Resistant biomacromolecules in the fossil record1

Rapid encapsulation of true ferns and arborane/fernane compounds fossilised in siderite concretions supports analytical distinction of plant fossils

Fossilised true ferns (Pecopteris sp.) preserved in siderite concretions from the Mazon Creek Lagerstätte (Illinois) presented a unique opportunity to characterise the organic signatures of these late Carboniferous plants. Localised analyses of true fern fossils showed several highly abundant phytohopanoids and fernane/arborane derived aromatic products, which were present only negligibly within their siderite matrix, as well as from other types of fossilised plants. These terpenoids had been recognised in some extant ferns, but scarcely in sedimentary organic matter and their exact source remained ambiguous. The present fossil biomarker data confirms an ancient true fern origin. Furthermore, the excellent concretion preservation of a series of related terpenoid products provided a rare insight into their diagenetic formation. The benign properties of carbonate concretions could be exploited further for biomarker evidence of other fossilised organisms, with one important caveat being that biomarker signals attributed to isolated fossils be significantly distinct from background organic matter pervading the concretion matrix. For instance, hydrocarbon profiles of seed ferns (pteridosperms) and articulates (horsetails) also preserved in Mazon Creek concretions were indistinguishable from separate analysis of their concretion matrix, preventing biomarker recognition.

Paleoproteomics of Mesozoic Dinosaurs and Other Mesozoic Fossils

Molecular studies have contributed greatly to our understanding of evolutionary processes that act upon virtually every aspect of living organisms. However, these studies are limited with regard to extinct organisms, particularly those from the Mesozoic because fossils pose unique challenges to molecular workflows, and because prevailing wisdom suggests no endogenous molecular components can persist into deep time. Here, the power and potential of a molecular approach to Mesozoic fossils is discussed. Molecular methods that have been applied to Mesozoic fossils-including iconic, non-avian dinosaurs- and the challenges inherent in such analyses, are compared and evaluated. Taphonomic processes resulting in the transition of living organisms from the biosphere into the fossil record are reviewed, and the possible effects of taphonomic alteration on downstream analyses that can be problematic for very old material (e.g., molecular modifications, limitations of on comparative databases) are addressed. Molecular studies applied to ancient remains are placed in historical context, and past and current studies are evaluated with respect to producing phylogenetically and/or evolutionarily significant data. Finally, some criteria for assessing the presence of endogenous biomolecules in very ancient fossil remains are suggested as a starting framework for such studies.

Paleo-inspired Systems: Durability, Sustainability, and Remarkable Properties

The process of mimicking properties of specific interest (such as mechanical, optical, and structural) observed in ancient and historical systems is designated here as paleo-inspiration. For instance, recovery in archaeology or paleontology identifies materials that are a posteriori extremely resilient to alteration. All the more encouraging is that many ancient materials were synthesized in soft chemical ways, often using low-energy resources and sometimes rudimentary manufacturing equipment. In this Minireview, ancient systems are presented as a source of inspiration for innovative material design in the Anthropocene.

Self-assembly as the underlying mechanism for exine development in Larix decidua D. C

Our findings suggest a new approach to pollen ontogenetic investigations, entailing consideration of physical factors, which enable a better understanding of exine developmental processes. The sporopollenin-containing part of the pollen wall-the exine-is one of the most complex cell walls in plants. By tracing each stage of microspore development in Larix decidua with TEM, we aimed to understand the underlying mechanisms of its exine establishment. Our hypothesis is that self-assembly interferes with exine development. Our specific aim is to generate experimental simulations of the exine developmental pattern. The sequence of events leading to exine development includes the appearance of spherical units in the periplasmic space, their rearrangement into radial columns, and the appearance of white-lined endexine lamellae. The final accumulation of sporopollenin proceeds in the post-tetrad period. The sequence of self-assembling micellar mesophases corresponds with that of the developmental events: spherical micelles; columns of spherical micelles; and laminate micelles separated by strata of water and visible as white-lined lamellae in TEM. Several patterns, simulating structures at different stages of exine development in Larix, were obtained from in vitro experiments. Purely physicochemical processes of self-assembly, which are not under direct genetic control, play an important role in exine development and share control with the genome. These findings suggest that a new approach to ontogenetic investigations, entailing consideration of physical factors (e.g., cell tensegrity), is required for a better understanding of developmental processes.

Organic molecular heterogeneities can withstand diagenesis

Reconstructing the original biogeochemistry of organic fossils requires quantifying the extent of the chemical transformations that they underwent during burial-induced maturation processes. Here, we performed laboratory experiments on chemically different organic materials in order to simulate the thermal maturation processes that occur during diagenesis. Starting organic materials were microorganisms and organic aerosols. Scanning transmission X-ray microscopy (STXM) was used to collect X-ray absorption near edge spectroscopy (XANES) data of the organic residues. Results indicate that even after having been submitted to 250 °C and 250 bars for 100 days, the molecular signatures of microorganisms and aerosols remain different in terms of nitrogen-to-carbon atomic ratio and carbon and nitrogen speciation. These observations suggest that burial-induced thermal degradation processes may not completely obliterate the chemical and molecular signatures of organic molecules. In other words, the present study suggests that organic molecular heterogeneities can withstand diagenesis and be recognized in the fossil record.

The biosynthesis, composition and assembly of the outer pollen wall: A tough case to crack

The formation of the durable outer pollen wall, largely composed of sporopollenin, is essential for the protection of the male gametophyte and plant reproduction. Despite its apparent strict conservation amongst land plants, the composition of sporopollenin and the biosynthetic pathway(s) yielding this recalcitrant biopolymer remain elusive. Recent molecular genetic studies in Arabidopsis thaliana (Arabidopsis) and rice have, however, identified key genes involved in sporopollenin formation, allowing a better understanding of the biochemistry and cell biology underlying sporopollenin biosynthesis and pollen wall development. Herein, current knowledge of the biochemical composition of the outer pollen wall is reviewed, with an emphasis on enzymes with characterized biochemical activities in sporopollenin and pollen coat biosynthesis. The tapetum, which forms the innermost sporophytic cell layer of the anther and envelops developing pollen, plays an essential role in sporopollenin and pollen coat formation. Recent studies show that several tapetum-expressed genes encode enzymes that metabolize fatty acid derived compounds to form putative sporopollenin precursors, including tetraketides derived from fatty acyl-CoA starter molecules, but analysis of mutants defective in pollen wall development indicate that other components are also incorporated into sporopollenin. Also highlighted are the many uncertainties remaining in the development of a sporopollenin-fortified pollen wall, particularly in relation to the mechanisms of sporopollenin precursor transport and assembly into the patterned form of the pollen wall. A working model for sporopollenin biosynthesis is proposed based on the data obtained largely from studies of Arabidopsis, and future challenges to complete our understanding of pollen wall biology are outlined.

Sporoderm and tapetum development in Eupomatia laurina (Eupomatiaceae). An interpretation

For the first time, the developmental events in the course of exine structure establishment have been traced in detail with TEM in Eupomatia, with the addition of cytochemical tests. A new look at unfolding events is suggested using our recent hypothesis on self-assembling micellar mesophases. The process proved to be unusual and includes "ghost" stages. The first units observed in the periplasmic space are spherical ones (= normal spherical micelles). These accumulate, resulting in a granular layer up to middle tetrad stage. Sporopollenin precursor accumulation on these units makes the ectexine layer looking as homogenous at late tetrad stage. Simultaneously, the columns of globules are added in the periplasmic space, which reminds an attempt to form columellae; but, the process failed. Instead, a fimbrillate endexine layer of compressed globules appears. The latter augments via additional globules, appearing in the periplasmic space in the free microspore period. The endexine formation is double-stepped spatially and temporally. The second, lamellate endexine layer (laminate micelles) appears late in development, when the channeled intine-I is already established-a very unusual feature. Moreover, a "fenestrated" stage comes unexpectedly at vacuolate stage, when hitherto amorphous ectexine appears pierced by cavernae-the results of reversal of normal spherical micelles (constituents of ectexine) to reverse the ones that open their cores for the entrance of hydrophilic nutrients from tapetum and give them over to the microspore cytoplasm by exchanging their solubilizates.

A new look at sporoderm ontogeny in Persea americana and the hidden side of development

BACKGROUND AND AIMS

The phenomenon of self-assembly, widespread in both the living and the non-living world, is a key mechanism in sporoderm pattern formation. Observations in developmental palynology appear in a new light if they are regarded as aspects of a sequence of micellar colloidal mesophases at genomically controlled initial parameters. The exine of Persea is reduced to ornamentation (spines and gemmae with underlying skin-like ectexine); there is no endexine. Development of Persea exine was analysed based on the idea that ornamentation of pollen occurs largely by self-assembly.

METHODS

Flower buds were collected from trees grown in greenhouses over 11 years in order to examine all the main developmental stages, including the very short tetrad period. After fixing, sections were examined using transmission electron microscopy.

KEY RESULTS AND CONCLUSIONS

The locations of future spines are determined by lipid droplets in invaginations of the microspore plasma membrane. The addition of new sporopollenin monomers into these invaginations leads to the appearance of chimeric polymersomes, which, after splitting into two individual assemblies, give rise to both liquid-crystal conical 'skeletons' of spines and spherical micelles. After autopolymerization of sporopollenin, spines emerge around their skeletons, nested into clusters of globules. These clusters and single globules between spines appear on a base of spherical micelles. The intine also develops on the base of micellar mesophases. Colloidal chemistry helps to provide a more general understanding of the processes and explains recurrent features of pollen walls from remote taxa.

Stable isotope ratios of carbon and nitrogen in pollen grains in order to characterize plant functional groups and photosynthetic pathway types

Measurements of delta(13)C, delta(15)N and C : N ratios on modern pollen grains from temperate plants, including whole grains as well as extracted sporopollenin, were analysed in order to characterize physiological plant types at the pollen level and to determine the variation of these parameters in modern pollen grains of the same climatic area. Measurements are presented for 95 batches of whole modern pollen from 58 temperate species and on the stable fraction of modern pollen grains, chemically extracted sporopollenin, for two modern species. Fourier transform infrared (FTIR) and cross-polarization and magic-angle spinning (CP/MAS) sporopollenin spectra were conducted in parallel. C(3) and C(4) plants can be separated by delta(13)C measurements based on pollen. Probabilistic assignments to plant functional groups (herbaceous, deciduous woody, evergreen woody) of C(3) plants by the means of a discriminant analysis can be made for C : N ratios and for delta(13)C. The results are related to other studies on sporopollenin in order to use this method in future work on fossil samples. Stable isotope measurements on pollen allow improved pollen diagrams, including forms that cannot be differentiated at species level, increasing the accuracy and resolution of plant physiological type distribution in quaternary and older fossil sediments.

The adsorption behavior of crystal violet in functionalized sporopollenin-mediated column arrangements

The adsorption behavior of Crystal Violet (CV) on a sporopollenin-based solid phase, carboxylated diaminoethane sporopollenin (CDAE-S), was investigated under column conditions, and the obtained breakthrough profiles were used in evaluations and quantifications. The adsorption capacity of the CDAE-S was observed to be considerably higher than that of diaminoethane sporopollenin (DAE-S), revealing the importance of electrostatic interactions and carboxyl groups in the adsorption of CV on the CDAE-S. The binding of CV on the DAE-S was found to be a typical nonspecific adsorption, whilst cation-exchange was proposed as the main mechanism for monolayer adsorption of CV on the CDAE-S. Hence in the present study, the cation-exchange is suggested as an effective process for removal and recovery of CV from aqueous effluents, and in view of the pH point of zero charge matter, multifunctionality of the CDAE-S is discussed in detail, and various application possibilities based on "aminocarboxylic acid" functionality are also drawn.

New insights from MALDI-ToF MS, NMR, and GC-MS: mass spectrometry techniques applied to palynology

The present study for the first time describes the application of matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-ToF MS) to palynology. With an accessible mass range of up to about 350,000 Da at subpicomolar range, this technique is ideal for the characterisation of bio-macromolecules, such as sporopollenin, found in fossil and extant pollen and spore walls, which often can only be isolated in very small quantities. At this stage, the limited solubility of sporopollenin allows for the identification of sections of this biopolymer, but with the optimisation of MALDI-ToF matrices, further structure elucidation will become possible. Furthermore, gas chromatography-mass spectrometry (GC-MS) and (1)H nuclear magnetic resonance ((1)H NMR) spectroscopy data obtained from a number of experiments revealed that some previously reported data were misinterpreted. These results add support to the hypothesis that common plasticizers were wrongly described as sporopollenin compounds.

UV-B absorbance and UV-B absorbing compounds (para-coumaric acid) in pollen and sporopollenin: the perspective to track historic UV-B levels

UV-B absorbance and UV-B absorbing compounds (UACs) of the pollen of Vicia faba, Betula pendula, Helleborus foetidus and Pinus sylvestris were studied. Sequential extraction demonstrated considerable UV-B absorbance both in the soluble (acid methanol) and insoluble sporopollenin (acetolysis resistant residue) fractions of UACs, while the wall-bound fraction of UACs was small. The UV-B absorbance of the soluble and sporopollenin fraction of pollen of Vicia faba plants exposed to enhanced UV-B (10 kJ m(-2) day(-1) UV-B(BE)) was higher than that of plants that received 0 kJ m(-2) day(-1) UV-B(BB). Pyrolysis gas chromatography-mass spectrometry (py-GC-MS) analysis of pollen demonstrated that p-coumaric acid and ferulic acid formed part of the sporopollenin fraction of the pollen. The amount of these aromatic monomers in the sporopollenin of Vicia faba appeared to increase in response to enhanced UV-B (10 kJ m(-2) day(-1) UV-B(BE)). The detection limit of pyGC-MS was sufficiently low to quantify these phenolic acids in ten pollen grains of Betula and Pinus. The experimental data presented provide evidence for the possibility that polyphenolic compounds in pollen of plants are indicators of solar UV-B and may be applied as a new proxy for the reconstruction of historic variation in solar UV-B levels.

Molecular insight into soil carbon turnover

Curie-point pyrolysis-gas chromatography coupled on-line to mass spectrometry (Py-GC/MS) and isotope ratio mass spectrometry (Py-GC/IRMS) were used to determine the individual turnover rate of specific carbohydrates, lignin, lipids and N-containing compounds from French arable soils. The analysed soils were cultivated, either continuously with a C3 plant (wheat delta(13)C-value = -25.2 per thousand), or transferred to a C4 plant (maize delta(13)C-value = -11.4 per thousand) cropping 23 years ago. Most pyrolysis products identified were related to carbohydrates (furans), lipids (hydrocarbons and derivatives of benzene), proteins (nitriles and pyrrole) and lignins (phenols). The relative yield of all individual pyrolysis products was similar in the samples from the maize and control wheat soil. The isotopic enrichment between identical pyrolysis products from the two soils varied from 1 to 12 delta (delta) units, indicating that after 23 years of cultivation 7 to 90% of their C was derived from maize. This suggests a slow mean turnover time varying from 9 to 220 years. Based on the differences in isotopic enrichment of chemical structures after vegetation change the pyrolysis products could be divided into three groups: (i) pyrolysis products with a nearly complete C4 signal, e. g. phenol, derived from lignin degradation products, (ii) pyrolysis products with an intermediate isotopic enrichment of 6-8 per thousand, most likely to be a composite of remaining (possibly physically protected) fragments derived from both maize and native wheat, and (iii) pyrolysis products showing only low enrichments in (13)C of 1-3 per thousand. Most of their precursors were found to be proteinaceaous materials. This indicates that proteins or peptides are indeed preserved during decomposition and humification processes occurring in the soil. Our study highlights the potential of Py-GC/MS-C-IRMS to further novel insights into the dynamics of soil organic constituents. Copyright 1999 John Wiley & Sons, Ltd.

Molecular taphonomy of animal and plant cuticles: selective preservation and diagenesis

The nature of organic material and the environment in which it is deposited exert a major influence on the extent to which biomacromolecules are preserved in the fossil record. The role of these factors is explored with a particular focus on the cuticle of arthropods and leaves. Preservation of the original chemistry of arthropod cuticles is favoured by their thickness and degree of sclerotization, and the presence of biominerals. Decay and burial in terrestrial as opposed to marine, and anoxic rather than oxygenated conditions, likewise appear to enhance preservation. The most important factor in the long–term preservation of the chemistry of both animal and plant cuticles, however, is diagenetic alteration to an aliphatic composition. This occurs even in amber, which encapsulates the fossil, eliminating almost all external factors. Some plants contain an original decay–resistant macromolecular aliphatic component but this is not the case in arthropods. It appears that the aliphatic components of many plant as well as animal fossils may be the result of diagenetic polymerization. Selective preservation as a result of decay resistance may explain the initial survival of organic materials in sediments, but in many cases longer–term preservation relies on chemical changes. Selective preservation is only a partial explanation for the origin of kerogen.