@article {45419, title = {Development of the annelid axochord: insights into notochord evolution.}, journal = {Science}, volume = {345}, year = {2014}, month = {2014 Sep 12}, pages = {1365-8}, abstract = {

The origin of chordates has been debated for more than a century, with one key issue being the emergence of the notochord. In vertebrates, the notochord develops by convergence and extension of the chordamesoderm, a population of midline cells of unique molecular identity. We identify a population of mesodermal cells in a developing invertebrate, the marine annelid Platynereis dumerilii, that converges and extends toward the midline and expresses a notochord-specific combination of genes. These cells differentiate into a longitudinal muscle, the axochord, that is positioned between central nervous system and axial blood vessel and secretes a strong collagenous extracellular matrix. Ancestral state reconstruction suggests that contractile mesodermal midline cells existed in bilaterian ancestors. We propose that these cells, via vacuolization and stiffening, gave rise to the chordate notochord.

}, issn = {1095-9203}, doi = {10.1126/science.1253396}, author = {Lauri, Antonella and Brunet, Thibaut and Handberg-Thorsager, Mette and Fischer, Antje H L and Simakov, Oleg and Steinmetz, Patrick R H and Tomer, Raju and Keller, Philipp J and Arendt, Detlev} } @article {5346, title = {Light sheet microscopy in cell biology.}, journal = {Methods in Molecular Biology}, volume = {931}, year = {2013}, month = {2013}, pages = {123-37}, abstract = {

Light sheet-based fluorescence microscopy (LSFM) is emerging as a powerful imaging technique for the life sciences. LSFM provides an exceptionally high imaging speed, high signal-to-noise ratio, low level of photo-bleaching, and good optical penetration depth. This unique combination of capabilities makes light sheet-based microscopes highly suitable for live imaging applications. Here, we provide an overview of light sheet-based microscopy assays for in vitro and in vivo imaging of biological samples, including cell extracts, soft gels, and large multicellular organisms. We furthermore describe computational tools for basic image processing and data inspection.

}, issn = {1940-6029}, doi = {10.1007/978-1-62703-056-4_7}, author = {Tomer, Raju and Khairy, Khaled and Keller, Philipp J} } @article {4898, title = {Quantitative high-speed imaging of entire developing embryos with simultaneous multiview light-sheet microscopy.}, journal = {Nature Methods}, volume = {9}, year = {2012}, month = {2012 Jun 3}, pages = {755-63}, abstract = {

Live imaging of large biological specimens is fundamentally limited by the short optical penetration depth of light microscopes. To maximize physical coverage, we developed the SiMView technology framework for high-speed in vivo imaging, which records multiple views of the specimen simultaneously. SiMView consists of a light-sheet microscope with four synchronized optical arms, real-time electronics for long-term sCMOS-based image acquisition at 175 million voxels per second, and computational modules for high-throughput image registration, segmentation, tracking and real-time management of the terabytes of multiview data recorded per specimen. We developed one-photon and multiphoton SiMView implementations and recorded cellular dynamics in entire Drosophila melanogaster embryos with 30-s temporal resolution throughout development. We furthermore performed high-resolution long-term imaging of the developing nervous system and followed neuroblast cell lineages in vivo. SiMView data sets provide quantitative morphological information even for fast global processes and enable accurate automated cell tracking in the entire early embryo.

High-resolution movies in the Digital Embryo repository
Nature News: "Fruitfly development, cell by cell" by Lauren Gravitz
Nature Methods Technology Feature: "Faster frames, clearer pictures" by Monya Baker
Andor Insight Awards: Life Sciences Winner

}, issn = {1548-7105}, doi = {10.1038/nmeth.2062}, author = {Tomer, Raju and Khairy, Khaled and Amat, Fernando and Keller, Philipp J} } @article {4070, title = {A computational statistics approach for estimating the spatial range of morphogen gradients.}, journal = {Development}, volume = {138}, year = {2011}, month = {2011 Nov}, pages = {4867-74}, abstract = {

A crucial issue in studies of morphogen gradients relates to their range: the distance over which they can act as direct regulators of cell signaling, gene expression and cell differentiation. To address this, we present a straightforward statistical framework that can be used in multiple developmental systems. We illustrate the developed approach by providing a point estimate and confidence interval for the spatial range of the graded distribution of nuclear Dorsal, a transcription factor that controls the dorsoventral pattern of the Drosophila embryo.

}, issn = {1477-9129}, doi = {10.1242/dev.071571}, author = {Kanodia, Jitendra S and Kim, Yoosik and Tomer, Raju and Khan, Zia and Chung, Kwanghun and Storey, John D and Lu, Hang and Keller, Philipp J and Shvartsman, Stansilas Y} } @article {3684, title = {Shedding light on the system: studying embryonic development with light sheet microscopy.}, journal = {Current Opinion in Genetics and Development}, volume = {21}, year = {2011}, month = {2011 Aug}, pages = {558-65}, abstract = {

Light sheet-based fluorescence microscopy (LSFM) is emerging as a powerful imaging technique for the life sciences. LSFM provides an exceptionally high imaging speed, high signal-to-noise ratio, low level of photo-bleaching and good optical penetration depth. This unique combination of capabilities makes light sheet-based microscopes highly suitable for live imaging applications. There is an outstanding potential in applying this technology to the quantitative study of embryonic development. Here, we provide an overview of the different basic implementations of LSFM, review recent technical advances in the field and highlight applications in the context of embryonic development. We conclude with a discussion of promising future directions.

}, issn = {1879-0380}, doi = {10.1016/j.gde.2011.07.003}, author = {Tomer, Raju and Khairy, Khaled and Keller, Philipp J} }