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Molecular Biology for Computer Scientists
CHAPTER 1 Molecular Biology for Computer Scientists Lawrence Hunter “Computers are to biology what mathematics is to physics.” — Harold Morowitz One of the major challenges for computer scientists who wish to work in the domain of molecular biology is becoming conversant with the daunting intri- cacies of existing biological knowledge and its extensive technical vocabu- lary. Questions about the origin, function, and structure of living systems have been pursued by nearly all cultures throughout history, and the work of the last two generations has been particularly fruitful. The knowledge of liv- ing systems resulting from this research is far too detailed and complex for any one human to comprehend. An entire scientific career can be based in the study of a single biomolecule. Nevertheless, in the following pages, I attempt to provide enough background for a computer scientist to understand much of the biology discussed in this book. This chapter provides the briefest of overviews; I can only begin to convey the depth, variety, complexity and stunning beauty of the universe of living things. Much of what follows is not about molecular biology per se. In order to 2ARTIFICIAL INTELLIGENCE & MOLECULAR BIOLOGY explain what the molecules are doing, it is often necessary to use concepts involving, for example, cells, embryological development, or evolution. Bi- ology is frustratingly holistic. Events at one level can effect and be affected by events at very different levels of scale or time. Digesting a survey of the basic background material is a prerequisite for understanding the significance of the molecular biology that is described elsewhere in the book. -
Department of Pharmacology (GRAD) 1
Department of Pharmacology (GRAD) 1 faculty participate fully at all levels. The department has the highest DEPARTMENT OF level of NIH funding of all pharmacology departments and a great diversity of research areas is available to trainees. These areas PHARMACOLOGY (GRAD) include cell surface receptors, G proteins, protein kinases, and signal transduction mechanisms; neuropharmacology; nucleic acids, cancer, Contact Information and antimicrobial pharmacology; and experimental therapeutics. Cell and molecular approaches are particularly strong, but systems-level research Department of Pharmacology such as behavioral pharmacology and analysis of knock-in and knock-out Visit Program Website (http://www.med.unc.edu/pharm/) mice is also well-represented. Excellent physical facilities are available for all research areas. Henrik Dohlman, Chair Students completing the training program will have acquired basic The Department of Pharmacology offers a program of study that leads knowledge of pharmacology and related fields, in-depth knowledge in to the degree of doctor of philosophy in pharmacology. The curriculum is their dissertation research area, the ability to evaluate scientific literature, individualized in recognition of the diverse backgrounds and interests of mastery of a variety of laboratory procedures, skill in planning and students and the broad scope of the discipline of pharmacology. executing an important research project in pharmacology, and the ability The department offers a variety of research areas including to communicate results, analysis, and interpretation. These skills provide a sound basis for successful scientific careers in academia, government, 1. Receptors and signal transduction or industry. 2. Ion channels To apply to BBSP, students must use The Graduate School's online 3. -
Biomolecules
biomolecules Communication MBLinhibitors.com, a Website Resource Offering Information and Expertise for the Continued Development of Metallo-β-Lactamase Inhibitors Zishuo Cheng 1, Caitlyn A. Thomas 1, Adam R. Joyner 2, Robert L. Kimble 1, Aidan M. Sturgill 1 , Nhu-Y Tran 1, Maya R. Vulcan 1, Spencer A. Klinsky 1, Diego J. Orea 1, Cody R. Platt 2, Fanpu Cao 2, Bo Li 2, Qilin Yang 2, Cole J. Yurkiewicz 1, Walter Fast 3 and Michael W. Crowder 1,* 1 Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA; [email protected] (Z.C.); [email protected] (C.A.T.); [email protected] (R.L.K.); [email protected] (A.M.S.); [email protected] (N.-Y.T.); [email protected] (M.R.V.); [email protected] (S.A.K.); [email protected] (D.J.O.); [email protected] (C.J.Y.) 2 Department of Computer Science and Software Engineering, Miami University, Oxford, OH 45056, USA; [email protected] (A.R.J.); [email protected] (C.R.P.); [email protected] (F.C.); [email protected] (B.L.); [email protected] (Q.Y.) 3 Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy and the LaMontagne Center for Infectious Disease, University of Texas, Austin, TX 78712, USA; [email protected] * Correspondence: [email protected]; Tel.: +1-513-529-2813 Received: 17 February 2020; Accepted: 12 March 2020; Published: 16 March 2020 Abstract: In an effort to facilitate the discovery of new, improved inhibitors of the metallo-β-lactamases (MBLs), a new, interactive website called MBLinhibitors.com was developed. -
To Undergraduate Studies in Chemistry, Chemical Engineering, and Chemical Biology College of Chemistry, University of California, Berkeley, 2011-12
Guide to Undergraduate Studies in Chemistry, Chemical Engineering, and -2012 Chemical Biology College of Chemistry 2011 University of California, Berkeley Academic Calendar 2011-12 Fall Semester 2011 Tele-BEARS Begins April 11 Monday Fee Payment Due August 15 Monday Fall Semester Begins August 18 Thursday Welcome Events August 22-26 Monday-Friday Instruction Begins August 25 Thursday Labor Day Holiday September 5 Monday Veterans Day Holiday November 11 Friday Thanksgiving Holiday November 24-25 Thursday-Friday Formal Classes End December 2 Friday Reading/Review/Recitation Week December 5-9 Monday-Friday Final Examinations December 12-16 Monday-Friday Fall Semester Ends December 16 Friday Winter Holiday December 26-27 Monday-Tuesday New Year’s Holiday December 29-30 Thursday-Friday Spring Semester 2012 Tele-BEARS Begins October 17, 2011 Monday Spring Semester Begins January 10 Tuesday Fee Payment Due January 15 Sunday Martin Luther King Jr. Holiday January 16 Monday Instruction Begins January 17 Tuesday Presidents’ Day Holiday February 20 Monday Spring Recess March 26-30 Monday-Friday César Chávez Holiday March 30 Friday Cal Day To Be Determined Formal Classes End April 27 Friday Reading/Review/Recitation Week April 30-May 4 Monday-Friday Final Examinations May 7-11 Monday-Friday Spring Semester Ends May 11 Friday Summer Sessions 2012 Tele-BEARS Begins February 6 Monday First Six-Week Session May 21-June 29 Monday-Friday Memorial Day Holiday May 28 Monday Ten-Week Session June 4-August 10 Monday-Friday Eight-Week Session June 18-August -
Molecular Biology and Applied Genetics
MOLECULAR BIOLOGY AND APPLIED GENETICS FOR Medical Laboratory Technology Students Upgraded Lecture Note Series Mohammed Awole Adem Jimma University MOLECULAR BIOLOGY AND APPLIED GENETICS For Medical Laboratory Technician Students Lecture Note Series Mohammed Awole Adem Upgraded - 2006 In collaboration with The Carter Center (EPHTI) and The Federal Democratic Republic of Ethiopia Ministry of Education and Ministry of Health Jimma University PREFACE The problem faced today in the learning and teaching of Applied Genetics and Molecular Biology for laboratory technologists in universities, colleges andhealth institutions primarily from the unavailability of textbooks that focus on the needs of Ethiopian students. This lecture note has been prepared with the primary aim of alleviating the problems encountered in the teaching of Medical Applied Genetics and Molecular Biology course and in minimizing discrepancies prevailing among the different teaching and training health institutions. It can also be used in teaching any introductory course on medical Applied Genetics and Molecular Biology and as a reference material. This lecture note is specifically designed for medical laboratory technologists, and includes only those areas of molecular cell biology and Applied Genetics relevant to degree-level understanding of modern laboratory technology. Since genetics is prerequisite course to molecular biology, the lecture note starts with Genetics i followed by Molecular Biology. It provides students with molecular background to enable them to understand and critically analyze recent advances in laboratory sciences. Finally, it contains a glossary, which summarizes important terminologies used in the text. Each chapter begins by specific learning objectives and at the end of each chapter review questions are also included. -
Independent Research Resources Demonstrations/Simulations
Independent Research Resources Independent Generation of Research (IGoR) - IGoR provides a platform for people to pool their knowledge, resources, time, and creativity so that everyone can pursue their own scientific curiosity. Virginia Junior Academy of Science Resource Library - Extensive collection of open-access resources for students in Biology & Medicine, Botany, Ecology, Environmental Sciences, Chemistry, Engineering and Physics The Society for Science and the Public Science Project Resources - A catalog of science resources that can support your quest to learn and do science Science Buddies - Ideas for science projects Teacher resources National Center for Science Education Scientist in the Classroom - Platform allows teachers to request classroom visits from scientists Genetics Education Outreach Network (GEON) - Network of genetics professionals HHMI BioInteractive Data Points - Explore and interpret primary data from published research Biotech in a Box Loan Kits - Shipped to your school from Fralin Life Sciences Institute at Virginia Tech Demonstrations/Simulations Genetic Science Learning Center- Simulations, videos and interactive activities that explore genetics, cell biology, neuroscience, ecology and health Remotely Accessible Instruments for Nanotechnology (RAIN) - Access and control nanoinstruments over the Internet in real-time with the assistance of an experienced engineer PhET Simulations - Interactive STEM simulations for all grade levels HHMI BioInteractive Interactive Media - Recommendations: Virus Explorer; Exploring -
Protein Identification Strategies in MALDI Imaging Mass Spectrometry
Available online at www.sciencedirect.com ScienceDirect Protein identification strategies in MALDI imaging mass spectrometry: a brief review 1,2 1,2,3 Daniel J Ryan , Jeffrey M Spraggins and 1,2,3,4,5 Richard M Caprioli Matrix assisted laser desorption/ionization (MALDI) imaging specimens [1,2 ,3,4]. MALDI IMS allows for the label- mass spectrometry (IMS) is a powerful technology used to free, multiplex analysis of thousands of analytes across a investigate the spatial distributions of thousands of molecules samples surface yielding 2-dimensional molecular maps throughout a tissue section from a single experiment. As that elucidate both the localization and relative abundance proteins represent an important group of functional molecules of endogenous species. The technology has been used to in tissue and cells, the imaging of proteins has been an study awiderangeofanalyteclasses,includingmetabolites, important point of focus in the development of IMS drugs, lipids, peptides, and proteins [5,6 ,7 ,8]. The imag- technologies and methods. Protein identification is crucial for ing of proteins has garnered particular attention due to the the biological contextualization of molecular imaging data. role the proteins play in cellular processes [9], and because However, gas-phase fragmentation efficiency of MALDI MALDI IMS allows for the visualization of a protein and its generated proteins presents significant challenges, making various proteoforms (i.e. varying post-translational modifi- protein identification directly from tissue difficult. This review cations) in a single imaging experiment [10,11 ,12]. As highlights methods and technologies specifically related to highlighted in Figure 1, MALDI IMS is performed by first protein identification that have been developed to overcome coating a tissue section with a MALDI matrix, which assists these challenges in MALDI IMS experiments. -
Suppression of Matrix Ions by N-Phosphorylation Labeling Using
Electronic Supplementary Material (ESI) for Chemical Communications This journal is © The Royal Society of Chemistry 2012 Supporting Information Suppression of Matrix Ions by N-Phosphorylation Labeling Using Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry Xiang Gao,a, b Zhi Tang,a Minghua Lu,a Hongxia Liu,b Yuyang Jiang,b Yufen Zhao c and Zongwei Cai*, a, b a Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, SAR, China b The Key Laboratory for Cancer Metabolomics of Shenzhen, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, China c Department of Chemistry and The Key Laboratory for Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, P. R. China * Corresponding author. E-mail: [email protected]. 1 Electronic Supplementary Material (ESI) for Chemical Communications This journal is © The Royal Society of Chemistry 2012 EXPERIMENTAL SECTION Materials and Reagents. L-Amino acids, D-(+)-glucosamine hydrochloride, agmatine sulfate salt, formic acid, magnesium sulfate (MgSO4), trifluoroacetic acid (TFA), triethylamine (TEA), tetrachloromethane (CCl4), -cyano-4-hydroxycinnamic acid (CHCA), and 2, 5-dihydroxybenzoic acid (DHB) were purchased from Sigma (St. Louis, MO, USA) and used without further purification. Diisopropyl phosphate (DIPP-H) and anhydrous ethanol were obtained from Alfa Aesar Chemical Ltd. (Tianjin, China). Peptide calibration standard used for calibration of MALDI-MS instrument was obtained from Bruker Daltonics (Bruker, Germany). Sep-Pak Vac C18 cartridges were purchased from Waters (MA, USA). Porous graphitic carbon (PGC) cartridges were obtained from Alltech Associates, Inc. (Deerfield, IL). Graphene nonopowder (8 nm flakes) was obtained from Graphene Laboratories Inc. -
Biochemistry and Molecular Biology
School of Life Sciences / Department of Biochemistry and Biophysics BIOCHEMISTRY AND MOLECULAR BIOLOGY Revealing how life works Department of Biochemistry and Biophysics Oregon State University 2011 Agriculture and Life Sciences Building Corvallis, OR 97331 OSUBB 541-737-4511 biochem.oregonstate.edu College of Science Oregon State University 128 Kidder Hall Corvallis, OR 97331 541-737-4811 science.oregonstate.edu This publication will be made available in an accessible alternative format upon request. Please contact the College COLLEGE OF SCIENCE of Science at 541-737-4811 or [email protected]. ACADEMIC BROCHURE / 2020 Highlights • Solve problems at the What will you discover? intersection of biological and physical sciences with our The Department of Biochemistry and Biophysics offers nationally accredited program world-class faculty, a tradition of interdisciplinary in biochemistry, molecular and research, teaching excellence and extraordinary cellular biology, chemistry, laboratories to facilitate undergraduate learning. molecular genetics, physics and statistics. The department ranks high nationally and internationally in many research areas, including signal transduction, gene • Tailor your education to expression, epigenetics, metabolic regulation, structural specific career goals with three biology, and genetic code expansion technology. different options. The department offers two Bachelor of Science degrees, • Thrive in a smaller, supportive both accredited by the American Society for Biochemistry department within a world-class and Molecular Biology (ASBMB): research university. • Biochemistry and Molecular Biology (BMB) with • Pursue interdisciplinary research options in Advanced Molecular Biology, Computational projects with faculty across OSU. Molecular Biology, and Pre-medicine; • Participate in the Biochemistry • Biochemistry and Biophysics (BB) with options in Club for community, leadership Advanced Biophysics, Neuroscience, and Pre-medicine. -
1 a Primer on Molecular Biology
1APrimer on Molecular Biology Alexander Zien Modern molecular biology provides a rich source of challenging machine learning problems. This tutorial chapter aims to provide the necessary biological background knowledge required to communicate with biologists and to understand and properly formalize a number of most interesting problems in this application domain. The largest part of the chapter (its first section) is devoted to the cell as the basic unit of life. Four aspects of cells are reviewed in sequence: (1) the molecules that cells make use of (above all, proteins, RNA, and DNA); (2) the spatial organization of cells (“compartmentalization”); (3) the way cells produce proteins (“protein expression”); and (4) cellular communication and evolution (of cells and organisms). In the second section, an overview is provided of the most frequent measurement technologies, data types, and data sources. Finally, important open problems in the analysis of these data (bioinformatics challenges) are briefly outlined. 1.1 The Cell The basic unit of all (biological) life is the cell. A cell is basically a watery solution of certain molecules, surrounded by a lipid (fat) membrane. Typical sizes of cells range from 1 µm (bacteria) to 100 µm (plant cells). The most important properties Life of a living cell (and, in fact, of life itself) are the following: It consists of a set of molecules that is separated from the exterior (as a human being is separated from his or her surroundings). It has a metabolism, that is, it can take up nutrients and convert them into other molecules and usable energy. The cell uses nutrients to renew its constituents, to grow, and to drive its actions (just like a human does). -
Biology 302 Course Syllabus Cell and Molecular Biology Fall 2014
Biology 302 Course Syllabus Cell and Molecular Biology Fall 2014 Instructor: Dr. Karen K. Resendes Office Phone: 724-946-7211 Office: 222 Hoyt Science Center e-mail: [email protected] Course Description: The primary emphasis of this course will be the basic structure and function of the cell. We begin the semester by looking at the “smaller picture” – the basic types of organic molecules that contribute to cells. We then explore cellular processes by starting on the cell surface and working our way into the interior of the cell. General topics include membrane transport and signaling, gene expression, intracellular transport, structure and motility, energy conversions, and cell division. Laboratory exercises will reinforce many of concepts covered in lecture. This course assumes the student has learned and retained a basic understanding of the fundamental cellular concepts presented in Foundations I and II. Course Structure: Lecture: T, R 9:20AM – 11:00AM Laboratory: R 2:00PM – 5:00PM HSC 206 Hoyt 343 Office Hours: M and W 1PM-2:30 PM OR other times by appointment Simply email, call or ask me for a time that will work for you. The sole purpose of making an appointment is that I want to be sure that I will be in my office at the time you want to meet with me. Required: 1. Text: Alberts A., et al. Molecular Biology of the Cell. Fifth Edition. Garland Science Publishers. New York, NY. 2008 2.Composition-style, quad-lined laboratory notebook 3. Frequent visits to the Bio 302 coursepage on my.westminster for: -Laboratory Handouts - Primary research articles - Online quizzes -Detailed reading lists - Electronic Resources Course Objectives: This course is intended for those students majoring in biology, molecular biology, biochemistry, or neuroscience. -
Biochemistry and Molecular Biology (BMB) 1
Biochemistry and Molecular Biology (BMB) 1 BMB 372. Advanced Molecular Biology. (3 h) BIOCHEMISTRY AND Presents molecular mechanisms by which stored genetic information is expressed including the mechanisms for and regulation of gene MOLECULAR BIOLOGY (BMB) expression, protein synthesis, and genome editing. Emphasizes analysis and interpretation of experimental data from the primary literature. Also Interdisciplinary Major listed as BIO 372. P-BIO 213 and 214 and BIO 370/BMB 370/CHM 370 or BIO 265 and BIO 370/BMB 370/CHM 370. This interdisciplinary Bachelor of Science major, jointly offered by the Departments of Biology and Chemistry, provides a strong foundation BMB 372L. Advanced Molecular Biology Laboratory. (1.5 h) in biological chemistry and molecular biology, and related topics at Introduces modern methods of molecular biology to analyze and the interface of these two disciplines. The major is designed to build manipulate expression of genes and function of gene products. Also conceptual understanding and practical and critical thinking skills to listed as BIO 372L. P or C-BIO 372/CHM 372 or BMB 373/CHM 373. address current biological, biochemical, and biomedical challenges. A BMB 373. Biochemistry II. (3 h) required research experience spanning multiple semesters, culminating Examines the structure, function, and synthesis of proteins and nucleic in a senior project, will give students strong experimental skills and acids and includes advanced topics in biochemistry including catalytic provide insight into biochemical and molecular biological experimental mechanisms of enzymes and ribozymes, use of sequence and structure approaches and results that demonstrate the function of biological databases, and molecular basis of disease and drug action.