Neil J. Gostling

Synchrotron X-ray tomographic microscopy of fossil embryos

Fossilized embryos from the late Neoproterozoic and earliest Phanerozoic have caused much excitement because they preserve the earliest stages of embryology of animals that represent the initial diversification of metazoans. However, the potential of this material has not been fully realized because of reliance on traditional, non-destructive methods that allow analysis of exposed surfaces only, and destructive methods that preserve only a single two-dimensional view of the interior of the specimen. Here, we have applied synchrotron-radiation X-ray tomographic microscopy (SRXTM), obtaining complete three-dimensional recordings at submicrometre resolution. The embryos are preserved by early diagenetic impregnation and encrustation with calcium phosphate, and differences in X-ray attenuation provide information about the distribution of these two diagenetic phases. Three-dimensional visualization of blastomere arrangement and diagenetic cement in cleavage embryos resolves outstanding questions about their nature, including the identity of the columnar blastomeres. The anterior and posterior anatomy of embryos of the bilaterian worm-like Markuelia confirms its position as a scalidophoran, providing new insights into body-plan assembly among constituent phyla. The structure of the developing germ band in another bilaterian, Pseudooides, indicates a unique mode of germ-band development. SRXTM provides a method of non-invasive analysis that rivals the resolution achieved even by destructive methods, probing the very limits of fossilization and providing insight into embryology during the emergence of metazoan phyla.

Dietary specializations and diversity in feeding ecology of the earliest stem mammals

The origin and radiation of mammals are key events in the history of life, with fossils placing the origin at 220 million years ago, in the Late Triassic period. The earliest mammals, representing the first 50 million years of their evolution and including the most basal taxa, are widely considered to be generalized insectivores. This implies that the first phase of the mammalian radiation—associated with the appearance in the fossil record of important innovations such as heterodont dentition, diphyodonty and the dentary–squamosal jaw joint—was decoupled from ecomorphological diversification. Finds of exceptionally complete specimens of later Mesozoic mammals have revealed greater ecomorphological diversity than previously suspected, including adaptations for swimming, burrowing, digging and even gliding, but such well-preserved fossils of earlier mammals do not exist, and robust analysis of their ecomorphological diversity has previously been lacking. Here we present the results of an integrated analysis, using synchrotron X-ray tomography and analyses of biomechanics, finite element models and tooth microwear textures. We find significant differences in function and dietary ecology between two of the earliest mammaliaform taxa, Morganucodon and Kuehneotherium—taxa that are central to the debate on mammalian evolution. Morganucodon possessed comparatively more forceful and robust jaws and consumed ‘harder’ prey, comparable to extant small-bodied mammals that eat considerable amounts of coleopterans. Kuehneotherium ingested a diet comparable to extant mixed feeders and specialists on ‘soft’ prey such as lepidopterans. Our results reveal previously hidden trophic specialization at the base of the mammalian radiation; hence even the earliest mammaliaforms were beginning to diversify—morphologically, functionally and ecologically. In contrast to the prevailing view, this pattern suggests that lineage splitting during the earliest stages of mammalian evolution was associated with ecomorphological specialization and niche partitioning.

Protochordate Zic genes define primitive somite compartments and highlight molecular changes underlying neural crest evolution.

SUMMARY The vertebrate Zic gene family encodes C2H2 zinc finger transcription factors closely related to the Gli proteins. Zic genes are expressed in multiple areas of developing vertebrate embryos, including the dorsal neural tube where they act as potent neural crest inducers. Here we describe the characterization of a Zic ortholog from the amphioxus Branchiostoma floridae and further describe the expression of a Zic ortholog from the ascidian Ciona intestinalis. Molecular phylogenetic analysis and sequence comparisons suggest the gene duplications that formed the vertebrate Zic family were specific to the vertebrate lineage. In Ciona maternal CiZic/Ci‐macho1 transcripts are localized during cleavage stages by asymmetric cell division, whereas zygotic expression by neural plate cells commences during neurulation. The amphioxus Zic ortholog AmphiZic is expressed in dorsal mesoderm and ectoderm during gastrulation, before being eliminated first from midline cells and then from all neurectoderm during neurulation. After neurulation, expression is reactivated in the dorsal neural tube and dorsolateral somite. Comparison of CiZic and AmphiZic expression with vertebrate Zic expression leads to two main conclusions. First, Zic expression allows us to define homologous compartments between vertebrate and amphioxus somites, showing primitive subdivision of vertebrate segmented mesoderm. Second, we show that neural Zic expression is a chordate synapomorphy, whereas the precise pattern of neural expression has evolved differently on the different chordate lineages. Based on these observations we suggest that a change in Zic regulation, specifically the evolution of a dorsal neural expression domain in vertebrate neurulae, was an important step in the evolution of the neural crest.

High resolution synchrotron imaging of wheat root hairs growing in soil and image based modelling of phosphate uptake

· Root hairs are known to be highly important for uptake of sparingly soluble nutrients, particularly in nutrient deficient soils. Development of increasingly sophisticated mathematical models has allowed uptake characteristics to be quantified. However, modelling has been constrained by a lack of methods for imaging live root hairs growing in real soils. · We developed a plant growth protocol and used Synchrotron Radiation X-ray Tomographic Microscopy (SRXTM) to uncover the three-dimensional (3D) interactions of root hairs in real soil. We developed a model of phosphate uptake by root hairs based directly on the geometry of hairs and associated soil pores as revealed by imaging. · Previous modelling studies found that root hairs dominate phosphate uptake. By contrast, our study suggests that hairs and roots contribute equally. We show that uptake by hairs is more localized than by roots and strongly dependent on root hair and aggregate orientation. · The ability to image hair-soil interactions enables a step change in modelling approaches, allowing a more realistic treatment of processes at the scale of individual root hairs in soil pores.

New dicynodonts (Therapsida, Anomodontia) and updated tetrapod stratigraphy of the Permian Ruhuhu Formation (Songea Group, Ruhuhu Basin) of southern Tanzania

ABSTRACT Permian tetrapod fossils were discovered in the Tanzanian Ruhuhu Formation in 1963, but they have received far less attention than the tetrapods of the overlying Usili (formerly Kawinga) Formation. Here, we describe two dicynodonts collected in the Ruhuhu Formation in 2008. Abajudon kaayai, gen. et sp. nov., is represented by a partial skull and mandible and is characterized by autapomorphic upper teeth that are triangular in cross-section, have procurved tips, and bear a deep groove on the mesial surface. Although it shows similarities to taxa such as Endothiodon and Chelydontops, the exact relationships between A. kaayai and other dicynodonts are uncertain. The second specimen also consists of a partial skull and mandible. We refer it to cf. Endothiodontia based on the medial placement of the long maxillary tooth rows, the presence of depressions on the palatine pad, a long posterior dentary sulcus, and similarities of the mandibular dentition. Tetrapods occur in three fossiliferous horizons in the Ruhuhu Formation. The likely Middle Permian lower horizon includes dinocephalians, temnospondyls, and the dicynodonts described here. The middle horizon includes a new, tusked species of Endothiodon and at least one other dicynodont. The upper horizon appears to sample an assemblage similar to that of the Usili Formation and therefore may be of Late Permian age. The discovery of Middle Permian fossils in Tanzania and Zambia provides the opportunity to test whether southern Gondwana was characterized by a cosmopolitan tetrapod fauna for an extended period of time before the biogeographic restructuring caused by the end-Permian mass extinction.

Deciphering the fossil record of early bilaterian embryonic development in light of experimental taphonomy

SUMMARY Experimental analyses of decay in a tunicate deuterostome and three lophotrochozoans indicate that the controls on decay and preservation of embryos, identified previously based on echinoids, are more generally applicable. Four stages of decay are identified regardless of the environment of death and decay. Embryos decay rapidly in oxic and anoxic conditions, although the gross morphology of embryos is maintained for longer under anoxic conditions. Under anoxic reducing conditions, the gross morphology of the embryos is maintained for the longest period of time, compatible with the timescale required for bacterially mediated mineralization of soft tissues. All four stages of decay were encountered under all environmental conditions, matching the spectrum of preservational qualities encountered in all fossil embryo assemblages. The preservation potential of embryos of deuterostomes and lophotrochozoans is at odds with the lack of such embryos in the fossil record. Rather, the fossil record of embryos, as sparse as it is, is dominated by forms interpreted as ecdysozoans, cnidarians, and stem‐metazoans. The dearth of deuterostome and lophotrochozoan embryos may be explained by the fact that ecdysozoans, at least, tend to deposit their eggs in the sediment rather than through broadcast spawning. However, fossil embryos remain very rare and the main controlling factor on their fossilization may be the unique conspiracy of environmental conditions at a couple of sites. The preponderance of fossilized embryos of direct developers should not be used in evidence against the existence of indirect development at this time in animal evolutionary history.

Scanning electron microscopy and synchrotron radiation x-ray tomographic microscopy of 330 million year old charcoalified seed fern fertile organs.

Abundant charcoalified seed fern (pteridosperm) pollen organs and ovules have been recovered from Late Viséan (Mississippian 330 Ma) limestones from Kingswood, Fife, Scotland. To overcome limitations of data collection from these tiny, sometimes unique, fossils, we have combined low vacuum scanning electron microscopy on uncoated specimens with backscatter detector and synchrotron radiation X-ray tomographic microscopy utilizing the Materials Science and TOMCAT beamlines at the Swiss Light Source of the Paul Scherrer Institut. In combination these techniques improve upon traditional cellulose acetate peel sectioning because they enable study of external morphology and internal anatomy in multiple planes of section on a single specimen that is retained intact. The pollen organ Melissiotheca shows a basal parenchymatous cushion bearing more than 100 sporangia on the distal face. Digital sections show the occurrence of pollen in some sporangia. The described ovule is new and has eight integumentary lobes that are covered in spirally arranged glandular hairs. Virtual longitudinal sections reveal the lobes are free above the pollen chamber. Results are applied in taxonomy and will subsequently contribute to our understanding of the former diversity and evolution of ovules, seeds, and pollen organs in the seed ferns, the first seed-bearing plants to conquer the land.

The earliest fossil embryos begin to mature

The Ediacaran Doushantuo Formation of South China is perhaps the most remarkable of all sites of exceptional fossilization. Fossils interpreted as animal embryos, which are otherwise vanishingly rare in the fossil record, are so abundant that in some layers they are the main constituent of the rock. The Doushantuo is of Precambrian age and the putative embryos predate the 542 million-year-old base of the Cambrian by as much as 40 million years. Indeed, these fossils constitute the oldest widely accepted record of animals. Viewed as embryos, the fossils provide a tantalizingly direct insight into development during the dawn of animal evolution. They provide a basis for addressing some of the classical questions in comparative embryology, such as the relative primitiveness of cleavage patterns, blastomere packing arrangements, and mechanisms of gastrulation. Peculiarly, however, only the very earliest cleavage stages have so far been recovered, leading to the suggestion that later stages were not preserved (Raff et al. 2006), or that the fossils are not embryos at all (Xue et al. 1999; Bailey et al. 2007). A radical recent proposal is that they represent giant sulfur-oxidizing bacteria occurring in clusters formed from reductive binary division of progenitors (Bailey et al. 2007). While this thesis explains some of the inadequacies of the animal embryo interpretation, it suffers from others (Donoghue 2007). A recent paper by Xiao et al. (2007) adds another twist (literally) to the story. Xiao and colleagues describe what appear to be late embryonic stages of Doushantuo embryos. These are comparable in size and in structure of the enveloping membrane to the putative fossil blastula/bacterium Megasphaera ornata, but in addition the outer membrane has a superficial helical groove, or else a tunnel with radiating canals running through its wall. Inside the membrane there are no blastomeres, but a large body with corresponding helically coiled invagination. If there really is a connection to the alleged cleavage-stage embryos, these fossils preclude a bacterial interpretation of the latter, but they are not much more help in terms of resolving affinity. Xiao and colleagues speculate that the helical fossils represent embryological stages of the stem-cnidarian Sinocyclocyclicus guizhouensis found in the same deposit, or that they represent larvae whose cilia were located in the radial canals of the helical tunnel. But in fact, they could be anythingFalthough they look like nothing seen before (Fig. 1).

The application of contrast media for in vivo feature enhancement in X-ray Computed Tomography of soil-grown plant roots

The use of in vivo X-ray microcomputed tomography (μCT) to study plant root systems has become routine, but is often hampered by poor contrast between roots, soil, soil water, and soil organic matter. In clinical radiology, imaging of poorly contrasting regions is frequently aided by the use of radio-opaque contrast media. In this study, we present evidence for the utility of iodinated contrast media (ICM) in the study of plant root systems using μCT. Different dilutions of an ionic and nonionic ICM (Gastrografin 370 and Niopam 300) were perfused into the aerial vasculature of juvenile pea plants via a leaf flap (Pisum sativum). The root systems were imaged via μCT, and a variety of image-processing approaches used to quantify and compare the magnitude of the contrast enhancement between different regions. Though the treatment did not appear to significantly aid extraction of full root system architectures from the surrounding soil, it did allow the xylem and phloem units of seminal roots and the vascular morphology within rhizobial nodules to be clearly visualized. The nonionic, low-osmolality contrast agent Niopam appeared to be well tolerated by the plant, whereas Gastrografin showed evidence of toxicity. In summary, the use of iodine-based contrast media allows usually poorly contrasting root structures to be visualized nondestructively using X-ray μCT. In particular, the vascular structures of roots and rhizobial nodules can be clearly visualized in situ.

Running a Question-and-Answer Website for Science Education: First-Hand Experiences

The online learning and outreach resource Ask A Biologist (AAB; http://www.askabiologist.org.uk/) has been operating for three years, and this paper reports our initial experience of running the site. To date, AAB has answered and archived online over 3,500 questions from the general public with contributions from more than 50 researchers, and attracted an estimated audience of half a million, all with relatively minimal investment. Simply, questions are posted by visitors to the site, and one or more of our registered academic experts then provide their answers which are available for all to see and browse. The system is simple and provides direct contact between the public and scientists on subjects that are guaranteed to be of interest. In this paper, we review the benefits and drawbacks of such a system based on our first-hand experiences, detailing how the site was originally conceived and built and how it operates. We offer this as a model for future projects and to highlight both the benefits and pitfalls of such a system.