Biology subjects

Evans, N. B.

Publications and source records attributed to Evans, N. B..

4 recordsLinked to original sources

bioRxiv2022

Integrated platform for multi-scale molecular imaging andphenotyping of the human brain

Understanding cellular architectures and their connectivity is essential for interrogating system function and dysfunction. However, we lack technologies for mapping the multi-scale details of individual cells in the human organ-scale system. To address this challenge, we developed a platform that simultaneously extracts spatial, molecular, morphological, and connectivity information of individual cells from the same human brain, by integrating novel chemical, mechanical, and computational tools. The platform includes three key tools: (i) a vibrating microtome for ultra-precision slicing of large-scale tissues without losing cellular connectivity (MEGAtome), (ii) a polymer hydrogel-based tissue processing technology for multiplexed multiscale imaging of human organ-scale tissues (mELAST), and (iii) a computational pipeline for reconstructing 3D connectivity across multiple brain slabs (UNSLICE). We demonstrated the transformative potential of our platform by analyzing human Alzheimers disease pathology at multiple scales and demonstrating scalable neural connectivity mapping in the human brain. One-Sentence SummaryWe developed an integrated, scalable platform for highly multiplexed, multi-scale phenotyping and connectivity mapping in the same human brain tissue, which incorporated novel tissue processing, labeling, imaging, and computational technologies.

bioengineering↗

bioRxiv2020

Functional dissection of neural circuitry using a genetic reporter for fMRI

The complex connectivity of the mammalian brain underlies its function, but understanding how interconnected brain regions interact in neural processing remains a formidable challenge. Here we address this problem by introducing a genetic probe that permits selective functional imaging of neural circuit elements defined by their synaptic interrelationships throughout the brain. The probe is an engineered enzyme that transduces cytosolic calcium dynamics of probe-expressing cells into localized hemodynamic responses that can be selectively visualized by functional magnetic resonance imaging. Using a viral vector that undergoes retrograde transport, we apply the probe to characterize a brain-wide network of monosynaptic inputs to the striatum activated in a deep brain stimulation paradigm in rats. The results reveal engagement of surprisingly diverse projection sources and inform an integrated model of striatal function relevant to reward behavior and therapeutic neurostimulation approaches. Our work thus establishes a potent strategy for mechanistic analysis of distributed neural systems.

neuroscience↗

bioRxiv2019

Ultrafast immunostaining of organ-scale tissues for scalable proteomic phenotyping

Studying the function and dysfunction of complex biological systems necessitates comprehensive understanding of individual cells. Advancements in three-dimensional (3D) tissue processing and imaging modalities have enabled rapid visualization and phenotyping of cells in their spatial context. However, system-wide interrogation of individual cells within large intact tissue remains challenging, low throughput, and error-prone owing to the lack of robust labeling technologies. Here we introduce a rapid, versatile, and scalable method, eFLASH, that enables complete and uniform labeling of organ-scale tissue within one day. eFLASH dynamically modulates chemical transport and reaction kinetics to establish system-wide uniform labeling conditions throughout the day-long labeling period. This unique approach enables the same protocol to be compatible with a wide range of tissue types and probes, enabling combinatorial molecular phenotyping across different organs and species. We applied eFLASH to generate quantitative maps of various cell types in mouse brains. We also demonstrated multidimensional cell profiling in a marmoset brain block. We envision that eFLASH will spur holistic phenotyping of emerging animal models and disease models to help assess their functions and dysfunctions.

bioengineering↗

bioRxiv2019

Scalable image processing techniques for quantitative analysis of volumetric biological images from light-sheet microscopy

Here we describe an image processing pipeline for quantitative analysis of terabyte-scale volumetric images of SHIELD-processed mouse brains imaged with light-sheet microscopy. The pipeline utilizes open-source packages for destriping, stitching, and atlas alignment that are optimized for parallel processing. The destriping step removes stripe artifacts, corrects uneven illumination, and offers over 100x speed improvements compared to previously reported algorithms. The stitching module builds upon Terastitcher to create a single volumetric image quickly from individual image stacks with parallel processing enabled by default. The atlas alignment module provides an interactive web-based interface that automatically calculates an initial alignment to a reference image which can be manually refined. The atlas alignment module also provides summary statistics of fluorescence for each brain region as well as region segmentations for visualization. The expected runtime of our pipeline on a whole mouse brain hemisphere is 1-2 d depending on the available computational resources and the dataset size.

bioengineering↗