Judith Mizrachi

All Publications

• Super-Resolution Oblique Light Sheet Microscopy for Meso- and Nanoscale Mapping of Brain Structure Mizrachi, J., Narasimhan, A., Qi, X., Drewes, R., Palaniswamy, R., Venkataraju, K. U., Albeanu, D. F., Osten, P. Cell Reports Methods. 2024
• Super Resolution Magnetic Resonance Fingerprinting International Society for Magnetic Resonance in Medicine Annual Conference Mizrachi, J., Barbieri, M., Chaudhari, A., Gold, G. 2023
• A multimodal cell census and atlas of the mammalian primary motor cortex NATURE Callaway, E. M., Dong, H., Ecker, J. R., Hawrylycz, M. J., Huang, Z., Lein, E. S., Ngai, J., Osten, P., Ren, B., Tolias, A., White, O., Zeng, H., Zhuang, X., Ascoli, G. A., Behrens, M., Chun, J., Feng, G., Gee, J. C., Ghosh, S. S., Halchenko, Y. O., Hertzano, R., Lim, B., Martone, M. E., Ng, L., Pachter, L., Ropelewski, A. J., Tickle, T. L., Yang, X., Zhang, K., Bakken, T. E., Berens, P., Daigle, T. L., Harris, J. A., Jorstad, N. L., Kalmbach, B. E., Kobak, D., Li, Y., Liu, H., Matho, K. S., Mukamel, E. A., Naeemi, M., Scala, F., Tan, P., Ting, J. T., Xie, F., Zhang, M., Zhang, Z., Zhou, J., Zingg, B., Bertagnolli, D., Casper, T., Crichton, K., Dee, N., Diep, D., Ding, S., Dong, W., Dougherty, E. L., Fong, O., Goldman, M., Goldy, J., Hodge, R. D., Hu, L., Keene, C., Krienen, F. M., Kroll, M., Lake, B. B., Lathia, K., Linnarsson, S., Liu, C. S., Macosko, E. Z., McCarroll, S. A., McMillen, D., Nadaf, N. M., Thuc Nghi Nguyen, Palmer, C. R., Thanh Pham, Plongthongkum, N., Reed, N. M., Regev, A., Rimorin, C., Romanow, W. J., Savoia, S., Siletti, K., Smith, K., Sulc, J., Tasic, B., Tieu, M., Torkelson, A., Tung, H., van Velthoven, C. J., Vanderburg, C. R., Yanny, A., Fang, R., Hou, X., Lucero, J. D., Osteen, J. K., Pinto-Duarte, A., Poirion, O., Preissl, S., Wang, X., Aldridge, A., Bartlett, A., Boggeman, L., O'Connor, C., Castanon, R. G., Chen, H., Fitzpatrick, C., Luo, C., Nery, J. R., Nunn, M., Rivkin, A. C., Tian, W., Dominguez, B., Ito-Cole, T., Jacobs, M., Jin, X., Lee, C., Lee, K., Miyazaki, P., Pang, Y., Rashid, M., Smith, J. B., Vu, M., Williams, E., Armand, E., Biancalani, T., Booeshaghi, A., Crow, M., Dudoit, S., Fischer, S., Gillis, J., Hu, Q., Kharchenko, P., Niu, S., Ntranos, V., Purdom, E., Risso, D., de Bezieux, H., Somasundaram, S., Street, K., Svensson, V., Vaishnav, E., Van den Berge, K., Welch, J. D., Yao, Z., An, X., Bateup, H. S., Bowman, I., Chance, R. K., Foster, N. N., Galbavy, W., Gong, H., Gou, L., Hatfield, J. T., Hintiryan, H., Hirokawa, K. E., Kim, G., Kramer, D. J., Li, A., Li, X., Luo, Q., Munoz-Castaneda, R., Stafford, D. A., Feng, Z., Jia, X., Jiang, S., Jiang, T., Kuang, X., Larsen, R., Lesnar, P., Li, Y., Li, Y., Liu, L., Peng, H., Qu, L., Ren, M., Ruan, Z., Shen, E., Song, Y., Wakeman, W., Wang, P., Wang, Y., Wang, Y., Yin, L., Yuan, J., Zhao, S., Zhao, X., Narasimhan, A., Palaniswamy, R., Banerjee, S., Ding, L., Huilgol, D., Huo, B., Kuo, H., Laturnus, S., Li, X., Mitra, P. P., Mizrachi, J., Wang, Q., Xie, P., Xiong, F., Yu, Y., Eichhorn, S. W., Berg, J., Bernabucci, M., Bernaerts, Y., Cadwell, C., Castro, J., Dalley, R., Hartmanis, L., Horwitz, G. D., Jiang, X., Ko, A. L., Miranda, E., Mulherkar, S., Nicovich, P. R., Owen, S. F., Sandberg, R., Sorensen, S. A., Tan, Z., Allen, S., Hockemeyer, D., Lee, A. Y., Veldman, M. B., Adkins, R. S., Ament, S. A., Bravo, H., Carter, R., Chatterjee, A., Colantuoni, C., Crabtree, J., Creasy, H., Felix, V., Giglio, M., Herb, B. R., Kancherla, J., Mahurkar, A., McCracken, C., Nickel, L., Olley, D., Orvis, J., Schor, M., Hood, G., Dichter, B., Grauer, M., Helba, B., Bandrowski, A., Barkas, N., Carlin, B., D'Orazi, F. D., Degatano, K., Gillespie, T. H., Khajouei, F., Konwar, K., Thompson, C., Kelly, K., Mok, S., Sunkin, S., BRAIN Initiative Cell Census Netwo 2021; 598 (7879): 86-102

  Abstract

  Here we report the generation of a multimodal cell census and atlas of the mammalian primary motor cortex as the initial product of the BRAIN Initiative Cell Census Network (BICCN). This was achieved by coordinated large-scale analyses of single-cell transcriptomes, chromatin accessibility, DNA methylomes, spatially resolved single-cell transcriptomes, morphological and electrophysiological properties and cellular resolution input-output mapping, integrated through cross-modal computational analysis. Our results advance the collective knowledge and understanding of brain cell-type organization1-5. First, our study reveals a unified molecular genetic landscape of cortical cell types that integrates their transcriptome, open chromatin and DNA methylation maps. Second, cross-species analysis achieves a consensus taxonomy of transcriptomic types and their hierarchical organization that is conserved from mouse to marmoset and human. Third, in situ single-cell transcriptomics provides a spatially resolved cell-type atlas of the motor cortex. Fourth, cross-modal analysis provides compelling evidence for the transcriptomic, epigenomic and gene regulatory basis of neuronal phenotypes such as their physiological and anatomical properties, demonstrating the biological validity and genomic underpinning of neuron types. We further present an extensive genetic toolset for targeting glutamatergic neuron types towards linking their molecular and developmental identity to their circuit function. Together, our results establish a unifying and mechanistic framework of neuronal cell-type organization that integrates multi-layered molecular genetic and spatial information with multi-faceted phenotypic properties.

  View details for DOI 10.1038/s41586-021-03950-0

  View details for Web of Science ID 000705847500002

  View details for PubMedID 34616075

  View details for PubMedCentralID PMC8494634

• Cellular anatomy of the mouse primary motor cortex NATURE Munoz-Castaneda, R., Zingg, B., Matho, K. S., Chen, X., Wang, Q., Foster, N. N., Li, A., Narasimhan, A., Hirokawa, K. E., Huo, B., Bannerjee, S., Korobkova, L., Park, C., Park, Y., Bienkowski, M. S., Chon, U., Wheeler, D. W., Li, X., Wang, Y., Naeemi, M., Xie, P., Liu, L., Kelly, K., An, X., Attili, S. M., Bowman, I., Bludova, A., Cetin, A., Ding, L., Drewes, R., D'Orazi, F., Elowsky, C., Fischer, S., Galbavy, W., Gao, L., Gillis, J., Groblewski, P. A., Gou, L., Hahn, J. D., Hatfield, J. T., Hintiryan, H., Huang, J., Kondo, H., Kuang, X., Lesnar, P., Li, X., Li, Y., Lin, M., Lo, D., Mizrachi, J., Mok, S., Nicovich, P. R., Palaniswamy, R., Palmer, J., Qi, X., Shen, E., Sun, Y., Tao, H. W., Wakemen, W., Wang, Y., Yao, S., Yuan, J., Zhan, H., Zhu, M., Ng, L., Zhang, L., Lim, B., Hawrylycz, M., Gong, H., Gee, J. C., Kim, Y., Chung, K., Yang, X., Peng, H., Luo, Q., Mitra, P. P., Zador, A. M., Zeng, H., Ascoli, G. A., Huang, Z., Osten, P., Harris, J. A., Dong, H. 2021; 598 (7879): 159-+

  Abstract

  An essential step toward understanding brain function is to establish a structural framework with cellular resolution on which multi-scale datasets spanning molecules, cells, circuits and systems can be integrated and interpreted1. Here, as part of the collaborative Brain Initiative Cell Census Network (BICCN), we derive a comprehensive cell type-based anatomical description of one exemplar brain structure, the mouse primary motor cortex, upper limb area (MOp-ul). Using genetic and viral labelling, barcoded anatomy resolved by sequencing, single-neuron reconstruction, whole-brain imaging and cloud-based neuroinformatics tools, we delineated the MOp-ul in 3D and refined its sublaminar organization. We defined around two dozen projection neuron types in the MOp-ul and derived an input-output wiring diagram, which will facilitate future analyses of motor control circuitry across molecular, cellular and system levels. This work provides a roadmap towards a comprehensive cellular-resolution description of mammalian brain architecture.

  View details for DOI 10.1038/s41586-021-03970-w

  View details for Web of Science ID 000733963000017

  View details for PubMedID 34616071

  View details for PubMedCentralID PMC8494646

• Super-resolution light-sheet fluorescence microscopy by SOFI bioRxiv Mizrachi, J., Narasimhan, A., Qi, X., Drewes, R., Palaniswamy, R., Wu, Z., Osten, P. 2020
• OLST protocol v1 (protocols.io.smwec7e) protocols.io Narasimhan, A., Umadevi Venkataraju, K., Mizrachi, J., Albeanu, D. F., Osten, P. 2018

  View details for DOI 10.17504/protocols.io.smwec7e

• SOFIA FORCAST Grism Study of the Mineralogy of Dust in the Winds of Proto-planetary Nebulae: RV Tauri Stars and SRd Variables ASTROPHYSICAL JOURNAL Arneson, R. A., Gehrz, R. D., Woodward, C. E., Helton, L. A., Shenoy, D., Evans, A., Keller, L. D., Hinkle, K. H., Jura, M., Lebzelter, T., Lisse, C. M., Rushton, M. T., Mizrachi, J. 2017; 843 (1)

  View details for DOI 10.3847/1538-4357/aa75cf

  View details for Web of Science ID 000404605200015

• Oblique light-sheet tomography: fast and high resolution volumetric imaging of mouse brains bioRxiv Narasimhan, A., Umadevi Venkataraju, K., Mizrachi, J., Albeanu, D. F., Osten, P. 2017

  View details for DOI 10.1101/132423

• A High Resolution Whole Brain Imaging Using Oblique Light Sheet Tomography Bioarxiv Narasimhan, A., Venkataraju, K. U., Mizrachi, J., Albeanu, D., Osten, P., 2017

  View details for DOI 10.1101/132423

• Development and Validation of Noninvasive Magnetic Resonance Relaxometry for the In Vivo Assessment of Tissue-Engineered Graft Oxygenation. Tissue engineering. Part C, Methods Einstein, S. A., Weegman, B. P., Firpo, M. T., Papas, K. K., Garwood, M. 2016; 22 (11): 1009-1017

  Abstract

  Techniques to monitor the oxygen partial pressure (pO2) within implanted tissue-engineered grafts (TEGs) are critically necessary for TEG development, but current methods are invasive and inaccurate. In this study, we developed an accurate and noninvasive technique to monitor TEG pO2 utilizing proton (1H) or fluorine (19F) magnetic resonance spectroscopy (MRS) relaxometry. The value of the spin-lattice relaxation rate constant (R1) of some biocompatible compounds is sensitive to dissolved oxygen (and temperature), while insensitive to other external factors. Through this physical mechanism, MRS can measure the pO2 of implanted TEGs. We evaluated six potential MRS pO2 probes and measured their oxygen and temperature sensitivities and their intrinsic R1 values at 16.4 T. Acellular TEGs were constructed by emulsifying porcine plasma with perfluoro-15-crown-5-ether, injecting the emulsion into a macroencapsulation device, and cross-linking the plasma with a thrombin solution. A multiparametric calibration equation containing R1, pO2, and temperature was empirically generated from MRS data and validated with fiber optic (FO) probes in vitro. TEGs were then implanted in a dorsal subcutaneous pocket in a murine model and evaluated with MRS up to 29 days postimplantation. R1 measurements from the TEGs were converted to pO2 values using the established calibration equation and these in vivo pO2 measurements were simultaneously validated with FO probes. Additionally, MRS was used to detect increased pO2 within implanted TEGs that received supplemental oxygen delivery. Finally, based on a comparison of our MRS data with previously reported data, ultra-high-field (16.4 T) is shown to have an advantage for measuring hypoxia with 19F MRS. Results from this study show MRS relaxometry to be a precise, accurate, and noninvasive technique to monitor TEG pO2 in vitro and in vivo.

  View details for DOI 10.1089/ten.TEC.2016.0106

  View details for PubMedID 27758135

  View details for PubMedCentralID PMC5116663

• Dust in the Winds of Proto-planetary Nebulae: RV Tauri Stars and SRd Variables Gehrz, R. D., Arneson, R., Helton, L. A., Woodward, C. E., Shenoy, D., Evans, A., Aneurin, L., Keller, L. D., Hinkle, K. H., Jura, M., Lebzelter, T., Lisse, C. M., Rushton, M. T., Mizrachi, J. 2016: 227
• Simultaneous Determination of Oxygen Partial Pressure and Temperature of Perfluorohexyloctane with 16.4 Tesla Magnetic Resonance Spectroscopy (MRS) University of Minnesota Digital Conservancy Mizrachi, J., et al 2013
• MRI in Practice, 4th ed.MRI in Practice, 4th ed. By Catherine Westbrook, Carolyn Kaut Roth, and John Talbot. West Sussex, UK: Wiley-Blackwell, 456 pp., 2011. $51.99 softcover (ISBN: 978-1444337433) American Journal of Roentgenology Stoffey, R. D., Mizrachi, J. S. 2012

  View details for DOI 10.2214/ajr.11.8252

• High Energy Particle Physics, NOvA Neutrino Detector Heller, K., et al Fermilab / University of Minnesota. 2012

  Abstract

  As a research assistant for the NOvA neutrino project, I worked to produce technology capable of measuring the flight, size, and identity of neutrinos. These particles barely interact with normal matter and move nearly at the speed of light. The detector, located a mile beneath the ground in Ash River, MN, was built in collaboration with Fermilab and is currently operational and used for many ongoing projects. http://novaexperiment.fnal.gov/publications/