High-speed Developments in Avian Genomics

Until recently, definitions of avian genome structure and function were based solely on our knowledge of the chicken genome. The expansion of genomic studies to include nonmodel avian species allows us not only to refine those definitions but also to begin collecting the necessary resources to initiate a truly ecological genomics of birds. In this article we review new genomic technologies that will speed up the investigation of avian genome function. The streamlined nature of avian genomes implies that large-scale transcriptional analyses, studies of the role of regulatory elements and of developmental genes, and even the annotation of avian genomes will yield interesting surprises. We review promising methods used to investigate genome evolution in birds as well as the means by which to integrate functional genomics approaches and transcriptional profiling information into ecological and evolutionary studies.Organismic and Evolutionary Biolog

Adaptive strategies of African horse sickness virus to facilitate vector transmission

African horse sickness virus (AHSV) is an orbivirus that is usually transmitted between its equid hosts by adult Culicoides midges. In this article, we review the ways in which AHSV may have adapted to this mode of transmission. The AHSV particle can be modified by the pH or proteolytic enzymes of its immediate environment, altering its ability to infect different cell types. The degree of pathogenesis in the host and vector may also represent adaptations maximising the likelihood of successful vectorial transmission. However, speculation upon several adaptations for vectorial transmission is based upon research on related viruses such as bluetongue virus (BTV), and further direct studies of AHSV are required in order to improve our understanding of this important virus

Innate Immunity and the Evolution of Resistance to an Emerging Infectious Disease in a Wild Bird

Innate immunity is expected to play a primary role in conferring resistance to novel infectious diseases, but few studies have attempted to examine its role in the evolution of resistance to emerging pathogens in wild vertebrate populations. Here, we used experimental infections and cDNA microarrays to examine whether changes in the innate and/or acquired immune responses likely accompanied the emergence of resistance in house finches (Carpodacus mexicanus) in the eastern United States subject to a recent outbreak of conjunctivitis-causing bacterium (Mycoplasma gallisepticum—MG). Three days following experimental infection with MG, we observed differences in the splenic transcriptional responses between house finches from eastern U.S. populations, with a 12-year history of MG exposure, versus western U.S. populations, with no history of exposure to MG. In particular, western birds down-regulated gene expression, while eastern finches showed no expression change relative to controls. Studies involving poultry have shown that MG can manipulate host immunity, and our observations suggest that pathogen manipulation occurred only in finches from the western populations, outside the range of MG. Fourteen days after infection, eastern finches, but not western finches, up-regulated genes associated with acquired immunity (cell-mediated immunity) relative to controls. These observations suggest population differences in the temporal course of the response to infection with MG and imply that innate immune processes were targets of selection in response to MG in the eastern U.S. population.Organismic and Evolutionary Biolog

Establishing Telepathology in Africa: Lessons From Botswana

Few reports of telepathology in Africa exist in the medical literature. With the strong need for improvement in health care infrastructure and personnel training in many African nations, telepathology provides a rapid and versatile tool to improve clinical care and foster educational and research opportunities. We describe the challenges faced in establishing robotic telepathology (RT) services at a government referral center in Botswana and reflect on conditions under which such initiatives may be most likely to succeed in sub-Saharan Africa and other parts of the developing world

Ecological resilience indicators for salt marsh ecosystems

Salt marshes are coastal ecosystems within the intertidal zone, characterized by hypoxic, saline, soil conditions and low biodiversity. Low diversity arises from frequent disturbance and stressful conditions (i.e., high salinity and hypoxia), where vegetative reproduction and low competition result in mostly monotypic stands, with some differences in plant community influenced by flooding regime (described below). While there are several types of salt marshes in the Northern Gulf of Mexico (NGoM), ranging from low to high salt marshes and salt flats (Tiner, 2013), Spartina alterniflora–dominated salt marshes in the Coastal and Marine Ecological Classification Standard (CMECS) Low and Intermediate Salt Marsh Biotic Group (FGDC, 2012) are the most extensive and are the focus of this project. These salt marshes are classified as “Gulf Coast Cordgrass Salt Marsh” (CEGL004190; USNVC, 2016). Within the NGoM region, some salt marsh areas are dominated by other species such as Spartina patens and Juncus roemerianus, which both occupy higher elevations in high-precipitation zones (e.g., Louisiana, Alabama, Mississippi, and Florida). In lower precipitation regions (southern Texas), hypersaline conditions often develop yielding communities of succulent salt marsh plants (Batis and Salicornia spp.). In climatic zones with warmer winter temperatures, temperate salt marshes naturally transition to mangrove (generally in the southern Gulf of Mexico range) or, in areas with lower precipitation, to salt flats (generally in western part of the study area)

Global profiling of alternative RNA splicing events provides insights into molecular differences between various types of hepatocellular carcinoma

Protein families encoded by transcripts that are differentially spliced in various types of HCC. Table S2. Bioinformatical prediction of functional changes caused by some of ASEs identified. Table S3. List of tumor suppressors for which AS is dysregulated in various types of HCC. Table S4. List of oncogenes for which AS is dysregulated in various types of HCC. Table S5. List of kinases for which AS is dysregulated in various types of HCC. Table S6. List of transcription factors for which AS is dysregulated in various types of HCC. Table S7. List of genes for which AS is dysregulated in all types of HCC. Table S8. List of genes uniquely dysregulated in HBV-associated HCC. Table S9. List of genes uniquely dysregulated in HCV-associated HCC. Table S10. List of genes uniquely dysregulated in HBV&HCV-associated HCC. Table S11. List of genes uniquely dysregulated in virus-free HCC. Figure S1. Characterization of splicing mysregulation in HCC. Figure S2. Characterization of ASEs that are modified in HBV- and HCV-associated HCC. Figure S3. AS modifications in transcripts encoded by kinases and transcriptions factores in HBV- and HCV-associated HCC. Figure S4. Global profiling of ASE modifications in both HBV&HCV-associated HCC and virus-free-associated HCC. Figure S5. RNA splicing factors in HCC. Figure S6. Modifications to AS of 96 transcripts in response to knockdown of splicing factors with specific siRNAs (PDF 6675 kb