Project description:Molecular profiles of neurons influence information processing, but bridging the gap between genes, circuits and behavior has been very difficult. Furthermore, the behavioral state of an animal continuously changes across development and as a result of sensory experience. How behavioral state influences molecular cell state is poorly understood. Here we present a complete atlas of the Drosophila larval nervous system. We develop polyseq, a python analysis package, and use single molecule RNA-FISH to validate our scRNAseq findings. To investigate how internal state affects cell state, we altered internal state with high-throughput behaviour protocols designed to mimic wasp sting and over activation of the memory system. We found nervous system-wide gene expression changes related to cell state. This work advances our understanding of how genes, neurons, and circuits generate behavior.
Project description:Molecular profiles of neurons influence neural development and function but bridging the gap between genes, circuits, and behavior has been very difficult. Here we used single cell RNAseq to generate a complete gene expression atlas of the Drosophila larval central nervous system composed of 131,077 single cells across three developmental stages (1 h, 24 h and 48 h after hatching). We identify 67 distinct cell clusters based on the patterns of gene expression. These include 31 functional mature larval neuron clusters, 1 ring gland cluster, 8 glial clusters, 6 neural precursor clusters, and 13 developing immature adult neuron clusters. Some clusters are present across all stages of larval development, while others are stage specific (such as developing adult neurons). We identify genes that are differentially expressed in each cluster, as well as genes that are differentially expressed at distinct stages of larval life. These differentially expressed genes provide promising candidates for regulating the function of specific neuronal and glial types in the larval nervous system, or the specification and differentiation of adult neurons. The cell transcriptome Atlas of the Drosophila larval nervous system is a valuable resource for developmental biology and systems neuroscience and provides a basis for elucidating how genes regulate neural development and function.
Project description:We have implemented an integrated Systems Biology approach to analyze overall transcriptomic reprogramming and systems level defense responses in the model plant Arabidopsis thaliana during an insect (Brevicoryne brassicae) and a bacterial (Pseudomonas syringae pv. tomato strain DC3000) attack. The main aim of this study was to identify the attacker-specific and general defense response signatures in the model plant Arabidopsis thaliana while attacked by phloem feeding aphids or pathogenic bacteria. Defense responses and networks, unique and specific for aphid or Pseudomonas stresses were identified. Our analysis revealed a probable link between biotic stress and microRNAs in Arabidopsis and thus opened up a new direction to conduct large-scale targeted experiments to explore detailed regulatory links among them. The presented results provide a first comprehensive understanding of Arabidopsis - B. brassicae and Arabidopsis - P. syringae interactions at a systems biology level.
Project description:We have implemented an integrated Systems Biology approach to analyze overall transcriptomic reprogramming and systems level defense responses in the model plant Arabidopsis thaliana during an insect (Brevicoryne brassicae) and a bacterial (Pseudomonas syringae pv. tomato strain DC3000) attack. The main aim of this study was to identify the attacker-specific and general defense response signatures in the model plant Arabidopsis thaliana while attacked by phloem feeding aphids or pathogenic bacteria. Defense responses and networks, unique and specific for aphid or Pseudomonas stresses were identified. Our analysis revealed a probable link between biotic stress and microRNAs in Arabidopsis and thus opened up a new direction to conduct large-scale targeted experiments to explore detailed regulatory links among them. The presented results provide a first comprehensive understanding of Arabidopsis - B. brassicae and Arabidopsis - P. syringae interactions at a systems biology level.
Project description:We report the application of single-molecule-based sequencing technology for high-throughput profiling of nervous system in locust Locusta migratoria manilensis. By obtaining over 57,000,000 bases of sequence from central nervous system, we generated 101836 contigs and 69440 scaffolds. We finally get 41179 unigene with an average length of 570bp. There are 5519 unigenes beyond the length of 1000bp. Using BLAST searches of the NR, NT, Swiss-Prot, KEGG and COG databases we are able to identify 13552 unigene (E<0.0001). Comprehensive assessment of all the unigenes by comparing with the studied genes of other insects nervous system reveals that our unigene are broadly representative of the transcriptome of insect nervous system. Our data provides the most large-scale EST-project for locust nervous system, which greatly benefits the exploring of this insect. In addition, we identify a large number of novel nervous genes which can be used in systematic studies of locust and other insects. Examination of 1 sample
Project description:In our study, we found that reprogrammed glia by activating PI3K and EGFR pathways promotes axon regeneration in the central nervous systems of Drosophila larvae. Thus, we analysized the transcriptome of the CNS collected from flies with or without repromgrammed glia by RNA-seq.
Project description:Queen pheromones are chemical signals that mediate reproductive division of labor in eusocial animals. Remarkably, queen pheromones are composed of identical or chemically similar compounds in some ants, wasps and bees, even though these taxa diverged >150MYA and evolved queens and workers independently. Here, we measure the transcriptomic consequences of experimental exposure to queen pheromones in workers from two ant and two bee species (genera: Lasius, Apis, Bombus), and test whether they are similar across species. Queen pheromone exposure affected transcription and splicing at many loci. Many genes responded consistently in multiple species, and the set of pheromone-sensitive genes was enriched for functions relating to lipid biosynthesis and transport, olfaction, production of cuticle, oogenesis, and histone (de)acetylation. Pheromone-sensitive genes tend to be evolutionarily ancient, positively selected, peripheral in the gene coexpression network, hypomethylated, and caste-specific in their expression. Our results reveal how queen pheromones achieve their effects, and suggest that ants and bees use similar genetic modules to achieve reproductive division of labor.
Project description:We report the application of single-molecule-based sequencing technology for high-throughput profiling of nervous system in locust Locusta migratoria manilensis. By obtaining over 57,000,000 bases of sequence from central nervous system, we generated 101836 contigs and 69440 scaffolds. We finally get 41179 unigene with an average length of 570bp. There are 5519 unigenes beyond the length of 1000bp. Using BLAST searches of the NR, NT, Swiss-Prot, KEGG and COG databases we are able to identify 13552 unigene (E<0.0001). Comprehensive assessment of all the unigenes by comparing with the studied genes of other insects nervous system reveals that our unigene are broadly representative of the transcriptome of insect nervous system. Our data provides the most large-scale EST-project for locust nervous system, which greatly benefits the exploring of this insect. In addition, we identify a large number of novel nervous genes which can be used in systematic studies of locust and other insects.