Steve Weiner

Persistence of soil organic matter as an ecosystem property

Globally, soil organic matter (SOM) contains more than three times as much carbon as either the atmosphere or terrestrial vegetation. Yet it remains largely unknown why some SOM persists for millennia whereas other SOM decomposes readily—and this limits our ability to predict how soils will respond to climate change. Recent analytical and experimental advances have demonstrated that molecular structure alone does not control SOM stability: in fact, environmental and biological controls predominate. Here we propose ways to include this understanding in a new generation of experiments and soil carbon models, thereby improving predictions of the SOM response to global warming.

Control of Aragonite or Calcite Polymorphism by Mollusk Shell Macromolecules

Many mineralizing organisms selectively form either calcite or aragonite, two polymorphs of calcium carbonate with very similar crystalline structures. Understanding how these organisms achieve this control has represented a major challenge in the field of biomineralization. Macromolecules extracted from the aragonitic shell layers of some mollusks induced aragonite formation in vitro when preadsorbed on a substrate of β-chitin and silk fibroin. Macromolecules from calcitic shell layers induced mainly calcite formation under the same conditions. The results suggest that these macromolecules are responsible for the precipitation of either aragonite or calcite in vivo.

An Overview of Biomineralization Processes and the Problem of the Vital Effect

“Biomineralization links soft organic tissues, which are compositionally akin to the atmosphere and oceans, with the hard materials of the solid Earth. It provides organisms with skeletons and shells while they are alive, and when they die these are deposited as sediment in environments from river plains to the deep ocean floor. It is also these hard, resistant products of life which are mainly responsible for the Earth’s fossil record. Consequently, biomineralization involves biologists, chemists, and geologists in interdisciplinary studies at one of the interfaces between Earth and life.” (Leadbeater and Riding 1986) Biomineralization refers to the processes by which organisms form minerals. The control exerted by many organisms over mineral formation distinguishes these processes from abiotic mineralization. The latter was the primary focus of earth scientists over the last century, but the emergence of biogeochemistry and the urgency of understanding the past and future evolution of the Earth are moving biological mineralization to the forefront of various fields of science, including the earth sciences. The growth in biogeochemistry has led to a number of new exciting research areas where the distinctions between the biological, chemical, and earth sciences disciplines melt away. Of the wonderful topics that are receiving renewed attention, the study of biomineral formation is perhaps the most fascinating. Truly at the interface of earth and life, biomineralization is a discipline that is certain to see major advancements as a new generation of scientists brings cross-disciplinary training and new experimental and computational methods to the most daunting problems. It is, however, by no means a new field. The first book on biomineralization was published in 1924 in German by W.J. Schmidt (Schmidt 1924), and the subject has continued to intrigue a dedicated community of scientists for many years. Until the early 1980s the field was known as …

Amorphous calcium phosphate is a major component of the forming fin bones of zebrafish: Indications for an amorphous precursor phase

A fundamental question in biomineralization is the nature of the first-formed mineral phase. In vertebrate bone formation, this issue has been the subject of a long-standing controversy. We address this key issue using the continuously growing fin bony rays of the Tuebingen long-fin zebrafish as a model for bone mineralization. Employing high-resolution scanning and transmission electron microscopy imaging, electron diffraction, and elemental analysis, we demonstrate the presence of an abundant amorphous calcium phosphate phase in the newly formed fin bones. The extracted amorphous mineral particles crystallize with time, and mineral crystallinity increases during bone maturation. Based on these findings, we propose that this amorphous calcium phosphate phase may be a precursor phase that later transforms into the mature crystalline mineral.

Mapping amorphous calcium phosphate transformation into crystalline mineral from the cell to the bone in zebrafish fin rays

The continuously forming fin bony rays of zebrafish represent a simple bone model system in which mineralization is temporally and spatially resolved. The mineralized collagen fibrils of the fin bones are identical in structure to those found in all known bone materials. We study the continuous mineralization process within the tissue by using synchrotron microbeam x-ray diffraction and small-angle scattering, combined with cryo-scanning electron microscopy. The former provides information on the mineral phase and the mineral particles size and shape, whereas the latter allows high-resolution imaging of native hydrated tissues. The integration of the two techniques demonstrates that new mineral is delivered and deposited as packages of amorphous calcium phosphate nanospheres, which transform into platelets of crystalline apatite within the collagen matrix.

Organization of extracellularly mineralized tissues: a comparative study of biological crystal growth

Biological mineralization processes are extremely diverse and, to date, it is an act of faith rather than an established principle that organisms utilize common mechanisms for forming crystals. A systematic analysis of the structural organization, as far as possible at the molecular level, of five different extracellularly mineralized tissues is presented to demonstrate that at least these mineralization processes are all part of the same continuum. The degrees of control exercised over crystal nucleation and crystal growth modulation are the basic variables. The five tissues, extracellularly mineralizing algae, radial and granular foraminifera, mammalian bone, mammalian enamel, and mollusk shell nacre, probably span the entire spectrum. Their crystal shapes, sizes, and the relations between the mineral phase and the organic phase, are primarily used to assess probable degrees of control exercised over crystal nucleation and modulation. Three different types of nucleation processes can be recognized: nonspecific, stereochemical, and epitaxial. Modulation of crystal growth after nucleation is either absent, achieved by adsorption of macromolecules onto specific crystal faces, or occurs by the prepositioning of matrix surfaces which interrupt crystal growth. The tissues in which active control is exercised over crystal growth all contain similar types of acidic matrix macromolecules. Significantly, the framework matrix macromolecules are all quite different and hence probably perform some tissue-specific functions. The study shows that there is a common basis for understanding these mineralization processes which is reflected in the nature of the protein-crystal interactions which occur in each tissue.

Mollusk shell acidic proteins: in search of individual functions.

Acidic proteins play a major role in the biomineralization process. These proteins are generally thought to control mineral formation and growth. Thus, characterization of individual acidic proteins is important as a first step toward linking function to individual proteins, which is our ultimate goal. In order to characterize the protein(s) responsible for the assemblage of biominerals, a new gel electrophoresis fixing and staining protocol was developed and many, if not all of the acidic proteins were visualized on the gel for the first time. In an in vitro assay we show that proteins extracted from an aragonitic shell layer induce the formation of amorphous calcium carbonate prior to its transformation into the aragonitic crystalline form. This study removes some major obstacles in the characterization of acidic proteins and sheds more light on the functions of these proteins in the biomineralization process.

On the relationship between the microstructure of bone and its mechanical stiffness

A recent study of bone structure shows that the plate-shaped carbonate apatite crystals in individual lamellae are arranged in layers across the lamellae, and that the orientation of these layers are different in alternate lamellae. Based on these findings, a new micromechanical model for the Youngs modulus of bone is proposed, which accounts for the anisotropy and geometrical characteristics of the material. The model incorporates the platelet-like geometry of the basic reinforcing unit, the presence of alternating thin and thick lamellae, and the orientations of the crystal platelets in the lamellae. The thin and thick lamellae are modeled as orthotropic composite layers made up of thin rectangular apatite platelets within a collagen matrix, and classical orthotropic elasticity theory is used to calculate the Youngs modulus of the lamellae. Bone is viewed as an assembly of such orthotropic lamellae bent into cylindrical structures, and having a constant, alternating angle between successive lamellae. The micromechanical model employs a modified rule-of-mixtures to account for the two types of lamellae. The model provides a curve similar to the published experimental data on the angular dependence of Youngs modulus, including a local maximum at an angle between 0 and 90 degrees. A rigorous testing of the model awaits additional experimental data.

Asprich: A novel aspartic acid-rich protein family from the prismatic shell matrix of the bivalve Atrina rigida.

Almost all mineralized tissues contain proteins that are unusually acidic. As they are also often intimately associated with the mineral phase, they are thought to fulfill important functions in controlling mineral formation. Relatively little is known about these important proteins, because their acidic nature causes technical difficulties during purification and characterization procedures. Much effort has been made to overcome these problems, particularly in the study of mollusk‐shell formation. To date about 16 proteins from mollusk‐shell organic matrices have been sequenced, but only two are unusually rich in aspartic and glutamic acids. Here we screened a cDNA library made from the mRNA of the shell‐forming cells of a bivalve, Atrina rigida, using probes for short Asp‐containing repeat sequences, and identified ten different proteins. Using more specific probes designed from one subgroup of conserved sequences, we obtained the full sequences of a family of seven aspartic acid‐rich proteins, which we named “Asprich”; a subfamily of the unusually acidic shell‐matrix proteins. Polyclonal antibodies raised against a synthetic peptide of the conserved acidic1 domain of these proteins reacted specifically with the matrix components of the calcitic prismatic layer, but not with those of the aragonitic nacreous layer. Thus the Asprich proteins are constituents of the prismatic layer shell matrix. We can identify different domains within these sequences, including a signal peptide characteristic of proteins destined for extracellular secretion, a conserved domain rich in aspartic acid that contains a sequence very similar to the calcium‐binding domain of Calsequestrin, and another domain rich in aspartic acid, that varies between the seven sequences. We also identified a domain with DEAD repeats that may have Mg‐binding capabilities. Although we do not know, as yet, the function of these proteins, their generally conserved sequences do indicate that they might well fulfill basic functions in shell formation.

Rotated plywood structure of primary lamellar bone in the rat: Orientations of the collagen fibril arrays

A basic structural motif of lamellar bone is the arrays of parallel collagen fibrils, with successive arrays having different orientations to form a plywood-like structure. Measurements of the angles between adjacent arrays from cryomicrotomed and vitrified thin sections of demineralized rat bone, cut approximately parallel to the lamellar boundary plane, show that most angles are around 30 degrees, although a subset are around 70 degrees. A structural model for collagen organization based on these measurements is proposed in which an individual lamellar unit (thick and thin lamellae together with transition zones) is composed of five arrays of parallel collagen fibrils, each offset by 30 degrees.