate biofilm growth and cellular organization observed for biofilms ofHelicobacter pylori, a common bacterial resident of human stomachs. To carry out this modeling, we modified an existing platform, Individual-based Dynamics of Microbial Communities Simulator (iDynoMiCS), to incorporate three-dimensional chemotaxis, planktonic cells that could join or leave the biofilm structure, and cellular production of AI-2. We simulated biofilm growth of previously characterizedH. pyloristrains with various AI-2 production and sensing capacities. Using biologically plausible parameters, we were able to recapitulate both the variation in biofilm mass and cellular distributions observed with these strains. Specifically, the strains that were competent to chemotax away from AI-2 produced smaller and more heterogeneously spaced biofilms, whereas the AI-2 chemotaxis-defective strains produced larger and more homogeneously spaced biofilms. The model also provided new insights into the cellular demographics contributing to the biofilm patterning of each strain. Our analysis supports the idea that cellular interactions at small spatial and temporal scales are sufficient to give rise to larger-scale emergent properties of biofilms.IMPORTANCEMost bacteria exist in aggregated, three-dimensional structures called biofilms. Although biofilms play important ecological roles in natural and engineered settings, they can also pose societal problems, for example, when they grow in plumbing systems or on medical implants. Understanding the processes that promote the growth and disassembly of biofilms could lead to better strategies to manage these structures. We had previously shown thatHelicobacter pyloribacteria are repulsed by high concentrations of a self-produced molecule, AI-2, and thatH. pylorimutants deficient in AI-2 sensing form larger and more homogeneously spaced biofilms. Here, we used computer simulations of biofilm formation to show that localH. pyloribehavior of repulsion from high AI-2 could explain the overall architecture ofH. pyloribiofilms. Our findings demonstrate that it is possible to change global biofilm organization by manipulating local cell behaviors, which suggests that simple strategies targeting cells at local scales could be useful for controlling biofilms in industrial and medical settings.


Plants ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 774
Author(s):  
Max Langer ◽  
Thomas Speck ◽  
Olga Speck

Although both the petiole and lamina of foliage leaves have been thoroughly studied, the transition zone between them has often been overlooked. We aimed to identify objectively measurable morphological and anatomical criteria for a generally valid definition of the petiole–lamina transition zone by comparing foliage leaves with various body plans (monocotyledons vs. dicotyledons) and spatial arrangements of petiole and lamina (two-dimensional vs. three-dimensional configurations). Cross-sectional geometry and tissue arrangement of petioles and transition zones were investigated via serial thin-sections and µCT. The changes in the cross-sectional geometries from the petiole to the transition zone and the course of the vascular bundles in the transition zone apparently depend on the spatial arrangement, while the arrangement of the vascular bundles in the petioles depends on the body plan. We found an exponential acropetal increase in the cross-sectional area and axial and polar second moments of area to be the defining characteristic of all transition zones studied, regardless of body plan or spatial arrangement. In conclusion, a variety of terms is used in the literature for describing the region between petiole and lamina. We prefer the term “petiole–lamina transition zone” to underline its three-dimensional nature and the integration of multiple gradients of geometry, shape, and size.


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