The axillary lymphoid organ - an external, experimentally accessible immune organ in the zebrafish
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ABSTRACT:
PROVIDER: PRJNA1128236 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR29551178_1.fastq.gz | Fastqsanger.gz | |||
| SRR29551178_2.fastq.gz | Fastqsanger.gz |
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Project description:Lymph nodes and other secondary lymphoid organs play critical roles in immune surveillance and immune activation in mammals, but the deep internal locations of these organs makes it challenging to study dynamic cellular mechanisms of immune cell interaction with pathogens or other host tissues such as the vasculature in living animals. Here, we describe a previously uncharacterized external immune organ located near the base of the zebrafish pectoral fin, the pectoral axillary lobe (PAL), with a variety of features that make it ideally suited for studying immune cell dynamics in vivo. This small, transparent organ consists of an outer cortex teeming with immune cells and an inner medulla with a mesh-like network of fibroblastic reticular cells along which immune cells migrate, and a network of lymphatic vessels draining to a large adjacent lymph sac. Noninvasive high-resolution imaging of transgenically marked immune cells can be carried out in the lobes of living animals, and the PAL is readily accessible to external treatment with antigens or pathogens. This newly discovered tissue provides a superb model for dynamic live imaging of immune cells and their interaction with pathogens and surrounding tissues, including blood and lymphatic vessels.
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Project description:Axillary bud outgrowth determines plant shoot architecture and is under control of endogenous hormones and a fine-tuned gene expression network. Some genes associated with shoot development are known targets of small RNAs (sRNAs). Although it is well known that sRNAs act broadly in plant development, our understanding about their roles in vegetative bud outgrowth remains limited. Moreover, the expression profiles of microRNAs (miRNAs) and their targets in axillary buds are unknown. In this study, we employed next-generation sequencing, gene expression analysis and metabolite profiling to identify sRNAs and quantify distinct hormones, respectively, in vegetative axillary buds of the tropical biofuel crop sugarcane (Saccharum spp.). Differential accumulation of abscisic acid (ABA), gibberellins (GA), and cytokinins indicates a dynamic balance of these hormones during sugarcane bud outgrowth. A number of repeat-associated siRNAs generated from distinct transposable elements and genes were highly expressed in both inactive and developing buds. RT-qPCR results revealed that specific miRNAs were differentially expressed in developing buds and some correlate negatively with the expression of their targets. Expression patterns of miR159 and its experimentally confirmed target GAMYB suggest they play roles in regulating ABA and GA-signaling pathways during bud outgrowth. Our work reveals, for the first time, differences in composition and expression profiles of small RNAs and targets between inactive and developing buds that, together with the endogenous balance of specific hormones, may be important to regulate axillary bud outgrowth in plants.
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