Spatial heterogeneity of the cytosol revealed by machine learning-based 3D particle tracking

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in McLaughlin, G. A., Langdon, E. M., Crutchley, J. M., Holt, L. J., Forest, M. G., Newby, J. M., & Gladfelter, A. S. (2020). Spatial heterogeneity of the cytosol revealed by machine learning-based 3D particle tracking. Molecular Biology of the Cell, 31(14), 1498-1511, doi:10.1091/mbc.E20-03-0210.The spatial structure and physical properties of the cytosol are not well understood. Measurements of the material state of the cytosol are challenging due to its spatial and temporal heterogeneity. Recent development of genetically encoded multimeric nanoparticles (GEMs) has opened up study of the cytosol at the length scales of multiprotein complexes (20-60 nm). We developed an image analysis pipeline for 3D imaging of GEMs in the context of large, multinucleate fungi where there is evidence of functional compartmentalization of the cytosol for both the nuclear division cycle and branching. We applied a neural network to track particles in 3D and then created quantitative visualizations of spatially varying diffusivity. Using this pipeline to analyze spatial diffusivity patterns, we found that there is substantial variability in the properties of the cytosol. We detected zones where GEMs display especially low diffusivity at hyphal tips and near some nuclei, showing that the physical state of the cytosol varies spatially within a single cell. Additionally, we observed significant cell-to-cell variability in the average diffusivity of GEMs. Thus, the physical properties of the cytosol vary substantially in time and space and can be a source of heterogeneity within individual cells and across populations.We would like to thank the 2016 Physiology course and Christina Termini at the Marine Biological Laboratory in Woods Hole, MA, Gregory Brittingham, and Marcus Roper for initial experiments and perspectives on pipeline. We thank David Adalsteinsson for help with DataTank software and many conversations about image analysis on large datasets. We thank Emmanual Levy (Weizmann Institute) for providing plasmids encoding synthetic phase separating peptides. This work was supported by Google Cloud, the National Science Foundation (NSF), the National Institutes of Health (NIH), and the Natural Sciences and Engineering Research Council of Canada (NSERC). ASG, EML, and GAM were supported by the NSF (RoLs: 1840273), HHMI faculty scholar award and the NIH (R01GM081506). JMN was supported by the NSERC (RGPIN-2019-06435, RGPAS-2019-00014, DGECR-2019-00321) and the NSF (DMS-171474). MGF was supported by the NSF (DMS-1816630, DMS-1664645). LJH was supported by the NIH (R01GM132447)

The Histone Methyltransferase SUV39H1 Suppresses Embryonal Rhabdomyosarcoma Formation in Zebrafish

Epigenetics, or the reversible and heritable marks of gene regulation not including DNA sequence, encompasses chromatin modifications on both the DNA and histones and is as important as the DNA sequence itself. Chromatin-modifying factors are playing an increasingly important role in tumorigenesis, particularly among pediatric rhabdomyosarcomas (RMS), revealing potential novel therapeutic targets. We performed an overexpression screen of chromatin-modifying factors in a KRASG12D-driven zebrafish model for RMS. Here, we describe the identification of a histone H3 lysine 9 histone methyltransferase, SUV39H1, as a suppressor of embryonal RMS formation in zebrafish. This suppression is specific to the histone methyltransferase activity of SUV39H1, as point mutations in the SET domain lacked the effect. SUV39H1-overexpressing and control tumors have a similar proliferation rate, muscle differentiation state, and tumor growth rate. Strikingly, SUV39H1-overexpressing fish initiate fewer tumors, which results in the observed suppressive phenotype. We demonstrate that the delayed tumor onset occurs between 5 and 7 days post fertilization. Gene expression profiling at these stages revealed that in the context of KRASG12D overexpression, SUV39H1 may suppress cell cycle progression. Our studies provide evidence for the role of SUV39H1 as a tumor suppressor

The Grizzly, November 16, 2006

Election Results Bring Significant Changes • Ursinus Maintains its Health • Peace Vigil on Campus • Lecture Examines the Ethical Treatment of Abandoned Embryos • SquadZilla Brings Hip-Hop to Life at Ursinus • Ursinus Campaign Surpasses Goal • HPV and Cervical Cancer: The Facts, Part II • Preview of the Upcoming UCDC Performance • The Labyrinth: Not Just David Bowie in Spandex • Review of The Sisters Rosensweig • Opinions: Nerf: Yardstick of the Pentagon; American Press Needs Revamping • Bears Down Dickinson in Battle of Top Teams in Centennial Conference • Bears Win Third Straight CC Championship!https://digitalcommons.ursinus.edu/grizzlynews/1725/thumbnail.jp

mRNA structure determines specificity of a polyQ-driven phase separation

Author Posting. © The Author(s), 2018. This is the author's version of the work. It is posted here by permission of American Association for the Advancement of Science for personal use, not for redistribution. The definitive version was published in American Association for the Advancement of Science 360 (2018): 922-927, doi:10.1126/science.aar7432.RNA promotes liquid-liquid phase separation (LLPS) to build membrane-less compartments in cells. How distinct molecular compositions are established and maintained in these liquid compartments is unknown. Here we report that secondary structure allows mRNAs to self-associate and determines if an mRNA is recruited to or excluded from liquid compartments. The polyQ-protein Whi3 induces conformational changes in RNA structure and generates distinct molecular fluctuations depending on the RNA sequence. These data support a model in which structure-based, RNA-RNA interactions promote assembly of distinct droplets and protein-driven, conformational dynamics of the RNA maintain this identity. Thus, the shape of RNA can promote the formation and coexistence of the diverse array of RNA-rich liquid compartments found in a single cell.This work was supported by NIH GM R01- GM081506, the HHMI Faculty Scholars program, R35 GM122532, ACS 130845-RSG-17-114- 01-RMC, NIH 1DP2 GM105453, and NIH R01 GM115631

The Grizzly, November 2, 2006

Escape Velocity Dancers Light Up the Stage in the Black Box Theater • Letter to the Editor • Drive to Support the Troops a Success • Ursinus Homecoming 2006: There\u27s No Place Like Home • Blood Drive a Success on Campus • Batteries Included • A Look at Muslim Women in History: Professor Barbara R. von Schlegell Speaks • UC\u27s Opportunity to Support American Troops • Haunting Tales from Main Street • 2008 Preview: Part I • Opinions: Iraq: Should We Stay or Should We Go? • Football Pounds Hopkins on Homecoming • One Win and In for Women\u27s Soccer • Homecoming Victory for Field Hockeyhttps://digitalcommons.ursinus.edu/grizzlynews/1723/thumbnail.jp

The Grizzly, October 26, 2006

Editorial: Putting the Pieces Back Together • Possible Scam Raises Concerns • Town Hall Meeting Brings Forth Campus Issues • Food Drive a Success • Fall is in the Air • Story Behind the Statue: Praha • Get to Know the Nominees • Opinions: Long Live Noise; Swept Under the Rug; Truth About Study Abroad • Women\u27s Volleyball Swept by Gettysburg • Bullets Offense Too Much for Bears • Bears Make Run for Playoffshttps://digitalcommons.ursinus.edu/grizzlynews/1722/thumbnail.jp

The Grizzly, March 1, 2007

Media Lecture: The Jailhouse Doesn\u27t Rock • Peanut Butter Recall Update • Annual UC Job and Internship Fair • Living in Sin • Creating Communication Elation • Spotlight on Coach Kevin Small • Laramie Hits Big at Ursinus • Nutrition Tips: Fad Diets • Opinions: English as the Official Language? • Bears Capture Centennial Conference Title • Men\u27s Lacrosse Season Previewhttps://digitalcommons.ursinus.edu/grizzlynews/1733/thumbnail.jp

The Grizzly, November 30, 2006

Alcohol Awareness on the Front Burner of the Ursinus Campus • Diversity Forum Held for Staff and Students • 2nd Annual Relay for Life Officially Kicked Off at Ursinus • Town Hall Discusses Incidents on Campus • An Oral Examination • UCDC Performs Superbly in Latest Show • People Seeing People: The Artwork of Seward Johnson • Highlights of the Exposure Week Events and Festivities • Opinions: The Meaning of Liberal Arts; Racism in Our World and Home • Ursinus 2006 Division III Field Hockey National Champions! • Swimming to Successhttps://digitalcommons.ursinus.edu/grizzlynews/1726/thumbnail.jp

The Grizzly, April 12, 2007

Project Pericles Continues to Succeed in Community Service • Macs Lag in Environmental Friendliness According to Greenpeace • New Dorm Progress • Ursinus Freshmen Fall Behind in Collegiate Learning Assessment • Spread Your Legs and Turn Your Head and Cough • Relay for Life Fast Approaching • Ursinus, Break the Silence! • Nutrition Tips: Veggie Report • Opinions: Dear Mahmoud • Bears Terrorize McDaniel, Sit Atop CC Standings • Bears Finish Second at NCGA Championshipshttps://digitalcommons.ursinus.edu/grizzlynews/1737/thumbnail.jp

The Grizzly, February 8, 2007

WeCAN Protest for Workers\u27 Rights • Letters to the Editor • Class of \u2749 UC Alum Speaks on Women in World War II • Now That I\u27m Ready • What is an RA? • Note from the Editor: Facebook Fallacy • Nutrition Tips for the UC Student • UC Spotlight: UCEA • Opinions: The American Threat • Tumbling to Success • Rain, Rain and More Reignhttps://digitalcommons.ursinus.edu/grizzlynews/1730/thumbnail.jp