Stability of Quiver Representations and Topology Change

We study phase structure of the moduli space of a D0-brane on the orbifold C^3/Z_2 \times Z_2 based on stability of quiver representations. It is known from an analysis using toric geometry that this model has multiple phases connected by flop transitions. By comparing the results of the two methods, we obtain a correspondence between quiver representations and geometry of toric resolutions of the orbifold. It is shown that a redundancy of coordinates arising in the toric description of the D-brane moduli space, which is a key ingredient of disappearance of non-geometric phases, is understood from the monodromy around the orbifold point. We also discuss why only geometric phases appear from the viewpoint of stability of D0-branes.Comment: 16 pages, 7 figures, minor corrections, references adde

Dynamic organization of cortical actin filaments during the ooplasmic segregation of ascidian Ciona eggs

© The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Ishii, H., & Tani, T. Dynamic organization of cortical actin filaments during the ooplasmic segregation of ascidian Ciona eggs. Molecular Biology of the Cell, 32(3), (2021): 274-288, https://doi.org/10.1091/mbc.E20-01-0083.Spatial reorganization of cytoplasm in zygotic cells is critically important for establishing the body plans of many animal species. In ascidian zygotes, maternal determinants (mRNAs) are first transported to the vegetal pole a few minutes after fertilization and then to the future posterior side of the zygotes in a later phase of cytoplasmic reorganization, before the first cell division. Here, by using a novel fluorescence polarization microscope that reports the position and the orientation of fluorescently labeled proteins in living cells, we mapped the local alignments and the time-dependent changes of cortical actin networks in Ciona eggs. The initial cytoplasmic reorganization started with the contraction of vegetal hemisphere approximately 20 s after the fertilization-induced [Ca2+] increase. Timing of the vegetal contraction was consistent with the emergence of highly aligned actin filaments at the cell cortex of the vegetal hemisphere, which ran perpendicular to the animal–vegetal axis. We propose that the cytoplasmic reorganization is initiated by the local contraction of laterally aligned cortical actomyosin in the vegetal hemisphere, which in turn generates the directional movement of cytoplasm within the whole egg.We deeply thank Shalin Mehta for use of his MATLAB codes for our fluorescence polarization analyses and Mark Terasaki for reading our manuscript and giving us helpful feedback. We thank William Jeffery for sharing information about local C. intestinalis around the Marine Biological Laboratory. We also thank Takahito Nishikata and Takehiro G. Kusakabe for their generous support and kind suggestions for our experiments. Our research was supported by National Institutes of Health grant R01 GM100160, Japan Society for the Promotion of Science KAKENHI grant JP18K19962 to T.T., institutional funds of the Marine Biological Laboratory to T.T. and H.I., and a TOYOBO Biotechnology Foundation long-term fellowship to H.I

Dynein-ADP as a Force-Generating Intermediate Revealed by a Rapid Reactivation of Flagellar Axoneme

AbstractFragmented flagellar axonemes of sand dollar spermatozoa were reactivated by rapid photolysis of caged ATP. After a time lag of 10ms, axonemes treated with protease started sliding disintegration. Axonemes without protease digestion started nanometer-scale high-frequency oscillation after a similar time lag. Force development in the sliding disintegration was measured with a flexible glass needle and its time course was corresponded well to that of the dynein-ADP intermediate production estimated using kinetic rates previously reported. However, with a high concentration (∼80μM) of vanadate, which binds to the dynein-ADP intermediate and forms a stable complex of dynein-ADP-vanadate, the time course of force development in sliding disintegration was not affected at all. In the case of high frequency oscillation, the time lag to start the oscillation, the initial amplitude, and the initial frequency were not affected by vanadate, though the oscillation once started was damped more quickly at higher concentrations of vanadate. These results suggest that during the initial turnover of ATP hydrolysis, force generation of dynein is not blocked by vanadate. A vanadate-insensitive dynein-ADP is postulated as a force-generating intermediate

Living cells and dynamic molecules observed with the polarized light microscope : the legacy of Shinya Inoué

Author Posting. © Marine Biological Laboratory, 2016. This article is posted here by permission of Marine Biological Laboratory for personal use, not for redistribution. The definitive version was published in Biological Bulletin 231 (2016): 85-95.In 1948, Shinya Inoué arrived in the United States for graduate studies at Princeton. A year later he came to Woods Hole, starting a long tradition of summer research at the Marine Biological Laboratory (MBL), which quickly became Inoué's scientific home. Primed by his Japanese mentor, Katsuma Dan, Inoué followed Dan's mantra to work with healthy, living cells, on a fundamental problem (mitosis), with a unique tool set that he refined for precise and quantitative observations (polarized light microscopy), and a fresh and brilliant mind that was unafraid of challenging current dogma. Building on this potent combination, Inoué contributed landmark observations and concepts in cell biology, including the notion that there are dynamic, fine structures inside living cells, in which molecular assemblies such as mitotic spindle fibers exist in delicate equilibrium with their molecular building blocks suspended in the cytoplasm. In the late 1970s and 1980s, Inoué and others at the MBL were instrumental in conceiving video microscopy, a groundbreaking technique which married light microscopy and electronic imaging, ushering in a revolution in how we know and what we know about living cells and the molecular mechanisms of life. Here, we recount some of Inoué's accomplishments and describe how his legacy has shaped current activities in polarized light imaging at the MBL.Preparation of this manuscript was supported by grants from the National Institutes of Health (no. GM100160 to TT; no. GM101701 to MS; and no. GM114274 to RO); and by the Marine Biological Laboratory start-up funds from the Inoue´ Family Endowment, to TT

Polarized light microscopy in reproductive and developmental biology

Author Posting. © The Author(s), 2013. This is the author's version of the work. It is posted here by permission of John Wiley & Sons for personal use, not for redistribution. The definitive version was published in Molecular Reproduction and Development (2013), doi:10.1002/mrd.22221.The polarized light microscope reveals orientational order in native molecular structures inside living cells, tissues, and whole organisms. Therefore, it is a powerful tool to monitor and analyze the early developmental stages of organisms that lend themselves to microscopic observations. In this article we briefly discuss the components specific to a traditional polarizing microscope and some historically important observations on chromosome packing in sperm head, first zygote division of the sea urchin, and differentiation initiated by the first uneven cell division in the sand dollar. We then introduce the LC-PolScope and describe its use for measuring birefringence and polarized fluorescence in living cells and tissues. Applications range from the enucleation of mouse oocytes to analyzing the polarized fluorescence of the water strider acrosome. We end by reporting first results on the birefringence of the developing chick brain, which we analyzed between developmental stages of days 12 through 20.This work was supported by funds from the National Institute of General Medical Sciences (grant 1R01GM100160-01A1 awarded to TT) and the National Institute of Biomedical Imaging and Bioengineering (grant EB002045 awarded to RO)

Imaging of the fluorescence spectrum of a single fluorescent molecule by prism-based spectroscopy

AbstractWe have devised a novel method to visualize the fluorescence spectrum of a single fluorescent molecule using prism-based spectroscopy. Equiping a total internal reflection microscope with a newly designed wedge prism, we obtained a spectral image of a single rhodamine red molecule attached to an essential light chain of myosin. We also obtained a spectral image of single-pair fluorescence resonance energy transfer between rhodamine red and Cy5 in a double-labeled myosin motor domain. This method could become a useful tool to investigate the dynamic processes of biomolecules at the single-molecule level

Reconstitution of dynamic microtubules with Drosophila XMAP215, EB1, and Sentin

© The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Journal of Cell Biology 199 (2012): 849-862, doi:10.1083/jcb.201206101.Dynamic microtubules (MTs) are essential for various intracellular events, such as mitosis. In Drosophila melanogaster S2 cells, three MT tip-localizing proteins, Msps/XMAP215, EB1, and Sentin (an EB1 cargo protein), have been identified as being critical for accelerating MT growth and promoting catastrophe events, thus resulting in the formation of dynamic MTs. However, the molecular activity of each protein and the basis of the modulation of MT dynamics by these three factors are unknown. In this paper, we showed in vitro that XMAP215msps had a potent growth-promoting activity at a wide range of tubulin concentrations, whereas Sentin, when recruited by EB1 to the growing MT tip, accelerated growth and also increased catastrophe frequency. When all three factors were combined, the growth rate was synergistically enhanced, and rescue events were observed most frequently, but frequent catastrophes restrained the lengthening of the MTs. We propose that MT dynamics are promoted by the independent as well as the cooperative action of XMAP215msps polymerase and the EB1–Sentin duo.This work was supported by a Next Generation grant (Japan Society for the Promotion of Science), the Inoue Foundation, and the Human Frontier Science Program (to G. Goshima). W. Li was supported by the Global Centers of Excellence program, the Leading Graduate School program, and the State Scholarship Study Abroad Program of the Chinese Scholarship Council.2013-05-2

Postnatal structural development of mammalian Basilar Membrane provides anatomical basis for the maturation of tonotopic maps and frequency tuning

The basilar membrane (BM) of the mammalian cochlea constitutes a spiraling acellular ribbon that is intimately attached to the organ of Corti. Its graded stiffness, increasing from apex to the base of the cochlea provides the mechanical basis for sound frequency analysis. Despite its central role in auditory signal transduction, virtually nothing is known about the BM’s structural development. Using polarized light microscopy, the present study characterized the architectural transformations of freshly dissected BM at time points during postnatal development and maturation. The results indicate that the BM structural elements increase progressively in size, becoming radially aligned and more tightly packed with maturation and reach the adult structural signature by postnatal day 20 (P20). The findings provide insight into structural details and developmental changes of the mammalian BM, suggesting that BM is a dynamic structure that changes throughout the life of an animal

Septin assemblies form by diffusion-driven annealing on membranes

Author Posting. © The Author(s), 2013. This is the author's version of the work. It is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences of the United States of America 111 (2014): 2146-2151, doi:10.1073/pnas.1314138111.Septins assemble into filaments and higher-order structures that act as scaffolds for diverse cell functions including cytokinesis, cell polarity, and membrane remodeling. Despite their conserved role in cell organization, little is known about how septin filaments elongate and are knit together into higher-order assemblies. Using fluorescence correlation spectroscopy (FCS), we determined that cytosolic septins are in small complexes suggesting that septin filaments are not formed in the cytosol. When the plasma membrane of live cells is monitored by total internal reflection fluorescence (TIRF) microscopy, we see that septin complexes of variable size diffuse in two dimensions. Diffusing septin complexes collide and make end-on associations to form elongated filaments and higher-order structures, an assembly process we call annealing. Septin assembly by annealing can be reconstituted in vitro on supported lipid bilayers with purified septin complexes. Using the reconstitution assay, we show that septin filaments are highly flexible, grow only from free filament ends and do not exchange subunits in the middle of filaments. This work shows for the first time that annealing is an intrinsic property of septins in the presence of membranes and demonstrates that cells exploit this mechanism to build large septin assemblies.This project was supported with funding from by NSF (MCB-507511, ASG) and NIH (GM100160, TT and ASG), and Colwin, Lemann and Spiegel summer fellowships and The Nikon Award for summer investigation at MBL in Woods Hole, MA (ASG) and instrument support from Micro Video Instruments (MVI).2014-07-2