Gapr for large-scale collaborative single-neuron reconstruction.

Whole-brain analysis of single-neuron morphology is crucial for unraveling the complex structure of the brain. However, large-scale neuron reconstruction from terabyte and even petabyte data of mammalian brains generated by state-of-the-art light microscopy is a daunting task. Here, we developed 'Gapr' (Gapr accelerates projectome reconstruction) that streamlines deep learning-based automatic reconstruction, 'automatic proofreading' that reduces human workloads at high-confidence sites, and high-throughput collaborative proofreading by crowd users through the Internet.

Single-neuron projectomes of mouse paraventricular hypothalamic nucleus oxytocin neurons reveal mutually exclusive projection patterns.

Oxytocin (OXT) plays important roles in autonomic control and behavioral modulation. However, it is unknown how the projection patterns of OXT neurons align with underlying physiological functions. Here, we present the reconstructed single-neuron, whole-brain projectomes of 264 OXT neurons of the mouse paraventricular hypothalamic nucleus (PVH) at submicron resolution.

Single-neuron analysis of dendrites and axons reveals the network organization in mouse prefrontal cortex.

The structures of dendrites and axons form the basis for the connectivity of neural network, but their precise relationship at single-neuron level remains unclear. Here we report the complete dendrite and axon morphology of nearly 2,000 neurons in mouse prefrontal cortex (PFC). We identified morphological variations of somata, dendrites and axons across laminar layers and PFC subregions and the general rules of somatodendritic scaling with cytoarchitecture.

Single-neuron projectome of mouse prefrontal cortex.

Prefrontal cortex (PFC) is the cognitive center that integrates and regulates global brain activity. However, the whole-brain organization of PFC axon projections remains poorly understood. Using single-neuron reconstruction of 6,357 mouse PFC projection neurons, we identified 64 projectome-defined subtypes.

Spatiotemporal single-cell analysis of gene expression in the mouse suprachiasmatic nucleus.

Mammalian circadian behaviors are orchestrated by the suprachiasmatic nucleus (SCN) in the ventral hypothalamus, but the number of SCN cell types and their functional roles remain unclear. We have used single-cell RNA-sequencing to identify the basic cell types in the mouse SCN and to characterize their circadian and light-induced gene expression patterns. We identified eight major cell types, with each type displaying a specific pattern of circadian gene expression.

Construction of microRNA- and microRNA*-mediated regulatory networks in plants.

The critical biological roles of microRNAs (miRNAs) have been well recognized. However, knowledge on the regulatory activities of miRNA*s is limited. Although several studies pointed to the capacity of this small RNA species to repress target genes in animals, few related analyses were performed in plants.

PmiRKB: a plant microRNA knowledge base.

MicroRNAs (miRNAs), one type of small RNAs (sRNAs) in plants, play an essential role in gene regulation. Several miRNA databases were established; however, successively generated new datasets need to be collected, organized and analyzed. To this end, we have constructed a plant miRNA knowledge base (PmiRKB) that provides four major functional modules.

High-throughput degradome sequencing can be used to gain insights into microRNA precursor metabolism.

The approximately 21 nucleotide microRNAs (miRNAs) are one type of well-defined small RNA species, and they play critical roles in various biological processes in organisms. In plants, most miRNAs exert repressive regulation on their targets through cleavage, and a number of miRNA-target pairs have been validated either by modified 5' RACE (rapid amplification of cDNA ends), or by newly developed high-throughput strategies. All these data have greatly advanced our understanding of the regulatory roles of plant miRNAs.