Katie McDole

Howard Hughes Medical Institute, Ашбърн, Virginia, United States

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Publications (7)95.42 Total impact

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    ABSTRACT: Light-sheet microscopy is a powerful method for imaging the development and function of complex biological systems at high spatiotemporal resolution and over long time scales. Such experiments typically generate terabytes of multidimensional image data, and thus they demand efficient computational solutions for data management, processing and analysis. We present protocols and software to tackle these steps, focusing on the imaging-based study of animal development. Our protocols facilitate (i) high-speed lossless data compression and content-based multiview image fusion optimized for multicore CPU architectures, reducing image data size 30-500-fold; (ii) automated large-scale cell tracking and segmentation; and (iii) visualization, editing and annotation of multiterabyte image data and cell-lineage reconstructions with tens of millions of data points. These software modules are open source. They provide high data throughput using a single computer workstation and are readily applicable to a wide spectrum of biological model systems.
    Nature Protocols 10/2015; 10(11):1679-1696. DOI:10.1038/nprot.2015.111 · 9.67 Impact Factor
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    ABSTRACT: Understanding how the brain works in tight concert with the rest of the central nervous system (CNS) hinges upon knowledge of coordinated activity patterns across the whole CNS. We present a method for measuring activity in an entire, non-transparent CNS with high spatiotemporal resolution. We combine a light-sheet microscope capable of simultaneous multi-view imaging at volumetric speeds 25-fold faster than the state-of-the-art, a whole-CNS imaging assay for the isolated Drosophila larval CNS and a computational framework for analysing multi-view, whole-CNS calcium imaging data. We image both brain and ventral nerve cord, covering the entire CNS at 2 or 5 Hz with two-or one-photon excitation, respectively. By mapping network activity during fictive behaviours and quantitatively comparing high-resolution whole-CNS activity maps across individuals, we predict functional connections between CNS regions and reveal neurons in the brain that identify type and temporal state of motor programs executed in the ventral nerve cord.
    Nature Communications 08/2015; 6:1-16. DOI:10.1038/ncomms8924 · 11.47 Impact Factor
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    ABSTRACT: The comprehensive reconstruction of cell lineages in complex multicellular organisms is a central goal of developmental biology. We present an open-source computational framework for the segmentation and tracking of cell nuclei with high accuracy and speed. We demonstrate its (i) generality by reconstructing cell lineages in four-dimensional, terabyte-sized image data sets of fruit fly, zebrafish and mouse embryos acquired with three types of fluorescence microscopes, (ii) scalability by analyzing advanced stages of development with up to 20,000 cells per time point at 26,000 cells min(-1) on a single computer workstation and (iii) ease of use by adjusting only two parameters across all data sets and providing visualization and editing tools for efficient data curation. Our approach achieves on average 97.0% linkage accuracy across all species and imaging modalities. Using our system, we performed the first cell lineage reconstruction of early Drosophila melanogaster nervous system development, revealing neuroblast dynamics throughout an entire embryo.
    Nature Methods 07/2014; 11(9). DOI:10.1038/nmeth.3036 · 32.07 Impact Factor
  • Katie McDole · Yixian Zheng ·
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    ABSTRACT: To understand cell fate specification and maintenance during development, it is essential to visualize both lineage markers and cell behaviors in real time using endogenous markers to report cell fate. We have generated a reporter line in which eGFP is fused to the endogenous locus of Cdx2, a transcription factor essential for trophectoderm specification, allowing us to visualize cell fate decisions in the preimplantation mouse embryo. We used two-photon laser scanning microscopy to visualize expression of the endogenous Cdx2 fusion protein and show that Cdx2 undergoes phases of upregulation. Additionally, we show that as late as the 32-cell stage, outer trophectoderm cells may change their fates by migrating inward and losing Cdx2 expression. Furthermore, the tools and techniques we report allow for dual-colored imaging, which will greatly facilitate the study of not only preimplantation development, but later stages of development and tissues where Cdx2 plays an important role. genesis 50:775-782, 2012. © 2012 Wiley Periodicals, Inc.
    genesis 10/2012; 50(10):775-82. DOI:10.1002/dvg.22049 · 2.02 Impact Factor
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    Youngjo Kim · Katie McDole · Yixian Zheng ·
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    ABSTRACT: Lamins are the major structural components of the nuclear lamina found in metazoan organisms. Extensive studies using tissue culture cells have shown that lamins are involved in a wide range of basic cell functions. This has led to the prevailing idea that a given animal cell needs at least one lamin protein for its basic proliferation and survival. However, recent studies have shown that lamins are dispensable for the proliferation and survival of mouse embryonic stem cells (ESC). In contrast to a lack of essential functions in ESCs, certain differentiated cells lacking B-type lamins exhibit increased cell cycle exit rates and enhanced senescence. In this Extra View, we discuss how studies using animal models and cell cultures have begun to reveal cell-type specific functions of lamins in tissue building and homeostasis.
    Nucleus (Austin, Texas) 05/2012; 3(3):256-62. DOI:10.4161/nucl.20392 · 3.03 Impact Factor
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    ABSTRACT: B-type lamins, the major components of the nuclear lamina, are believed to be essential for cell proliferation and survival. We found that mouse embryonic stem cells (ESCs) do not need any lamins for self-renewal and pluripotency. Although genome-wide lamin-B binding profiles correlate with reduced gene expression, such binding is not directly required for gene silencing in ESCs or trophectoderm cells. However, B-type lamins are required for proper organogenesis. Defects in spindle orientation in neural progenitor cells and migration of neurons probably cause brain disorganizations found in lamin-B null mice. Thus, our studies not only disprove several prevailing views of lamin-Bs but also establish a foundation for redefining the function of the nuclear lamina in the context of tissue building and homeostasis.
    Science 11/2011; 334(6063):1706-10. DOI:10.1126/science.1211222 · 33.61 Impact Factor
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    Katie McDole · Yuan Xiong · Pablo A Iglesias · Yixian Zheng ·
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    ABSTRACT: The first lineage segregation in the pre-implantation mouse embryo gives rise to cells of the inner cell mass and the trophectoderm. Segregation into these two lineages during the 8-cell to 32-cell stages is accompanied by a significant amount of cell displacement, and as such it has been difficult to accurately track cellular behavior using conventional imaging techniques. Consequently, how cellular behaviors correlate with cell fate choices is still not fully understood. To achieve the high spatial and temporal resolution necessary for tracking individual cell lineages, we utilized two-photon light-scanning microscopy (TPLSM) to visualize and follow every cell in the embryo using fluorescent markers. We found that cells undergoing asymmetric cell fate divisions originate from a unique population of cells that have been previously classified as either outer or inner cells. This imaging technique coupled with a tracking algorithm we developed allows us to show that these cells, which we refer to as intermediate cells, share features of inner cells but exhibit different dynamic behaviors and a tendency to expose their cell surface in the mouse embryo between the fourth and fifth cleavages. We provide an accurate description of the correlation between cell division order and cell fate, and demonstrate that cell cleavage angle is a more accurate indicator of cellular polarity than cell fate. Our studies demonstrate the utility of two-photon imaging in answering questions in the pre-implantation field that have previously been difficult or impossible to address. Our studies provide a framework for the future use of specific markers to track cell fate molecularly and with high accuracy.
    Developmental Biology 07/2011; 355(2):239-49. DOI:10.1016/j.ydbio.2011.04.024 · 3.55 Impact Factor

Publication Stats

154 Citations
95.42 Total Impact Points


  • 2014-2015
    • Howard Hughes Medical Institute
      Ашбърн, Virginia, United States
  • 2011-2012
    • Johns Hopkins University
      • Department of Biology
      Baltimore, Maryland, United States
    • Carnegie Institution for Science
      • Department of Embryology
      Вашингтон, West Virginia, United States