@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{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{cleland_voegele_schweitzer_2012, title={Empirical evaluation of bone extraction protocols}, volume={7}, number={2}, journal={PLoS One}, author={Cleland, T. P. and Voegele, K. and Schweitzer, M. H.}, year={2012} }
 @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{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} }
 @article{boyd_cleland_novas_2011, title={Osteogenesis, homology, and function of the intercostal plates in ornithischian dinosaurs (Tetrapoda, Sauropsida)}, volume={130}, number={4}, journal={Zoomorphology}, author={Boyd, C. A. and Cleland, T. P. and Novas, F.}, year={2011}, pages={305–313} }