James D. Schiffbauer

Effects of Immersion on Visual Analysis of Volume Data

In our research agenda to study the effects of immersion (level of fidelity) on various tasks in virtual reality (VR) systems, we have found that the most generalizable findings come not from direct comparisons of different technologies, but from controlled simulations of those technologies. We call this the mixed reality (MR) simulation approach. However, the validity of MR simulation, especially when different simulator platforms are used, can be questioned. In this paper, we report the results of an experiment examining the effects of field of regard (FOR) and head tracking on the analysis of volume visualized micro-CT datasets, and compare them with those from a previous study. The original study used a CAVE-like display as the MR simulator platform, while the present study used a high-end head-mounted display (HMD). Out of the 24 combinations of system characteristics and tasks tested on the two platforms, we found that the results produced by the two different MR simulators were similar in 20 cases. However, only one of the significant effects found in the original experiment for quantitative tasks was reproduced in the present study. Our observations provide evidence both for and against the validity of MR simulation, and give insight into the differences caused by different MR simulator platforms. The present experiment also examined new conditions not present in the original study, and produced new significant results, which confirm and extend previous existing knowledge on the effects of FOR and head tracking. We provide design guidelines for choosing display systems that can improve the effectiveness of volume visualization applications.

Novel application of focused ion beam electron microscopy (FIB-EM) in preparation and analysis of microfossil ultrastructures: A new view of complexity in early eukaryotic organisms

Abstract Coupled dual-beam focused ion beam electron microscopy (FIB-EM) has gained popularity across multiple disciplines over the past decade. Widely utilized as a stand-alone instrument for micromachining and metal or insulator deposition in numerous industries, the submicron-scale ion milling and cutting capabilities of FIB-EM systems have been well documented in the materials science literature. These capacities make FIB-EM a powerful tool for in situ, site-specific transmission electron microscopy (TEM) ultrathin foil preparation. Recent advancements in the field-emission guns (FEGs) of FIB-EM systems have provided spatial resolution comparable to that of many high-end scanning electron microscopes (SEM), thus providing enhanced imaging capacities with material deposition and material removal capabilities. More recently, FIB-EM preparation techniques have been applied to geological samples to characterize mineral inclusions, grain boundaries, and microfossils. Here, we demonstrate a novel method for analyzing three-dimensional (3-D) ultrastructures of microfossils using FIB-EM. Our method, FIB-EM nanotomography, consists of sequential ion milling, or cross sectioning, and concurrent SEM imaging. This technique with coupled dual-beam systems allows for real-time, 3-D ultrastructural analysis and compositional mapping with precise site selectivity and may provide new insights in fossil ultrastructures. Using the FIB-EM nanotomography method, we investigated herkomorphic and acanthomorphic acritarchs (organic-walled microfossils) extracted from the ≥999 Ma Mesoproterozoic Ruyang Group of North China. The 3-D characteristics of such important but controversial acritarch features as processes and vesicularly enclosed central bodies are described. Through these case studies, we demonstrate that FIB-EM nanotomography is a powerful and useful tool for investigating the three-dimensionality of microfossil ultra- and nanostructures.

A unifying model for Neoproterozoic–Palaeozoic exceptional fossil preservation through pyritization and carbonaceous compression

Soft-tissue fossils capture exquisite biological detail and provide our clearest views onto the rise of animals across the Ediacaran-Cambrian transition. The processes contributing to fossilization of soft tissues, however, have long been a subject of debate. The Ediacaran Gaojiashan biota displays soft-tissue preservational styles ranging from pervasive pyritization to carbonaceous compression, and thus provides an excellent opportunity to dissect the relationships between these taphonomic pathways. Here geochemical analyses of the Gaojiashan fossil Conotubus hemiannulatus show that pyrite precipitation was fuelled by the degradation of labile tissues through bacterial sulfate reduction (BSR). Pyritization initiated with nucleation on recalcitrant tube walls, proceeded centripetally, decelerated with exhaustion of labile tissues and possibly continued beneath the BSR zone. We propose that pyritization and kerogenization are regulated principally by placement and duration of the decaying organism in different microbial zones of the sediment column, which hinge on post-burial sedimentation rate and/or microbial zone thickness.

BIOSTRATINOMY OF THE LATE EDIACARAN PYRITIZED GAOJIASHAN LAGERSTÄTTE FROM SOUTHERN SHAANXI, SOUTH CHINA: IMPORTANCE OF EVENT DEPOSITS

Abstract The upper Ediacaran Gaojiashan Lagerstätte (551–541 Ma) in southern Shaanxi Province, South China, hosts a variety of soft-bodied or lightly biomineralized tubular fossils (Shaanxilithes, Conotubus, Gaojiashania, Sinotubulites, and Cloudina) and calcareous microfossils (Protolagena). This study focuses on the fossiliferous middle Gaojiashan Member at the Gaojiashan section, where pyritization of soft-bodied or lightly skeletonized tubular fossils is the primary mode of preservation. Integrated paleoecological, sedimentological, and taphonomic analysis shows that event deposition played an important role in the biostratinomy of the Gaojiashan Lagerstätte. Gaojiashan fossils, particularly pyritized fossils, preferentially occur in mm-thick, normally graded calcisiltite-siltstone layers, interpreted as distal event deposits, but are rarely present in calcilutite-mudstone beds. Two taphofacies are recognized in the middle Gaojiashan calcisiltites-siltstones, on the basis of biostratinomic data (e.g., fossil fragmentation and disarticulation). Both taphofacies contain fossils (Conotubus, Gaojiashania, and Protolagena) that were buried in situ by distal event deposits below the average storm wave base; evidence for in situ burial includes oblique orientation, rejuvenation, growth interruption, and reorientation. This research represents one of the few biostratinomic studies of Precambrian Lagerstätten. Results show that the Gaojiashan Lagerstätte, like many Phanerozoic Konservat-Lagerstätten, was influenced strongly by event deposition that provides an obrution mechanism for quick burial. Although some taphonomic processes—those responsible for Ediacara-type and Burgess Shale-type preservation—may be restricted to certain geological time intervals, others such as sedimentary obrution and rapid burial may have been continuously and universally important in exceptional preservation throughout geologic history.

The origin of intracellular structures in Ediacaran metazoan embryos

Animal embryo-like fossils from the Ediacaran Doushantuo Formation, South China, have been interpreted as the earliest metazoan fossils, significantly predating the radiation of biomineralizing animals and macroscopic bilaterians during the Ediacaran–Cambrian transition. The exceptional cellular and intracellular preservation of the Doushantuo fossils can provide tantalizing glimpses into the organellic structures of these multicellular eukaryotes. The organelle-like features are distinguishable in light, electron, and X-ray imaging, a distinction that has been assumed to be a result of compositional variation. Combined electron microscopic and X-ray tomographic analyses, however, reveal that crystalline textural variation may also contribute to the visibility of these intracellular structures. Specifically, cell lumina and lipid vesicle-like (or yolk granule-like) structures are preserved as nanometer-sized, randomly oriented apatite crystals, whereas cell boundaries and nucleus-like structures are preserved as botryoidal aggregates of micrometer-sized apatite crystals. These textural differences render contrast in electron and X-ray imaging, and they also indicate two mineralization stages, with the botryoidal aggregates at the cell boundaries and nucleus-like structures representing late-stage overgrowth or void-filling cementation. These findings suggest that, while the Doushantuo intracellular structures may occupy the same topological position as strongly degraded nuclei and vesicles, they do not represent organelles with intact enclosing membranes. Instead, the membrane-like structures that characterize the nucleus-like structures are mostly late-stage cements, critically undermining recent hypotheses about the nature of nuclear division and the non-animal holozoan affinity of the Doushantuo fossils, which assume a biological origin of such membrane-like structures.

Taphonomic study of Ediacaran organic-walled fossils confirms the importance of clay minerals and pyrite in Burgess Shale−type preservation

Burgess Shale−type (BST) macrofossils and organic-walled microfossils are preserved as carbonaceous compressions and may share similar taphonomic processes. Previous taphonomic investigations of carbonaceous compressions have primarily focused on the microchemistry of Cambrian BST fossils, but comparative data from organic-walled microfossils were not available. To address these issues, we analyzed two organic-walled taxa from the Yangtze Gorges area of the South China block, Chuaria (an acritarch) and Vendotaenia (a ribbon-shaped fossil). Their abundance offers the opportunity for destructive microanalysis, including petrography, electron microscopy, and elemental mapping on both bedding planes and in cross sections. Our data suggest that Chuaria preservation is remarkably similar to BST fossils in that its vesicle walls are closely associated with clay minerals. In addition, like many BST macrofossils, Chuaria and Vendotaenia are also closely associated with pyrite; Chuaria vesicles are often filled with framboidal pyrite, and Vendotaenia fossils are associated with sulfate, partly derived from pyrite oxidation. The comparative taphonomy of Chuaria and Vendotaenia and BST macrofossils indicates that the preservation of organic-walled acritarchs may be aided by clay and pyrite mineralization, and that these abundant microfossils may serve as proxies for uncovering in more detail the taphonomic histories of BST preservation.

Taphonomy of the Upper Ediacaran Enigmatic Ribbonlike Fossil Shaanxilithes

Abstract Shaanxilithes ningqiangensis is an enigmatic ribbon-shaped fossil from the upper Ediacaran Gaojiashan Member of the Dengying Formation, southern Shaanxi Province, South China. This taxon has also been reported from Ediacaran successions in North China and possibly in Siberia, making it a potential index fossil for interregional biostratigraphic correlation of upper Ediacaran successions. At Gaojiashan, Shaanxilithes ningqiangensis is often preserved along bedding planes of phosphate-rich silty and calcareous shale, with no evidence of vertical intrusion into adjacent beds and containing little to no carbonaceous material. Here, through detailed microstructural and microchemical investigation using a combination of analytical techniques, taphonomic details of Shaanxilithes ningqiangensis and potentially related forms are revealed, showing that these enigmatic fossils are preserved as clay molds. Together with other taphonomic features, such as abruptly bent ribbons, overlapping but not crosscutting ribbons, and co-occurring discoidal structures interpreted as disarticulated sections of the original organism, the new data suggest that Shaanxilithes ningqiangensis is a body fossil consisting of serially arranged units that are discoidal, lensoidal, or crescentic in shape. Shaanxilithes ningqiangensis is not a trace fossil as some previous researchers have suggested.

Experimental Formation of a Microbial Death Mask

Abstract This study represents a first attempt to observe soft-tissue decay in association with microbial mats, in order to recreate the death-mask model proposed for terminal Neoproterozoic Lagerstätten. This model explains the precipitation of authigenic iron sulfide minerals on, and around, decaying carcasses in association with microbial mats, cementing the sediment as a sole veneer and retaining the external morphology of the organism in relief on the upper and lower surface of coarse-grained sandy event beds. Although this model has been substantiated by the discovery of abundant microbially induced sedimentary structures (MISS) and pyrite veneers in close association with Ediacaran fossils, it has not been tested previously by experimental taphonomic studies under controlled laboratory conditions. Arthropod larvae that decayed on top of a cyanobacterial mat demonstrated higher quality preservation of fine-scale anatomy than larvae that decayed in the absence of a mat. Decay experiments involving bacterial mats and organic-rich sands generated a black ring extending radially from the decaying carcasses. When this precipitate was analyzed using XPS and ESEM-EDS it revealed the presence of likely iron sulfides, or at least spatially associated Fe and S, and localized concentrations of common aluminosilicate elements (Al, K, Fe, and Mg), which is a composition that has been documented in association with Ediacaran fossil preservation.

The nature and origin of nucleus‐like intracellular inclusions in Paleoproterozoic eukaryote microfossils

The well-known debate on the nature and origin of intracellular inclusions (ICIs) in silicified microfossils from the early Neoproterozoic Bitter Springs Formation has recently been revived by reports of possible fossilized nuclei in phosphatized animal embryo-like fossils from the Ediacaran Doushantuo Formation of South China. The revisitation of this discussion prompted a critical and comprehensive investigation of ICIs in some of the oldest indisputable eukaryote microfossils-the ornamented acritarchs Dictyosphaera delicata and Shuiyousphaeridium macroreticulatum from the Paleoproterozoic Ruyang Group of North China-using a suite of characterization approaches: scanning electron microscopy (SEM), transmission electron microscopy (TEM), and focused ion beam scanning electron microscopy (FIB-SEM). Although the Ruyang acritarchs must have had nuclei when alive, our data suggest that their ICIs represent neither fossilized nuclei nor taphonomically condensed cytoplasm. We instead propose that these ICIs likely represent biologically contracted and consolidated eukaryotic protoplasts (the combination of the nucleus, surrounding cytoplasm, and plasma membrane). As opposed to degradational contraction of prokaryotic cells within a mucoidal sheath-a model proposed to explain the Bitter Springs ICIs-our model implies that protoplast condensation in the Ruyang acritarchs was an in vivo biologically programmed response to adverse conditions in preparation for encystment. While the discovery of bona fide nuclei in Paleoproterozoic acritarchs would be a substantial landmark in our understanding of eukaryote evolution, the various processes (such as degradational and biological condensation of protoplasts) capable of producing nuclei-mimicking structures require that interpretation of ICIs as fossilized nuclei be based on comprehensive investigations.

Comment on "Fossilized Nuclei and Germination Structures Identify Ediacaran 'Animal Embryos' as Encysting Protists"

On the basis of putative nuclei and endospores, Huldtgren et al. (Reports, 23 December 2011, p. 1696) propose that embryo-like Doushantuo microfossils are nonmetazoan holozoans akin to mesomycetozoeans. However, both size and preservation preclude interpretation of internal structures as nuclei. Moreover, the authors may have conflated two different populations; some specimens display a pseudoparenchymatous organization incompatible with a mesomycetozoean comparison.