• Comparative and demographic analysis of orang-utan genomes

      Locke, Devin P.; Hillier, LaDeana W.; Warren, Wesley C.; Worley, Kim C.; Nazareth, Lynne V.; Muzny, Donna M.; Yang, Shiaw-Pyng; Wang, Zhengyuan; Chinwalla, Asif T.; Minx, Pat; et al. (2011)
      ‘Orang-utan’ is derived from a Malay term meaning ‘man of the forest’ and aptly describes the southeast Asian great apes native to Sumatra and Borneo. The orang-utan species, Pongo abelii (Sumatran) and Pongo pygmaeus (Bornean), are the most phylogenetically distant great apes from humans, thereby providing an informative perspective on hominid evolution. Here we present a Sumatran orang-utan draft genome assembly and short read sequence data from five Sumatran and five Bornean orang-utan genomes. Our analyses reveal that, compared to other primates, the orang-utan genome has many unique features. Structural evolution of the orang-utan genome has proceeded much more slowly than other great apes, evidenced by fewer rearrangements, less segmental duplication, a lower rate of gene family turnover and surprisingly quiescent Alu repeats, which have played a major role in restructuring other primate genomes. We also describe a primate polymorphic neocentromere, found in both Pongo species, emphasizing the gradual evolution of orang-utan genome structure. Orang-utans have extremely low energy usage for a eutherian mammal1, far lower than their hominid relatives. Adding their genome to the repertoire of sequenced primates illuminates new signals of positive selection in several pathways including glycolipid metabolism. From the population perspective, both Pongo species are deeply diverse; however, Sumatran individuals possess greater diversity than their Bornean counterparts, and more species-specific variation. Our estimate of Bornean/Sumatran speciation time, 400,000 years ago, is more recent than most previous studies and underscores the complexity of the orang-utan speciation process. Despite a smaller modern census population size, the Sumatran effective population size (Ne) expanded exponentially relative to the ancestral Ne after the split, while Bornean Ne declined over the same period. Overall, the resources and analyses presented here offer new opportunities in evolutionary genomics, insights into hominid biology, and an extensive database of variation for conservation efforts.
    • Depositional diseases

      Graham, E.A.; Burns, Rachel E.; Ossiboff, R. J.; Garner, Michael M.; Jacobson, Elliott R. (CRC Press, 2021)
      This book accompanies Infectious Diseases and Pathology of Reptiles, Second Edition to cover noninfectious diseases of reptiles, meeting the need for a similar, authoritative single-source reference. The volume features color photos of normal anatomy and histology, as well as gross, light, and electron microscopic imagery of diseases. Subjects range from neoplasia, nutrition, and metabolic disease, and deposition disorders to developmental anomalies, trauma, and physical diseases, and the unique contribution of paleopathology and diseases of bone. Each chapter is supported by numerous figures, many of which are unique and cannot be found in the published literature. Readers will note that some of the chapters are based on organ system, a trend that will continue into the next edition to encompass all of the basic organ systems. This book holds the most information ever accrued into one publication on noninfectious diseases and pathology of this class of animals, providing information on every aspect of the anatomy, pathophysiology, and differential diagnosis. With up-to-the-minute data, a never-before-seen collection of images, and a stellar panel of contributors, Noninfectious Diseases and Pathology of Reptiles is the definitive resource for veterinarians, biologists, and researchers involved in the study of reptile diseases.
    • Sex-specific epigenetic profile of inner cell mass of mice conceived in vivo or by IVF

      Ruggeri, Elena; Lira-Albarrán, Saúl; Grow, Edward J; Liu, Xiaowei; Harner, Royce; Maltepe, Emin; Ramalho-Santos, Miguel; Donjacour, Annemarie; Rinaudo, Paolo (2020)
      …Animal studies indicate that IVF offspring display metabolic alterations, including hypertension, glucose intolerance and cardiac hypertrophy, often in a sexual dimorphic fashion. The detailed nature of epigenetic changes following in-vitro culture is, however, unknown. This study was performed to evaluate the epigenetic (using whole-genome bisulfite sequencing (WGBS) and assay for transposase-accessible chromatin using sequencing (ATAC-seq)) and transcriptomic changes (using RNA-seq) occurring in the inner cell mass (ICM) of male or female mouse embryos generated in vivo or by IVF....
    • Wildlife-microbiome interactions and disease: Exploring opportunities for disease mitigation across ecological scales

      Williams, Candace L.; Caraballo-Rodríguez, Andrés Mauricio; Allaband, Celeste; Zarrinpar, Amir; Knight, Rob; Gauglitz, Julia M. (2018)
      … we will examine how the microbiome influences gastrointestinal disorders, metabolic dysregulation, reproduction, and disease susceptibility in captive wildlife. Investigation of wildlife, and specifically captive wildlife, affords a unique opportunity to gain understanding of the broad diversity of the associated microbiota and learn from nature’s molecular and microbial responses to disease. Studies like these could lead to the discovery of new interventions, ranging from dietary changes to the use of microbes or their natural products as treatment…