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Reduced paucimannosidic N‐glycan formation by suppression of a specific β‐hexosaminidase from Nicotiana benthamiana 下载免费PDF全文
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Trygve Bakken Lindsay Cowell Brian D. Aevermann Mark Novotny Rebecca Hodge Jeremy A. Miller Alexandra Lee Ivan Chang Jamison McCorrison Bali Pulendran Yu Qian Nicholas J. Schork Roger S. Lasken Ed S. Lein Richard H. Scheuermann 《BMC bioinformatics》2017,18(17):559
Background
A fundamental characteristic of multicellular organisms is the specialization of functional cell types through the process of differentiation. These specialized cell types not only characterize the normal functioning of different organs and tissues, they can also be used as cellular biomarkers of a variety of different disease states and therapeutic/vaccine responses. In order to serve as a reference for cell type representation, the Cell Ontology has been developed to provide a standard nomenclature of defined cell types for comparative analysis and biomarker discovery. Historically, these cell types have been defined based on unique cellular shapes and structures, anatomic locations, and marker protein expression. However, we are now experiencing a revolution in cellular characterization resulting from the application of new high-throughput, high-content cytometry and sequencing technologies. The resulting explosion in the number of distinct cell types being identified is challenging the current paradigm for cell type definition in the Cell Ontology.Results
In this paper, we provide examples of state-of-the-art cellular biomarker characterization using high-content cytometry and single cell RNA sequencing, and present strategies for standardized cell type representations based on the data outputs from these cutting-edge technologies, including “context annotations” in the form of standardized experiment metadata about the specimen source analyzed and marker genes that serve as the most useful features in machine learning-based cell type classification models. We also propose a statistical strategy for comparing new experiment data to these standardized cell type representations.Conclusion
The advent of high-throughput/high-content single cell technologies is leading to an explosion in the number of distinct cell types being identified. It will be critical for the bioinformatics community to develop and adopt data standard conventions that will be compatible with these new technologies and support the data representation needs of the research community. The proposals enumerated here will serve as a useful starting point to address these challenges.998.
Norma Nitschke Anne Ebeling Tanja Rottstock Christoph Scherber Cornelius Middelhoff Sylvia Creutzburg Alexandra Weigelt Teja Tscharntke Markus Fischer Wolfgang W. Weisser 《Journal of Plant Ecology》2010,3(2):109
Aims Invasion resistance in experimental plant communities is known to increase with increasing diversity and further to depend on the presence of particular functional groups. To test whether these effects also hold true for the invader establishment phase beyond the seedling stage, we studied survival and performance of Centaurea jacea L. (brown knapweed) planted into experimental grassland communities of varying plant biodiversity over three consecutive years. Moreover, we analysed the role of insect herbivory and biomass of the recipient community for mediating diversity effects.Methods In 2005, seedlings of Centaurea were transplanted into experimental grassland communities (the Jena Experiment) covering a species richness (1–60) and functional group richness (1–4) gradient. Half of these transplants and the community surrounding them in each plot were sprayed with insecticide while the other half served as control. In 2006 and 2007 (during the second and third year after transplantation), we recorded survival, growth-related (e.g. transplant biomass, height) and reproduction-related traits (e.g. number of flower heads). Annual data on community aboveground biomass served as covariate to investigate mediating effects of aboveground competition with the recipient community.Important findings Species richness was the most important factor responsible for Centaurea limitation. Higher levels of diversity decreased survival and all performance traits in both years. These diversity effects were partly driven by community biomass, but not fully explained by that covariate, suggesting the importance also of further processes. The influence of functional group richness was strong in the second year after transplantation and weaker in the third year. Among the particular functional groups, only the presence of legumes showed strong negative effects on Centaurea survival and weak negative effects on growth and reproduction, the latter two being mediated by biomass. Insect herbivore reduction considerably benefited Centaurea in sprayed monocultures, where it grew significantly larger than in all other diversity levels and than in the control subplots. We conclude that effects of plant community properties on invading individuals change in the course of establishment, that plant species richness effects are also important during later stages of establishment, and that biomass (especially at high diversity) and herbivory (especially at low diversity) of the recipient community are important in mediating community effects on invaders. 相似文献
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Jacob B Landis Christopher M Miller Amanda K Broz Alexandra A Bennett Noelia Carrasquilla-Garcia Douglas R Cook Robert L Last Patricia A Bedinger Gaurav D Moghe 《Molecular biology and evolution》2021,38(8):3202
Evolutionary dynamics at the population level play a central role in creating the diversity of life on our planet. In this study, we sought to understand the origins of such population-level variation in mating systems and defensive acylsugar chemistry in Solanum habrochaites—a wild tomato species found in diverse Andean habitats in Ecuador and Peru. Using Restriction-site-Associated-DNA-Sequencing (RAD-seq) of 50 S. habrochaites accessions, we identified eight population clusters generated via isolation and hybridization dynamics of 4–6 ancestral populations. Detailed characterization of mating systems of these clusters revealed emergence of multiple self-compatible (SC) groups from progenitor self-incompatible populations in the northern part of the species range. Emergence of these SC groups was also associated with fixation of deleterious alleles inactivating acylsugar acetylation. The Amotape-Huancabamba Zone—a geographical landmark in the Andes with high endemism and isolated microhabitats—was identified as a major driver of differentiation in the northern species range, whereas large geographical distances contributed to population structure and evolution of a novel SC group in the central and southern parts of the range, where the species was also inferred to have originated. Findings presented here highlight the role of the diverse ecogeography of Peru and Ecuador in generating population differentiation, and enhance our understanding of the microevolutionary processes that create biological diversity. 相似文献
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Alla Shvaleva Filipe Costa e Silva Joaquim Miguel Costa Alexandra Correia Margaret Anderson Raquel Lobo-do-Vale David Fangueiro Catarina Bicho João Santos Pereira Maria Manuela Chaves Ute Skiba Cristina Cruz 《Plant and Soil》2014,374(1-2):883-898