@article {59911, title = {Molecular logic of spinocerebellar tract neuron diversity and connectivity.}, journal = {Cell Reports}, volume = {27}, year = {2019}, month = {2019 May 27}, pages = {2620-35}, abstract = {

Coordinated motor behaviors depend on feedback communication between peripheral sensory systems and central circuits in the brain and spinal cord. Relay of muscle and tendon-derived sensory information to the CNS is facilitated by functionally and anatomically diverse groups of spinocerebellar tract neurons (SCTNs), but the molecular logic by which SCTN diversity and connectivity is achieved is poorly understood. We used single cell RNA sequencing and genetic manipulations to define the mechanisms governing the molecular profile and organization of SCTN subtypes. We found that SCTNs relaying proprioceptive sensory information from limb and axial muscles are generated through segmentally-restricted actions of specific Hox genes. Loss of Hox function disrupts SCTN subtype-specific transcriptional programs, leading to defects in the connections between proprioceptive sensory neurons, SCTNs, and the cerebellum. These results indicate that Hox-dependent genetic programs play essential roles in the assembly of the neural circuits required for proprioception.

}, doi = {10.1016/j.celrep.2019.04.113}, author = {Baek, Myungin and Menon, Vilas and Jessell, Thomas M and Hantman, Adam W and Dasen, Jeremy} } @article {47262, title = {Simultaneous denoising, deconvolution, and demixing of calcium imaging data.}, journal = {Neuron}, volume = {89}, year = {2016}, month = {2016 Jan 20}, pages = {285-99}, abstract = {

We present a modular approach for analyzing calcium imaging recordings of large neuronal ensembles. Our goal is to simultaneously identify the locations of the neurons, demix spatially overlapping components, and denoise and deconvolve the spiking activity from the slow dynamics of the calcium indicator. Our approach relies on a constrained nonnegative matrix factorization that expresses the spatiotemporal fluorescence activity as the product of a spatial matrix that encodes the spatial footprint of each neuron in the optical field and a temporal matrix that characterizes the calcium concentration of each neuron over time. This framework is combined with a novel constrained deconvolution approach that extracts estimates of neural activity from fluorescence traces, to create a spatiotemporal processing algorithm that requires minimal parameter tuning. We demonstrate the general applicability of our method by applying it to in\ vitro and in\ vivo multi-neuronal imaging data, whole-brain light-sheet imaging data, and dendritic imaging data.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2015.11.037}, author = {Pnevmatikakis, Eftychios A and Soudry, Daniel and Gao, Yuanjun and Machado, Timothy A and Merel, Josh and Pfau, David and Reardon, Thomas and Mu, Yu and Lacefield, Clay and Yang, Weijian and Ahrens, Misha and Bruno, Randy and Jessell, Thomas M and Peterka, Darcy S and Yuste, Rafael and Paninski, Liam} } @article {5896, title = {Clarke{\textquoteright}s column neurons as the focus of a corticospinal corollary circuit.}, journal = {Nature Neuroscience}, volume = {13}, year = {2010}, month = {2010 Oct}, pages = {1233-9}, abstract = {

Proprioceptive sensory signals inform the CNS of the consequences of motor acts, but effective motor planning involves internal neural systems capable of anticipating actual sensory feedback. Just where and how predictive systems exert their influence remains poorly understood. We explored the possibility that spinocerebellar neurons that convey proprioceptive sensory information also integrate information from cortical command systems. Analysis of the circuitry and physiology of identified dorsal spinocerebellar tract neurons in mouse spinal cord revealed distinct populations of Clarke{\textquoteright}s column neurons that received direct excitatory and/or indirect inhibitory inputs from descending corticospinal axons. The convergence of these descending inhibitory and excitatory inputs to Clarke{\textquoteright}s column neurons established local spinal circuits with the capacity to mark or modulate incoming proprioceptive input. Together, our genetic, anatomical and physiological results indicate that Clarke{\textquoteright}s column spinocerebellar neurons nucleate local spinal corollary circuits that are relevant to motor planning and evaluation.

}, keywords = {3-dione, 6-Cyano-7-nitroquinoxaline-2, Animals, beta-Galactosidase, Bicuculline, Cerebellum, Cholera Toxin, Electric Stimulation, Estrogen Antagonists, Excitatory Amino Acid Antagonists, Feedback, GABA Antagonists, Gene Expression Regulation, Glial Cell Line-Derived Neurotrophic Factor, Glycine Agents, Glycine Plasma Membrane Transport Proteins, Green Fluorescent Proteins, Homeodomain Proteins, Lysine, Membrane Potentials, Messenger, Mice, Models, Nerve Net, Neural Inhibition, Neural Pathways, Neurological, Newborn, Parvalbumins, Patch-Clamp Techniques, Protein Kinase C, RNA, Sensory, Sensory Receptor Cells, Spinal Cord, Stilbamidines, Strychnine, Tamoxifen, tau Proteins, Transcription Factors, Transgenic, Vesicular Glutamate Transport Protein 1}, issn = {1546-1726}, doi = {10.1038/nn.2637}, author = {Hantman, Adam W and Jessell, Thomas M} }