Xiangning Li

High-throughput dual-colour precision imaging for brain-wide connectome with cytoarchitectonic landmarks at the cellular level.

The precise annotation and accurate identification of neural structures are prerequisites for studying mammalian brain function. The orientation of neurons and neural circuits is usually determined by mapping brain images to coarse axial-sampling planar reference atlases. However, individual differences at the cellular level likely lead to position errors and an inability to orient neural projections at single-cell resolution. Here, we present a high-throughput precision imaging method that can acquire a co-localized brain-wide data set of both fluorescent-labelled neurons and counterstained cell bodies at a voxel size of 0.32 × 0.32 × 2.0 μm in 3 days for a single mouse brain. We acquire mouse whole-brain imaging data sets of multiple types of neurons and projections with anatomical annotation at single-neuron resolution. The results show that the simultaneous acquisition of labelled neural structures and cytoarchitecture reference in the same brain greatly facilitates precise tracing of long-range projections and accurate locating of nuclei.

Developing neuronal networks: Self-organized criticality predicts the future

Self-organized criticality emerged in neural activity is one of the key concepts to describe the formation and the function of developing neuronal networks. The relationship between critical dynamics and neural development is both theoretically and experimentally appealing. However, whereas it is well-known that cortical networks exhibit a rich repertoire of activity patterns at different stages during in vitro maturation, dynamical activity patterns through the entire neural development still remains unclear. Here we show that a series of metastable network states emerged in the developing and “aging” process of hippocampal networks cultured from dissociated rat neurons. The unidirectional sequence of state transitions could be only observed in networks showing power-law scaling of distributed neuronal avalanches. Our data suggest that self-organized criticality may guide spontaneous activity into a sequential succession of homeostatically-regulated transient patterns during development, which may help to predict the tendency of neural development at early ages in the future.

Visible rodent brain-wide networks at single-neuron resolution

There are some unsolvable fundamental questions, such as cell type classification, neural circuit tracing and neurovascular coupling, though great progresses are being made in neuroscience. Because of the structural features of neurons and neural circuits, the solution of these questions needs us to break through the current technology of neuroanatomy for acquiring the exactly fine morphology of neuron and vessels and tracing long-distant circuit at axonal resolution in the whole brain of mammals. Combined with fast-developing labeling techniques, efficient whole-brain optical imaging technology emerging at the right moment presents a huge potential in the structure and function research of specific-function neuron and neural circuit. In this review, we summarize brain-wide optical tomography techniques, review the progress on visible brain neuronal/vascular networks benefit from these novel techniques, and prospect the future technical development.

Monitoring calcium concentration in neurons with cameleon.

The calcium ion, a second messenger in the brain, plays key roles in neuronal signaling pathways. Ca(2+) signals in neurons are often highly localized and difficult to measure accurately. The quantification of calcium concentration is thus critical for understanding neuronal signaling. In this study, a yellow cameleon (YC3.60) excited using a 458 nm laser was used to monitor the calcium signals in neurons, and the dynamic range (R(max)/R(min)) of YC3.60 was found to reach 250%. The spatial distribution of calcium and the physiological changes in hippocampal neurons and even in spines were determined by the fluorescence resonance energy transfer (FRET) method. It was proved that cameleon could be used for the quantitative measurement of calcium concentration in neurons. Fluorescence readout of the calcium concentration in neurons by FRET is nondestructive, quantifiable with high spatiotemporal resolution, and even applicable to dendritic spines.

A Quantitative Analysis of the Distribution of CRH Neurons in Whole Mouse Brain

Corticotropin-releasing hormone (CRH), with widespread expression in the brain, plays a key role in modulating a series of behaviors, including anxiety, arousal, motor function, learning and memory. Previous studies have focused on some brain regions with densely distributed CRH neurons such as paraventricular hypothalamic nucleus (PVH) and bed nuclei of the stria terminalis (BST) and revealed some basic structural and functional knowledge of CRH neurons. However, there is no systematic analysis of brain-wide distribution of CRH neurons. Here, we performed a comprehensive study of CRH neurons in CRH-IRES-Cre;Ai3 mice via automatic imaging and stereoscopic cell counting in a whole mouse brain. We acquired four datasets of the CRH distributions with co-localized cytoarchitecture at a voxel resolution of 0.32 μm × 0.32 μm × 2 μm using brain-wide positioning system (BPS). Next, we precisely located and counted the EYFP-labeled neurons in different regions according to propidium iodide counterstained anatomical reference using Neuronal Global Position System. In particular, dense EYFP expression was found in piriform area, BST, central amygdalar nucleus, PVH, Barrington’s nucleus, and inferior olivary complex. Considerable CRH neurons were also found in main olfactory bulb, medial preoptic nucleus, pontine gray, tegmental reticular nucleus, external cuneate nucleus, and midline thalamus. We reconstructed and compared the soma morphology of CRH neurons in 11 brain regions. The results demonstrated that CRH neurons had regional diversities of both cell distribution and soma morphology. This anatomical knowledge enhances the current understanding of the functions of CRH neurons. These results also demonstrated the ability of our platform to accurately orient, reconstruct and count neuronal somas in three-dimension for type-specific neurons in the whole brain, making it feasible to answer the fundamental neuroscience question of exact numbers of various neurons in the whole brain.

Homeostatically regulated synchronized oscillations induced by short-term tetrodotoxin treatment in cultured neuronal network.

Homeostatic plasticity plays a critical role in the stability of neuronal activities. Here, with high-density hippocampal networks cultured on multi-electrode arrays (MEAs), the transformation of spontaneous neuronal firing patterns induced by 1microM tetrodotoxin was clarified. Once tetrodotoxin was washed out after a 4-h treatment, spontaneous activities rose significantly with spike rate increasing approximately three times, and synchronized burst oscillations appeared throughout the network, with the cross-correlation coefficient between the active sites rising from 0.06+/-0.03 to 0.27+/-0.05. The long-term recording showed that the oscillations lasted for more than 4h before the network recovered. These results suggest that short-term treatment by tetrodotoxin may induce the homeostatically enhanced neuronal excitability, and that the spontaneous synchronized oscillations should be an indicator of homeostatic plasticity in cultured neuronal network. Furthermore, the non-invasive and long-term recording with MEAs as a novel sensing system is identified to be appropriate for pharmacological investigations of neuronal plasticity at the network level.

In Vivo Visualization of Tumor Antigen-containing Microparticles Generated in Fluorescent-protein-elicited Immunity

In vivo optical spatio-temporal imaging of the tumor microenvironment is useful to explain how tumor immunotherapies work. However, the lack of fluorescent antigens with strong immunogenicity makes it difficult to study the dynamics of how tumors are eliminated by any given immune response. Here, we develop an effective fluorescent model antigen based on the tetrameric far-red fluorescent protein KatushkaS158A (tfRFP), which elicits both humoral and cellular immunity. We use this fluorescent antigen to visualize the dynamic behavior of immunocytes as they attack and selectively eliminate tfRFP-expressing tumors in vivo; swarms of immunocytes rush toward tumors with high motility, clusters of immunocytes form quickly, and numerous antigen-antibody complexes in the form of tfRFP+ microparticles are generated in the tumor areas and ingested by macrophages in the tumor microenvironment. Therefore, tfRFP, as both a model antigen and fluorescent reporter, is a useful tool to visualize specific immune responses in vivo.

Precise Cerebral Vascular Atlas in Stereotaxic Coordinates of Whole Mouse Brain

Understanding amazingly complex brain functions and pathologies requires a complete cerebral vascular atlas in stereotaxic coordinates. Making a precise atlas for cerebral arteries and veins has been a century-old objective in neuroscience and neuropathology. Using micro-optical sectioning tomography (MOST) with a modified Nissl staining method, we acquired five mouse brain data sets containing arteries, veins, and microvessels. Based on the brain-wide vascular spatial structures and brain regions indicated by cytoarchitecture in one and the same mouse brain, we reconstructed and annotated the vascular system atlas of both arteries and veins of the whole mouse brain for the first time. The distributing patterns of the vascular system within the brain regions were acquired and our results show that the patterns of individual vessels are different from each other. Reconstruction and statistical analysis of the microvascular network, including derivation of quantitative vascular densities, indicate significant differences mainly in vessels with diameters less than 8 μm and large than 20 μm across different brain regions. Our precise cerebral vascular atlas provides an important resource and approach for quantitative studies of brain functions and diseases.

Synchronized spontaneous spikes on multi-electrode array show development of cultured neuronal network

Spontaneous firing play an important role in development of neuronal network. Activity-dependent modification of synaptic efficacy is widely recognized as a cellular basis of learning, memory, and development plasticity. Little is known of the activity-dependent modification of the synchronized spontaneous firing of the hippocampal networks. Long-term recording of spontaneous activity in cultured hippocampal neuronal networks was carried out using substrates containing multi-electrode array (MEA). Spontaneous uncorrelated firing appeared within a week and transformed progressively into synchronized pattern. During the development, these synchronized firings became into oscillation pattern and the synchronization has little change. By paired stimulation from adjacent electrodes in the network, the synchronized firing form a larger network burst. These results suggest that synchronized spontaneous spikes show the development of neuronal network and electronical stimulation could change the development

TDat: An Efficient Platform for Processing Petabyte-Scale Whole-Brain Volumetric Images

Three-dimensional imaging of whole mammalian brains at single-neuron resolution has generated terabyte (TB)- and even petabyte (PB)-sized datasets. Due to their size, processing these massive image datasets can be hindered by the computer hardware and software typically found in biological laboratories. To fill this gap, we have developed an efficient platform named TDat, which adopts a novel data reformatting strategy by reading cuboid data and employing parallel computing. In data reformatting, TDat is more efficient than any other software. In data accessing, we adopted parallelization to fully explore the capability for data transmission in computers. We applied TDat in large-volume data rigid registration and neuron tracing in whole-brain data with single-neuron resolution, which has never been demonstrated in other studies. We also showed its compatibility with various computing platforms, image processing software and imaging systems.