Calcite and aragonite seas and the de novo acquisition of carbonate skeletons

A longstanding question in paleontology has been the influence of calcite and aragonite seas on the evolution of carbonate skeletons. An earlier study based on 21 taxa that evolved skeletons during the Ediacaran through Ordovician suggested that carbonate skeletal mineralogy is determined by seawater chemistry at the time skeletons first evolve in a clade. Here I test this hypothesis using an expanded dataset comprising 40 well‐defined animal taxa that evolved skeletons de novo in the last 600 Myr. Of the 37 taxa whose mineralogy is known with some confidence, 25 acquired mineralogies that matched seawater chemistry of the time, whereas only two taxa acquired non‐matching mineralogies. (Ten appeared during times when seawater chemistry is not well constrained.) The results suggest that calcite and aragonite seas do have a strong influence on carbonate skeletal mineralogy, however, this appears to be true only at the time mineralized skeletons first evolve. Few taxa switch mineralogies (from calcite to aragonite or vice versa) despite subsequent changes in seawater chemistry, and those that do switch do not appear to do so in response to changing aragonite–calcite seas. This suggests that there may be evolutionary constraints on skeletal mineralogy, and that although there may be increased costs associated with producing a mineralogy not favored by seawater, the costs of switching mineralogies are even greater.     

S-Nitrosylation of platelet alphaIIbbeta3 as revealed by Raman spectroscopy

The exact mechanisms regulating conformational changes in the platelet-specific integrin alphaIIbbeta3 are not fully understood. However, a role exists for thiol/disulfide exchange in integrin conformational changes leading to altered disulfide bonding patterns, via its endogenous thiol isomerase activity. Nitric oxide (NO) accelerates this intrinsic enzymatic activity and, in doing so, reverses the activational state of the integrin on the platelet surface toward a more unactivated one. We propose that it is an S-nitrosylation-induced "shuffling" of thiol/disulfide exchange that regulates this reversal of the activated state of the integrin. In this study, we use Raman spectroscopy to explore S-nitrosylation of purified alphaIIbbeta3. Using S-nitrosoglutathione (GSNO) as a model system, we identify Raman markers which show a direct interaction between NO and the thiol groups of the integrin and reveal many of the structural changes that occur in alphaIIbbeta3 in the course of not only its activation but also its deactivation. Key conformational changes are detected within the integrin when treated with manganese (Mn2+), occurring mainly in the cysteine and disulfide regions of the protein, confirming the importance of thiol/disulfide exchange in integrin activation. These changes are subsequently shown to be reversed in the presence of NO.     

Skeletal ultrastructure and phylogeny of cyclostome bryozoans

Recent research on the ultrastructure of the calcareous skeleton in the bryozoan order Cyclostomata is summarized and updated, based on field emission SEM studies of 87 species. Six fundamental ultrastructural fabrics are recognized which differ in the crystallographic orientations, shapes and prevailing growth directions of the constituent crystallites. During the growth of individual walls a succession of fabrics is secreted, defining a fabric suite. Five fabric suites are described in interior walls and four in exterior walls. Nine ultrastructural characters were combined with 37 other skeletal characters in a PAUP analysis of the relationships between 28 post-Palaeozoic cyclostomes chosen to include representatives of all suborders. A single tree of length 142 steps was found. Comparison of tree statistics for three categories of characters showed ultrastructural characters to be more homoplastic than zooidal characters, and the latter more homoplastic than colonial characters. Rooting the tree on the paleotubuliporine Cuffeyella gave four transitions from fixed- to free-walled organization and no reversals. With respect to the five extant suborders of cyclostomes, this first, preliminary analysis implies that Rectangulata and Cancellata are monophyletic groups, whereas Articulata are diphyletic, and both Tubuliporina and Cerioporina paraphyletic.     

The structure of nucleosome core particles as revealed by difference Raman spectroscopy.

Raman spectra have been observed of nucleosome core particles (I) prepared from chicken erythrocyte chromatin, its isolated 146 bp DNA (II), and its isolated histone octamer (H2A+H2B+H3+H4)2 (III). By examining the difference Raman spectra, (I)-(II), (I)-(III), and (I)-(II)-(III), several pieces of information have been obtained on the conformation of the DNA moiety, the conformation of the histone moiety, and the DNA-histone interaction in the nucleosome core particles. In the nucleosome core particles, about 15 bp (A.T rich) portions of the whole 146 bp DNA are considered to take an A-form conformation. These are considered to correspond to its bent portions which appear at intervals of 10 bp.     

Structural heterogeneity of wheat arabinoxylans revealed by Raman spectroscopy

A set of arabinoxylan samples differing in their arabinose composition and various samples of arabino-xylo-oligosaccharide samples were analysed by Raman spectroscopy. Specific signatures for arabinose substitution were found in several spectral regions, that is, 400-600, 800-950 and 1030-1100 cm(-1). A linear relationship was observed between the peak ratio 855/895 cm(-1) of the second derivative spectra and the A/X ratio determined by chemical analysis. Moreover, spectral changes were observed in the 400-600 cm(-1) region assigned to the coupled vibrations mode in the skeleton: while the intensity of the band at 570 cm(-1) increased with the degree of substitution, that at 494 cm(-1) decreased. Similarly, a linear relationship was observed between the peak intensity ratio 570/494 cm(-1) calculated on the second derivative spectra and the composition data. Analysis of Raman spectra of arabino-xylo-oligosaccharides allowed to identify specific spectral features of disubstitution.     

Structural and functional properties of hemoglobins from unicellular organisms as revealed by resonance Raman spectroscopy

Hemoglobins have been discovered in organisms from virtually all kingdoms. Their presence in unicellular organisms suggests that the gene for hemoglobin is very ancient and that the hemoglobins must have functions other than oxygen transport, in view of the fact that O2 delivery is a diffusion-controlled process in these organisms. Based on sequence alignment, three groups of hemoglobins have been characterized in unicellular organisms. The group-one hemoglobins, termed truncated hemoglobins, consist of proteins with 110-140 amino acid residues and a novel two-over-two alpha-helical sandwich motif. The group-two hemoglobins, termed flavohemoglobins, consist of a hemoglobin domain, with a classical three-over-three alpha-helical sandwich motif, and a flavin-containing reductase domain that is covalently attached to it. The group-three hemoglobins consist of myoglobin-like proteins that have high sequence homology and structural similarity to the hemoglobin domain of flavohemoglobins. In this review, recent resonance Raman studies of each group of these proteins are presented. Their implications are discussed in the context of the structural and functional properties of these novel hemoglobins.     

Precipitation of Calcite by Indigenous Microorganisms to Strengthen Liquefiable Soils

Enrichments for indigenous microorganisms capable of hydrolyzing urea in the presence of CaCl₂ were performed on potentially liquefiable saturated soils in both the laboratory and in situ. Following enrichment, treatment of soils with nutrients, CaCl₂ and urea resulted in significant in situ precipitation of calcite, even at depth, by indigenous microorganisms. The biomineralized soils showed properties that indicate calcite precipitation increased their resistance to seismic-induced liquefaction.     

Calcite precipitation and dissolution of biogenic aragonite in shallow Ordovician calcite seas

The Ordovician was a time of extensive and pervasive low-magnesium calcite (LMC) precipitation on shallow marine sea floors. The evidence comes from field study (extensive hardgrounds and other early cementation fabrics in shallow-water carbonate sequences) and petrography (large volumes of marine calcite cement in grainstones). Contemporaneous sea-floor events, particularly relationships with boring and encrusting organisms and reworking in sequences of intraformational conglomerates, confirm the early timing of such LMC cementation, and also of widespread associated aragonite dissolution. Local evidence points to the dissolved aragonite as a significant source of the calcite cement. This scenario, and the fabrics that provide the evidence for it, are likely to be pointers to other times in the stratigraphic record when LMC was the predominant shallow marine precipitate (Calcite Sea times). The combination of rapid calcite precipitation and aragonite dissolution at a time early in the Phanerozoic when many major invertebrate groups were becoming established may have acted as an influence on the evolution of both their skeletal mineralogy and their ecology.     

Structural similarities and differences of the heme pockets of various P450 isoforms as revealed by resonance Raman spectroscopy

Cytochromes P450 CYP102 A1, 1A2, and 3A4, all belonging to the class II type of P450 enzymes, were studied by resonance Raman spectroscopy. Spectra were measured for the oxidized substrate-free, oxidized substrate-bound, and reduced forms of each of these P450s. The analysis of the resonance Raman spectra indicates that the individual isoforms differ with respect to orientation and conformations of the heme side chains, whereas the overall porphyrin geometry is essentially the same. In the oxidized state, the vinyl groups exhibit both a coplanar and an out-of-plane orientation with respect to the heme, albeit with different relative propensities in the various isoforms. In the reduced state, both vinyl groups are forced into a coplanar orientation. In addition to the differences in behavior of the vinyl groups, the redox-linked spectral changes also include the bending mode of the propionate side chains. The spectral differences associated with the porphyrin substituents are likely to reflect subtle conformational differences in the heme pocket of various P450 isoforms which may constitute the structural basis for the known variability of their functions.     

Biomineralization in bryozoans: present,past and future

Many animal phyla have the physiological ability to produce biomineralized skeletons with functional roles that have been shaped by natural selection for more than 500 million years. Among these are bryozoans, a moderately diverse phylum of aquatic invertebrates with a rich fossil record and importance today as bioconstructors in some shallow‐water marine habitats. Biomineralizational patterns and, especially, processes are poorly understood in bryozoans but are conventionally believed to be similar to those of the related lophotrochozoan phyla Brachiopoda and Mollusca. However, bryozoan skeletons are more intricate than those of these two phyla. Calcareous skeletons have been acquired independently in two bryozoan clades – Stenolaemata in the Ordovician and Cheilostomata in the Jurassic – providing an evolutionary replicate. This review aims to highlight the importance of biomineralization in bryozoans and focuses on their skeletal ultrastructures, mineralogy and chemistry, the roles of organic components, the evolutionary history of bimineralization in bryozoans with respect to changes in seawater chemistry, and the impact of contemporary global changes, especially ocean acidification, on bryozoan skeletons. Bryozoan skeletons are constructed from three different wall types (exterior, interior and compound) differing in the presence/absence and location of organic cuticular layers. Skeletal ultrastructures can be classified into wall‐parallel (i.e. laminated) and wall‐perpendicular (i.e. prismatic) fabrics, the latter apparently found in only one of the two biomineralizing clades (Cheilostomata), which is also the only clade to biomineralize aragonite. A plethora of ultrastructural fabrics can be recognized and most occur in combination with other fabrics to constitute a fabric suite. The proportion of aragonitic and bimineralic bryozoans, as well as the Mg content of bryozoan skeletons, show a latitudinal increase into the warmer waters of the tropics. Responses of bryozoan mineralogy and skeletal thickness to oscillations between calcite and aragonite seas through geological time are equivocal. Field and laboratory studies of living bryozoans have shown that predicted future changes in pH (ocean acidification) combined with global warming are likely to have detrimental effects on calcification, growth rate and production of polymorphic zooids for defence and reproduction, although some species exhibit reasonable levels of resilience. Some key questions about bryozoan biomineralization that need to be addressed are identified.     

Calcite and aragonite in the egg shell of Chelonia mydas L.

The structure of the calcified layer of egg shells from farm-reared and wild turtles has been examined using scanning electron microscopy and infrared analysis. Farm-reared egg shells contained discrete morphologically distinct regions of blocks of calcite and spherulites of aragonite. In contrast, the egg shells from feral populations consisted only of the spherulites. Differences in the impurity contents of the calcite and aragonite structures have been observed. SEM revealed a thin cuticular membrane.     

Structural changes in plasma membranes prepared from irradiated Chinese hamster V79 cells as revealed by Raman spectroscopy

The effect of gamma irradiation on the integrity of plasma membranes isolated from Chinese hamster V79 cells was investigated by Raman spectroscopy. Plasma membranes of control V79 cells show transitions between (-) 10 and 5 degrees C (low-temperature transition), 10 and 22 degrees C (middle-temperature transition), and 32 and 40 degrees C (high-temperature transition). Irradiation (5 Gy) alters these transitions markedly. First, the low-temperature transition shifts to higher temperature (onset and completion temperatures 4 and 14 degrees C). Second, the middle-temperature transition shifts up to the range of about 20-32 degrees C, but the width remains unchanged. Third, the higher temperature transition broadens markedly and shifts to the range of about 15-40 degrees C. Protein secondary structure as determined by least-squares analysis of the amide I bands shows 36% total helix, 55% total beta-strand, and 9% turn plus undefined for control plasma membrane proteins. Plasma membrane proteins of irradiated V79 cells show an increase in total helix (40 and 45% at 5 and 10 Gy, respectively) and a decrease in the total beta-strand (48 and 44% at 5 and 10 Gy, respectively) structures. The qualitative analysis of the Raman features of plasma membranes and model compounds in the 1600 cm-1 region, assigned to tyrosine groups, revealed that irradiation alters the microenvironment of these groups. We conclude that the radiation dose used in the survival range of Chinese hamster V79 cells can cause damage to plasma membrane proteins without detectable lipid peroxidation, and that the altered proteins react differently with lipids, yielding a shift in the thermal transition properties.     

Picosecond structural dynamics of myoglobin following photodissociation of carbon monoxide as revealed by ultraviolet time-resolved resonance Raman spectroscopy

Picosecond protein dynamics of myoglobin in response to structural changes in heme upon CO dissociation were observed in a site-specific fashion for the first time using time-resolved UV resonance Raman spectroscopy. Transient UV resonance Raman spectra showed several phases of intensity changes in both tryptophan and tyrosine Raman bands. Five picoseconds after dissociation, the W18, W16, and W3 bands of tryptophan residues and the Y8a band of tyrosine residues decreased in intensity, followed by recovery of the Y8a band intensity in hundreds of picoseconds and recovery of the tryptophan bands in nanoseconds. These spectral changes suggest that the change in heme structure impulsively drives concerted movement of the EF helical section and that rearrangements toward a deoxy structure occur in the heme vicinity and in the A helix within a time frame of sub-nanoseconds to nanoseconds.     

Phylogeny and diversification of bryozoans

Although only a small fraction of the estimated 6000 extant bryozoan species has been analysed in a molecular phylogenetic context, the resultant trees have increased our understanding of the interrelationships between major bryozoan groups, as well as between bryozoans and other metazoan phyla. Molecular systematic analyses have failed to recover the Lophophorata as a monophyletic clade until recently, when phylogenomic data placed the Brachiopoda as sister to a clade formed by Phoronida + Bryozoa. Among bryozoans, class Phylactolaemata has been shown to be the sister group of Gymnolaemata + Stenolaemata, corroborating earlier anatomical inferences. Despite persistent claims, there are no unequivocal bryozoans of Cambrian age: the oldest bryozoans are stenolaemates from the Tremadocian of China. Stenolaemates underwent a major radiation during the Ordovician, but the relationships between the six orders involved are poorly understood, mostly because the simple and plastic skeletons of stenolaemates make phylogenetic analyses difficult. Bryozoans were hard‐hit by the mass extinction/s in the late Permian and it was not until the Middle Jurassic that they began to rediversify, initially through the cyclostome stenolaemates. The most successful post‐Palaeozoic order (Cheilostomata) evolved a calcareous skeleton de novo from a soft‐bodied ancestor in the Late Jurassic, maintained a low diversity until the mid‐Cretaceous and then began to radiate explosively. A remarkable range of morphological structures in the form of highly modified zooidal polymorphs, or non‐zooidal or intrazooidal modular elements, is postulated to have evolved repeatedly in this group. Crucially, many of these structures have been linked to micropredator protection and can be interpreted as key traits linked to the diversification of cheilostomes.     

Protein secondary structure and orientation in silk as revealed by Raman spectromicroscopy

Taking advantage of recent advances in polarized Raman microspectroscopy, and based on a rational decomposition of the amide I band, the conformation and orientation of proteins have been determined for cocoon silks of the silkworms Bombyx mori and Samia cynthia ricini and dragline silks of the spiders Nephila clavipes and Nephila edulis. This study distinguished between band components due to beta-sheets, beta-turns, 3(1)-helices, and unordered structure for the four fibers. For B. mori, the beta-sheet content is 50%, which matches the proportion of residues that form the GAGAGS fibroin motifs. For the Nephila dragline and S. c. ricini cocoon, the beta-sheet content (36-37% and 45%, respectively) is higher than the proportion of residues that belong to polyalanine blocks (18% and 42%, respectively), showing that adjacent GGA motifs are incorporated into the beta-sheets. Nephila spidroins contain fewer beta-sheets and more flexible secondary structures than silkworm fibroins. The amorphous polypeptide chains are preferentially aligned parallel to the fiber direction, although their level of orientation is much lower than that of beta-sheets. Overall, the results show that the four silks exhibit a common molecular organization, with mixtures of different amounts of beta-sheets and flexible structures, which are organized with specific orientation levels.     

Active site heterogeneity in dimethyl sulfoxide reductase from Rhodobacter capsulatus revealed by Raman spectroscopy

Raman spectroscopy has been used to investigate the structure of the molybdenum cofactor in DMSO reductase from Rhodobacter capsulatus. Three oxidized forms of the enzyme, designated 'redox cycled', 'as prepared', and DMSOR(mod)D, have been studied using 752 nm laser excitation. In addition, two reduced forms of DMSO reductase, prepared either anaerobically using DMS or using dithionite, have been characterized. The 'redox cycled' form has a single band in the Mo=O stretching region at 865 cm(-1) consistent with other studies. This oxo ligand is found to be exchangeable directly with DMS(18)O or by redox cycling. Furthermore, deuteration experiments demonstrate that the oxo ligand in the oxidized enzyme has some hydroxo character, which is ascribed to a hydrogen bonding interaction with Trp 116. There is also evidence from the labeling studies for a modified dithiolene sulfur atom, which could be present as a sulfoxide. In addition to the 865 cm(-1) band, an extra band at 818 cm(-1) is observed in the Mo=O stretching region of the 'as prepared' enzyme which is not present in the 'redox cycled' enzyme. Based on the spectra of unlabeled and labeled DMS reduced enzyme, the band at 818 cm(-1) is assigned to the S=O stretch of a coordinated DMSO molecule. The DMSOR(mod)D form, identified by its characteristic Raman spectrum, is also present in the 'as prepared' enzyme preparation but not after redox cycling. The complex mixture of forms identified in the 'as prepared' enzyme reveals a substantial degree of active site heterogeneity in DMSO reductase.     

The ‘biomineralization toolkit’ and the origin of animal skeletons

Biomineralized skeletons are widespread in animals, and their origins can be traced to the latest Ediacaran or early Cambrian fossil record, in virtually all animal groups. The origin of animal skeletons is inextricably linked with the diversification of animal body plans and the dramatic changes in ecology and geosphere–biosphere interactions across the Ediacaran–Cambrian transition. This apparent independent acquisition of skeletons across diverse animal clades has been proposed to have been driven by co‐option of a conserved ancestral genetic toolkit in different lineages at the same time. This ‘biomineralization toolkit’ hypothesis makes predictions of the early evolution of the skeleton, predictions tested herein through a critical review of the evidence from both the fossil record and development of skeletons in extant organisms. Furthermore, the distribution of skeletons is here plotted against a time‐calibrated animal phylogeny, and the nature of the deep ancestors of biomineralizing animals interpolated using ancestral state reconstruction. All these lines of evidence point towards multiple instances of the evolution of biomineralization through the co‐option of an inherited organic skeleton and genetic toolkit followed by the stepwise acquisition of more complex skeletal tissues under tighter biological control. This not only supports the ‘biomineralization toolkit’ hypothesis but also provides a model for describing the evolution of complex biological systems across the Ediacaran–Cambrian transition.     

Contribution of Raman spectroscopy to identification of biominerals present in teeth of Acanthopleura rehderi,Acanthopleura curtisiana,and Onithochiton quercinus

Raman spectroscopic investigations of the major lateral teeth of the chitons Acanthopleura rehderi and Acanthopleura curtisiana indicate that, in addition to the magnetite of the cutting surface and a carbonated hydroxyapatite in the central tooth core, these species deposit limonite in place of the lepidocrocite reported for other members of the genus Acanthopleura. A comparison of the spectra from these species with those of Onithochiton quercinus, which also deposits limonite, indicates that the current assignment of these species to Acanthopleura may not be appropriate. Biomineralization of the major lateral teeth may be a useful parameter to include in the taxonomic classification of chiton species.     

Terrestrial adaptations in the postcranial skeletons of guenons

Arboreal and semiterrestrial guenons show similar osteological features of the limbs across a wide range of species, environments, and geography, while the more terrestrially committed guenons exhibit greater morphological divergence. An ecomorphological comparison of two sympatric guenons living in Kibale Forest, Uganda, reveals an array of anatomical adaptations for terrestriality in the limbs of Cercopithecus lhoesti similar to those found in Erythrocebus patas. In contrast, Cercopithecus aethiops, although also frequent users of the terrestrial environment, generally exhibit fewer morphological adaptations characteristic of a terrestrial lifestyle. It appears that significant morphological modification for terrestriality has occurred twice within the diverse radiation of living guenons with C. aethiops perhaps representing a third group in the making. © 1994 Wiley-Liss, Inc.