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PDW CV March 2014
Curriculum Vitae Dr. ir. Peter De Wulf Contact information European Institute of Oncology Department of Experimental Oncology Via Adamello 16 20139 Milan, Italy E-mail: [email protected] Tel: (++39) 0294375036 Fax: (++39) 0294375990 Position 08/2005 - present Principal Investigator Director Kinetochore and Chromosome Segregation Research Unit Department of Experimental Oncology European Institute of Oncology Milan, Italy Education and training 11/1999 - 06/2005 Post-Doctoral Research in Yeast Kinetochore Biology Department of Biology Massachusetts Institute of Technology 77 Massachusetts Avenue 02139 Cambridge (MA), USA Mentor: Prof. Dr. Peter K. Sorger (now at Harvard Medical School, Department of Systems Biology) 07/1996 - 10/1999 Post-Doctoral Research in Bacterial Two-Component Signal Transduction Department of Microbiology and Molecular Genetics Harvard Medical School 210 Longwood Avenue 02115 Boston (MA), USA Mentor: Prof. Dr. Edmund C.C. Lin (deceased) 04-20/07/1999 Course in Protein Purification and Characterization Cold Spring Harbor Laboratory. Cold Spring Harbor (NY), USA Instructors: Dr. Richard Burgess, Dr. Albert Courey, Dr. Sue-Hwa Lin, Dr. Sheenah Mische 06-20/06/1997 Course in Advanced Bacterial Genetics Cold Spring Harbor Laboratory. Cold Spring Harbor (NY), USA Instructors: Dr. Bonnie Bassler, Dr. Colin Manoil, Dr. James Slauch 06/1995 - 06/1996 Training in Yeast Cell Biology Department of Applied Biochemistry University of Milan via Celoria 26 20133 Milan, Italy Mentor: Prof. Dr. Lilia Alberghina (now at the University of Milan-Bicocca, Department of Biotechnology and Biosciences) 1 01/1992-05/1995 Ph.D. in Industrial Microbiology and Biocatalysis Department of Biochemical and Microbial Technology School of Bioengineering University of Ghent Coupure Links 653 B-9000 Ghent, Belgium Mentor: Prof. -
Spindle Assembly in Xenopus Egg Extracts
Spindle Assembly in Xenopus Egg Extracts: Respective Roles of Centrosomes and Microtubule Self-Organization Rebecca Heald, Régis Tournebize, Anja Habermann, Eric Karsenti, and Anthony Hyman Cell Biology Program, European Molecular Biology Laboratory, 69117 Heidelberg, Germany Abstract. In Xenopus egg extracts, spindles assembled end–directed translocation of microtubules by cytoplas- around sperm nuclei contain a centrosome at each pole, mic dynein, which tethers centrosomes to spindle poles. while those assembled around chromatin beads do not. However, in the absence of pole formation, microtu- Poles can also form in the absence of chromatin, after bules are still sorted into an antiparallel array around addition of a microtubule stabilizing agent to extracts. mitotic chromatin. Therefore, other activities in addi- Using this system, we have asked (a) how are spindle tion to dynein must contribute to the polarized orienta- poles formed, and (b) how does the nucleation and or- tion of microtubules in spindles. When centrosomes are ganization of microtubules by centrosomes influence present, they provide dominant sites for pole forma- spindle assembly? We have found that poles are mor- tion. Thus, in Xenopus egg extracts, centrosomes are not phologically similar regardless of their origin. In all cases, necessarily required for spindle assembly but can regu- microtubule organization into poles requires minus late the organization of microtubules into a bipolar array. uring cell division, the correct organization of mi- and Lloyd, 1994). In the absence of centrosomes, bipolar crotubules in bipolar spindles is necessary to dis- spindle assembly seems to occur through the self-organiza- D tribute chromosomes to the daughter cells. The tion of microtubules around mitotic chromatin (McKim slow growing or minus ends of the microtubules are fo- and Hawley, 1995; Heald et al., 1996; Waters and Salmon, cused at each pole, while the plus ends interact with the 1997). -
Mechanistic Mathematical Modeling of Spatiotemporal Microtubule Dynamics and Regulation in Vivo
Research Collection Doctoral Thesis Mechanistic mathematical modeling of spatiotemporal microtubule dynamics and regulation in vivo Author(s): Widmer, Lukas A. Publication Date: 2018 Permanent Link: https://doi.org/10.3929/ethz-b-000328562 Rights / License: In Copyright - Non-Commercial Use Permitted This page was generated automatically upon download from the ETH Zurich Research Collection. For more information please consult the Terms of use. ETH Library diss. eth no. 25588 MECHANISTICMATHEMATICAL MODELINGOFSPATIOTEMPORAL MICROTUBULEDYNAMICSAND REGULATION INVIVO A thesis submitted to attain the degree of DOCTOR OF SCIENCES of ETH ZURICH (dr. sc. eth zurich) presented by LUKASANDREASWIDMER msc. eth cbb born on 11. 03. 1987 citizen of luzern and ruswil lu, switzerland accepted on the recommendation of Prof. Dr. Jörg Stelling, examiner Prof. Dr. Yves Barral, co-examiner Prof. Dr. François Nédélec, co-examiner Prof. Dr. Linda Petzold, co-examiner 2018 Lukas Andreas Widmer Mechanistic mathematical modeling of spatiotemporal microtubule dynamics and regulation in vivo © 2018 ACKNOWLEDGEMENTS We are all much more than the sum of our work, and there is a great many whom I would like to thank for their support and encouragement, without which this thesis would not exist. I would like to thank my supervisor, Prof. Jörg Stelling, for giving me the opportunity to conduct my PhD research in his group. Jörg, you have been a great scientific mentor, and the scientific freedom you give your students is something I enjoyed a lot – you made it possible for me to develop my own theories, and put them to the test. I thank you for the trust you put into me, giving me a challenge to rise up to, and for always having an open door, whether in times of excitement or despair. -
Intracellular Scaling Mechanisms
Downloaded from http://cshperspectives.cshlp.org/ on September 29, 2021 - Published by Cold Spring Harbor Laboratory Press Intracellular Scaling Mechanisms Simone Reber1,2 and Nathan W. Goehring3 1Max Planck Institute of Molecular Genetics and Cell Biology, 01307 Dresden, Germany 2Integrative Research Institute (IRI) for the Life Sciences, Humboldt-Universita¨t zu Berlin, 10115 Berlin, Germany 3MRC Laboratory of Molecular Cell Biology, University College London, WC1E 6BT London, United Kingdom Correspondence: [email protected] Organelle function is often directly related to organelle size. However, it is not necessarily absolute size but the organelle-to-cell-size ratio that is critical. Larger cells generally have increased metabolic demands, must segregate DNA over larger distances, and require larger cytokinetic rings to divide. Thus, organelles often must scale to the size of the cell. The need for scaling is particularly acute during early development during which cell size can change rapidly. Here, we highlight scaling mechanisms for cellular structures as diverse as centro- somes, nuclei, and the mitotic spindle, and distinguish them from more general mechanisms of size control. In some cases, scaling is a consequence of the underlying mechanism of organelle size control. In others, size-control mechanisms are not obviously related to cell size, implying that scaling results indirectly from cell-size-dependent regulation of size- control mechanisms. cell is a highly organized unit in which We also know that cell size can vary dra- Afunctions are compartmentalized into spe- matically even within one organism. Xenopus cific organelles. Each cellular organelle carries laevis is an extreme example. The smallest so- out a distinct function, which is not only related matic cells are only a few micrometers in diam- to its molecular composition but, in many cas- eter, whereas the oocyte and one-cell embryo es, also to its size. -
Findings Magazine
FindingsFALL 2017 U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Institute of General Medical Sciences features 1 Protein Paradox: Enrique De La Cruz Aims to Understand Actin 18 The Science of Size: Rebecca Heald Explores Size Control in Amphibians articles 5 A World Without Pain 6 Demystifying General Anesthetics 10 There’s an “Ome” for That —TORSTEN WITTMANN, UNIVERSITY OF CALIFORNIA, SAN FRANCISCO ON THE COVER This human skin cell was bathed 17 Lighting Up the Promise of Gene Therapy in a liquid containing a growth factor. The procedure for Glaucoma triggered the formation of specialized protein structures that enable the cell to move. We depend on our cells 24 NIGMS Is on Instagram! being able to move for basic functions such as the healing of wounds and the launch of immune responses. departments 3 Cool Tools: High-Resolution Microscopy— Editor In Living Color Chris Palmer 9 Spotlight on Videos: Scientists in Action Contributing Writers Carolyn Beans 14 S potlight on the Cell: The Extracellular Matrix, Kathryn Calkins Emily Carlson a Multitasking Marvel Alisa Zapp Machalek Chris Palmer Erin Ross Ruchi Shah activities Production Manager 22 Superstars of Science Quiz Susan Athey Online Editor The Last Word (inside back cover) Susan Athey Find Us At Image credits: Unless otherwise credited, images are royalty-free stock images. https://twitter.com/nigms https://www.facebook.com/nigms.nih.gov Produced by the Offce of Communications and Public Liaison https://www.instagram.com/nigms_nih National Institute of General Medical Sciences National Institutes of Health https://www.youtube.com/user/NIGMS U.S. -
Josephine Bay Paul Center for Comparative Molecular Biology And
OCTOBER 2, 2014 CONTACT US DIRECTIONS TO MBL HOME ABOUT MBL EDUCATION RESEARCH GIVING MBL NEWS HOME Josephine Bay Paul Center for Comparative Molecular Biology and Evolution RESOURCES HIGHLIGHTS RESEARCH Josephine Bay Paul Center for Comparative Molecular Biology and Evolution Eugene Bell Center for Regenerative Biology & Tissue Engineering Cellular Dynamics Program The Ecosystems Center Program in Sensory Physiology and Behavior Whitman Center for Research and Discovery EDUCATION MBLWHOI LIBRARY GIFTS PEOPLE In the Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, scientists explore the evolution and interaction of genomes of diverse organisms with significant roles in environmental biology and human health. Bay Paul Center scientists integrate the powerful tools of genome science, molecular phylogenetics, and molecular ecology to advance our understanding of how living organisms are related to each other, to provide the tools to quantify and assess biodiversity, and to identify genes and metabolic processes of ecological and biomedical importance. Publications | Staff List © 1996-2014, The Marine Biological Laboratory MARINE BIOLOGICAL LABORATORY, MBL, and the Join the MBL community: 1888 logo are registered trademarks and service marks of The Marine Biological Laboratory. OCTOBER 2, 2014 CONTACT US DIRECTIONS TO MBL HOME ABOUT MBL EDUCATION RESEARCH GIVING MBL NEWS HOME Bay Paul Center Publications RESOURCES Akerman, NH; Butterfield, DA; and Huber, JA. 2013. Phylogenetic Diversity and Functional Gene Patterns of Sulfur- oxidizing Subseafloor Epsilonproteobacteria in Diffuse Hydrothermal Vent Fluids. Front Microbiol. 4, 185. HIGHLIGHTS RESEARCH Alliegro, MC; and Alliegro, MA. 2013. Localization of rRNA Transcribed Spacer Domains in the Nucleolinus and Maternal Procentrosomes of Surf Clam (Spisula) Oocytes.” RNA Biol. -
Machine-Learning Based Classification of Textual Stimuli To
MACHINE-LEARNING BASED CLASSIFICATION OF TEXTUAL STIMULI TO PROMOTE IDEATION IN BIOINSPIRED DESIGN A Dissertation by MICHAEL W. GLIER Submitted to the Office of Graduate Studies of Texas A&M University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Chair of Committee, Daniel A. McAdams Co-Chair of Committee, Julie S. Linsey Committee Members, Richard J Malak Tracy A. Hammond Head of Department, Andreas Polycarpou August 2013 Major Subject: Mechanical Engineering Copyright 2013 Michael W. Glier ABSTRACT Bioinspired design uses biological systems to inspire engineering designs. One of bioinspired design’s challenges is identifying relevant information sources in biology for an engineering design task. Currently information can be retrieved by searching biology texts or journals using biology-focused keywords that map to engineering functions. However, this search technique can overwhelm designers with unusable results. This work explores the use of text classification tools to identify relevant biology passages for design. Further, this research examines the effects of using biology passages as stimuli during idea generation. Four human-subjects studies are examined in this work. Two surveys are performed in which participants evaluate sentences from a biology corpus and indicate whether each sentence prompts an idea for solving a specific design problem. The surveys are used to develop and evaluate text classification tools. Two idea generation studies are performed in which participants generate and record solutions for designing a corn shucker using either different sets of biology passages as design stimuli, or no stimuli. Based 286 sentences from the surveys, a k Nearest Neighbor classifier is developed that is able to identify helpful sentences relating to the function “separate” with a precision of 0.62 and recall of 0.48. -
Molecular Determinants of the Ska-Ndc80 Interaction and Their
RESEARCH ARTICLE Molecular determinants of the Ska-Ndc80 interaction and their influence on microtubule tracking and force-coupling Pim J Huis in ’t Veld1†, Vladimir A Volkov2†, Isabelle D Stender1, Andrea Musacchio1,3*, Marileen Dogterom2* 1Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany; 2Department of Bionanoscience, Faculty of Applied Sciences, Delft University of Technology, Delft, Netherlands; 3Centre for Medical Biotechnology, Faculty of Biology, University Duisburg, Essen, Germany Abstract Errorless chromosome segregation requires load-bearing attachments of the plus ends of spindle microtubules to chromosome structures named kinetochores. How these end-on kinetochore attachments are established following initial lateral contacts with the microtubule lattice is poorly understood. Two microtubule-binding complexes, the Ndc80 and Ska complexes, are important for efficient end-on coupling and may function as a unit in this process, but precise conditions for their interaction are unknown. Here, we report that the Ska-Ndc80 interaction is phosphorylation-dependent and does not require microtubules, applied force, or several previously identified functional determinants including the Ndc80-loop and the Ndc80-tail. Both the Ndc80- tail, which we reveal to be essential for microtubule end-tracking, and Ndc80-bound Ska stabilize microtubule ends in a stalled conformation. Modulation of force-coupling efficiency demonstrates *For correspondence: that the duration of stalled microtubule -
A Study of the Cell Biology of Motility in Eimeria Tenella Sporozoites
A STUDY OF THE CELL BIOLOGY OF MOTILITY IN Eimeria tenella SPOROZOITES by David Robert Bruce Department of Biology University College London A thesis presented for the degree of Doctor of Philosophy in the University of London 2000 ProQuest Number: U643145 All rights reserved INFORMATION TO ALL USERS The quality of this reproduction is dependent upon the quality of the copy submitted. In the unlikely event that the author did not send a complete manuscript and there are missing pages, these will be noted. Also, if material had to be removed, a note will indicate the deletion. uest. ProQuest U643145 Published by ProQuest LLC(2016). Copyright of the Dissertation is held by the Author. All rights reserved. This work is protected against unauthorized copying under Title 17, United States Code. Microform Edition © ProQuest LLC. ProQuest LLC 789 East Eisenhower Parkway P.O. Box 1346 Ann Arbor, Ml 48106-1346 ABSTRACT A study on the cell biology of motility inEimeria tenella sporozoites Eimeria tenella is an obligate intracellular parasite within the phylum Apicomplexa. It is the causative agent of coccidiosis in domesticated chickens and under modem farming conditions can have a considerable economic impact. Motility is employed by the sporozoite to effect release from the sporocyst and enable invasion of appropriate host cells and occurs at an average speed of 16.7 ± 6 pms'\ Frame by frame video analysis of gliding motility shows it to be an erratic non substrate specific process and this observation was confirmed by studies of bead translocation across the cell surface occurring at an average speed of 16.9 ± 7.6 pms'^ Incubation with cytochalasin D, 2,3-butanedione monoxime and colchicine, known inhibitors of the motility associated proteins actin, myosin and tubulin respectively, indicated that it is an actomyosin complex which generates the force to power sporozoite motility. -
Structure of Human Mad1 C-Terminal Domain Reveals Its Involvement in Kinetochore Targeting
Structure of human Mad1 C-terminal domain reveals its involvement in kinetochore targeting Soonjoung Kima,b,1, Hongbin Suna,1,2, Diana R. Tomchickc, Hongtao Yua,b,3, and Xuelian Luoa,3 aDepartment of Pharmacology, bHoward Hughes Medical Institute, and cDepartment of Biochemistry, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390 Edited by Edward D. Salmon, University of North Carolina, Chapel Hill, NC, and accepted by the Editorial Board February 28, 2012 (received for review November 4, 2011) The spindle checkpoint prevents aneuploidy by delaying anaphase and sufficient for its kinetochore localization and checkpoint func- onset until all sister chromatids achieve proper microtubule attach- tion (18). By contrast, an N-terminal fragment of Xenopus Mad1 ment. The kinetochore-bound checkpoint protein complex Mad1- lacking the CTD has been shown to localize to kinetochores (19). Mad2 promotes the conformational activation of Mad2 and serves Finally, mutation of T680, a residue within the CTD and a poten- as a catalytic engine of checkpoint signaling. How Mad1 is targeted tial Plk1 phosphorylation site, in human Mad1 has been reported to kinetochores is not understood. Here, we report the crystal to diminish its kinetochore localization (20). It is thus unclear structure of the conserved C-terminal domain (CTD) of human whether Mad1 has conserved kinetochore-targeting domains. Mad1. Mad1 CTD forms a homodimer and, unexpectedly, has a fold The kinetochore receptor or receptors of Mad1 are also unknown. similar to those of the kinetochore-binding domains of Spc25 and In this study, we have determined the crystal structure of the Csm1. -
Spatial Organization of Large Cells
Spatial Organization of Large Cells A dissertation presented by Martin Helmut Wuehr to The Committee on Higher Degrees in Systems Biology in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the subject of Systems Biology Harvard University Cambridge, Massachusetts March 2010 i © 2010 – Martin H. Wuehr All rights reserved. ii Timothy John Mitchison Martin Helmut Wuehr Spatial Organization of Large Cells Abstract The rationale for my research was to investigate unusually large cells, fertilized frog and fish eggs, to obtain a unique perspective on a cell’s spatial organization with a focus on cell division. First, we investigated how spindle size changes during cleavage stages while cell size changes by orders of magnitude. To do so we improved techniques for immunofluorescence in amphibian embryos and generated a transgenic fish line with fluorescently labeled microtubules. We show that in smaller cells spindle length scales with cell length, but in very large cells spindle length approaches an upper limit and seems uncoupled from cell size. Furthermore, we were able to assemble mitotic spindles in embryonic extract that had similar size as in vivo spindles. This indicates that spindle size is set by a mechanism that is intrinsic to the spindle and not downstream of cell size. Second we investigated how relatively small spindles in large cells are positioned, and oriented for symmetric cell division. We show that the localization and orientation of these spindles are determined by location and iii orientation of sister centrosomes set by the anaphase-telophase aster of the previous cycle. Third we researched the mechanism by which asters center and align centrosomes relative to the longest axis. -
Cell Biology Annual Meeting Program
Cell Biology Annual Meeting Program Shirley Tilghman, President Julie Theriot, Program Chair Karen Oegema, Local Organizer ascb.org/2015meeting Search Your Smartphone App Store for ASCB2015 Submit Your Research Committed to Excellence, Rigor, and Breadth eNeuro has joined JNeurosci in the PubMed Central database. Learn more at SfN.org DON’T MISS OUT ON ANOTHER ISSUE! SUBSCRIBE Sign up now to receive FOR FREE* the monthly print magazine. TODAY! Each issue contains feature articles on hot new trends in science, profiles of top-notch researchers, reviews of the latest tools and technologies, and much, much more. * Only available for a limited time. Not all requests qualify for a free subscription. www.the-scientist.com/subscribe The Company of Biologists is a UK based charity and not-for-profit publisher run by biologists for biologists. The Company aims to promote research and study across all branches of biology through the publication of its five journals. Development Advances in developmental biology and stem cells dev.biologists.org Journal of Cell Science The science of cells jcs.biologists.org The Journal of Experimental Biology At the forefront of comparative physiology and integrative biology jeb.biologists.org Disease Models & Mechanisms Basic research with translational impact dmm.biologists.org Biology Open Facilitating rapid peer review for accessible research bio.biologists.org In addition to publishing, The Company makes an important contribution to the scientific community, providing grants, travelling fellowships and sponsorship