@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={Abstract}, 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{voegele_boles_ullmann_schroeter_zheng_lacovara_2022, title={Soft Tissue and Biomolecular Preservation in Vertebrate Fossils from Glauconitic, Shallow Marine Sediments of the Hornerstown Formation, Edelman Fossil Park, New Jersey}, volume={11}, ISSN={["2079-7737"]}, DOI={10.3390/biology11081161}, abstractNote={Endogenous biomolecules and soft tissues are known to persist in the fossil record. To date, these discoveries derive from a limited number of preservational environments, (e.g., fluvial channels and floodplains), and fossils from less common depositional environments have been largely unexplored. We conducted paleomolecular analyses of shallow marine vertebrate fossils from the Cretaceous–Paleogene Hornerstown Formation, an 80–90% glauconitic greensand from Jean and Ric Edelman Fossil Park in Mantua Township, NJ. Twelve samples were demineralized and found to yield products morphologically consistent with vertebrate osteocytes, blood vessels, and bone matrix. Specimens from these deposits that are dark in color exhibit excellent histological preservation and yielded a greater recovery of cells and soft tissues, whereas lighter-colored specimens exhibit poor histology and few to no cells/soft tissues. Additionally, a well-preserved femur of the marine crocodilian Thoracosaurus was found to have retained endogenous collagen I by immunofluorescence and enzyme-linked immunosorbent assays. Our results thus not only corroborate previous findings that soft tissue and biomolecular recovery from fossils preserved in marine environments are possible but also expand the range of depositional environments documented to preserve endogenous biomolecules, thus broadening the suite of geologic strata that may be fruitful to examine in future paleomolecular studies.}, number={8}, journal={BIOLOGY-BASEL}, author={Voegele, Kristyn K. and Boles, Zachary M. and Ullmann, Paul V and Schroeter, Elena R. and Zheng, Wenxia and Lacovara, Kenneth J.}, year={2022}, month={Aug} }
 @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{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}, 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{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={Abstract}, 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{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={Abstract}, 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={Abstract}, 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{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}, 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.}, 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_sjovall_zheng_uvdal_engdahl_moyer_gren_kamezaki_et al._2017, title={Biochemistry and adaptive colouration of an exceptionally preserved juvenile fossil sea turtle}, volume={7}, journal={Scientific Reports}, author={Lindgren, J. and Kuriyama, T. and Madsen, H. and Sjovall, P. and Zheng, W. X. and Uvdal, P. and Engdahl, A. and Moyer, A. E. and Gren, J. A. and Kamezaki, N. and et al.}, year={2017} }
 @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{schweitzer_zheng_zanno_werning_sugiyama_2016, title={Chemistry supports the identification of gender-specific reproductive tissue in Tyrannosaurus rex}, volume={6}, journal={Scientific Reports}, author={Schweitzer, M. H. and Zheng, W. X. and Zanno, L. and Werning, S. and Sugiyama, T.}, year={2016} }
 @article{moyer_zheng_schweitzer_2016, title={Keratin durability has implications for the fossil record: Results from a 10 year feather degradation experiment}, volume={11}, number={7}, journal={PLoS One}, author={Moyer, A. E. and Zheng, W. X. and Schweitzer, M. H.}, year={2016} }
 @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}, 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}, number={2}, journal={PLoS One}, author={Schweitzer, M. H. and Moyer, A. E. and Zheng, W. X.}, year={2016} }
 @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{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}, journal={Scientific Reports}, author={Moyer, A. E. and Zheng, W. X. and Johnson, E. A. and Lamanna, M. C. and Li, D. Q. and Lacovara, K. J. and Schweitzer, M. H.}, year={2014} }
 @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} }
 @article{weaver_doguzhaeva_lawver_tacker_ciampaglio_crate_zheng_2011, title={Characterization of Organics Consistent with beta-Chitin Preserved in the Late Eocene Cuttlefish Mississaepia mississippiensis}, volume={6}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0028195}, abstractNote={Background Preservation of original organic components in fossils across geological time is controversial, but the potential such molecules have for elucidating evolutionary processes and phylogenetic relationships is invaluable. Chitin is one such molecule. Ancient chitin has been recovered from both terrestrial and marine arthropods, but prior to this study had not been recovered from fossil marine mollusks. Methodology/Principal Findings Organics consistent with β-chitin are recovered in cuttlebones of Mississaepia mississippiensis from the Late Eocene (34.36 million years ago) marine clays of Hinds County, Mississippi, USA. These organics were determined and characterized through comparisons with extant taxa using Scanning Electron Microscopy/Energy Dispersive Spectrometry (SEM/EDS), Field Emission Scanning Electron Microscopy (Hyperprobe), Fourier Transmission Infrared Spectroscopy (FTIR) and Immunohistochemistry (IHC). Conclusions/Significance Our study presents the first evidence for organics consistent with chitin from an ancient marine mollusk and discusses how these organics have been degraded over time. As mechanisms for their preservation, we propose that the inorganic/organic lamination of the cuttlebone, combined with a suboxic depositional environment with available free Fe2+ ions, inhibited microbial or enzymatic degradation.}, number={11}, journal={PLOS ONE}, author={Weaver, Patricia G. and Doguzhaeva, Larisa A. and Lawver, Daniel R. and Tacker, R. Christopher and Ciampaglio, Charles N. and Crate, Jon M. and Zheng, Wenxia}, year={2011}, month={Nov} }
 @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}, 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} }