Biological Physics
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Structural Data in Synthetic Biology Approaches for Studying General Design Principles of Cellular Signaling Networks
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Structure Perspective Structural Data in Synthetic Biology Approaches for Studying General Design Principles of Cellular Signaling Networks Christina Kiel1,2,* and Luis Serrano1,2,3 1EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain 2Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain 3ICREA, Pg. Lluı´s Companys 23, 08010 Barcelona, Spain *Correspondence: [email protected] http://dx.doi.org/10.1016/j.str.2012.10.002 In recent years, high-throughput discovery of macromolecular protein structures and complexes has played a major role in advancing a more systems-oriented view of protein interaction and signaling networks. The design of biological systems often employs structural information or structure-based protein design to successfully implement synthetic signaling circuits or for rewiring signaling flows. Here, we summarize the latest advances in using structural information for studying protein interaction and signaling networks, and in synthetic biology approaches. We then provide a perspective of how combining structural biology with engineered cell signaling modules—using additional information from quantitative biochemistry and proteo- mics, gene evolution, and mathematical modeling—can provide insight into signaling modules and the general design principles of cell signaling. Ultimately, this will improve our understanding of cell- and tissue-type-specific signal transduction. Integrating the quantitative effects of disease mutations into these systems may provide a basis for elucidating the molecular mechanisms of diseases. Introduction further complicated by the fact that often proteins recruit binding There is growing three-dimensional (3D) structural information partners using several domain or linear motifs. -
ASB M B Annual Meeting Highlights from the 2009
2010 ANNUAL MEETING, APRIL 24-28. ANAHEIM AWAITS! hlights fr ig om H June 2009 t h e 2 0 0 9 A S B M B A n n u al Meeting American Society for Biochemistry and Molecular Biology ANNUAL REVIEWS A Nonprofit Scientific Publisher INSIGHTFUL ANNUAL REVIEW OF TABLE OF CONTENTS BIOCHEMISTRY Without a License, or Accidents Waiting to Happen, E. Peter Geiduschek RESEARCH IN • A Journey in the World of DNA Rings and Beyond, James C. Wang BIOCHEMISTRY Vol. 78 • JUlY 2009 • The Biochemistry of Disease: Desperately Seeking Syzygy, John W. Kozarich • Biosynthesis of Phosphonic and Phosphinic Acid Natural STARTS WITH Editor: Products, William W. Metcalf, Wilfred A. van der Donk • New Antivirals and Drug Resistance, Peter M. Colman • Multidrug Resistance in Bacteria, Roger D. Kornberg ANNUAL Hiroshi Nikaido • Conformational Pathology of the Serpins: Themes, REVIEWS Stanford University School Variations, and Therapeutic Strategies, Bibek Gooptu, David A. Lomas of Medicine • Getting a Grip on Prions: Oligomers, Amyloids, and Pathological Membrane Interactions, Byron Caughey, Gerald S. Baron, Bruce Chesebro, Annual Review of Martin Jeffrey • RING Domain E3 Ubiquitin Ligases, Raymond J. Deshaies, Biochemistry, in publication Claudio A.P. Joazeiro • Regulation and Cellular Roles of Ubiquitin- since 1932, sets the standard Specific Deubiquitinating Enzymes, Francisca E. Reyes-Turcu, Karen H. Ventii, Keith D. Wilkinson • Recognition and Processing of Ubiquitin- for review articles in biological Protein Conjugates by the Proteasome, Daniel Finley • Degradation of chemistry and molecular biology. Activated Protein Kinases by Ubiquitination, Zhimin Lu, Tony Hunter • The Since its inception, these volumes Role of Ubiquitin in the NFκB Regulatory Pathways, Brian Skaug, Xiaomo have served as an indispensable Jiang, Zhijian J. -
Synthetic Biology Applying Engineering to Biology
Synthetic Biology Applying Engineering to Biology Report of a NEST High-Level Expert Group EUR 21796 PROJECT REPORT Interested in European research? RTD info is our quarterly magazine keeping you in touch with main developments (results, programmes, events, etc). It is available in English, French and German. A free sample copy or free subscription can be obtained from: European Commission Directorate-General for Research Information and Communication Unit B-1049 Brussels Fax : (32-2) 29-58220 E-mail: [email protected] Internet: http://europa.eu.int/comm/research/rtdinfo/index_en.html EUROPEAN COMMISSION Directorate-General for Research Directorate B — Structuring the European Research Area Unit B1 — Anticipation of Scientific and Technological Needs (NEST activity); Basic Research E-mail: [email protected] Contact: Christian Krassnig European Commission Office SDME 01/37 B-1049 Brussels Tel. (32-2) 29-86445 Fax (32-2) 29-93173 E-mail: [email protected] For further information on the NEST activity please refer to the following website: http://www.cordis.lu/nest/home.html EUROPEAN COMMISSION Synthetic Biology Applying Engineering to Biology Report of a NEST High-Level Expert Group NEST - New and Energing Science and Technology - is a research activity under the European Community’s 6th Framework Programme Directorate-General for Research Structuring the European Research Area 2005 Anticipating Scientific and Technological Needs; Basic Research EUR 21796 Europe Direct is a service to help you find answers to your questions about the European Union Freephone number: 00 800 6 7 8 9 10 11 LEGAL NOTICE: Neither the European Commission nor any person acting on behalf of the Commission is responsible for the use which might be made of the following information. -
Pages 459 To
459 University Organization Board of Trustees The dean of the Heller School for Social study abroad, international students and Policy and Management oversees the scholars, and student enrichment services), academic activities of the school and its Hiatt Career Center, research and planning, Under Massachusetts law, the Board of work in such policy areas as children, and student life (including athletics, Trustees is the governing body of the youth, families, health, mental health, chaplaincy, community service, health university. There are four faculty substance abuse, disabilities, aging, social services, intercultural center, judicial representatives and three student change, and economic inequalities. orientation, psychological counseling, representatives to the board who participate residence life, and student activities). in board meetings and have votes on the The dean of the Brandeis International several committees. The president of the Business School oversees the academic, The senior vice president for university, the chair of the Fellows, the professional, and development activities communications administers and executes president of the Brandeis National of the university’s second professional critical university-wide internal and Committee, and the president of the school. Research areas of the school external communications, overseeing the Alumni Association serve ex officio. The include economic policy, finance, global communications emergency response plan board annually elects an alumni term entrepreneurship, international business, and directing all crisis communications. trustee who serves a four-year term with regional economics integration, and trade Further, she is responsible for an integrated full voting privileges. and exports. marketing communications program that highlights Brandeis’s research The President accomplishments, academic excellence, The president, the chief executive officer of The Faculty Senate social justice mission, and scholarly the university, is appointed by the Board of contributions to the Jewish community. -
Biochemistry Biotechnology Cell Biology
Undergraduate Biochemistry Opportunities www.ed.ac.uk/biology Biotechnology Cell Biology Biochem_Biotech_CellBio_A5.indd 1 21/05/2019 14:25 Biochemistry The programme combines coverage of the Biochemistry is the study of living systems at basic principles and knowledge underpinning the cellular and molecular level. This dynamic biotechnology and an appreciation of the field draws on a variety of subjects and has processes involved in converting an idea widespread application. Biochemistry applies a into a product. The objective is to provide a knowledge of chemistry and physical sciences firm foundation in molecular and microbial to investigate basic life processes. The subject biotechnology through compulsory sections has a major impact on modern medical research dealing with topics such as expression vectors, and upon the pharmaceutical, bioengineering, microbial fermentation, protein structure, drug agricultural and environmental industries. design and the development of antimicrobials and vaccines. The programme encourages the critical assessment of current developments in areas of Cell Biology biological interest. Modern cell biology is a dynamic discipline that combines the interests and techniques of many Biotechnology scientific fields. Cell biologists investigate the Biotechnology is concerned with industrial basic structural and functional units of life, the and biomedical applications of fundamental cells that compose all living organisms. They aim knowledge derived from biology. This covers to understand: cellular structure, composition many facets from making useful products and regulation, the organelles that cells contain, using microbial, plant or animal cells to using cell growth, nuclear and cellular division, and bioinformatics and structural biology to design cell death. Understanding how cells work is new drugs. Biotechnology is an exciting area fundamental to many areas of biology and is of with new developments each year in areas that particular importance to fields such as cancer affect us all. -
BCH 6746: Structural Biology Course Prerequisites: CRN 12063 Section 001, 3 Credit Hours
Please note: Each college and department may have their own requirements, in addition to those stated in the Syllabus Guidelines. BCH 6746: Structural Biology Course Prerequisites: CRN 12063 Section 001, 3 Credit hours College of Arts and Sciences, CMMB COURSE SYLLABUS Insert USF Logo here Instructor Name: Yu Chen Semester/Term & Year: Spring 2019 Class Meeting Days: TR Class Meeting Time: 11:00 – 12:20 pm Class Meeting Location: MDC 1507 Lab Meeting Location: N/A Delivery Method: Lecture I. Welcome! II. University Course Description The theory and application of modern physical biochemical techniques. III. Course Objectives This course focuses on relating theoretical concepts and experimental approaches to a wide range of potential research problems in the area of structural biology. The course aims to provide a solid foundation and breadth of understanding in structural biology that will facilitate application to current and future research problems. IV. Course Purpose Major Topics: Introduction to Structural Biology; From Structure to Function I; From Structure to Function II; From Structure to Function III; From Structure fo Function IV; Control of Protein Function I; Strategies for Protein Separation; Strategies for Protein Identification; Chemical and Immunochemical Probes of Structure; Methods in Structural Bio I, II, II; Structure Determination I, II, III, IV; Control of Protein Function II, III, IV V. Learning Outcomes Students will gain an understanding of the basic science of Protein Structure, including first principles of the physical interactions that maintain proteins and the mechanisms that make them tic. They will also learn about different techniques and experimental approaches that represent the state-of-the-art and are widely used in the study of proteins. -
2014-Program-For-Lecture-Gregory
OKLAHOMA SCHOOL OF SCIENCE AND MATHEMATICS Oklahoma stands out among other states in our dedication to providing OSSM an outstanding science and mathematics education to its gifted students at a time when our nation falls behind other countries in these areas. Senator Penny Williams Distinguished Lecture Series With just 22 classes graduated, OSSM alumni/alumnae are already Presents bringing substantial benefits to our state as they complete their degrees and move into their professions. “How Parkinson’s Disease Starts and •••••••••••••••••••••••• How It Might Be Stopped” • Eighty-five percent of OSSM alumni are remaining in scientific, technology, By engineering, and mathematics (STEM) fields for their careers! 2014 Capra Scholar • Of OSSM graduates now employed (many are still in undergraduate and graduate school or completing residencies in medical school), more than 60% GreGory A. PetSko, D.PHIl. are employed in Oklahoma. The fields of study and careers most chosen by OSSM graduates are engineering Arthur J. Mahon Professor of Neurology and Neuroscience and • Director, Helen and Robert Appel Alzheimer’s Disease Research Institute Weill Cornell Medical College (aerospace, biomedical, chemical, civil, computer, electrical, mechanical, Adjunct Professor of Biomedical Engineering Cornell University petroleum); medicine, medical research, and other health sciences; and other fields including computer science, technology, education, scientific research, Gyula and Katica Tauber Professor of Biochemistry and Chemistry, Emeritus Brandeis University business, and law. Adjunct Professor of Neurology Harvard Medical School Many OSSM alums are employed in many of Oklahoma’s finest corporations, Past-President, American Society for Biochemistry and Molecular Biology • President, International Union of Biochemistry and Molecular Biology hospitals and technical firms such as AT&T, Artificial Lift Company, Baptist Hospital, Benham Companies, Boeing, Chesapeake Energy, C. -
MATHEMATICAL TECHNIQUES in STRUCTURAL BIOLOGY Contents 0. Introduction 4 1. Molecular Genetics: DNA 6 1.1. Genetic Code 6 1.2. T
MATHEMATICAL TECHNIQUES IN STRUCTURAL BIOLOGY J. R. QUINE Contents 0. Introduction 4 1. Molecular Genetics: DNA 6 1.1. Genetic code 6 1.2. The geometry of DNA 6 1.3. The double helix 6 1.4. Larger organization of DNA 7 1.5. DNA and proteins 7 1.6. Problems 7 2. Molecular Genetics: Proteins 10 2.1. Amino Acids 10 2.2. The genetic code 10 2.3. Amino acid template 11 2.4. Tetrahedral geometry 11 2.5. Amino acid structure 13 2.6. The peptide bond 13 2.7. Protein structure 14 2.8. Secondary structure 14 3. Frames and moving frames 19 3.1. Basic definitions 19 3.2. Frames and gram matrices 19 3.3. Frames and rotations 20 3.4. Frames fixed at a point 20 3.5. The Frenet Frame 20 3.6. The coiled-coil 22 3.7. The Frenet formula 22 3.8. Problems 24 4. Orthogonal transformations and Rotations 25 4.1. The rotation group 25 4.2. Complex form of a rotation 28 4.3. Eigenvalues of a rotation 28 4.4. Properties of rotations 29 4.5. Problems 30 5. Torsion angles and pdb files 33 5.1. Torsion Angles 33 5.2. The arg function 34 5.3. The torsion angle formula 34 5.4. Protein torsion angles. 35 5.5. Protein Data Bank files. 35 1 2 J. R. QUINE 5.6. Ramachandran diagram 36 5.7. Torsion angles on the diamond packing 37 5.8. Appendix, properties of cross product 38 5.9. Problems 38 6. -
Biophysical Society 58Th Annual Meeting February 15–19, 2014 | San Francisco, California
ABSTRACT DEADLINE: OCTOBER 1, 2013 | EARLY REGISTRATION DEADLINE: JANUARY 8, 2014 Biophysical Society 58th Annual Meeting FEBRUARY 15–19, 2014 | SAN FRANCISCO, CALIFORNIA BIOPHYSICS OF CELL DIVISION AND National Lecturer SPATIAL RELATIONSHIPS Workshops Susan Biggins, Fred Hutchinson Cancer Workshops will be held on Sunday and Carlos Bustamante Research Center, Co-Chair Tuesday evenings. University of California, Berkeley Wallace Marshall, University of California, San Francisco, Co-Chair POLARIZABLE FORCE FIELDS FROM Daniel Fletcher, University of California, BIOMOLECULAR SIMULATIONS A Journey Through Cellular Processes: Berkeley One Molecule at a Time Matthieu Piel, Curie Institute, France Benoit Roux, University of Chicago, Co-Chair Alexander Mackerell, University FORCE GENERATION IN CELL AND of Maryland, Co-Chair TISSUE NETWORKS Vijay Pande, Stanford University Michael Sheetz, Columbia University, MOLECULAR BASIS FOR REGULATION Teresa Head-Gordon, University Co-Chair Symposia 2+ of California, Berkeley OF CA CHANNELS Clare Waterman, NHLBI, Co-Chair Stephen Long, Memorial Sloan- Symposia will be held Sunday through Alexander Bershadsky, Weizmann Kettering Cancer Center, Co-Chair SINGLE MOLECULE DYNAMICS USING Wednesday. Institute of Science, Israel FRET/LRET Amy Lee, University of Iowa, Co-Chair Frank Jülicher, Max Planck Institute for the Achillefs Kapanidis, University of Annette Dolphin, University College Physics of Complex Systems, Germany FORCE SENSING IN MUSCLE London, United Kingdom Oxford, United Kingdom, Co-Chair Mathias Gautel, -
Experimentally Demonstrated the Intrinsic Instability of the Fluorite-Type Zr Cation Network
0246110 Rta(i) 1 1,2 l,4 1,6 1,l 2 22 Rta(i) Figure 2. Temperature dependence of Zr-FTfor pure orthorhombic zirconia Figure 3 Temperature dependence of Zr-0 shell in tetragonal zirconia solid solution Our study has experimentally demonstrated the intrinsic instability of the fluorite-type Zr cation network. Coherent scattering beween Conclusions central Zr ion and distant cations is weaker and vibration modes of the Zr-cation network are It is found that, for all of zirconia solid softer in tetragonal zirconia than in monoclmic, solutions studied, the dopant-oxygen distances are orthorhombic, or stabilized cubic zirconia. In si@icantly ddferent from the Zr-0 distances. addition, the outer foux oxygens in the 8-fold The dopant-cation distances, on the other hand, coordinated Zr-0 polyhedron are only loosely are usually very close to the Zr-Zr distance, solutions. A bonded and are subject to very large static and confirming the formation of solid dynamic distortions. This effect is illustrated by general structural picture for zirconia solid the expanded portion of the Fourier transform solutions is one that places the dopant cations shown in Figure 3. randomly on tbe Zr sites in the cation network, but with distorted and sometimes very different Dopant Structure dopant-oxygen polyhedra surrounding these dopants. In the case of Ge4+ doping and Y-Nb We have also successfully performed co-doping, short-rangecation ordering has been EXAFS experiments at the dopant absorption suggested from our EXAFS results. edges for doped zirconia solid solutions. Dopants Based on the above structural information studied include the Ce-,Nb-, and Y-K edges as and other EXAFS results obtained from NSLS, well as Ce-LIn edge. -
Cell Biology in Sudan
See discussions, stats, and author profiles for this publication at: https://www.researchgate.net/publication/290440842 Science on the Banks of the Nile: Cell Biology in Sudan Article · September 2014 READS 162 4 authors, including: Marmar A. El Siddig Adil Ali EL Hussein University of Khartoum University of Khartoum 40 PUBLICATIONS 25 CITATIONS 44 PUBLICATIONS 67 CITATIONS SEE PROFILE SEE PROFILE Sakina Yagi University of Khartoum 36 PUBLICATIONS 174 CITATIONS SEE PROFILE Available from: Marmar A. El Siddig Retrieved on: 17 May 2016 ASCB MARCH 2014 NEWSLETTER VOLUME 37, NUMBER 2 The ASCB in 2018 Page 3 ASCB Task Force to Explore Annual Meeting Reproducibility of Scientific Data Highlights The apparent irreproducibility of some published scientific Page 9 results is an issue of growing concern to industry and to the scientific community. It has begun to receive attention in the news media as well, and if one believes the popular press as MBoC Call for Papers much as 80% of scientific research cannot be reproduced. Is in Quantitative that really true? Does that apply to all research or just some Biology areas? These are just two of the questions a task force of the Page 36 ASCB’s Public Policy Committee (PPC) will attempt to answer as it conducts an in-depth analysis of the issue. If reports of widespread difficulty in reproducing published Inside research results are true, it is a problem that could threaten the scientific enterprise and undermine the authority of the COMPASS Outreach Awards 2 scientific community. In his charge to the task force, ASCB Executive Director’s Column 3 Executive Director Stefano Bertuzzi listed four potential causes for difficulties in reproducing results: DORA Panel Discussion 9 n A hyper-competitive culture that overemphasizes results BSCB Young Cell Biologist 10 n A bias in favor of positive results Young French Cell Biologists 11 Reproducibility, continued on p.17 Mark Winey Local Meeting Highlights 12 Nominate a Colleague for an ASCB Award! Deadline April 1. -
The Institute of Botany
FEATURE ARTICLE Taiwan’s Academia Sinica Forges Ahead Research in the life sciences has expanded and improved, and is conforming to international standards institutes and research projects, to promote academic collaboration between Taiwan and other countries, and to make plans for academic development when requested by the government. It is also responsible for nominating three candidates for the presidency when the president vacates, as well as formulation of rules pertaining to the Academia. The Central Advisory Committee consists of chairpersons of the advisory committee of the individual institutes, and two to three specialists from each of the Academia’s three divisions. One of the vice presidents of the Academia serves as its chairperson. The committee recruits national and international specialists for the Academia and also creates long-term interdisciplinary research plans. It is also he development of science and 188 associate research fellows, 134 responsible for evaluating and promoting T technology has been given much assistant research fellows, 123 assistant inter-institutional large-scale research importance by the Taiwan government in fellows, and 20 research assistants. projects, evaluating applications of recent years. This can be seen from the postdoctoral researchers, and selecting Organization increased expenditure on science and winners for the Academia’s annual technology, and the annual increase in The Academia is headed by Dr. Yuan- awards for outstanding publications by national R&D budget. The government Tseh Lee, its president. Dr. Lee is the junior research faculties. is determined to improve the quality of 1986 Nobel Laureate in Chemistry. He Division of Life Sciences research carried out in the country.