Colón-Ramos Daniel

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Last Name
Colón-Ramos
First Name
Daniel
ORCID
0000-0003-0223-7717

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  • Preprint
    Visualizing calcium flux in freely moving nematode embryos
    ( 2017-02) Ardiel, Evan L. ; Kumar, Abhishek ; Marbach, Joseph ; Christensen, Ryan ; Gupta, Rishi ; Duncan, William ; Daniels, Jonathan S. ; Stuurman, Nico ; Colón-Ramos, Daniel ; Shroff, Hari
    The lack of physiological recordings from Caenorhabditis elegans embryos stands in stark contrast to the comprehensive anatomical and gene expression datasets already available. Using light-sheet fluorescence microscopy (LSFM) to address the challenges associated with functional imaging at this developmental stage, we recorded calcium dynamics in muscles and neurons and developed analysis strategies to relate activity and movement. In muscles, we found that the initiation of twitching was associated with a spreading calcium wave in a dorsal muscle bundle. Correlated activity in muscle bundles was linked with early twitching and eventual coordinated movement. To identify neuronal correlates of behavior, we monitored brain-wide activity with subcellular resolution and identified a particularly active cell associated with muscle contractions. Finally, imaging neurons of a well-defined adult motor circuit, we found that reversals in the eggshell correlated with calcium transients in AVA interneurons.
  • Article
    Differential adhesion regulates neurite placement via a retrograde zippering mechanism
    (eLife Sciences Publications, 2021-11-16) Sengupta, Titas ; Koonce, Noelle L. ; Vázquez-Martínez, Nabor ; Moyle, Mark W. ; Duncan, Leighton H. ; Emerson, Sarah E. ; Han, Xiaofei ; Shao, Lin ; Wu, Yicong ; Santella, Anthony ; Fan, Li ; Bao, Zhirong ; Mohler, William A. ; Shroff, Hari ; Colón-Ramos, Daniel
    During development, neurites and synapses segregate into specific neighborhoods or layers within nerve bundles. The developmental programs guiding placement of neurites in specific layers, and hence their incorporation into specific circuits, are not well understood. We implement novel imaging methods and quantitative models to document the embryonic development of the C. elegans brain neuropil, and discover that differential adhesion mechanisms control precise placement of single neurites onto specific layers. Differential adhesion is orchestrated via developmentally regulated expression of the IgCAM SYG-1, and its partner ligand SYG-2. Changes in SYG-1 expression across neuropil layers result in changes in adhesive forces, which sort SYG-2-expressing neurons. Sorting to layers occurs, not via outgrowth from the neurite tip, but via an alternate mechanism of retrograde zippering, involving interactions between neurite shafts. Our study indicates that biophysical principles from differential adhesion govern neurite placement and synaptic specificity in vivo in developing neuropil bundles.
  • Article
    A genetically encoded tool for reconstituting synthetic modulatory neurotransmission and reconnect neural circuits in vivo
    (Nature Research, 2021-08-09) Hawk, Josh D. ; Wisdom, Elias M. ; Sengupta, Titas ; Kashlan, Zane D. ; Colón-Ramos, Daniel
    Chemogenetic and optogenetic tools have transformed the field of neuroscience by facilitating the examination and manipulation of existing circuits. Yet, the field lacks tools that enable rational rewiring of circuits via the creation or modification of synaptic relationships. Here we report the development of HySyn, a system designed to reconnect neural circuits in vivo by reconstituting synthetic modulatory neurotransmission. We demonstrate that genetically targeted expression of the two HySyn components, a Hydra-derived neuropeptide and its receptor, creates de novo neuromodulatory transmission in a mammalian neuronal tissue culture model and functionally rewires a behavioral circuit in vivo in the nematode Caenorhabditis elegans. HySyn can interface with existing optogenetic, chemogenetic and pharmacological approaches to functionally probe synaptic transmission, dissect neuropeptide signaling, or achieve targeted modulation of specific neural circuits and behaviors.
  • Article
    Incorporating the image formation process into deep learning improves network performance
    (Nature Research, 2022-10-31) Li, Yue ; Su, Yijun ; Guo, Min ; Han, Xiaofei ; Liu, Jiamin ; Vishwasrao, Harshad D ; Li, Xuesong ; Christensen, Ryan ; Sengupta, Titas ; Moyle, Mark W ; Rey-Suarez, Ivan ; Chen, Jiji ; Upadhyaya, Arpita ; Usdin, Ted B ; Colón-Ramos, Daniel Alfonso ; Liu, Huafeng ; Wu, Yicong ; Shroff, Hari
    We present Richardson–Lucy network (RLN), a fast and lightweight deep learning method for three-dimensional fluorescence microscopy deconvolution. RLN combines the traditional Richardson–Lucy iteration with a fully convolutional network structure, establishing a connection to the image formation process and thereby improving network performance. Containing only roughly 16,000 parameters, RLN enables four- to 50-fold faster processing than purely data-driven networks with many more parameters. By visual and quantitative analysis, we show that RLN provides better deconvolution, better generalizability and fewer artifacts than other networks, especially along the axial dimension. RLN outperforms classic Richardson–Lucy deconvolution on volumes contaminated with severe out of focus fluorescence or noise and provides four- to sixfold faster reconstructions of large, cleared-tissue datasets than classic multi-view pipelines. We demonstrate RLN’s performance on cells, tissues and embryos imaged with widefield-, light-sheet-, confocal- and super-resolution microscopy.