@misc{ayala_schroeter_schweitzer_2024, title={Porphyrin-Based Molecules in the Fossil Record Shed Light on the Evolution of Life}, volume={14}, ISSN={["2075-163X"]}, url={https://www.mdpi.com/2075-163X/14/2/201}, DOI={10.3390/min14020201}, abstractNote={The fossil record demonstrates the preservation of porphyrins (e.g., heme) in organic sediments and the fossilized remains of animals. These molecules are essential components in modern metabolic processes, such as electron transport (cytochromes) and oxygen transport (hemoglobin), and likely originated before the emergence of life. The integration and adaptation of porphyrins and structurally similar molecules (e.g., chlorophylls) are key aspects in the evolution of energy production (i.e., aerobic respiration and photosynthesis) and complex life (i.e., eukaryotes and multicellularity). Here, we discuss the evolution and functional diversity of heme-bound hemoglobin proteins in vertebrates, along with the preservation of these molecules in the fossil record. By elucidating the pivotal role of these molecules in the evolution of life, this review lays the groundwork necessary to explore hemoglobin as a means to investigate the paleobiology of extinct taxa, including non-avian dinosaurs.}, number={2}, journal={MINERALS}, author={Ayala, Juan D. and Schroeter, Elena R. and Schweitzer, Mary H.}, year={2024}, month={Feb} }
 @article{ullmann_schweitzer_2023, title={A STATISTICAL META-ANALYSIS OF LITHOLOGIC AND OTHER POTENTIAL CONTROLS ON FOSSIL BONE CELLULAR AND SOFT TISSUE PRESERVATION}, volume={38}, ISSN={["1938-5323"]}, DOI={10.2110/palo.2022.026}, abstractNote={ABSTRACT
               Demineralization assays, utilizing weak acids to isolate organics from biomineralized tissues, have recently been applied with increasing frequency to explore soft tissue preservation in fossils, revealing frequent retention of cells and other pliable microstructures in fossil bones. However, factors controlling long-term preservation of such labile structures remain mysterious. To address this, we compiled a database of bone demineralization results from 29 studies, then conducted a statistical meta-analysis of these data to evaluate the importance of specimen age, taxonomy, entombing lithology, and bone tissue type on microstructure recovery. Our database encompasses results from 137 bones from 44 formations spanning the Permian to the Holocene. Osteocytes, blood vessels, and fibrous/proteinaceous matrix each exhibit bimodal recovery patterns in which most fossil bones either yield many or none of these microstructures. Though their relative abundances in any given fossil bone are extremely variable, statistically significant Fisher's Exact tests found that if a bone yields one of these types of microstructures in abundance then the others are usually also abundant. None of the variables examined significantly influence osteocyte recovery, but Kruskal-Wallis and subsequent pairwise Mann-Whitney tests revealed that bones collected from unconsolidated sediments, of Paleocene age, and/or deriving from birds, amphibians, marine reptiles, or crocodylians often yield few or no vessels and fibrous matrix. Although these findings hint at possible controls on cellular and soft tissue preservation in fossil bones, they should be viewed cautiously as they are demonstrably biased by uneven sampling. For example, many of the apparent trends are substantially controlled by overrepresentation of data from nonavian dinosaur specimens from Cretaceous fluvio-lacustrine deposits. Future demineralization assays should therefore focus on non-mammalian specimens from the Cenozoic and Jurassic-and-older nondinosaurian specimens, especially those preserved in less-common depositional environments (e.g., eolian settings).}, number={5}, journal={PALAIOS}, author={Ullmann, Paul V. and Schweitzer, Mary H.}, year={2023}, month={May}, pages={246–257} }
 @article{anne_canoville_edwards_schweitzer_zanno_2023, title={Independent Evidence for the Preservation of Endogenous Bone Biochemistry in a Specimen of Tyrannosaurus rex}, volume={12}, ISSN={["2079-7737"]}, DOI={10.3390/biology12020264}, abstractNote={Biomolecules preserved in deep time have potential to shed light on major evolutionary questions, driving the search for new and more rigorous methods to detect them. Despite the increasing body of evidence from a wide variety of new, high resolution/high sensitivity analytical techniques, this research is commonly met with skepticism, as the long standing dogma persists that such preservation in very deep time (>1 Ma) is unlikely. The Late Cretaceous dinosaur Tyrannosaurus rex (MOR 1125) has been shown, through multiple biochemical studies, to preserve original bone chemistry. Here, we provide additional, independent support that deep time bimolecular preservation is possible. We use synchrotron X-ray fluorescence imaging (XRF) and X-ray absorption spectroscopy (XAS) to investigate a section from the femur of this dinosaur, and demonstrate preservation of elements (S, Ca, and Zn) associated with bone remodeling and redeposition. We then compare these data to the bone of an extant dinosaur (bird), as well as a second non-avian dinosaur, Tenontosaurus tilletti (OMNH 34784) that did not preserve any sign of original biochemistry. Our data indicate that MOR 1125 bone cortices have similar bone elemental distributions to that of an extant bird, which supports preservation of original endogenous chemistry in this specimen.}, number={2}, journal={BIOLOGY-BASEL}, author={Anne, Jennifer and Canoville, Aurore and Edwards, Nicholas P. and Schweitzer, Mary H. and Zanno, Lindsay E.}, year={2023}, month={Feb} }
 @article{schweitzer_2023, title={Paleontology in the 21st Century}, volume={12}, ISSN={["2079-7737"]}, url={https://www.mdpi.com/2079-7737/12/3/487}, DOI={10.3390/biology12030487}, abstractNote={For much of its 300+ year history, “modern” paleontology has been a descriptive science, firmly housed within geological sciences [...]}, number={3}, journal={BIOLOGY-BASEL}, author={Schweitzer, Mary H.}, year={2023}, month={Mar} }
 @article{garza_madsen_sjoevall_osbaeck_zheng_jarenmark_schweitzer_engdahl_uvdal_eriksson_et al._2022, title={An ancestral hard-shelled sea turtle with a mosaic of soft skin and scutes}, volume={12}, ISSN={["2045-2322"]}, DOI={10.1038/s41598-022-26941-1}, abstractNote={AbstractThe transition from terrestrial to marine environments by secondarily aquatic tetrapods necessitates a suite of adaptive changes associated with life in the sea, e.g., the scaleless skin in adult individuals of the extant leatherback turtle. A partial, yet exceptionally preserved hard-shelled (Pan-Cheloniidae) sea turtle with extensive soft-tissue remains, including epidermal scutes and a virtually complete flipper outline, was recently recovered from the Eocene Fur Formation of Denmark. Examination of the fossilized limb tissue revealed an originally soft, wrinkly skin devoid of scales, together with organic residues that contain remnant eumelanin pigment and inferred epidermal transformation products. Notably, this stem cheloniid—unlike its scaly living descendants—combined scaleless limbs with a bony carapace covered in scutes. Our findings show that the adaptive transition to neritic waters by the ancestral pan-chelonioids was more complex than hitherto appreciated, and included at least one evolutionary lineage with a mosaic of integumental features not seen in any living turtle.}, number={1}, journal={SCIENTIFIC REPORTS}, author={Garza, Randolph Glenn and Madsen, Henrik and Sjoevall, Peter and Osbaeck, Frank and Zheng, Wenxia and Jarenmark, Martin and Schweitzer, Mary H. and Engdahl, Anders and Uvdal, Per and Eriksson, Mats E. and et al.}, year={2022}, month={Dec} }
 @article{schweitzer_zheng_equall_2022, title={Environmental Factors Affecting Feather Taphonomy}, volume={11}, ISSN={["2079-7737"]}, DOI={10.3390/biology11050703}, abstractNote={The exceptional preservation of feathers in the fossil record has led to a better understanding of both phylogeny and evolution. Here we address factors that may have contributed to the preservation of feathers in ancient organisms using experimental taphonomy. We show that the atmospheres of the Mesozoic, known to be elevated in both CO2 and with temperatures above present levels, may have contributed to the preservation of these soft tissues by facilitating rapid precipitation of hydroxy- or carbonate hydroxyapatite, thus outpacing natural degradative processes. Data also support that that microbial degradation was enhanced in elevated CO2, but mineral deposition was also enhanced, contributing to preservation by stabilizing the organic components of feathers.}, number={5}, journal={BIOLOGY-BASEL}, author={Schweitzer, Mary Higby and Zheng, Wenxia and Equall, Nancy}, year={2022}, month={May} }
 @article{schroeter_ullmann_macauley_ash_zheng_schweitzer_lacovara_2022, title={Soft-Tissue, Rare Earth Element, and Molecular Analyses of Dreadnoughtus schrani, an Exceptionally Complete Titanosaur from Argentina}, volume={11}, ISSN={["2079-7737"]}, DOI={10.3390/biology11081158}, abstractNote={Evidence that organic material preserves in deep time (>1 Ma) has been reported using a wide variety of analytical techniques. However, the comprehensive geochemical data that could aid in building robust hypotheses for how soft-tissues persist over millions of years are lacking from most paleomolecular reports. Here, we analyze the molecular preservation and taphonomic history of the Dreadnougtus schrani holotype (MPM-PV 1156) at both macroscopic and microscopic levels. We review the stratigraphy, depositional setting, and physical taphonomy of the D. schrani skeletal assemblage, and extensively characterize the preservation and taphonomic history of the humerus at a micro-scale via: (1) histological analysis (structural integrity) and X-ray diffraction (exogenous mineral content); (2) laser ablation-inductively coupled plasma mass spectrometry (analyses of rare earth element content throughout cortex); (3) demineralization and optical microscopy (soft-tissue microstructures); (4) in situ and in-solution immunological assays (presence of endogenous protein). Our data show the D. schrani holotype preserves soft-tissue microstructures and remnants of endogenous bone protein. Further, it was exposed to LREE-enriched groundwaters and weakly-oxidizing conditions after burial, but experienced negligible further chemical alteration after early-diagenetic fossilization. These findings support previous hypotheses that fossils that display low trace element uptake are favorable targets for paleomolecular analyses.}, number={8}, journal={BIOLOGY-BASEL}, author={Schroeter, Elena R. and Ullmann, Paul V and Macauley, Kyle and Ash, Richard D. and Zheng, Wenxia and Schweitzer, Mary H. and Lacovara, Kenneth J.}, year={2022}, month={Aug} }
 @article{schroeter_cleland_schweitzer_2021, title={Deep Time Paleoproteomics: Looking Forward}, volume={12}, ISSN={["1535-3907"]}, DOI={10.1021/acs.jproteome.1c00755}, abstractNote={The goal of paleoproteomics is to characterize proteins from specimens that have been subjected to the degrading and obscuring effects of time, thus obtaining biological information about tissues or organisms both unobservable in the present and unobtainable through morphological study. Although the description of sequences from Tyrannosaurus rex and Brachylophosaurus canadensis suggested that proteins may persist over tens of millions of years, the majority of paleoproteomic analyses have focused on historical, archeological, or relatively young paleontological samples that rarely exceed 1 million years in age. However, recent advances in methodology and analyses of diverse tissues types (e.g., fossil eggshell, dental enamel) have begun closing the large window of time that remains unexplored in the fossil history of the Cenozoic. In this perspective, we discuss the history and current state of deep time paleoproteomics (DTPp), here defined as paleoproteomic study of samples ∼1 million years (1 Ma) or more in age. We then discuss the future of DTPp research, including what we see as critical ways the field can expand, advancements in technology that can be utilized, and the types of questions DTPp can address if such a future is realized.}, journal={JOURNAL OF PROTEOME RESEARCH}, author={Schroeter, Elena R. and Cleland, Timothy P. and Schweitzer, Mary H.}, year={2021}, month={Dec} }
 @book{schweitzer_schroeter_czajka_2020, title={Dinosaurs}, ISBN={9780429466717}, url={http://dx.doi.org/10.1201/9780429466717}, DOI={10.1201/9780429466717}, abstractNote={This textbook introduces research on dinosaurs by describing the science behind how we know what we know about dinosaurs. A wide range of topics is covered, from fossils and taphonomy to dinosaur physiology, evolution, and extinction. In addition, sedimentology, paleo-tectonics, and non-dinosaurian Mesozoic life are discussed. There is a special opportunity to capitalize on the enthusiasm for dinosaurs that students bring to classrooms to foster a deeper engagement in all sciences. Students are encouraged to synthesize information, employ critical thinking, construct hypotheses, devise methods to test these hypotheses, and come to new defensible conclusions, just as paleontologists do. Key Features Clear and easy to read dinosaur text with well-defined terminology Over 600 images and diagrams to illustrate concepts and aid learning Reading objectives for each chapter section to guide conceptual learning and encourage active reading Companion website (teachingdinosaurs.com) that includes supporting materials such as in-class activities, question banks, lists of suggested specimens, and more to encourage student participation and active learning Ending each chapter with a specific "What We Don't Know" section to encourage student curiosity Related Titles Singer, R. Encyclopedia of Paleontology (ISBN 978-1-884964-96-1) Fiorillo, A. R. Alaska Dinosaurs: An Ancient Arctic World (ISBN 978-1-138-06087-6) Caldwell, M. W. The Origin of Snakes: Morphology and the Fossil Record (ISBN 978-1-4822-5134-0)}, publisher={CRC Press}, author={Schweitzer, Mary Higby and Schroeter, Elena Rita and Czajka, Charles Doug}, year={2020}, month={Nov} }
 @article{canoville_schweitzer_zanno_2020, title={Identifying medullary bone in extinct avemetatarsalians: challenges, implications and perspectives}, volume={375}, ISSN={["1471-2970"]}, DOI={10.1098/rstb.2019.0133}, abstractNote={Medullary bone (MB) is a sex-specific tissue produced by female birds during the laying cycle, and it is hypothesized to have arisen within Avemetatarsalia, possibly outside Avialae. Over the years, researchers have attempted to define a set of criteria from which to evaluate the nature of purported MB-like tissues recovered from fossil specimens. However, we argue that the prevalence, microstructural and chemical variability of MB in Neornithes is, as of yet, incompletely known and thus current diagnoses of MB do not capture the extent of variability that exists in modern birds. Based on recently published data and our own observations of MB distribution and structure using computed tomography and histochemistry, we attempt to advance the discourse on identifying MB in fossil specimens. We propose: (i) new insights into the phylogenetic breadth and structural diversity of MB within extant birds; (ii) a reevaluation and refinement of the most recently published list of criteria suggested for confidently identifying MB in the fossil record; (iii) reconsideration of some prior identifications of MB-like tissues in fossil specimens by taking into account the newly acquired data; and (iv) discussions on the challenges of characterizing MB in Neornithes with the goal of improving its diagnosis in extinct avemetatarsalians.This article is part of the theme issue ‘Vertebrate palaeophysiology’.}, number={1793}, journal={PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES}, author={Canoville, Aurore and Schweitzer, Mary H. and Zanno, Lindsay}, year={2020}, month={Mar} }
 @article{ullmann_voegele_grandstaff_ash_zheng_schroeter_schweitzer_lacovara_2020, title={Molecular tests support the viability of rare earth elements as proxies for fossil biomolecule preservation}, volume={10}, ISSN={["2045-2322"]}, DOI={10.1038/s41598-020-72648-6}, abstractNote={AbstractThe rare earth element (REE) composition of a fossil bone reflects its chemical alteration during diagenesis. Consequently, fossils presenting low REE concentrations and/or REE profiles indicative of simple diffusion, signifying minimal alteration, have been proposed as ideal candidates for paleomolecular investigation. We directly tested this prediction by conducting multiple biomolecular assays on a well-preserved fibula of the dinosaur Edmontosaurus from the Cretaceous Hell Creek Formation previously found to exhibit low REE concentrations and steeply-declining REE profiles. Gel electrophoresis identified the presence of organic material in this specimen, and subsequent immunofluorescence and enzyme-linked immunosorbant assays identified preservation of epitopes of the structural protein collagen I. Our results thereby support the utility of REE profiles as proxies for soft tissue and biomolecular preservation in fossil bones. Based on considerations of trace element taphonomy, we also draw predictions as to the biomolecular recovery potential of additional REE profile types exhibited by fossil bones.}, number={1}, journal={SCIENTIFIC REPORTS}, author={Ullmann, Paul V. and Voegele, Kristyn K. and Grandstaff, David E. and Ash, Richard D. and Zheng, Wenxia and Schroeter, Elena R. and Schweitzer, Mary H. and Lacovara, Kenneth J.}, year={2020}, month={Sep} }
 @article{bailleul_o’connor_schweitzer_2019, title={Dinosaur paleohistology: review, trends and new avenues of investigation}, volume={7}, ISSN={2167-8359}, url={http://dx.doi.org/10.7717/peerj.7764}, DOI={10.7717/peerj.7764}, abstractNote={In the mid-19th century, the discovery that bone microstructure in fossils could be preserved with fidelity provided a new avenue for understanding the evolution, function, and physiology of long extinct organisms. This resulted in the establishment of paleohistology as a subdiscipline of vertebrate paleontology, which has contributed greatly to our current understanding of dinosaurs as living organisms. Dinosaurs are part of a larger group of reptiles, the Archosauria, of which there are only two surviving lineages, crocodilians and birds. The goal of this review is to document progress in the field of archosaur paleohistology, focusing in particular on the Dinosauria. We briefly review the “growth age” of dinosaur histology, which has encompassed new and varied directions since its emergence in the 1950s, resulting in a shift in the scientific perception of non-avian dinosaurs from “sluggish” reptiles to fast-growing animals with relatively high metabolic rates. However, fundamental changes in growth occurred within the sister clade Aves, and we discuss this major evolutionary transition as elucidated by histology. We then review recent innovations in the field, demonstrating how paleohistology has changed and expanded to address a diversity of non-growth related questions. For example, dinosaur skull histology has elucidated the formation of curious cranial tissues (e.g., “metaplastic” tissues), and helped to clarify the evolution and function of oral adaptations, such as the dental batteries of duck-billed dinosaurs. Lastly, we discuss the development of novel techniques with which to investigate not only the skeletal tissues of dinosaurs, but also less-studied soft-tissues, through molecular paleontology and paleohistochemistry—recently developed branches of paleohistology—and the future potential of these methods to further explore fossilized tissues. We suggest that the combination of histological and molecular methods holds great potential for examining the preserved tissues of dinosaurs, basal birds, and their extant relatives. This review demonstrates the importance of traditional bone paleohistology, but also highlights the need for innovation and new analytical directions to improve and broaden the utility of paleohistology, in the pursuit of more diverse, highly specific, and sensitive methods with which to further investigate important paleontological questions.}, journal={PeerJ}, publisher={PeerJ}, author={Bailleul, Alida M. and O’Connor, Jingmai and Schweitzer, Mary H.}, year={2019}, month={Sep}, pages={e7764} }
 @article{bailleul_zheng_horner_hall_holliday_schweitzer_2020, title={Evidence of proteins, chromosomes and chemical markers of DNA in exceptionally preserved dinosaur cartilage}, volume={7}, ISSN={["2053-714X"]}, DOI={10.1093/nsr/nwz206}, abstractNote={Abstract
               A histological ground-section from a duck-billed dinosaur nestling (Hypacrosaurus stebingeri) revealed microstructures morphologically consistent with nuclei and chromosomes in cells within calcified cartilage. We hypothesized that this exceptional cellular preservation extended to the molecular level and had molecular features in common with extant avian cartilage. Histochemical and immunological evidence supports in situ preservation of extracellular matrix components found in extant cartilage, including glycosaminoglycans and collagen type II. Furthermore, isolated Hypacrosaurus chondrocytes react positively with two DNA intercalating stains. Specific DNA staining is only observed inside the isolated cells, suggesting endogenous nuclear material survived fossilization. Our data support the hypothesis that calcified cartilage is preserved at the molecular level in this Mesozoic material, and suggest that remnants of once-living chondrocytes, including their DNA, may preserve for millions of years.}, number={4}, journal={NATIONAL SCIENCE REVIEW}, author={Bailleul, Alida M. and Zheng, Wenxia and Horner, John R. and Hall, Brian K. and Holliday, Casey M. and Schweitzer, Mary H.}, year={2020}, month={Apr}, pages={815–822} }
 @article{boatman_goodwin_holman_fakra_zheng_gronsky_schweitzer_2019, title={Mechanisms of soft tissue and protein preservation in Tyrannosaurus rex}, volume={9}, ISSN={["2045-2322"]}, DOI={10.1038/s41598-019-51680-1}, abstractNote={AbstractThe idea that original soft tissue structures and the native structural proteins comprising them can persist across geological time is controversial, in part because rigorous and testable mechanisms that can occur under natural conditions, resulting in such preservation, have not been well defined. Here, we evaluate two non-enzymatic structural protein crosslinking mechanisms, Fenton chemistry and glycation, for their possible contribution to the preservation of blood vessel structures recovered from the cortical bone of a Tyrannosaurus rex (USNM 555000 [formerly, MOR 555]). We demonstrate the endogeneity of the fossil vessel tissues, as well as the presence of type I collagen in the outermost vessel layers, using imaging, diffraction, spectroscopy, and immunohistochemistry. Then, we use data derived from synchrotron FTIR studies of the T. rex vessels to analyse their crosslink character, with comparison against two non-enzymatic Fenton chemistry- and glycation-treated extant chicken samples. We also provide supporting X-ray microprobe analyses of the chemical state of these fossil tissues to support our conclusion that non-enzymatic crosslinking pathways likely contributed to stabilizing, and thus preserving, these T. rex vessels. Finally, we propose that these stabilizing crosslinks could play a crucial role in the preservation of other microvascular tissues in skeletal elements from the Mesozoic.}, journal={Scientific Reports}, author={Boatman, E.M. and Goodwin, M.B. and Holman, H-Y N and Fakra, S and Zheng, W and Gronsky, R and Schweitzer, M.H.}, year={2019}, month={Oct}, pages={15678} }
 @article{schweitzer_schroeter_cleland_zheng_2019, title={Paleoproteomics of Mesozoic Dinosaurs and Other Mesozoic Fossils}, volume={19}, ISSN={1615-9853 1615-9861}, url={http://dx.doi.org/10.1002/pmic.201800251}, DOI={10.1002/pmic.201800251}, abstractNote={AbstractMolecular 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.}, number={16}, journal={PROTEOMICS}, publisher={Wiley}, author={Schweitzer, Mary Higby and Schroeter, Elena R. and Cleland, Timothy P. and Zheng, Wenxia}, year={2019}, month={Jul}, pages={1800251} }
 @article{schroeter_blackburn_goshe_schweitzer_2019, title={Proteomic method to extract, concentrate, digest and enrich peptides from fossils with coloured (humic) substances for mass spectrometry analyses}, volume={6}, ISSN={["2054-5703"]}, DOI={10.1098/rsos.181433}, abstractNote={Humic substances are breakdown products of decaying organic matter that co-extract with proteins from fossils. These substances are difficult to separate from proteins in solution and interfere with analyses of fossil proteomes. We introduce a method combining multiple recent advances in extraction protocols to both concentrate proteins from fossil specimens with high humic content and remove humics, producing clean samples easily analysed by mass spectrometry (MS). This method includes: (i) a non-demineralizing extraction buffer that eliminates protein loss during the demineralization step in routine methods; (ii) filter-aided sample preparation (FASP) of peptides, which concentrates and digests extracts in one filter, allowing the separation of large humics after digestion; (iii) centrifugal stage tipping, which further clarifies and concentrates samples in a uniform process performed simultaneously on multiple samples. We apply this method to a moa fossil (approx. 800–1000 years) dark with humic content, generating colourless samples and enabling the detection of more proteins with greater sequence coverage than previous MS analyses on this same specimen. This workflow allows analyses of low-abundance proteins in fossils containing humics and thus may widen the range of extinct organisms and regions of their proteomes we can explore with MS.}, number={8}, journal={ROYAL SOCIETY OPEN SCIENCE}, author={Schroeter, Elena R. and Blackburn, Kevin and Goshe, Michael B. and Schweitzer, Mary H.}, year={2019}, month={Aug} }
 @article{canoville_schweitzer_zanno_2019, title={Systemic distribution of medullary bone in the avian skeleton: ground truthing criteria for the identification of reproductive tissues in extinct Avemetatarsalia}, volume={19}, ISSN={1471-2148}, url={http://dx.doi.org/10.1186/s12862-019-1402-7}, DOI={10.1186/s12862-019-1402-7}, abstractNote={Medullary bone (MB) is an estrogen-dependent, sex-specific tissue produced by female birds during lay and inferred to be present in extinct avemetatarsalians (bird-line archosaurs). Although preliminary studies suggest that MB can be deposited within most skeletal elements, these are restricted to commercial layers or hormonally treated male pigeons, which are poor analogues for wild birds. By contrast, studies in wild bird species noted the presence of MB almost exclusively within limb bones, spurring the misconception that MB deposition is largely restricted to these regions. These disparate claims have cast doubt on the nature of MB-like tissues observed in some extinct avemetatarsalians because of their "unusual" anatomical locations. Furthermore, previous work reported that MB deposition is related to blood supply and pneumatization patterns, yet these hypotheses have not been tested widely in birds. To document the skeletal distribution of MB across Neornithes, reassess previous hypotheses pertaining to its deposition/distribution patterns, and refine the set of criteria by which to evaluate the nature of purported MB tissue in extinct avemetatarsalians, we CT-scanned skeletons of 40 female birds (38 species) that died during the egg-laying cycle, recorded presence or absence of MB in 19 skeletal regions, and assessed pneumatization of stylopods. Selected elements were destructively analyzed to ascertain the chemical and histological nature of observed endosteal bone tissues in contentious skeletal regions. Although its skeletal distribution varies interspecifically, we find MB to be a systemic tissue that can be deposited within virtually all skeletal regions, including cranial elements. We also provide evidence that the deposition of MB is dictated by skeletal distribution patterns of both pneumaticity and bone marrow; two factors linked to ecology (body size, foraging). Hence, skeletal distribution of MB can be extensive in small-bodied and diving birds, but more restricted in large-bodied species or efficient flyers. Previously outlined anatomical locations of purported MB in extinct taxa are invalid criticisms against their potential reproductive nature. Moreover, the proposed homology of lung tissues between birds and some extinct avemetatarsalians permit us to derive a series of location-based predictions that can be used to critically evaluate MB-like tissues in fossil specimens.}, number={1}, journal={BMC Evolutionary Biology}, publisher={Springer Nature}, author={Canoville, Aurore and Schweitzer, Mary H. and Zanno, Lindsay E.}, year={2019}, month={Mar} }
 @article{pan_zheng_sawyer_pennington_zheng_wang_wang_hu_o’connor_zhao_et al._2019, title={The molecular evolution of feathers with direct evidence from fossils}, volume={116}, ISSN={0027-8424 1091-6490}, url={http://dx.doi.org/10.1073/pnas.1815703116}, DOI={10.1073/pnas.1815703116}, abstractNote={Significance
          
            During the dinosaur–bird transition, feathers of bird ancestors must have been molecularly modified to become biomechanically suitable for flight. We report molecular moieties in fossil feathers that shed light on that transition. Pennaceous feathers attached to the right forelimb of the Jurassic dinosaur
            Anchiornis
            were composed of both feather β-keratins and α-keratins, but were dominated by α-keratins, unlike mature feathers of extant birds, which are dominated by β-keratins. Data suggest that the pennaceous feathers of
            Anchiornis
            had some, but not all, of the ultrastructural and molecular characteristics of extant feathers, and may not yet have attained molecular modifications required for powered flight.
          }, number={8}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Pan, Yanhong and Zheng, Wenxia and Sawyer, Roger H. and Pennington, Michael W. and Zheng, Xiaoting and Wang, Xiaoli and Wang, Min and Hu, Liang and O’Connor, Jingmai and Zhao, Tao and et al.}, year={2019}, month={Jan}, pages={3018–3023} }
 @article{schweitzer_zheng_moyer_sjövall_lindgren_2018, title={Preservation potential of keratin in deep time}, volume={13}, ISSN={1932-6203}, url={http://dx.doi.org/10.1371/journal.pone.0206569}, DOI={10.1371/journal.pone.0206569}, abstractNote={Multiple fossil discoveries and taphonomic experiments have established the durability of keratin. The utility and specificity of antibodies to identify keratin peptides has also been established, both in extant feathers under varying treatment conditions, and in feathers from extinct organisms. Here, we show localization of feather-keratin antibodies to control and heat-treated feathers, testifying to the repeatability of initial data supporting the preservation potential of keratin. We then show new data at higher resolution that demonstrates the specific response of these antibodies to the feather matrix, we support the presence of protein in heat-treated feathers using ToF-SIMS, and we apply these methods to a fossil feather preserved in the unusual environment of sinter hot springs. We stress the importance of employing realistic conditions such as sediment burial when designing experiments intended as proxies for taphonomic processes occurring in the fossil record. Our data support the hypothesis that keratin, particularly the β-keratin that comprises feathers, has potential to preserve in fossil remains.}, number={11}, journal={PLOS ONE}, publisher={Public Library of Science (PLoS)}, author={Schweitzer, Mary Higby and Zheng, Wenxia and Moyer, Alison E. and Sjövall, Peter and Lindgren, Johan}, editor={Mishra, Yogendra KumarEditor}, year={2018}, month={Nov}, pages={e0206569} }
 @article{long_zheng_schweitzer_hallen_2018, title={Resonance Raman Imagery of Semi-Fossilized Soft Tissues}, volume={10753}, ISSN={["1996-756X"]}, DOI={10.1117/12.2321298}, abstractNote={The discovery of soft structures in dinosaur bone with the morphological and molecular characteristics of blood vessels in extant vertebrates was both surprising and controversial. Mounting evidence suggests that these soft tissues are blood vessels, their preservation driven in part by reactive oxygen species derived from hemoglobin degradation. More data are needed to support this hypothesis. Raman spectroscopy, and resonance Raman in particular, can provide detailed information as to the chemical makeup of these samples. We used two different excitation wavelengths in microscale Raman measurements to look for lines characteristic of degraded heme molecules, both in ancient vessels and modern analogues taken from semi-fossilized, hemoglobin-soaked ostrich bones. In both samples, we observed two regimes: dark colored, stiff regions and more transparent, elastic regions. We discovered that the two apparent regimes in the samples had different strengths of Raman returns, and that resonance effects greatly affected the Raman intensity. In all cases, there was some evidence of degraded heme spectra, though the increased returns indicated that the dark regimes had reacted more strongly with the heme specie. The modern vessels displayed a resonance Raman intensity consistent with hemoglobin molecular structures, which indicated resonance spectra would provide understanding of the ancient heme molecule. To investigate the two regimes more thoroughly, we acquired Raman spectra over areas where the sample transitioned from one regime to another. Variable wavelength resonance Raman measurements over the whole sample were used to give more information about the heme species present, in both ancient and modern samples.}, journal={ULTRAFAST NONLINEAR IMAGING AND SPECTROSCOPY VI}, author={Long, Brandon and Zheng, Wenxia and Schweitzer, Mary and Hallen, Hans}, year={2018} }
 @article{lindgren_sjövall_thiel_zheng_ito_wakamatsu_hauff_kear_engdahl_alwmark_et al._2018, title={Soft-tissue evidence for homeothermy and crypsis in a Jurassic ichthyosaur}, volume={564}, ISSN={0028-0836 1476-4687}, url={http://dx.doi.org/10.1038/s41586-018-0775-x}, DOI={10.1038/s41586-018-0775-x}, abstractNote={Ichthyosaurs are extinct marine reptiles that display a notable external similarity to modern toothed whales. Here we show that this resemblance is more than skin deep. We apply a multidisciplinary experimental approach to characterize the cellular and molecular composition of integumental tissues in an exceptionally preserved specimen of the Early Jurassic ichthyosaur Stenopterygius. Our analyses recovered still-flexible remnants of the original scaleless skin, which comprises morphologically distinct epidermal and dermal layers. These are underlain by insulating blubber that would have augmented streamlining, buoyancy and homeothermy. Additionally, we identify endogenous proteinaceous and lipid constituents, together with keratinocytes and branched melanophores that contain eumelanin pigment. Distributional variation of melanophores across the body suggests countershading, possibly enhanced by physiological adjustments of colour to enable photoprotection, concealment and/or thermoregulation. Convergence of ichthyosaurs with extant marine amniotes thus extends to the ultrastructural and molecular levels, reflecting the omnipresent constraints of their shared adaptation to pelagic life. The presence of blubber and distribution of melanophores in a countershading pattern in an Early Jurassic ichthyosaur demonstrate that the evolutionary convergence of these reptiles with extant marine amniotes extends to the cellular and molecular levels.}, number={7736}, journal={Nature}, publisher={Springer Nature}, author={Lindgren, Johan and Sjövall, Peter and Thiel, Volker and Zheng, Wenxia and Ito, Shosuke and Wakamatsu, Kazumasa and Hauff, Rolf and Kear, Benjamin P. and Engdahl, Anders and Alwmark, Carl and et al.}, year={2018}, month={Dec}, pages={359–365} }
 @article{lindgren_kuriyama_madsen_sjövall_zheng_uvdal_engdahl_moyer_gren_kamezaki_et al._2017, title={Biochemistry and adaptive colouration of an exceptionally preserved juvenile fossil sea turtle}, volume={7}, ISSN={2045-2322}, url={http://dx.doi.org/10.1038/S41598-017-13187-5}, DOI={10.1038/S41598-017-13187-5}, abstractNote={AbstractThe holotype (MHM-K2) of the Eocene cheloniine Tasbacka danica is arguably one of the best preserved juvenile fossil sea turtles on record. Notwithstanding compactional flattening, the specimen is virtually intact, comprising a fully articulated skeleton exposed in dorsal view. MHM-K2 also preserves, with great fidelity, soft tissue traces visible as a sharply delineated carbon film around the bones and marginal scutes along the edge of the carapace. Here we show that the extraordinary preservation of the type of T. danica goes beyond gross morphology to include ultrastructural details and labile molecular components of the once-living animal. Haemoglobin-derived compounds, eumelanic pigments and proteinaceous materials retaining the immunological characteristics of sauropsid-specific β-keratin and tropomyosin were detected in tissues containing remnant melanosomes and decayed keratin plates. The preserved organics represent condensed remains of the cornified epidermis and, likely also, deeper anatomical features, and provide direct chemical evidence that adaptive melanism – a biological means used by extant sea turtle hatchlings to elevate metabolic and growth rates – had evolved 54 million years ago.}, number={1}, journal={Scientific Reports}, publisher={Springer Science and Business Media LLC}, author={Lindgren, Johan and Kuriyama, Takeo and Madsen, Henrik and Sjövall, Peter and Zheng, Wenxia and Uvdal, Per and Engdahl, Anders and Moyer, Alison E. and Gren, Johan A. and Kamezaki, Naoki and et al.}, year={2017}, month={Oct} }
 @article{schroeter_dehart_cleland_zheng_thomas_kelleher_bern_schweitzer_2017, title={Expansion for the Brachylophosaurus canadensis Collagen I Sequence and Additional Evidence of the Preservation of Cretaceous Protein}, volume={16}, ISSN={["1535-3907"]}, DOI={10.1021/acs.jproteome.6b00873}, abstractNote={Sequence data from biomolecules such as DNA and proteins, which provide critical information for evolutionary studies, have been assumed to be forever outside the reach of dinosaur paleontology. Proteins, which are predicted to have greater longevity than DNA, have been recovered from two nonavian dinosaurs, but these results remain controversial. For proteomic data derived from extinct Mesozoic organisms to reach their greatest potential for investigating questions of phylogeny and paleobiology, it must be shown that peptide sequences can be reliably and reproducibly obtained from fossils and that fragmentary sequences for ancient proteins can be increasingly expanded. To test the hypothesis that peptides can be repeatedly detected and validated from fossil tissues many millions of years old, we applied updated extraction methodology, high-resolution mass spectrometry, and bioinformatics analyses on a Brachylophosaurus canadensis specimen (MOR 2598) from which collagen I peptides were recovered in 2009. We recovered eight peptide sequences of collagen I: two identical to peptides recovered in 2009 and six new peptides. Phylogenetic analyses place the recovered sequences within basal archosauria. When only the new sequences are considered, B. canadensis is grouped more closely to crocodylians, but when all sequences (current and those reported in 2009) are analyzed, B. canadensis is placed more closely to basal birds. The data robustly support the hypothesis of an endogenous origin for these peptides, confirm the idea that peptides can survive in specimens tens of millions of years old, and bolster the validity of the 2009 study. Furthermore, the new data expand the coverage of B. canadensis collagen I (a 33.6% increase in collagen I alpha 1 and 116.7% in alpha 2). Finally, this study demonstrates the importance of reexamining previously studied specimens with updated methods and instrumentation, as we obtained roughly the same amount of sequence data as the previous study with substantially less sample material. Data are available via ProteomeXchange with identifier PXD005087.}, number={2}, journal={JOURNAL OF PROTEOME RESEARCH}, author={Schroeter, Elena R. and DeHart, Caroline J. and Cleland, Timothy P. and Zheng, Wenxia and Thomas, Paul M. and Kelleher, Neil L. and Bern, Marshall and Schweitzer, Mary H.}, year={2017}, month={Feb}, pages={920–932} }
 @article{schroeter_dehart_schweitzer_thomas_kelleher_2016, title={Bone protein “extractomics”: comparing the efficiency of bone protein extractions of Gallus gallus in tandem mass spectrometry, with an eye towards paleoproteomics}, volume={4}, ISSN={2167-8359}, url={http://dx.doi.org/10.7717/peerj.2603}, DOI={10.7717/peerj.2603}, abstractNote={Proteomic studies of bone require specialized extraction protocols to demineralize and solubilize proteins from within the bone matrix. Although various protocols exist for bone protein recovery, little is known about how discrete steps in each protocol affect the subset of the bone proteome recovered by mass spectrometry (MS) analyses. Characterizing these different “extractomes” will provide critical data for development of novel and more efficient protein extraction methodologies for fossils. Here, we analyze 22 unique sub-extractions of chicken bone and directly compare individual extraction components for their total protein yield and diversity and coverage of bone proteins identified by MS. We extracted proteins using different combinations and ratios of demineralizing reagents, protein-solubilizing reagents, and post-extraction buffer removal methods, then evaluated tryptic digests from 20 µg aliquots of each fraction by tandem MS/MS on a 12T FT-ICR mass spectrometer. We compared total numbers of peptide spectral matches, peptides, and proteins identified from each fraction, the redundancy of protein identifications between discrete steps of extraction methods, and the sequence coverage obtained for select, abundant proteins. Although both alpha chains of collagen I (the most abundant protein in bone) were found in all fractions, other collagenous and non-collagenous proteins (e.g., apolipoprotein, osteonectin, hemoglobin) were differentially identified. We found that when a standardized amount of extracted proteins was analyzed, extraction steps that yielded the most protein (by weight) from bone were oftennotthe ones that produced the greatest diversity of bone proteins, or the highest degree of protein coverage. Generally, the highest degrees of diversity and coverage were obtained from demineralization fractions, and the proteins found in the subsequent solubilization fractions were highly redundant with those in the previous fraction. Based on these data, we identify future directions and parameters to consider (e.g., proteins targeted, amount of sample required) when applying discrete parts of these protocols to fossils.}, journal={PeerJ}, publisher={PeerJ}, author={Schroeter, Elena R. and DeHart, Caroline J. and Schweitzer, Mary H. and Thomas, Paul M. and Kelleher, Neil L.}, year={2016}, month={Oct}, pages={e2603} }
 @article{schweitzer_zheng_zanno_werning_sugiyama_2016, title={Chemistry supports the identification of gender-specific reproductive tissue in Tyrannosaurus rex}, volume={6}, ISSN={2045-2322}, url={http://dx.doi.org/10.1038/srep23099}, DOI={10.1038/srep23099}, abstractNote={AbstractMedullary bone (MB), an estrogen-dependent reproductive tissue present in extant gravid birds, is texturally, histologically and compositionally distinct from other bone types. Phylogenetic proximity led to the proposal that MB would be present in non-avian dinosaurs and recent studies have used microscopic, morphological and regional homologies to identify this reproductive tissue in both theropod and ornithischian dinosaurs. Here, we capitalize on the unique chemical and histological fingerprint of MB in birds to characterize, at the molecular level, MB in the non-avian theropod Tyrannosaurus rex (MOR 1125) and show that the retention of original molecular components in fossils allows deeper physiological and evolutionary questions to be addressed.}, number={1}, journal={Scientific Reports}, publisher={Springer Science and Business Media LLC}, author={Schweitzer, Mary Higby and Zheng, Wenxia and Zanno, Lindsay and Werning, Sarah and Sugiyama, Toshie}, year={2016}, month={Mar} }
 @article{moyer_zheng_schweitzer_2016, title={Keratin Durability Has Implications for the Fossil Record: Results from a 10 Year Feather Degradation Experiment}, volume={11}, ISSN={1932-6203}, url={http://dx.doi.org/10.1371/journal.pone.0157699}, DOI={10.1371/journal.pone.0157699}, abstractNote={Keratinous ‘soft tissue’ structures (i.e. epidermally derived and originally non-biomineralized), include feathers, skin, claws, beaks, and hair. Despite their relatively common occurrence in the fossil record (second only to bone and teeth), few studies have addressed natural degradation processes that must occur in all organic material, including those keratinous structures that are incorporated into the rock record as fossils. Because feathers have high preservation potential and strong phylogenetic signal, in the current study we examine feathers subjected to different burial environments for a duration of ~10 years, using transmission electron microscopy (TEM) and in situ immunofluorescence (IF). We use morphology and persistence of specific immunoreactivity as indicators of preservation at the molecular and microstructural levels. We show that feather keratin is durable, demonstrates structural and microstructural integrity, and retains epitopes suitable for specific antibody recognition in even the harshest conditions. These data support the hypothesis that keratin antibody reactivity can be used to identify the nature and composition of epidermal structures in the rock record, and to address evolutionary questions by distinguishing between alpha- (widely distributed) and beta- (limited to sauropsids) keratin.}, number={7}, journal={PLOS ONE}, publisher={Public Library of Science (PLoS)}, author={Moyer, Alison E. and Zheng, Wenxia and Schweitzer, Mary H.}, editor={Beatty, Brian LeeEditor}, year={2016}, month={Jul}, pages={e0157699} }
 @article{moyer_zheng_schweitzer_2016, title={Microscopic and immunohistochemical analyses of the claw of the nesting dinosaur, Citipati osmolskae}, volume={283}, number={1842}, journal={Proceedings of the Royal Society of London. Series B}, author={Moyer, A. E. and Zheng, W. X. and Schweitzer, M. H.}, year={2016} }
 @article{pan_zheng_moyer_jingmai k. o'connor_wang_zheng_wang_schroeter_zhou_schweitzer_2016, title={Molecular evidence of keratin and melanosomes in feathers of the Early Cretaceous bird Eoconfuciusornis}, volume={113}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.1617168113}, abstractNote={Significance
          
            We report fossil evidence of feather structural protein (beta-keratin) from a 130-My-old basal bird (
            Eoconfuciusornis
            ) from the famous Early Cretaceous Jehol Biota, which has produced many feathered dinosaurs, early birds, and mammals. Multiple independent molecular analyses of both microbodies and associated matrix recovered from the fossil feathers confirm that these microbodies are indeed melanosomes. We use transmission electron microscopy and immunogold to show localized binding of antibodies raised against feather protein to matrix filaments within these ancient feathers. Our work sheds new light on molecular constituents of tissues preserved in fossils.
          }, number={49}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Pan, Yanhong and Zheng, Wenxia and Moyer, Alison E. and Jingmai K. O'Connor and Wang, Min and Zheng, Xiaoting and Wang, Xiaoli and Schroeter, Elena R. and Zhou, Zhonghe and Schweitzer, Mary H.}, year={2016}, month={Dec}, pages={E7900–E7907} }
 @article{schweitzer_moyer_zheng_2016, title={Testing the Hypothesis of Biofilm as a Source for Soft Tissue and Cell-Like Structures Preserved in Dinosaur Bone}, volume={11}, ISSN={1932-6203}, url={http://dx.doi.org/10.1371/journal.pone.0150238}, DOI={10.1371/journal.pone.0150238}, abstractNote={Recovery of still-soft tissue structures, including blood vessels and osteocytes, from dinosaur bone after demineralization was reported in 2005 and in subsequent publications. Despite multiple lines of evidence supporting an endogenous source, it was proposed that these structures arose from contamination from biofilm-forming organisms. To test the hypothesis that soft tissue structures result from microbial invasion of the fossil bone, we used two different biofilm-forming microorganisms to inoculate modern bone fragments from which organic components had been removed. We show fundamental morphological, chemical and textural differences between the resultant biofilm structures and those derived from dinosaur bone. The data do not support the hypothesis that biofilm-forming microorganisms are the source of these structures.}, number={2}, journal={PLOS ONE}, publisher={Public Library of Science (PLoS)}, author={Schweitzer, Mary Higby and Moyer, Alison E. and Zheng, Wenxia}, editor={Claessens, LeonEditor}, year={2016}, month={Feb}, pages={e0150238} }
 @article{dacke_elsey_trosclair_sugiyama_nevarez_schweitzer_2015, title={Alligator osteoderms as a source of labile calcium for eggshell formation}, volume={297}, ISSN={["1469-7998"]}, DOI={10.1111/jzo.12272}, abstractNote={AbstractThe calcium (Ca) demand on alligators in active reproduction is significant, yet the source of this additional Ca is unclear. Three possible sources for Ca mobilization are endolymphatic deposits, as in anurans and some lizards; short‐lived skeletal medullary bone or analogous deposits, as in birds; or some other source such as the osteoderm layer of the integument or simply mobilization of structural bone. Here, we investigate possible extra‐skeletal sources for labile Ca in the reproducing alligator, including endolymphatic Ca deposits, by analogy with anuran amphibian and some reptiles and integumentary osteodermal (scale) Ca deposits. We conducted X‐ray image analyses of skulls for the presence of significant endolymphatic Ca deposits. We also examined dermal bone of scutes (osteoderm, scales) from the dorsal integument using both X‐ray and histological analyses. Tissues from reproducing females containing mature but unovulated follicles were compared with those from specimens that had nested (laid eggs) or contained eggs within the oviduct at advanced stages of calcification. A small number of immature specimens and an adult male were also compared. No clear differences were observed in endolymphatic deposits between pre‐ and post‐ovulatory specimens. Scute (osteoderm) X‐ray density was significantly greater in females with ripe ovarian follicles compared with those that had recently laid (nested) or contained heavily calcified eggs within their oviducts. The latter groups also showed histological evidence of scute resorption compared with the former, suggesting that the scutes play a role in Ca storage during egglay.}, number={4}, journal={JOURNAL OF ZOOLOGY}, author={Dacke, C. G. and Elsey, R. M. and Trosclair, P. L., III and Sugiyama, T. and Nevarez, J. G. and Schweitzer, M. H.}, year={2015}, month={Dec}, pages={255–264} }
 @article{cleland_schroeter_schweitzer_2015, title={Biologically and diagenetically derived peptide modifications in moa collagens}, volume={282}, ISSN={0962-8452 1471-2954}, url={http://dx.doi.org/10.1098/rspb.2015.0015}, DOI={10.1098/rspb.2015.0015}, abstractNote={
            The modifications that occur on proteins in natural environments over time are not well studied, yet characterizing them is vital to correctly interpret sequence data recovered from fossils. The recently extinct moa (Dinornithidae) is an excellent candidate for investigating the preservation of proteins, their post-translational modifications (PTMs) and diagenetic alterations during degradation. Moa protein extracts were analysed using mass spectrometry, and peptides from collagen I, collagen II and collagen V were identified. We also identified biologically derived PTMs (i.e. methylation, di-methylation, alkylation, hydroxylation, fucosylation) on amino acids at locations consistent with extant proteins. In addition to these
            in vivo
            modifications, we detected novel modifications that are probably diagenetically derived. These include loss of hydroxylation/glutamic semialdehyde, carboxymethyllysine and peptide backbone cleavage, as well as previously noted deamidation. Moa collagen sequences and modifications provide a baseline by which to evaluate proteomic studies of other fossils, and a framework for defining the molecular relationship of moa to other closely related taxa.
          }, number={1808}, journal={Proceedings of the Royal Society B: Biological Sciences}, publisher={The Royal Society}, author={Cleland, Timothy P. and Schroeter, Elena R. and Schweitzer, Mary H.}, year={2015}, month={Jun}, pages={20150015} }
 @misc{lindgren_moyer_schweitzer_sjovall_uvdal_nilsson_heimdal_engdahl_gren_schultz_et al._2015, title={Interpreting melanin-based coloration through deep time: A critical review}, volume={282}, ISSN={0962-8452 1471-2954}, url={http://dx.doi.org/10.1098/rspb.2015.0614}, DOI={10.1098/rspb.2015.0614}, abstractNote={Colour, derived primarily from melanin and/or carotenoid pigments, is integral to many aspects of behaviour in living vertebrates, including social signalling, sexual display and crypsis. Thus, identifying biochromes in extinct animals can shed light on the acquisition and evolution of these biological traits. Both eumelanin and melanin-containing cellular organelles (melanosomes) are preserved in fossils, but recognizing traces of ancient melanin-based coloration is fraught with interpretative ambiguity, especially when observations are based on morphological evidence alone. Assigning microbodies (or, more often reported, their ‘mouldic impressions’) as melanosome traces without adequately excluding a bacterial origin is also problematic because microbes are pervasive and intimately involved in organismal degradation. Additionally, some forms synthesize melanin. In this review, we survey both vertebrate and microbial melanization, and explore the conflicts influencing assessment of microbodies preserved in association with ancient animal soft tissues. We discuss the types of data used to interpret fossil melanosomes and evaluate whether these are sufficient for definitive diagnosis. Finally, we outline an integrated morphological and geochemical approach for detecting endogenous pigment remains and associated microstructures in multimillion-year-old fossils.}, number={1813}, journal={Proceedings of the Royal Society of London. Series B}, publisher={The Royal Society}, author={Lindgren, J. and Moyer, A. and Schweitzer, M. H. and Sjovall, P. and Uvdal, P. and Nilsson, D. E. and Heimdal, J. and Engdahl, A. and Gren, J. A. and Schultz, B. P. and et al.}, year={2015}, pages={20150614} }
 @article{cleland_schroeter_zamdborg_zheng_lee_tran_bern_duncan_lebleu_ahlf_et al._2015, title={Mass Spectrometry and Antibody-Based Characterization of Blood Vessels from Brachylophosaurus canadensis}, volume={14}, ISSN={["1535-3907"]}, DOI={10.1021/acs.jproteome.5b00675}, abstractNote={Structures similar to blood vessels in location, morphology, flexibility, and transparency have been recovered after demineralization of multiple dinosaur cortical bone fragments from multiple specimens, some of which are as old as 80 Ma. These structures were hypothesized to be either endogenous to the bone (i.e., of vascular origin) or the result of biofilm colonizing the empty osteonal network after degradation of original organic components. Here, we test the hypothesis that these structures are endogenous and thus retain proteins in common with extant archosaur blood vessels that can be detected with high-resolution mass spectrometry and confirmed by immunofluorescence. Two lines of evidence support this hypothesis. First, peptide sequencing of Brachylophosaurus canadensis blood vessel extracts is consistent with peptides comprising extant archosaurian blood vessels and is not consistent with a bacterial, cellular slime mold, or fungal origin. Second, proteins identified by mass spectrometry can be localized to the tissues using antibodies specific to these proteins, validating their identity. Data are available via ProteomeXchange with identifier PXD001738.}, number={12}, journal={JOURNAL OF PROTEOME RESEARCH}, author={Cleland, Timothy P. and Schroeter, Elena R. and Zamdborg, Leonid and Zheng, Wenxia and Lee, Ji Eun and Tran, John C. and Bern, Marshall and Duncan, Michael B. and Lebleu, Valerie S. and Ahlf, Dorothy R. and et al.}, year={2015}, month={Dec}, pages={5252–5262} }
 @article{schweitzer_lindgren_moyer_2015, title={Melanosomes and ancient coloration re-examined: A response to Vinther 2015}, volume={37}, ISSN={["1521-1878"]}, DOI={10.1002/bies.201500061}, abstractNote={Round to elongate microbodies associated with fossil vertebrate soft tissues were interpreted as microbial traces until 2008, when they were re‐described as remnant melanosomes – intracellular, pigment‐containing eukaryotic organelles. Since then, multiple claims for melanosome preservation and inferences of organismal color, behavior, and physiology have been advanced, based upon the shape and size of these microstructures. Here, we re‐examine evidence for ancient melanosomes in light of information reviewed in Vinther (2015), and literature regarding the preservation potential of microorganisms and their exopolymeric secretions. We: (i) address statements in Vinther's recent (2015) review that are incorrect or which misrepresent published data; (ii) discuss the need for caution in interpreting “voids” and microbodies associated with degraded fossil soft tissues; (iii) present evidence that microorganisms are in many cases an equally parsimonious source for these “voids” as are remnant melanosomes; and (iv) suggest methods/criteria for differentiating melanosomes from microbial traces in the fossil record.}, number={11}, journal={BioEssays}, author={Schweitzer, M.H. and Lindgren, J. and Moyer, A.E.}, year={2015}, pages={1174–1183} }
 @article{cadena_schweitzer_2014, title={A Pelomedusoid Turtle from the Paleocene-Eocene of Colombia Exhibiting Preservation of Blood Vessels and Osteocytes}, volume={48}, ISSN={["1937-2418"]}, DOI={10.1670/13-046}, abstractNote={Abstract We describe a Paleocene–Eocene pelomedusoid turtle from tropical South America in a new fossiliferous locality, from Los Cuervos Formation, at the Calenturitas Coal Mine, Colombia. Although no further systematic precision beyond Pelomedusoides incertae sedis can be supported, the presence of an ischial scar positioned far anteriorly to the anal notch, and a strongly decorated ventral surface of the plastron, indicate that this specimen is potentially related to the bothremydid clade formed by Puentemys–Foxemys. We also demonstrate the potential organic preservation of osteocytes and blood vessels for this specimen, indicating that preservation of soft tissue such as vessels and bone cells in the fossil record is independent of bone type, fossil site, or locality; occurring in different lineages of vertebrates; and that it is even possible to occur in tropical depositional environments during a period of maximum global warming such as the Paleocene–Eocene. Resumen Aqui describimos la primera ocurencia de tortugas pelomedusoid del Paleoceno–Eoceno en la parte tropical de Suramérica, en una nueva localidad fósilifera, de la Formación Los Cuervos, en la mina de carbón Calenturitas, Colombia. Aunque, no mayor precisión sistemática puede ser soportada más que Pelomedusoides incertae sedis, la presencia de una cicatriz isquial posicionada muy anteriormente a la escotadura anal y una fuertemente decorada superficie ventral del plastron, indican que el especimen esta relacionado con el clado bothremydido formado por Puentemys–Foxemys. También demostramos la posible preservación orgánica de osteocitos y vasos sanguineos para este especimen; indicando que la preservación de tejidos blandos como vasos y celulas oseas en el registro fósil es independiente del tipo de hueso, sitio fósil o localidad, ocurriendo en diferentes linajes de vertebrados, y que es possible que ocurra en ambientes deposicionales tropicales, durante periodos de maximo calentamiento global como el Paleoceno–Eoceno.}, number={4}, journal={JOURNAL OF HERPETOLOGY}, author={Cadena, Edwin A. and Schweitzer, Mary H.}, year={2014}, month={Dec}, pages={461–465} }
 @article{schweitzer_zheng_cleland_goodwin_boatman_theil_marcus_fakra_2014, title={A role for iron and oxygen chemistry in preserving soft tissues, cells and molecules from deep time}, volume={281}, number={1775}, journal={Proceedings of the Royal Society of London. Series B}, author={Schweitzer, M. H. and Zheng, W. X. and Cleland, T. P. and Goodwin, M. B. and Boatman, E. and Theil, E. and Marcus, M. A. and Fakra, S. C.}, year={2014} }
 @article{schweitzer_2014, title={Blood from Stone}, volume={23}, ISSN={1936-1513}, url={http://dx.doi.org/10.1038/scientificamericandinosaurs0514-104}, DOI={10.1038/scientificamericandinosaurs0514-104}, number={2s}, journal={Scientific American}, publisher={Springer Nature}, author={Schweitzer, Mary H.}, year={2014}, month={May}, pages={104–111} }
 @article{schweitzer_2014, title={Dinosaurs are important}, volume={310}, DOI={10.1038/scientificamerican0614-12}, number={6}, journal={Scientific American}, publisher={Scientific American}, author={Schweitzer, M.H.}, year={2014}, month={Jun}, pages={12} }
 @article{schweitzer_2014, title={Dinosaurs are important yesterday's big reptiles can help us figure out how the human era is shaping up}, volume={310}, number={6}, journal={Scientific American}, author={Schweitzer, M. H.}, year={2014}, pages={12–12} }
 @article{moyer_zheng_johnson_lamanna_li_lacovara_schweitzer_2014, title={Melanosomes or Microbes: Testing an Alternative Hypothesis for the Origin of Microbodies in Fossil Feathers}, volume={4}, ISSN={2045-2322}, url={http://dx.doi.org/10.1038/srep04233}, DOI={10.1038/srep04233}, abstractNote={Microbodies associated with fossil feathers, originally attributed to microbial biofilm, have been reinterpreted as melanosomes: pigment-containing, eukaryotic organelles. This interpretation generated hypotheses regarding coloration in non-avian and avian dinosaurs. Because melanosomes and microbes overlap in size, distribution and morphology, we re-evaluate both hypotheses. We compare melanosomes within feathers of extant chickens with patterns induced by microbial overgrowth on the same feathers, using scanning (SEM), field emission (FESEM) and transmission (TEM) electron microscopy. Melanosomes are always internal, embedded in a morphologically distinct keratinous matrix. Conversely, microbes grow across the surface of feathers in continuous layers, more consistent with published images from fossil feathers. We compare our results to both published literature and new data from a fossil feather ascribed to Gansus yumenensis (ANSP 23403). 'Mouldic impressions' were observed in association with both the feather and sediment grains, supporting a microbial origin. We propose criteria for distinguishing between these two microbodies.}, number={1}, journal={Scientific Reports}, publisher={Springer Science and Business Media LLC}, author={Moyer, Alison E. and Zheng, Wenxia and Johnson, Elizabeth A. and Lamanna, Matthew C. and Li, Da-qing and Lacovara, Kenneth J. and Schweitzer, Mary H.}, year={2014}, month={Mar} }
 @article{schweitzer_schroeter_goshe_2014, title={Protein Molecular Data from Ancient (>1 million years old) Fossil Material: Pitfalls, Possibilities and Grand Challenges}, volume={86}, ISSN={0003-2700 1520-6882}, url={http://dx.doi.org/10.1021/ac500803w}, DOI={10.1021/ac500803w}, abstractNote={Advances in resolution and sensitivity of analytical techniques have provided novel applications, including the analyses of fossil material. However, the recovery of original proteinaceous components from very old fossil samples (defined as >1 million years (1 Ma) from previously named limits in the literature) is far from trivial. Here, we discuss the challenges to recovery of proteinaceous components from fossils, and the need for new sample preparation techniques, analytical methods, and bioinformatics to optimize and fully utilize the great potential of information locked in the fossil record. We present evidence for survival of original components across geological time, and discuss the potential benefits of recovery, analyses, and interpretation of fossil materials older than 1 Ma, both within and outside of the fields of evolutionary biology.}, number={14}, journal={Analytical Chemistry}, publisher={American Chemical Society (ACS)}, author={Schweitzer, Mary Higby and Schroeter, Elena R. and Goshe, Michael B.}, year={2014}, month={Jul}, pages={6731–6740} }
 @article{boatman_goodwin_holman_fakra_schweitzer_gronsky_horner_2014, title={Synchrotron Chemical and Structural Analysis of Tyrannosaurus rex Blood Vessels: The Contribution of Collagen Hypercrosslinking to Tissue Longevity}, volume={20}, ISSN={1431-9276 1435-8115}, url={http://dx.doi.org/10.1017/S1431927614008885}, DOI={10.1017/S1431927614008885}, abstractNote={Recent descriptions of blood vessels recovered from dinosaur bones have raised many questions regarding tissue diagenesis and the associated chemical pathways that led to preservation. Previous analyses have identified preserved elastin and collagen proteins in a variety of specimens [1][2]. In particular, the mechanical, chemical, and thermal susceptibility of fibrillar collagen is partially dependent on the degree of intermolecular crosslinking. While collagen crosslinking can be either enzymatically or non-enzymatically driven in life, in death, only non-enzymatic pathways are available. Hence, non-enzymatic intermolecular crosslinking of fibrillar collagen supermolecular networks in fossil blood vessels has been suggested as a possible contributor to tissue longevity.}, number={S3}, journal={Microscopy and Microanalysis}, publisher={Cambridge University Press (CUP)}, author={Boatman, Elizabeth M. and Goodwin, Mark B. and Holman, Hoi-Ying and Fakra, Sirine and Schweitzer, Mary H. and Gronsky, Ronald and Horner, John R.}, year={2014}, month={Aug}, pages={1430–1431} }
 @article{hertzog_schweitzer_zanno_2013, title={Willo’s change of heart}, journal={The Naturalist}, author={Hertzog, L. and Schweitzer, M.H. and Zanno, L.}, year={2013}, pages={6–7} }
 @inbook{zheng_schweitzer_2012, title={Chemical Analyses of Fossil Bone}, ISBN={9781617799761 9781617799778}, ISSN={1064-3745 1940-6029}, url={http://dx.doi.org/10.1007/978-1-61779-977-8_10}, DOI={10.1007/978-1-61779-977-8_10}, abstractNote={The preservation of microstructures consistent with soft tissues, cells, and other biological components in demineralized fragments of dinosaur bone tens of millions of years old was unexpected, and counter to current hypotheses of tissue, cellular, and molecular degradation. Although the morphological similarity of these tissues to extant counterparts was unmistakable, after at least 80 million years exposed to geochemical influences, morphological similarity is insufficient to support an endogenous source. To test this hypothesis, and to characterize these materials at a molecular level, we applied multiple independent chemical, molecular, and microscopic analyses to identify the presence of original components produced by the extinct organisms. Microscopic techniques included field emission scanning electron microscopy, analytical transmission electron microscopy, transmitted light microscopy (LM), and fluorescence microscopy (FM). The chemical and molecular techniques include enzyme-linked immunosorbant assay, sodium dodecyl sulfate polyacrylamide gel electrophoresis, western blot (immunoblot), and attenuated total reflectance infrared spectroscopy. In situ analyses performed directly on tissues included immunohistochemistry and time-of-flight secondary ion mass spectrometry. The details of sample preparation and methodology are described in detail herein.}, booktitle={Methods in Molecular Biology}, publisher={Humana Press}, author={Zheng, Wenxia and Schweitzer, Mary Higby}, year={2012}, pages={153–172} }
 @inbook{schweitzer_marshall_2012, place={Bloomington, IN}, edition={2nd}, title={Claws, scales, beaks and feathers: Molecular traces in the fossil record}, booktitle={The Complete Dinosaur}, publisher={Indiana University Press}, author={Schweitzer, M.H. and Marshall, M.}, editor={Brett-Surman, M.K. and Holtz, T.R. and Farlow, J.O.Editors}, year={2012}, pages={273–284} }
 @article{cleland_voegele_schweitzer_2012, title={Empirical Evaluation of Bone Extraction Protocols}, volume={7}, ISSN={1932-6203}, url={http://dx.doi.org/10.1371/journal.pone.0031443}, DOI={10.1371/journal.pone.0031443}, abstractNote={The application of high-resolution analytical techniques to characterize ancient bone proteins requires clean, efficient extraction to obtain high quality data. Here, we evaluated many different protocols from the literature on ostrich cortical bone and moa cortical bone to evaluate their yield and relative purity using the identification of antibody-antigen complexes on enzyme-linked immunosorbent assay and gel electrophoresis. Moa bone provided an ancient comparison for the effectiveness of bone extraction protocols tested on ostrich bone. For the immunological part of this study, we focused on collagen I, osteocalcin, and hemoglobin because collagen and osteocalcin are the most abundant proteins in the mineralized extracellular matrix and hemoglobin is common in the vasculature. Most of these procedures demineralize the bone first, and then the remaining organics are chemically extracted. We found that the use of hydrochloric acid, rather than ethylenediaminetetraacetic acid, for demineralization resulted in the cleanest extractions because the acid was easily removed. In contrast, the use of ethylenediaminetetraacetic acid resulted in smearing upon electrophoretic separation, possibly indicating these samples were not as pure. The denaturing agents sodium dodecyl sulfate, urea, and guanidine HCl have been used extensively for the solubilization of proteins in non-biomineralized tissue, but only the latter has been used on bone. We show that all three denaturing agents are effective for extracting bone proteins. One additional method tested uses ammonium bicarbonate as a solubilizing buffer that is more appropriate for post-extraction analyses (e.g., proteomics) by removing the need for desalting. We found that both guanidine HCl and ammonium bicarbonate were effective for extracting many bone proteins, resulting in similar electrophoretic patterns. With the increasing use of proteomics, a new generation of scientists are now interested in the study of proteins from not only extant bone but also from ancient bone.}, number={2}, journal={PLoS ONE}, publisher={Public Library of Science (PLoS)}, author={Cleland, Timothy P. and Voegele, Kristyn and Schweitzer, Mary H.}, editor={Evans, Alistair RobertEditor}, year={2012}, month={Feb}, pages={e31443} }
 @article{schweitzer_zheng_cleland_bern_2013, title={Molecular analyses of dinosaur osteocytes support the presence of endogenous molecules}, volume={52}, ISSN={["1873-2763"]}, DOI={10.1016/j.bone.2012.10.010}, abstractNote={The discovery of soft, transparent microstructures in dinosaur bone consistent in morphology with osteocytes was controversial. We hypothesize that, if original, these microstructures will have molecular features in common with extant osteocytes. We present immunological and mass spectrometry evidence for preservation of proteins comprising extant osteocytes (Actin, Tubulin, PHEX, Histone H4) in osteocytes recovered from two non-avian dinosaurs. Furthermore, antibodies to DNA show localized binding to these microstructures, which also react positively with DNA intercalating stains propidium iodide (PI) and 4',6'-diamidino-2-phenylindole dihydrochloride (DAPI). Each antibody binds dinosaur cells in patterns similar to extant cells. These data are the first to support preservation of multiple proteins and to present multiple lines of evidence for material consistent with DNA in dinosaurs, supporting the hypothesis that these structures were part of the once living animals. We propose mechanisms for preservation of cells and component molecules, and discuss implications for dinosaurian cellular biology.}, number={1}, journal={BONE}, author={Schweitzer, Mary Higby and Zheng, Wenxia and Cleland, Timothy P. and Bern, Marshall}, year={2013}, month={Jan}, pages={414–423} }
 @misc{cadena_schweitzer_2012, title={Variation in osteocytes morphology vs bone type in turtle shell and their exceptional preservation from the Jurassic to the present}, volume={51}, ISSN={["1873-2763"]}, DOI={10.1016/j.bone.2012.05.002}, abstractNote={Here we describe variations in osteocytes derived from each of the three bone layers that comprise the turtle shell. We examine osteocytes in bone from four extant turtle species to form a morphological 'baseline', and then compare these with morphologies of osteocytes preserved in Cenozoic and Mesozoic fossils. Two different morphotypes of osteocytes are recognized: flattened-oblate osteocytes (FO osteocytes), which are particularly abundant in the internal cortex and lamellae of secondary osteons in cancellous bone, and stellate osteocytes (SO osteocytes), principally present in the interstitial lamellae between secondary osteons and external cortex. We show that the morphology of osteocytes in each of the three bone layers is conserved through ontogeny. We also demonstrate that these morphological variations are phylogenetically independent, as well as independent of the bone origin (intramembranous or endochondral). Preservation of microstructures consistent with osteocytes in the morphology in Cenozoic and Mesozoic fossil turtle bones appears to be common, and occurs in diverse diagenetic environments including marine, freshwater, and terrestrial deposits. These data have potential to illuminate aspects of turtle biology and evolution previously unapproachable, such as estimates of genome size of extinct species, differences in metabolic rates among different bones from a single individual, and potential function of osteocytes as capsules for preservation of ancient biomolecules.}, number={3}, journal={BONE}, author={Cadena, Edwin A. and Schweitzer, Mary H.}, year={2012}, month={Sep}, pages={614–620} }
 @article{antonio_schweitzer_jensen_kalluri_buckley_orgel_2011, title={Dinosaur peptides suggest mechanisms of protein survival}, volume={6}, number={6}, journal={PLoS One}, author={Antonio, J. D. S. and Schweitzer, M. H. and Jensen, S. T. and Kalluri, R. and Buckley, M. and Orgel, J. P. R. O.}, year={2011} }
 @article{cleland_stoskopf_schweitzer_2011, title={Histological, chemical, and morphological reexamination of the "heart" of a small Late Cretaceous Thescelosaurus}, volume={98}, ISSN={["1432-1904"]}, DOI={10.1007/s00114-010-0760-1}, abstractNote={A three-dimensional, iron-cemented structure found in the anterior thoracic cavity of articulated Thescelosaurus skeletal remains was hypothesized to be the fossilized remains of the animal's four-chambered heart. This was important because the finding could be interpreted to support a hypothesis that non-avian dinosaurs were endothermic. Mammals and birds, the only extant organisms with four-chambered hearts and single aortae, are endotherms. The hypothesis that this Thescelosaurus has a preserved heart was controversial, and therefore, we reexamined it using higher-resolution computed tomography, paleohistological examination, X-ray diffraction analysis, X-ray photoelectron spectroscopy, and scanning electron microscopy. This suite of analyses allows for detailed morphological and chemical examination beyond what was provided in the original work. Neither the more detailed examination of the gross morphology and orientation of the thoracic "heart" nor the microstructural studies supported the hypothesis that the structure was a heart. The more advanced computed tomography showed the same three areas of low density as the earlier studies with no evidence of additional low-density areas as might be expected from examinations of an ex situ ostrich heart. Microstructural examination of a fragment taken from the "heart" was consistent with cemented sand grains, and no chemical signal consistent with a biological origin was detected. However, small patches of cell-like microstructures were preserved in the sandstone matrix of the thoracic structure. A possible biological origin for these microstructures is the focus of ongoing investigation.}, number={3}, journal={NATURWISSENSCHAFTEN}, author={Cleland, Timothy P. and Stoskopf, Michael K. and Schweitzer, Mary H.}, year={2011}, month={Mar}, pages={203–211} }
 @misc{schweitzer_2011, title={Soft tissue preservation in terrestrial mesozoic vertebrates}, volume={39}, ISSN={0084-6597 1545-4495}, url={http://dx.doi.org/10.1146/annurev-earth-040610-133502}, DOI={10.1146/annurev-earth-040610-133502}, abstractNote={Exceptionally preserved fossils—i.e., those that retain, in some manner, labile components of organisms that are normally degraded far too quickly to enter the fossil record—hold the greatest potential for understanding aspects of the biology of long-extinct animals and are the best targets for the search for endogenous biomolecules. Yet the modes of preservation of these labile components, and exactly what remains of the original composition, are not well understood. Here, I review a selection of cases of soft tissue preservation in Mesozoic vertebrates, examine chemical and environmental factors that may influence such preservation, explore the potential of these fossils for high-resolution analytical studies, and suggest clarification of terminologies and criteria for determining the endogeneity of source and the degree of preservation of these well-preserved tissues.}, number={1}, journal={Annual review of earth and planetary sciences, vol 39}, publisher={Annual Reviews}, author={Schweitzer, M. H.}, year={2011}, pages={187–216} }
 @article{schweitzer_2010, title={BLOOD FROM STONE}, volume={303}, ISSN={["0036-8733"]}, DOI={10.1038/scientificamerican1210-62}, number={6}, journal={SCIENTIFIC AMERICAN}, author={Schweitzer, Mary H.}, year={2010}, month={Dec}, pages={62–69} }
 @article{green_schweitzer_lamm_2010, title={Limb bone histology and growth in Placerias hesternus (Therapsida: Anomodontia) from the upper triassic of North America}, volume={53}, journal={Palaeontology}, author={Green, J. L. and Schweitzer, M. H. and Lamm, E. T.}, year={2010}, pages={347–364} }
 @article{schweitzer_zheng_organ_avci_suo_freimark_lebleu_duncan_heiden_neveu_et al._2009, title={Biomolecular characterization and protein sequences of the Campanian hadrosaur Brachylophosaurus canadensis}, volume={324}, ISSN={["1095-9203"]}, DOI={10.1126/science.1165069}, abstractNote={The Birds and the Dinosaurs
          
            The extent to which primary tissues are preserved in ancient fossils remains controversial.
            
              Schweitzer
              et al.
            
            (p.
            626
            ; see the news story by
            Service
            ) describe well-preserved tissues and primary collagen sequences from the femur of an 80-million-year-old hadrosaur. The fossil preserved structures resembling primary bone tissues and vessels. Both extracts and tissue pieces were analyzed in multiple laboratories by mass spectrometry, which revealed ancient collagen sequences that support a close relation between birds and dinosaurs.
          }, number={5927}, journal={Science}, author={Schweitzer, Mary H. and Zheng, Wenxia and Organ, Chris L. and Avci, Recep and Suo, Zhiyong and Freimark, Lisa M. and Lebleu, Valerie S. and Duncan, Michael B. and Heiden, Matthew G. Vander and Neveu, John M. and et al.}, year={2009}, month={May}, pages={626–631} }
 @article{schweitzer_avci_collier_goodwin_2008, title={Microscopic, chemical and molecular methods for examining fossil specimens}, volume={7}, ISSN={["1777-571X"]}, DOI={10.1016/j.crpv.2008.02.005}, abstractNote={Advances in technology over the past two decades have resulted in unprecedented access to data from biological specimens. These data have expanded our understanding of physical characteristics, physiological, cellular and subcellular processes, and evolutionary relationships at the molecular level and beyond. Paleontological and archaeological sciences have recently begun to apply these technologies to fossil and subfossil representatives of extinct organisms. Data derived from multidisciplinary, non-traditional techniques can be difficult to decipher, and without a basic understanding of the type of information provided by these methods, their usefulness for fossil studies may be overlooked. This review describes some of these powerful new analytical tools, the data that may be accessible through their use, advantages and limitations, and how they can be applied to fossil material to elucidate characteristics of extinct organisms and their paleoecological environments. Des avancées technologiques intervenues au cours des deux dernières décades ont permis d'accéder à des données sans précédent sur des échantillons biologiques. Ces données ont élargi notre compréhension des caractéristiques physiques, des processus physiologiques cellulaires et subcellulaires, ainsi que des relations évolutives au niveau de la molécule et au-delà. Les sciences paléontologiques et archéologiques se sont récemment orientées vers l'application de ces technologies à des représentants fossiles ou subfossiles d'organismes disparus. Les bénéfices de ces techniques, qui sont du domaine de multiples disciplines, sont difficiles à déchiffrer et, sans une connaissance de base du type d'information fourni par ces méthodes, leur utilité pour l'étude des fossiles peut ne pas être bien mesurée. Cet article décrit certains de ces nouveaux outils analytiques puissants, les données qu'ils permettent d'obtenir, leurs avantages et leurs limites, et comment ils peuvent être appliqués au matériel fossile pour élucider les caractéristiques d'organismes disparus et leurs environnements paléoécologiques.}, number={2-3}, journal={Comptes Rendus Palevol}, author={Schweitzer, M.H. and Avci, R. and Collier, T. and Goodwin, M.B.}, year={2008}, month={Apr}, pages={159–184} }
 @article{organ_schweitzer_zheng_freimark_cantley_asara_2008, title={Molecular phylogenetics of mastodon and Tyrannosaurus rex}, volume={320}, ISSN={["0036-8075"]}, DOI={10.1126/science.1154284}, abstractNote={
            We report a molecular phylogeny for a nonavian dinosaur, extending our knowledge of trait evolution within nonavian dinosaurs into the macromolecular level of biological organization. Fragments of collagen α1(I) and α2(I) proteins extracted from fossil bones of
            Tyrannosaurus rex
            and
            Mammut americanum
            (mastodon) were analyzed with a variety of phylogenetic methods. Despite missing sequence data, the mastodon groups with elephant and the
            T. rex
            groups with birds, consistent with predictions based on genetic and morphological data for mastodon and on morphological data for
            T. rex
            . Our findings suggest that molecular data from long-extinct organisms may have the potential for resolving relationships at critical areas in the vertebrate evolutionary tree that have, so far, been phylogenetically intractable.
          }, number={5875}, journal={SCIENCE}, author={Organ, Chris L. and Schweitzer, Mary H. and Zheng, Wenxia and Freimark, Lisa M. and Cantley, Lewis C. and Asara, John M.}, year={2008}, month={Apr}, pages={499–499} }
 @article{asara_schweitzer_2008, title={Response to comment on "protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry"}, volume={319}, number={5859}, journal={Science}, author={Asara, J. M. and Schweitzer, M. H.}, year={2008} }
 @article{asara_schweitzer_cantley_cottrell_2008, title={Response to comment on "protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry"}, volume={321}, number={5892}, journal={Science}, author={Asara, J. M. and Schweitzer, M. H. and Cantley, L. C. and Cottrell, J. S.}, year={2008} }
 @article{schweitzer_suo_avci_asara_allen_arce_horner_2007, title={Analyses of soft tissue from Tyrannosaurus rex suggest the presence of protein}, volume={316}, ISSN={["1095-9203"]}, DOI={10.1126/science.1138709}, abstractNote={
            We performed multiple analyses of
            Tyrannosaurus rex
            (specimen MOR 1125) fibrous cortical and medullary tissues remaining after demineralization. The results indicate that collagen I, the main organic component of bone, has been preserved in low concentrations in these tissues. The findings were independently confirmed by mass spectrometry. We propose a possible chemical pathway that may contribute to this preservation. The presence of endogenous protein in dinosaur bone may validate hypotheses about evolutionary relationships, rates, and patterns of molecular change and degradation, as well as the chemical stability of molecules over time.
          }, number={5822}, journal={SCIENCE}, author={Schweitzer, Mary Higby and Suo, Zhiyong and Avci, Recep and Asara, John M. and Allen, Mark A. and Arce, Fernando Teran and Horner, John R.}, year={2007}, month={Apr}, pages={277–280} }
 @article{schweitzer_elsey_dacke_horner_lamm_2007, title={Do egg-laying crocodilian (Alligator mississippiensis) archosaurs form medullary bone?}, volume={40}, ISSN={["8756-3282"]}, DOI={10.1016/j.bone.2006.10.029}, abstractNote={It is beyond question that Mesozoic dinosaurs, like Aves and Crocodylia, are archosaurs. However, within the archosaurian clade, the origin and distribution of some major features are less clear, particularly with respect to reproductive physiology. Medullary bone, a highly mineralized, bony reproductive tissue present in the endosteal cavities of all extant egg-laying birds thus far examined, has recently been reported in Tyrannosaurus rex. Its presence or absence in extant crocodilians, therefore, may shed light on the timing of its evolutionary appearance. If medullary bone is present in all three taxa, it arose before the three lineages diverged. However, if medullary bone arose after this divergence, it may be present in both extinct dinosaurs and birds, or in birds only. If present in extinct dinosaurs and birds, but not crocodilians, it would indicate that it arose in the common ancestor of this clade, thus adding support to the closer phylogenetic relationship of dinosaurs and birds relative to crocodilians. Thus, the question of whether the crocodilian Alligator mississippiensis forms medullary bone during the production of eggs has important evolutionary significance. Our examination of long bones from several alligators (two alligators with eggs in the oviducts, one that had produced eggs in the past but was not currently in reproductive phase, an immature female and an adult male) shows no differences on the endosteal surfaces of the long bones, and no evidence of medullary bone, supporting the hypothesis that medullary bone first evolved in the dinosaur–bird line, after the divergence of crocodilians from this lineage.}, number={4}, journal={BONE}, author={Schweitzer, M. H. and Elsey, R. M. and Dacke, C. G. and Horner, J. R. and Lamm, E. -T.}, year={2007}, month={Apr}, pages={1152–1158} }
 @misc{asara_garavelli_slatter_schweitzer_freimark_phillips_cantley_2007, title={Interpreting sequences from mastodon and T-rex}, volume={317}, ISSN={["1095-9203"]}, DOI={10.1126/science.317.5843.1324}, abstractNote={J. Asara et al. reported that collagen proteins from well-preserved ancient fossil bones from a 160,000- to 600,000-year-old mastodon and a 68-million-year-old T. rex can be extracted and sequenced (“Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry,” 13 April,}, number={5843}, journal={SCIENCE}, author={Asara, John M. and Garavelli, John S. and Slatter, David A. and Schweitzer, Mary H. and Freimark, Lisa M. and Phillips, Matthew and Cantley, Lewis C.}, year={2007}, month={Sep}, pages={1324–1325} }
 @article{schweitzer_2007, title={New Avenues of Investigation for Old Bones}, volume={13}, ISSN={1431-9276 1435-8115}, url={http://dx.doi.org/10.1017/S1431927607079160}, DOI={10.1017/S1431927607079160}, abstractNote={Extended abstract of a paper presented at Microscopy and Microanalysis 2007 in Ft. Lauderdale, Florida, USA, August 5 – August 9, 2007}, number={S02}, journal={Microscopy and Microanalysis}, publisher={Cambridge University Press (CUP)}, author={Schweitzer, MH}, year={2007}, month={Aug} }
 @article{suo_avci_schweitzer_deliorman_2007, title={Porphyrin as an ideal biomarker in the search for extraterrestrial life}, volume={7}, ISSN={["1531-1074"]}, DOI={10.1089/ast.2006.0120}, abstractNote={A key issue in astrobiological research is identifying target molecules that are unambiguously biological in origin and can be easily detected and recognized. We suggest porphyrin derivatives as an ideal target, because these chromophores are global in distribution and found in virtually all living organisms on Earth, including microorganisms that may approximate the early evolution of life on Earth. We discuss the inherent qualities that make porphyrin ideally suited for astrobiological research and discuss methods for detecting porphyrin molecules in terrestrial sedimentary environments. We present preliminary data to support the use of ToFSIMS as a powerful technique in the identification of porphyrins.}, number={4}, journal={ASTROBIOLOGY}, author={Suo, Zhiyong and Avci, Recep and Schweitzer, Mary Higby and Deliorman, Muhammedin}, year={2007}, month={Aug}, pages={605–615} }
 @article{asara_schweitzer_freimark_phillips_cantley_2007, title={Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry}, volume={316}, ISSN={["1095-9203"]}, DOI={10.1126/science.1137614}, abstractNote={
            Fossilized bones from extinct taxa harbor the potential for obtaining protein or DNA sequences that could reveal evolutionary links to extant species. We used mass spectrometry to obtain protein sequences from bones of a 160,000- to 600,000-year-old extinct mastodon (
            Mammut americanum
            ) and a 68-million-year-old dinosaur (
            Tyrannosaurus rex
            ). The presence of
            T. rex
            sequences indicates that their peptide bonds were remarkably stable. Mass spectrometry can thus be used to determine unique sequences from ancient organisms from peptide fragmentation patterns, a valuable tool to study the evolution and adaptation of ancient taxa from which genomic sequences are unlikely to be obtained.
          }, number={5822}, journal={SCIENCE}, author={Asara, John M. and Schweitzer, Mary H. and Freimark, Lisa M. and Phillips, Matthew and Cantley, Lewis C.}, year={2007}, month={Apr}, pages={280–285} }
 @misc{schweitzer_2007, title={The Sauropods}, volume={2007}, DOI={10.1643/0045-8511(2007)7[234:TSEAP]2.0.CO;2}, abstractNote={THE SAUROPODS: EVOLUTION AND PALEOBIOLOGY. Kristina A. Curry Rogers and Jeffrey A. Wilson (eds). 2005. The University of California Press, Berkeley, California. ISBN 978-0-52024623-2 (hard cover). 358 p. $65.00 (hard cover).—The giant sauropods have captured the imagination of the public since their discovery. Their enormous size and morphological oddities embody the exotic nature of dinosaurs and present conundrums of physiology and biomechanics that have, for decades, challenged scientists who study them. The monophyly of sauropods as a group is unquestioned (Upchurch, 1998; Wilson and Sereno, 1998; Wilson, 2002; Upchurch et al., 2004), and their close relationship to prosauropods as an ancestral taxon is likewise robustly supported. However, relationships within the clade are less clear, a problem exacerbated by fragmentary remains and missing or incomplete skull material that would be diagnostic. Evolutionary relationships aside, this dinosaurian taxon poses many questions that were thought to be unanswerable. However, in the book The Sauropods, edited by K. Curry-Rogers and J. Wilson, many of these issues are addressed, and new light is being shed, not only on relationships, but on many aspects of the paleobiology of the group as a whole. New techniques, analytical approaches, and comparisons, coupled with new sauropod discoveries, are beginning to provide answers to questions regarding growth strategies (Chapter 11), feeding mechanisms and strategies (Chapters 4–6), behavior (Chapter 9) and even reproduction (Chapter 10). Most chapters in the multi-authored book end with a heartfelt dedication to Jack MacIntosh, whose unfailing passion for this wonderful group of animals has inspired many present and future generations of scientists. I am not a morphologist, or an expert in phylogenetic analyses, and sauropods are not the focus of my research. But I love dinosaurs, and I will not soon forget the pleasure of sitting next to Jack at a dinner after one of many meetings celebrating dinosaur diversity. I have never met a nicer, more humble, kind, warm human being—a rarity among academics devoted to obscure and esoteric studies, including paleontology. Jack’s passion for sauropods was and is immediately apparent, but his childlike curiosity for all things dinosaurian is captivating—and motivating as well. He has a gift for encouraging beginning and ‘old guard’ scientists alike, and his enthusiasm radiates to all who study any aspect of dinosaur science. These accolades to an exceptional scientist, and more, a wonderful human being, and the high praise and recognition of his contributions to this discipline, are richly deserved. The book ranges from overly technical in places to an almost folksy discussion of topics. The early chapters in this book are dedicated to the history of scientific investigation of the sauropods, and to the evolutionary relationships between sauropod clades and of sauropods to other dinosaurian taxa. The copious reference list at the end of every chapter provides a comprehensive summary of work done in the area discussed, and provides a wonderful starting place for students of dinosaur biology interested in any area of study. Chapter 1 is a thorough description of diagnostic characters that nest the sauropod clade within Saurischia, and that diagnose individual clades within Sauropoda. It also presents a brief history of the attempts to classify this group of dinosaurs and the various methods employed to do so. It also discusses the various ‘defining’ characters of sauropods, including elongation of cervical vertebrae and adaptations of the limbs to a columnar stance, requirements for terrestrial animals of such great mass. Chapter 2 embraces the outlandish and bizarre features of titanosaurs, arguably one of the most successful of sauropod linages, and describes the geographical and temporal distributions of this clade. CurryRogers segues nicely from the phylogenetic overview of sauropods presented in Chapter 1 to a narrower cladistic analysis of characters defining the titanosaurs within the sauropods. The discussion and diagnosis of Rapetosaurus krausei as a ‘keystone titanosaur’ provides some resolution to the phylogenetic and evolutionary picture of this dominant, widespread, diverse clade. The list of diagnostic characters provided in the appendix is impressive, and forms a robust framework for future phylogenetic hypotheses as new specimens are discovered and described. An informative discussion of fluctuating patterns of sauropod diversity is the focus of Chapter 3. The attempts to distinguish taphonomic artifacts from true evolutionary trends is thoughtful and emphasizes the need for consideration of sedimentary and stratigraphic context when attempting to discern true extinction and/or diversification events vs. number of opportunities to observe. This is not often directly addressed in}, number={1}, journal={Copeia}, author={Schweitzer, M.H.}, year={2007}, month={Feb}, pages={234–237} }
 @article{smejkal_schweitzer_2007, title={Will current technologies enable dinosaur proteomics?}, volume={4}, ISSN={1478-9450 1744-8387}, url={http://dx.doi.org/10.1586/14789450.4.6.695}, DOI={10.1586/14789450.4.6.695}, number={6}, journal={Expert Review of Proteomics}, publisher={Informa UK Limited}, author={Smejkal, Gary B and Schweitzer, Mary H}, year={2007}, month={Dec}, pages={695–699} }
 @article{schweitzer_wittmeyer_horner_2007, title={Soft tissue and cellular preservation in vertebrate skeletal elements from the Cretaceous to the present}, volume={274}, ISSN={["1471-2954"]}, DOI={10.1098/rspb.2006.3705}, abstractNote={
            Soft tissues and cell-like microstructures derived from skeletal elements of a well-preserved
            Tyrannosaurus rex
            (MOR 1125) were represented by four components in fragments of demineralized cortical and/or medullary bone: flexible and fibrous bone matrix; transparent, hollow and pliable blood vessels; intravascular material, including in some cases, structures morphologically reminiscent of vertebrate red blood cells; and osteocytes with intracellular contents and flexible filipodia. The present study attempts to trace the occurrence of these four components in bone from specimens spanning multiple geological time periods and varied depositional environments. At least three of the four components persist in some skeletal elements of specimens dating to the Campanian. Fibrous bone matrix is more altered over time in morphology and less likely to persist than vessels and/or osteocytes. Vessels vary greatly in preservation, even within the same specimen, with some regions retaining pliability and other regions almost crystalline. Osteocytes also vary, with some retaining long filipodia and transparency, while others present with short and stubby filipodia and deeply pigmented nuclei, or are pigmented throughout with no nucleus visible. Alternative hypotheses are considered to explain the origin/source of observed materials. Finally, a two-part mechanism, involving first cross-linking of molecular components and subsequent mineralization, is proposed to explain the surprising presence of
            still
            -soft elements in fossil bone. These results suggest that present models of fossilization processes may be incomplete and that soft tissue elements may be more commonly preserved, even in older specimens, than previously thought. Additionally, in many cases, osteocytes with defined nuclei are preserved, and may represent an important source for informative molecular data.
          }, number={1607}, journal={PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES}, author={Schweitzer, Mary Higby and Wittmeyer, Jennifer L. and Horner, John R.}, year={2007}, month={Jan}, pages={183–197} }
 @article{channing_schweitzer_horner_mceneaney_2005, title={A silicified bird from Quaternary hot spring deposits}, volume={272}, ISSN={["1471-2954"]}, DOI={10.1098/rspb.2004.2989}, abstractNote={
            The first avian fossil recovered from high-temperature hot spring deposits is a three-dimensional external body mould of an American coot (
            Fulica americana
            ) from Holocene sinters of Yellowstone National Park, Wyoming, USA. Silica encrustation of the carcass, feathers and colonizing microbial communities occurred within days of death and before substantial soft tissue degradation, allowing preservation of gross body morphology, which is usually lost under other fossilization regimes. We hypothesize that the increased rate and extent of opal-A deposition, facilitated by either passive or active microbial mediation following carcass colonization, is required for exceptional preservation of relatively large, fleshy carcasses or soft-bodied organisms by mineral precipitate mould formation. We suggest physico-chemical parameters conducive to similar preservation in other vertebrate specimens, plus distinctive sinter macrofabric markers of hot spring subenvironments where these parameters are met.
          }, number={1566}, journal={PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES}, author={Channing, A and Schweitzer, MH and Horner, JR and McEneaney, T}, year={2005}, month={May}, pages={905–911} }
 @article{schweitzer_wittmeyer_avci_pincus_2005, title={Experimental support for an immunological approach to the search for life on other planets}, volume={5}, ISSN={["1557-8070"]}, DOI={10.1089/ast.2005.5.30}, abstractNote={We propose a three-phase approach to test for evidence of life in extraterrestrial samples. The approach capitalizes on the flexibility, sensitivity, and specificity of antibody-antigen interactions. Data are presented to support the first phase, in which various extraction protocols are compared for efficiency, and in which a preliminary suite of antibodies are tested against various antigens. The antigens and antibodies were chosen on the basis of criteria designed to optimize the detection of extraterrestrial biomarkers unique to living or once-living organisms.}, number={1}, journal={ASTROBIOLOGY}, author={Schweitzer, MH and Wittmeyer, J and Avci, R and Pincus, S}, year={2005}, month={Feb}, pages={30–47} }
 @article{schweitzer_wittmeyer_horner_2005, title={Gender-specific reproductive tissue in ratites and Tyrannosaurus rex}, volume={308}, ISSN={["0036-8075"]}, DOI={10.1126/science.1112158}, abstractNote={
            Unambiguous indicators of gender in dinosaurs are usually lost during fossilization, along with other aspects of soft tissue anatomy. We report the presence of endosteally derived bone tissues lining the interior marrow cavities of portions of
            Tyrannosaurus rex
            (Museum of the Rockies specimen number 1125) hindlimb elements, and we hypothesize that these tissues are homologous to specialized avian tissues known as medullary bone. Because medullary bone is unique to female birds, its discovery in extinct dinosaurs solidifies the link between dinosaurs and birds, suggests similar reproductive strategies, and provides an objective means of gender differentiation in dinosaurs.
          }, number={5727}, journal={SCIENCE}, author={Schweitzer, MH and Wittmeyer, JL and Horner, JR}, year={2005}, month={Jun}, pages={1456–1460} }
 @article{schweitzer_chiappe_garrido_lowenstein_pincus_2005, title={Molecular preservation in Late Cretaceous sauropod dinosaur eggshells}, volume={272}, ISSN={["0962-8452"]}, DOI={10.1098/rspb.2004.2876}, abstractNote={Exceptionally preserved sauropod eggshells discovered in Upper Cretaceous (Campanian) deposits in Patagonia, Argentina, contain skeletal remains and soft tissues of embryonic Titanosaurid dinosaurs. To preserve these labile embryonic remains, the rate of mineral precipitation must have superseded post-mortem degradative processes, resulting in virtually instantaneous mineralization of soft tissues. If so, mineralization may also have been rapid enough to retain fragments of original biomolecules in these specimens. To investigate preservation of biomolecular compounds in these well-preserved sauropod dinosaur eggshells, we applied multiple analytical techniques. Results demonstrate organic compounds and antigenic structures similar to those found in extant eggshells.}, number={1565}, journal={PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES}, author={Schweitzer, MH and Chiappe, L and Garrido, AC and Lowenstein, JM and Pincus, SH}, year={2005}, month={Apr}, pages={775–784} }
 @inproceedings{schweitzer_wittmeyer_2005, title={One pretty amazing T.rex : A presentation for "100 years of tyrannosaurus rex}, author={Schweitzer, M.H. and Wittmeyer, J.L.}, editor={Carpenter, K. and Larson, P.Editors}, year={2005} }
 @article{avci_schweitzer_boyd_wittmeyer_arce_calvo_2005, title={Preservation of bone collagen from the late cretaceous period studied by immunological techniques and atomic force microscopy}, volume={21}, ISSN={["0743-7463"]}, DOI={10.1021/la047682e}, abstractNote={Late Cretaceous avian bone tissues from Argentina demonstrate exceptional preservation. Skeletal elements are preserved in partial articulation and suspended in three dimensions in a medium-grained sandstone matrix, indicating unusual perimortem taphonomic conditions. Preservation extends to the microstructural and molecular levels. Bone tissues respond to collagenase digestion and histochemical stains. In situ immunohistochemistry localizes binding sites for avian collagen antibodies in fossil tissues. Immunohistochemical studies do not, however, guarantee the preservation of molecular integrity. A protein may retain sufficient antigenicity for antibody binding even though degradation may render it incapable of original function. Therefore, we have applied atomic force microscopy to address the integrity and functionality of retained organic structures. Collagen pull-off measurements not only support immunochemical evidence for collagen preservation for antibody recognition but also imply preservation of the whole molecular integrity. No appreciable differences in collagen pull-off properties were measured between fossil and extant bone samples under physiological conditions.}, number={8}, journal={LANGMUIR}, author={Avci, R and Schweitzer, MH and Boyd, RD and Wittmeyer, JL and Arce, FT and Calvo, JO}, year={2005}, month={Apr}, pages={3584–3590} }
 @article{schweitzer_wittmeyer_horner_toporski_2005, title={Soft-tissue vessels and cellular preservation in Tyrannosaurus rex}, volume={307}, ISSN={["1095-9203"]}, DOI={10.1126/science.1108397}, abstractNote={
            Soft tissues are preserved within hindlimb elements of
            Tyrannosaurus rex
            (Museum of the Rockies specimen 1125). Removal of the mineral phase reveals transparent, flexible, hollow blood vessels containing small round microstructures that can be expressed from the vessels into solution. Some regions of the demineralized bone matrix are highly fibrous, and the matrix possesses elasticity and resilience. Three populations of microstructures have cell-like morphology. Thus, some dinosaurian soft tissues may retain some of their original flexibility, elasticity, and resilience.
          }, number={5717}, journal={SCIENCE}, author={Schweitzer, MH and Wittmeyer, JL and Horner, JR and Toporski, JK}, year={2005}, month={Mar}, pages={1952–1955} }
 @article{schweitzer_2005, title={Warm-blooded}, volume={114}, number={4}, journal={Natural History Magazine}, author={Schweitzer, M. H.}, year={2005}, pages={50–51} }
 @article{avci_schweitzer_boyd_wittmeyer_steele_toporski_beech_arce_spangler_cole_et al._2004, title={Comparison of antibody-antigen interactions on collagen measured by conventional immunological techniques and atomic force microscopy}, volume={20}, ISSN={["0743-7463"]}, DOI={10.1021/la036376i}, abstractNote={We have developed a means of using atomic force microscopy (AFM) to repeatedly localize a small area of interest (4 x 4 microm(2)) within a 0.5-cm(2) area on a heterogeneous sample, to obtain and localize high-resolution images and force measurements on nonideal samples (i.e., samples that better reflect actual biological systems, not prepared on atomically flat surfaces). We demonstrate the repeated localization and measurement of unbinding forces associated with antibody--antigen (ab--ag) interactions, by applying AFM in air and in liquid to visualize and measure polyclonal ab--ag interactions, using chicken collagen as a model system. We demonstrate that molecular interactions, in the form of ab--ag complexes, can be visualized by AFM when secondary antibodies are conjugated to 20-nm colloidal gold particles. We then compare those results with established immunological techniques, to demonstrate broader application of AFM technology to other systems. Data from AFM studies are compared with results obtained using immunological methods traditionally employed to investigate ab--ag interactions, including enzyme-linked immunosorbent assay, immunoblotting, and in situ immunofluorescence. Finally, using functionalized AFM tips with a flexible tether [poly(ethylene glycol) 800] to which a derivatized antibody was attached, we analyzed force curve data to measure the unbinding force of collagen antibody from its antigen, obtaining a value of approximately 90 +/- 40 pN with a MatLab code written to automate the analyses of force curves obtained in force--volume mode. The methodology we developed for embedded collagen sections can be readily applied to the investigation of other receptor--ligand interactions.}, number={25}, journal={LANGMUIR}, author={Avci, R and Schweitzer, M and Boyd, RD and Wittmeyer, J and Steele, A and Toporski, J and Beech, W and Arce, FT and Spangler, B and Cole, KM and et al.}, year={2004}, month={Dec}, pages={11053–11063} }
 @article{higby schweitzer_2004, title={Molecular paleontology: some current advances and problems}, volume={90}, ISSN={0753-3969}, url={http://dx.doi.org/10.1016/j.annpal.2004.02.001}, DOI={10.1016/j.annpal.2004.02.001}, abstractNote={Molecular paleontology is the application of molecular analytical techniques to fossil or subfossil material in order to test for the presence of original biomolecules. These molecules may be proteins, DNA, carbohydrates or lipids, or their diagenetic products. Molecular investigations of fossil specimens seek to assess if any original chemical/molecular material persists, whether or not this material retains systematic significance, if molecular preservation can be or is linked to morphological preservation, and to understand degradation patterns for biomolecules that may enter the geologic record. La paléontologie moléculaire est l'application des techniques d'analyse moléculaire à des matériaux fossiles ou subfossiles de façon à y tester la présence de biomolécules originelles. Ces molécules peuvent être des protéines, de l'ADN, des hydrates de carbone ou des lipides, ou les produits de leur diagenèse. Les analyses moléculaires de matériels fossiles cherchent à vérifier si quelques structures chimiques ou moléculaires originelles persistent, si elles conservent ou non une valeur systématique, et si la conservation moléculaire peut être ou est effectivement liée à la conservation de la morphologie. Enfin elles permettent de comprendre les voies de dégradation de biomolécules susceptibles de s'intégrer au registre géologique. Bien qu'il soit exact que les biomolécules riches en information soient en général dégradées au cours de la diagenèse et de la fossilisation des tissus, bien des facteurs modulent ces processus de telle sorte que, dans des circonstances très rares, il est possible que des fragments identifiables des biomolécules originelles soient conservés dans les tissus fossilisés. Beaucoup d'informations sur les organismes éteints peuvent être révélées par l'étude de ces restes moléculaires, particulièrement dans la mesure où les techniques continuent à gagner en spécificité et en sensibilité. Grâce au potentiel que ces fragments moléculaires ont conservé pour nous permettre de mieux comprendre les organismes éteints, les recherches futures devraient porter non seulement sur l'amélioration des techniques que nous employons pour étudier le matériel fossile, mais aussi sur l'élucidation des paramètres environnementaux qui contribuent à une bonne conservation, et sur la compréhension des modifications chimiques potentielles, de façon à mieux lier les produits de dégradation à leurs molécules d'origine. Ce type d'investigations nécessite clairement d'accroître les interactions transdisciplinaires et la communication entre divers domaines de recherche.}, number={2}, journal={Annales de Paléontologie}, publisher={Elsevier BV}, author={Higby Schweitzer, Mary}, year={2004}, month={Apr}, pages={81–102} }
 @article{chin_eberth_schweitzer_rando_sloboda_horner_2003, title={Remarkable Preservation of Undigested Muscle Tissue Within a Late Cretaceous Tyrannosaurid Coprolite from Alberta, Canada}, volume={18}, ISSN={0883-1351}, url={http://dx.doi.org/10.1669/0883-1351(2003)018<0286:rpoumt>2.0.co;2}, DOI={10.1669/0883-1351(2003)018<0286:rpoumt>2.0.co;2}, abstractNote={Abstract Exceptionally detailed soft tissues have been identified within the fossilized feces of a large Cretaceous tyrannosaurid. Microscopic cord-like structures in the coprolitic ground mass are visible in thin section and with scanning electron microscopy. The morphology, organization, and context of these structures indicate that they are the fossilized remains of undigested muscle tissue. This unusual discovery indicates specific digestive and taphonomic conditions, including a relatively short gut-residence time, rapid lithification, and minimal diagenetic recrystallization. Rapid burial of the feces probably was facilitated by a flood event on the ancient coastal lowland plain on which the fecal mass was deposited.}, number={3}, journal={PALAIOS}, publisher={Society for Sedimentary Geology}, author={Chin, K. and Eberth, D. A. and Schweitzer, M. H. and Rando, T. A. and Sloboda, W. J. and Horner, J. R.}, year={2003}, month={Jun}, pages={286–294} }
 @article{schweitzer_2003, title={The future of molecular paleontology}, volume={5}, number={2}, journal={Paleontologica Electronica}, author={Schweitzer, M.H.}, year={2003}, pages={editorial 2} }
 @inbook{chapman_matthews_schweitzer_horner_2002, place={Alexandria, VA}, title={Applying 21st century technology to very old animals}, ISBN={9780922152629}, booktitle={Dinosaurs: The Science Behind the Stories}, publisher={Society of Vertebrate Paleontology, The Paleontological Society, American Geological Institute}, author={Chapman, R.E. and Matthews, N.A. and Schweitzer, M.H. and Horner, C.C.}, editor={Scotchmoor, J.G. and Springer, D.A. and Breithaupt, B.H. and Fiorillo, T.Editors}, year={2002}, pages={137–144} }
 @article{jackson_schweitzer_schmitt_2006, title={Dinosaur eggshell study using scanning electron microscopy}, volume={24}, ISSN={0161-0457 1932-8745}, url={http://dx.doi.org/10.1002/sca.4950240501}, DOI={10.1002/sca.4950240501}, abstractNote={AbstractVisualization and analysis of structural features in fossil dinosaur eggs by scanning electron microscopy augment information from traditional petrographic light microscopy. Comparison of characteristics in fossil and modern eggshells allows inferences to be made regarding dinosaur reproductive biology, physiology, and evolutionary relationships. Assessment of diagenetic alteration of primary eggshell calcite structure that occurs during fossilization provides important information necessary for taxonomic identification and paleoenvironmental interpretations.}, number={5}, journal={Scanning}, publisher={Wiley}, author={Jackson, Frankie D. and Schweitzer, Mary H. and Schmitt, James G.}, year={2006}, month={Dec}, pages={217–223} }
 @article{schweitzer_hill_asara_lane_pincus_2002, title={Identification of Immunoreactive Material in Mammoth Fossils}, volume={55}, ISSN={0022-2844 1432-1432}, url={http://dx.doi.org/10.1007/s00239-002-2365-6}, DOI={10.1007/s00239-002-2365-6}, abstractNote={The fossil record represents a history of life on this planet. Attempts to obtain molecular information from this record by analysis of nucleic acids found within fossils of extreme age have been unsuccessful or called into question. However, previous studies have demonstrated the long-term persistence of peptides within fossils and have used antibodies to extant proteins to demonstrate antigenic material. In this study we address two questions: Do immunogenic/antigenic materials persist in fossils? and; Can fossil material be used to raise antibodies that will cross-react with extant proteins? We have used material extracted from a well-preserved 100,000–300,000-year-old mammoth skull to produce antisera. The specificity of the antisera was tested by ELISA, western blotting, and immunohistochemistry. It was demonstrated that antisera reacted specifically with the fossils and not the surrounding sediments. Reactivity of antisera with modern proteins and tissues was also demonstrated, as was the ability to detect evolutionary relationships via antibody–antigen interactions. Mass spectrometry demonstrated the presence of amino acids and specific peptides within the fossil. Peptides were purified by anion-exchange chromatography and sequenced by tandem mass spectrometry. The collagen-derived peptides may have been the source of at least some of the immunologic reactivity, but the antisera identified molecules that were not observed by mass spectrometry, indicating that immunologic methods may have greater sensitivity. Although the presence of peptides and amino acids was demonstrated, the exact nature of the antigenic material was not fully clarified. This report demonstrates that antibodies may be used to obtain information from the fossil record.}, number={6}, journal={Journal of Molecular Evolution}, publisher={Springer Science and Business Media LLC}, author={Schweitzer, Mary and Hill, Christopher L. and Asara, John M. and Lane, William S. and Pincus, Seth H.}, year={2002}, month={Dec}, pages={696–705} }
 @article{schweitzer_jackson_chiappe_schmitt_calvo_rubilar_2002, title={Late Cretaceous avian eggs with embryos from Argentina}, volume={22}, ISSN={0272-4634 1937-2809}, url={http://dx.doi.org/10.1671/0272-4634(2002)022[0191:lcaewe]2.0.co;2}, DOI={10.1671/0272-4634(2002)022[0191:lcaewe]2.0.co;2}, abstractNote={MARY H. SCHWEITZER1,2, FRANKIE D. JACKSON2, LUIS M. CHIAPPE3, JAMES G. SCHMITT2, JORGE O. CALVO4, and DAVID E. RUBILAR5 1Department of Microbiology, Montana State University, Bozeman, Montana 59717, schweitz@montana.edu; 2Department of Earth Sciences and Museum of the Rockies, Montana State University, Bozeman, Montana 59717; 3Natural History Museum of Los Angeles, Los Angeles, California 90007; 4Museo de Geologia y Paleontologia, Universidad Nacional del Comahue, Neuqu6n, Argentina; 5Instituto de Geociencias, Universidad Austral de Chile, Casilla 567, Valdivia, Chile, and Secci6n Paleontologia, Museo Nacional de Historia Natural, Casilla 787, Santiago, Chile}, number={1}, journal={Journal of Vertebrate Paleontology}, publisher={Informa UK Limited}, author={Schweitzer, Mary H. and Jackson, Frankie D. and Chiappe, Luis M. and Schmitt, James G. and Calvo, Jorge O. and Rubilar, David E.}, year={2002}, month={Mar}, pages={191–195} }
 @article{schweitzer_marshall_2001, title={A molecular model for the evolution of endothermy in the theropod-bird lineage}, volume={291}, ISSN={0022-104X 1097-010X}, url={http://dx.doi.org/10.1002/jez.1132}, DOI={10.1002/jez.1132}, abstractNote={AbstractEctothermy is a primitive state; therefore, a shared common ancestor of crocodiles, dinosaurs, and birds was at some point ectothermic. Birds, the extant descendants of the dinosaurs, are endothermic. Neither the metabolic transition within this lineage nor the place the dinosaurs held along the ectothermic‐endothermic continuum is defined. This paper presents a conceptual model for the evolution of endothermy in the theropod‐bird lineage. It is recognized that other animals (some fish, insects, etc.) are functionally endothermic. However, endothermy in other clades is beyond the scope of this paper, and we address the onset of endothermy in only the theropod/bird clade. The model begins with simple changes in a single gene of a common ancestor, and it includes a series of concomitant physiological and morphological changes, beginning perhaps as early as the first archosaurian common ancestor of dinosaurs and crocodiles. These changes continued to accumulate within the theropod‐avian lineage, were maintained and refined through selective forces, and culminated in extant birds. Metabolic convergence or homoplasy is evident in the inherent differences between the endothermy of mammals and the endothermy of extant birds. The strength and usefulness of this model lie in the phylogenetic, genetic, evolutionary, and adaptive plausibility of each of the suggested developmental steps toward endothermy. The model, although conceptual in nature, relies on an extensive knowledge base developed by numerous workers in each of these areas. In addition, the model integrates known genetic, metabolic, and developmental aspects of extant taxa that phylogenetically bracket theropod dinosaurs for comparison with information derived from the fossil record of related extinct taxa. J. Exp. Zool. (Mol. Dev. Evol.) 291:317–338, 2001. © 2001 Wiley‐Liss, Inc.}, number={4}, journal={Journal of Experimental Zoology}, publisher={Wiley}, author={Schweitzer, Mary Higby and Marshall, Cynthia Lee}, year={2001}, pages={317–338} }
 @inproceedings{schweitzer_2001, place={New Haven, Connecticut}, title={Evolutionary implications of possible protofeather structures associated with a specimen of Shuvuuia deserti}, booktitle={New Perspectives on the Origin and Evolution of Birds: Proceedings of the International Symposium in Honor of John H. Ostrom}, publisher={Peabody Museum of Natural History Special Publication}, author={Schweitzer, M.H.}, editor={Gauthier, J.Editor}, year={2001}, pages={181–194} }
 @inproceedings{steele_mckay_allen_thomas-keprta_warmflash_schweitzer_priscu_hedgecock_pincus_sears_et al._2001, place={Houston, TX}, series={LPI contribution}, title={Mars immunoassay life detection instrument for astrobiology (MILDI)}, booktitle={Lunar and Planetary Science XXXII : papers presented at the thirty-second Lunar and Planetary Science Conference : March 12-16, 2001, Houston, Texas}, publisher={Lunar and Planetary Institute}, author={Steele, A. and McKay, D. and Allen, C. and Thomas-Keprta, K. and Warmflash, D. and Schweitzer, M.H. and Priscu, J and Hedgecock, J and Pincus, S. and Sears, J. and et al.}, year={2001}, collection={LPI contribution} }
 @inproceedings{steele_toporski_mckay_schweitzer_pincus_pérez-mercader_parro_2001, place={Noordwijk}, series={European Space Agency}, title={Micro-array assay for solar system exploration}, booktitle={Exo-/astro-biology : proceedings of the first European workshop, 21-23 May 2001, ESRIN, Frascati, Italy}, publisher={European Space Agency Publications Division}, author={Steele, A. and Toporski, J. and McKay, D.S. and Schweitzer, M.H. and Pincus, S. and Pérez-Mercader, J. and Parro, V.G.}, year={2001}, pages={91–97}, collection={European Space Agency} }
 @article{schweitzer_watt_avci_knapp_chiappe_norell_marshall_1999, title={Beta-keratin specific immunological reactivity in feather-like structures of the Cretaceous Alvarezsaurid,Shuvuuia deserti}, volume={285}, ISSN={0022-104X 1097-010X}, url={http://dx.doi.org/10.1002/(SICI)1097-010X(19990815)285:2<146::AID-JEZ7>3.0.CO;2-A}, DOI={10.1002/(sici)1097-010x(19990815)285:2<146::aid-jez7>3.3.co;2-1}, number={2}, journal={Journal of Experimental Zoology}, publisher={Wiley}, author={Schweitzer, M.H. and Watt, J.A. and Avci, R. and Knapp, L. and Chiappe, L. and Norell, M. and Marshall, M.}, year={1999}, month={Aug}, pages={146–157} }
 @article{higby schweitzer_horner_1999, title={Intravascular microstructures in trabecular bone tissues of Tyrannosaurus rex}, volume={85}, ISSN={0753-3969}, url={http://dx.doi.org/10.1016/s0753-3969(99)80013-5}, DOI={10.1016/s0753-3969(99)80013-5}, abstractNote={Histological analyses of trabecular tissue from the limb bones of a Tyrannosaurus rex revealed the presence of small (average 25 μm) round microstructures in the vascular channels of the bone. These bony tissues otherwise evidenced minimal diagenetic change, and no secondary mineral deposition was observed in the vessel channels. While we have published analyses of the bony tissues of this specimen, we have not published data obtained on these small intravascular microstructures. Several characteristics link these microstructures to endogenous biological components, although their origin is not confirmed, and several hypotheses are considered. A discussion of the meaning of the term 'organic preservation' and a suggestion of criteria that should be met to be described as such is included. L'examen histologique d'os trabéculaire provenant d'os longs de Tyrannosaurus rex a révélé la présence de petites microstructures arrondies (de 25 μm en moyenne) dans la lumière des canaux vasculaires. Ces tissus osseux ne présentent par ailleurs qu'un minimum de transformations diagénétiques, et l'on n'a pas observé de dépôts secondaires de minéraux dans la lumière des canaux vasculaires. Nous avons déjà publié des analyses concernant ce tissu osseux mais nous présentons ici les premières données concernant les microstructures globulaires observées dans la lumière des canaux vasculaires. Plusieurs caractéristiques les rapprochent de composés biologiques d'origine endogène et bien que leur origine et signification ne puissent encore être démontrées avec certitude, nous passons en revue plusieurs hypothèses les concernant. Ceci nous conduit à discuter ce que l'on entend par « conservation organiqueet à proposer des critères à remplir pour que ce type de conservation soit acceptable en tant que tel en paléontologie.}, number={3}, journal={Annales de Paléontologie}, publisher={Elsevier BV}, author={Higby Schweitzer, Mary and Horner, John R.}, year={1999}, month={Jul}, pages={179–192} }
 @article{schweitzer_watt_avci_forster_krause_knapp_rogers_beech_marshall_1999, title={Keratin immunoreactivity in the Late Cretaceous bird Rahonavis ostromi}, volume={19}, ISSN={0272-4634 1937-2809}, url={http://dx.doi.org/10.1080/02724634.1999.10011183}, DOI={10.1080/02724634.1999.10011183}, abstractNote={ABSTRACT Immunohistochemical studies, supported by additional lines of evidence, suggest that original proteinaceous components of keratin claw sheath material may be preserved in the pedal ungual phalanx associated with the primitive bird, Rahonavis ostromi, from the Late Cretaceous of Madagascar. This conclusion is based upon immunohistochemical analyses, and supported by brightfield, transmission, and scanning electron microscopy, mass spectrometry, and x-ray photoelectron spectroscopy. Although keratinous structures such as hair, nails, claws, scales and feathers have been identified in the fossil record, these identifications were based on morphological similarity rather than molecular analyses. Chemical or immunological evidence for the survival of keratin has not previously been established in fossils older than ~33,000 BP. This study demonstrates immunological staining and amino acid composition consistent with the presence of fragments of beta keratin, a protein family unique to reptiles and bird...}, number={4}, journal={Journal of Vertebrate Paleontology}, publisher={Informa UK Limited}, author={Schweitzer, Mary H. and Watt, John A. and Avci, Recep and Forster, Catherine A. and Krause, David W. and Knapp, Loren and Rogers, Raymond R. and Beech, Iwona and Marshall, Mark}, year={1999}, month={Dec}, pages={712–722} }
 @article{hill_schweitzer_1999, title={Mammoth (Mammuthus) from the Doden Gravels, Eastern Montana: biometric and molecular analyses}, volume={16}, journal={Current Research in the Pleistocene}, author={Hill, C.L. and Schweitzer, M.}, year={1999}, pages={120–123} }
 @inproceedings{schweitzer_marshall_barnard_bohle_arnold_starkey_1997, place={Philadelphia, PA}, title={Blood from a stone?}, booktitle={Dinofest International : proceedings of a symposium held at Arizona State University}, publisher={Academy of Natural Sciences}, author={Schweitzer, M.H. and Marshall, M. and Barnard, D. and Bohle, S. and Arnold, K. and Starkey, JR}, editor={Wolberg, D. and Stump, E. and Rosenberg, G.D.Editors}, year={1997}, pages={101–104} }
 @article{schweitzer_marshall_carron_bohle_busse_arnold_barnard_horner_starkey_1997, title={Heme compounds in dinosaur trabecular bone}, volume={94}, ISSN={0027-8424 1091-6490}, url={http://dx.doi.org/10.1073/pnas.94.12.6291}, DOI={10.1073/pnas.94.12.6291}, abstractNote={
            Six independent lines of evidence point to the existence of heme-containing compounds and/or hemoglobin breakdown products in extracts of trabecular tissues of the large theropod dinosaur
            Tyrannosaurus rex
            . These include signatures from nuclear magnetic resonance and electron spin resonance that indicate the presence of a paramagnetic compound consistent with heme. In addition, UV/visible spectroscopy and high performance liquid chromatography data are consistent with the Soret absorbance characteristic of this molecule. Resonance Raman profiles are also consistent with a modified heme structure. Finally, when dinosaurian tissues were extracted for protein fragments and were used to immunize rats, the resulting antisera reacted positively with purified avian and mammalian hemoglobins. The most parsimonious explanation of this evidence is the presence of blood-derived hemoglobin compounds preserved in the dinosaurian tissues.
          }, number={12}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Schweitzer, M. H. and Marshall, M. and Carron, K. and Bohle, D. S. and Busse, S. C. and Arnold, E. V. and Barnard, D. and Horner, J. R. and Starkey, J. R.}, year={1997}, month={Jun}, pages={6291–6296} }
 @inbook{schweitzer_lessom_1997, title={Jurassic Park}, booktitle={The Encyclopedia of Dinosaurs}, publisher={Academic Press}, author={Schweitzer, M.H. and Lessom, D.}, editor={Currie, P.J. and Padian, K.Editors}, year={1997}, pages={385–387} }
 @inbook{schweitzer_1997, title={Molecular paleontology: rationale and techniques for the study of ancient molecules}, booktitle={The Complete Dinosaur}, publisher={Indiana University Press}, author={Schweitzer, M.H.}, editor={Farlow, J.O. and Brett-Surman, M.K.Editors}, year={1997}, pages={137–149} }
 @article{schweitzer_johnson_zocco_horner_starkey_1997, title={Preservation of biomolecules in cancellous bone of Tyrannosaurus rex}, volume={17}, ISSN={0272-4634 1937-2809}, url={http://dx.doi.org/10.1080/02724634.1997.10010979}, DOI={10.1080/02724634.1997.10010979}, abstractNote={ABSTRACT An exceptionally well preserved specimen of the tyrannosaurid dinosaur Tyrannosaurus rex Osborn shows little evidence of permineralization or other diagenetic effects. It appears that the cancellous bone tissues of the specimen may have been protected from water infiltration or mineral deposition by the very dense cortical bone which surrounds them. The cancellous tissues provided an opportunity to test the hypothesis that indigenous biomolecules might be preserved over the course of millions of years under the appropriate conditions. HPLC analysis of extracts from the bone tissues revealed the presence of molecules with light absorbance maxima consistent with nucleic acids and peptides/proteins. Analyses of bone extracts for amino acid content yielded ratios similar to those found for modern ostrich and horse bone. A high molar glycine ratio and the presence of hydroxylysine peaks in bony tissue samples from the T. rex suggests the presence of collagen type I remnants. Results indicate that the ...}, number={2}, journal={Journal of Vertebrate Paleontology}, publisher={Informa UK Limited}, author={Schweitzer, Mary Higby and Johnson, Craig and Zocco, Thomas G. and Horner, John R. and Starkey, Jean R.}, year={1997}, month={Jun}, pages={349–359} }
 @article{hedges_schweitzer_1995, title={Detecting dinosaur DNA}, volume={268}, ISSN={0036-8075 1095-9203}, url={http://dx.doi.org/10.1126/science.7761839}, DOI={10.1126/science.7761839}, number={5214}, journal={Science}, publisher={American Association for the Advancement of Science (AAAS)}, author={Hedges, S. and Schweitzer, M.}, year={1995}, month={May}, pages={1191–1192} }