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Abstract Motivation Spatially resolved single-cell transcriptomics have provided unprecedented insights into gene expression in situ, particularly in the context of cell interactions or organization of tissues. However, current technologies for profiling spatial gene expression at single-cell resolution are generally limited to the measurement of a small number of genes. To address this limitation, several algorithms have been developed to impute or predict the expression of additional genes that were not present in the measured gene panel. Current algorithms do not leverage the rich spatial and gene relational information in spatial transcriptomics. To improve spatial gene expression predictions, we introduce Spatial Propagation and Reinforcement of Imputed Transcript Expression (SPRITE) as a meta-algorithm that processes predictions obtained from existing methods by propagating information across gene correlation networks and spatial neighborhood graphs.
Results SPRITE improves spatial gene expression predictions across multiple spatial transcriptomics datasets. Furthermore, SPRITE predicted spatial gene expression leads to improved clustering, visualization, and classification of cells. SPRITE can be used in spatial transcriptomics data analysis to improve inferences based on predicted gene expression.
Availability and implementation The SPRITE software package is available at https://github.com/sunericd/SPRITE. Code for generating experiments and analyses in the manuscript is available at https://github.com/sunericd/sprite-figures-and-analyses.
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null (Ed.)Abstract Yarrowia lipolytica has emerged as a biomanufacturing platform for a variety of industrial applications. It has been demonstrated to be a robust cell factory for the production of renewable chemicals and enzymes for fuel, feed, oleochemical, nutraceutical and pharmaceutical applications. Metabolic engineering of this non-conventional yeast started through conventional molecular genetic engineering tools; however, recent advances in gene/genome editing systems, such as CRISPR–Cas9, transposons, and TALENs, has greatly expanded the applications of synthetic biology, metabolic engineering and functional genomics of Y. lipolytica . In this review we summarize the work to develop these tools and their demonstrated uses in engineering Y. lipolytica , discuss important subtleties and challenges to using these tools, and give our perspective on important gaps in gene/genome editing tools in Y. lipolytica .more » « less
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The genes that encode the α- and β-chain subunits of vertebrate hemoglobin have served as a model system for elucidating general principles of gene family evolution, but little is known about patterns of evolution in amniotes other than mammals and birds. Here, we report a comparative genomic analysis of the α- and β-globin gene clusters in sauropsids (archosaurs and nonavian reptiles). The objectives were to characterize changes in the size and membership composition of the α- and β-globin gene families within and among the major sauropsid lineages, to reconstruct the evolutionary history of the sauropsid α- and β-globin genes, to resolve orthologous relationships, and to reconstruct evolutionary changes in the developmental regulation of gene expression. Our comparisons revealed contrasting patterns of evolution in the unlinked α- and β-globin gene clusters. In the α-globin gene cluster, which has remained in the ancestral chromosomal location, evolutionary changes in gene content are attributable to the differential retention of paralogous gene copies that were present in the common ancestor of tetrapods. In the β-globin gene cluster, which was translocated to a new chromosomal location, evolutionary changes in gene content are attributable to differential gene gains (via lineage-specific duplication events) and gene losses (via lineage-specific deletions and inactivations). Consequently, all major groups of amniotes possess unique repertoires of embryonic and postnatally expressed β-type globin genes that diversified independently in each lineage. These independently derived β-type globins descend from a pair of tandemly linked paralogs in the most recent common ancestor of sauropsids.more » « less
