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Scaling up Genetic Circuit Design for Cellular Computing
Edinburgh Research Explorer Scaling up genetic circuit design for cellular computing Citation for published version: Xiang, Y, Dalchau, N & Wang, B 2018, 'Scaling up genetic circuit design for cellular computing: advances and prospects', Natural Computing, vol. 17, no. 4, pp. 833-853. https://doi.org/10.1007/s11047-018-9715-9 Digital Object Identifier (DOI): 10.1007/s11047-018-9715-9 Link: Link to publication record in Edinburgh Research Explorer Document Version: Publisher's PDF, also known as Version of record Published In: Natural Computing Publisher Rights Statement: This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creative commons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. General rights Copyright for the publications made accessible via the Edinburgh Research Explorer is retained by the author(s) and / or other copyright owners and it is a condition of accessing these publications that users recognise and abide by the legal requirements associated with these rights. Take down policy The University of Edinburgh has made every reasonable effort to ensure that Edinburgh Research Explorer content complies with UK legislation. If you believe that the public display of this file breaches copyright please contact [email protected] providing details, and -
The Bio Revolution: Innovations Transforming and Our Societies, Economies, Lives
The Bio Revolution: Innovations transforming economies, societies, and our lives economies, societies, our and transforming Innovations Revolution: Bio The The Bio Revolution Innovations transforming economies, societies, and our lives May 2020 McKinsey Global Institute Since its founding in 1990, the McKinsey Global Institute (MGI) has sought to develop a deeper understanding of the evolving global economy. As the business and economics research arm of McKinsey & Company, MGI aims to help leaders in the commercial, public, and social sectors understand trends and forces shaping the global economy. MGI research combines the disciplines of economics and management, employing the analytical tools of economics with the insights of business leaders. Our “micro-to-macro” methodology examines microeconomic industry trends to better understand the broad macroeconomic forces affecting business strategy and public policy. MGI’s in-depth reports have covered more than 20 countries and 30 industries. Current research focuses on six themes: productivity and growth, natural resources, labor markets, the evolution of global financial markets, the economic impact of technology and innovation, and urbanization. Recent reports have assessed the digital economy, the impact of AI and automation on employment, physical climate risk, income inequal ity, the productivity puzzle, the economic benefits of tackling gender inequality, a new era of global competition, Chinese innovation, and digital and financial globalization. MGI is led by three McKinsey & Company senior partners: co-chairs James Manyika and Sven Smit, and director Jonathan Woetzel. Michael Chui, Susan Lund, Anu Madgavkar, Jan Mischke, Sree Ramaswamy, Jaana Remes, Jeongmin Seong, and Tilman Tacke are MGI partners, and Mekala Krishnan is an MGI senior fellow. -
The Biological Microprocessor, Or How to Build a Computer with Biological Parts
Volume No: 7, Issue: 8, April 2013, e201304003, http://dx.doi.org/10.5936/csbj.201304003 CSBJ The biological microprocessor, or how to build a computer with biological parts Gerd HG Moe-Behrens a,* Abstract: Systemics, a revolutionary paradigm shift in scientific thinking, with applications in systems biology, and synthetic biology, have led to the idea of using silicon computers and their engineering principles as a blueprint for the engineering of a similar machine made from biological parts. Here we describe these building blocks and how they can be assembled to a general purpose computer system, a biological microprocessor. Such a system consists of biological parts building an input / output device, an arithmetic logic unit, a control unit, memory, and wires (busses) to interconnect these components. A biocomputer can be used to monitor and control a biological system. Introduction Nature and computers are words that used to mean unrelated Other important contributions to systemics are by the Nobel-prize things. However, this view changed, starting in the 1940s, when a winning work of Ilya Prigogine on self-organization and his systems revolutionary scientific paradigm, systemics based on platonic theory concepts in thermodynamics [10]. Furthermore: Mitchell idealistic philosophy, gained popularity [1] [2] [3]. Feigenbaums work on Chaos theory [11]. Contemporary application The roots of philosophical idealism based systemics goes back to finds systems theory in bioscience in fields such as systems biology, Plato. A centerpiece of Plato’s (428/7 to 348/7 BC) work is his and its practical application synthetic biology [12]. The term systems theory of forms, also called theory of ideas [2]. -
Mechanisms of Microbial Genetics 443
Chapter 11 | Mechanisms of Microbial Genetics 443 Chapter 11 Mechanisms of Microbial Genetics Figure 11.1 Escherichia coli (left) may not appear to have much in common with an elephant (right), but the genetic blueprints for these vastly different organisms are both encoded in DNA. (credit left: modification of work by NIAID; credit right: modification of work by Tom Lubbock) Chapter Outline 11.1 The Functions of Genetic Material 11.2 DNA Replication 11.3 RNA Transcription 11.4 Protein Synthesis (Translation) 11.5 Mutations 11.6 How Asexual Prokaryotes Achieve Genetic Diversity 11.7 Gene Regulation: Operon Theory Introduction In 1954, French scientist and future Nobel laureate Jacques Monod (1910–1976) famously said, “What is true in E. coli is true in the elephant,” suggesting that the biochemistry of life was maintained throughout evolution and is shared in all forms of known life. Since Monod’s famous statement, we have learned a great deal about the mechanisms of gene regulation, expression, and replication in living cells. All cells use DNA for information storage, share the same genetic code, and use similar mechanisms to replicate and express it. Although many aspects of genetics are universally shared, variations do exist among contemporary genetic systems. We now know that within the shared overall theme of the genetic mechanism, there are significant differences among the three domains of life: Eukarya, Archaea, and Bacteria. Additionally, viruses, cellular parasites but not themselves living cells, show dramatic variation in their genetic material and the replication and gene expression processes. Some of these differences have allowed us to engineer clinical tools such as antibiotics and antiviral drugs that specifically inhibit the reproduction of pathogens yet are harmless to their hosts. -
Microbial Genetics 428L/528L - Laboratory Course Dr
MIC et al. 428/528L D. Baltrus Microbial Genetics 428L/528L - Laboratory Course Dr. David Baltrus Spring 2015 INTRODUCTION Welcome to the exciting world of Microbial Genetics. MIC428L/528L is going to be your opportunity to experience the hands-on experimental part of microbial genetics. It is important to remember that the field of Microbial Genetics consists of an extremely large area; in this laboratory we will expose you to some of the major theories and techniques used daily in thousands of microbial genetics research labs around the world. In fact, most of the experiments you will perform are used regularly in the research of Dr. Baltrus. Microbial Genetics 428L/528L is a constantly evolving course. Most students take the lecture (MIC428R/528R) and lab simultaneously. Although the laboratory runs concurrently with the lecture, it is impossible to match the laboratory exercises with the lecture material due to the different rates with which the information can be imparted to you and the limited laboratory periods available. At several points the laboratory utilizes techniques not yet covered in lecture. In addition, several laboratory periods are devoted to the DNA sequence analysis module taught in the Bioscience Learning Center (BLC) located in the Henry Koffler building. LABORATORY GOALS The overall goal of this laboratory course is to expose you to realistic microbial genetics research. Some laboratory periods will be short. Occasionally you will be required to come in during a non-scheduled lab time or day to continue the experimental protocol. Experience over the past several years re-enforces the maxim that your success and failure is directly related to your preparation and carefulness in the laboratory. -
Microbial Genetics and Genomics 11:680:480
COURSE SYLLABUS Microbial Genetics and Genomics 11:680:480 COURSE OVERVIEW: Microbial Genetics and Genomics 11:680:480 Spring Semester CONTACT INFORMATION: Instructor(s): Dr. Gerben Zylstra Office Location: Foran, Room 322 Email: [email protected] Office Hours: By arrangement COURSE WEBSITE, RESOURCES AND MATERIALS: • Canvas COURSE DESCRIPTION: Genetics of bacteria and phage, focusing on replication, repair, transcription, translation, gene regulation, genetic networks, plasmids, conjugation, transformation, microbial and phage interactions, and different types of phage and their lifestyles. LEARNING GOALS: Understand the biochemical mechanisms underpinning replication, transcription, and translation Appreciate the diversity of mechanisms used by bacteria to regulate gene expression Demonstrate knowledge of the biochemistry behind conjugation and transformation Recognize the diverse types and lifestyles of phage ASSIGNMENTS/RESPONSIBILITIES, GRADING & ASSESSMENT: Three exams each covering one third of the course (100 points each) and repeated questions from exam 1 and 2 on the third exam (40 points) ACCOMODATIONS FOR STUDENTS WITH DISABILITIES Please follow the procedures outlined at https://ods.rutgers.edu/students/registration-form. Full policies and procedures are at https://ods.rutgers.edu/ ABSENCE POLICY If you miss class please check with other students about what you missed. All lecture notes and all important announcements will be posted on Canvas. If you arrive late for class please come in quietly and find an open seat. -
Moving from Observation to Predictive Design Corey J. Wilson
Biomolecular Assemblies: Moving from Observation to Predictive Design Corey J. Wilson,† Andreas S. Bommarius,† Julie A. Champion,† Yury O. Chernoff,‡,≡ David G. Lynn,‖ Anant K. Paravastu,† Chen Liang,‖ Ming-Chien Hsieh,‖ Jennifer M. Heemstra‖,* †School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States ‡School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, United States ≡Laboratory of Amyloid Biology & Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg 199034, Russia ‖Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States *corresponding author, [email protected] ABSTRACT: Biomolecular assembly is a key driving force in nearly all life processes, providing structure, information storage, and communication within cells and at the whole organism level. These assembly processes rely on precise interactions between functional groups on nucleic acids, proteins, carbohydrates, and small molecules, and can be fine tuned to span a range of time, length, and complexity scales. Recognizing the power of these motifs, researchers have sought to emulate and engineer biomolecular assemblies in the laboratory, with goals ranging from modulating cellular function to the creation of new polymeric materials. In most cases, engineering efforts are inspired or informed by understanding the structure and properties of naturally occurring assemblies, which has in turn fueled the development of predictive -
Microbiology and Molecular Genetics 1
Microbiology and Molecular Genetics 1 For certification and completion of the BS degree, students will take MICROBIOLOGY AND one year of clinical internship in program accredited by the National Accrediting Agency for Clinical Laboratory Science (NAACLS) and MOLECULAR GENETICS affiliated with Oklahoma State University. Students have the options of the following hospitals/programs: Comanche County Memorial Hospital, Microbiology/Cell and Molecular Biology Lawton, OK; St. Francis Hospital, Tulsa, OK; Mercy Hospital, Ada, OK; Mercy Hospital, Ardmore, OK. Microbiology is the hands-on study of bacteria, viruses, fungi and algae and their many relationships to humans, animals, plants and the Medical Laboratory Science is unique in allowing students to enter environment. Cell and molecular biology bridges the fields of chemistry, the health profession directly after obtaining a BS degree. Clinical biochemistry and biology as it seeks to understand life and cellular laboratory scientists comprise the third-largest segment of the healthcare processes at the molecular level. Microbiologists apply their knowledge professions and are an important member of the healthcare team, to infectious diseases and pathogenic mechanisms; food production working alongside doctors and nurses. Students who complete and preservation, industrial fermentations which produce chemicals, Microbiology/Cell and Molecular Biology with the MLS option enjoy a drugs, antibiotics, alcoholic beverages and various food products; 100% employment rate upon graduation. biodegradation of toxic chemicals and other materials present in the environment; insect pathology; the exciting and expanding field of Courses biotechnology which endeavors to utilize living organisms to solve GENE 5102 Molecular Genetics important problems in medicine, agriculture, and environmental science; Prerequisites: BIOC 3653 or MICR 3033 and one course in genetics or infectious diseases; and public health and sanitation. -
Actuator 125, 126 Adleman's DNA Computer 16–17 Allosteric
383 Index a binary-coded decimal (BCD) code 236 actuator 125, 126 biocompatibility 125, 147, 166, 241, Adleman’s DNA computer 16–17 329 allosteric biosensors 64 biomolecular computing 1, 2, 3, 5, 15, allosteric effector 111, 113 353, 371, 381 allosteric inhibiter 113 (bio)molecular realizations 363 allosteric toehold 266 biomolecular scaffolds 80–81 -Hemolysin (HL) 331 biomolecular switches 105 7-amino-4-methyl coumarin (AMC) Black Hole Quencher 374 131 blocking amplitude 331 AND Boolean logic 68, 164 Boolean algebra 65, 279 3-AND gate 359, 360 Boolean logic gate 1, 2, 10, 88, 133, AND gate implementation 38 134, 140, 155, 156, 157, 164, 282, 3-AND logic gate operation 358 284, 362 anti-anti-terminator/anti-terminator Boolean operations 1, 113, 155, 279, hairpin (aat/at-HP) 255 363 anti-fuel strand complementary 270 branch migration 97, 158, 248, 249, anti-gRNA bind 257 254, 258, 265–268, 282, 285, 287, antioxidant indicator 241 297, 298 application-specific integrated circuits Broccoli RNA aptamer 68–70 (ASICs) 39 aptamer–fluorophore complex 61 c aptamer ligand binding 125 cadmium chalcogenide semiconductors Arbona’s biophysical model 313 159 arithmetic DNA logic devices carbon dots (CDs) 159, 174–175 full-adder, full-subtractor 234 Cas9 + gRNA 255 half-adder, half-subtractor 232–234 catalytic hairpin assembly (CHA) 131, asynchronization circuits 38 261 asynchronous circuits 38 cationic conjugated polymers (CCPs) automatic writing–reading DNA 176 processes 9, 10 cell entry vehicles 81, 82 Cello computing language 7 b cellular environment 93, 251, 281, 285, bi-dynamic DNA origami 289 nanostructures 309 central processing unit (CPU) 275 DNA- and RNA-Based Computing Systems, First Edition. -
Biosc1280 2017 Syllabus 1-3-17
BIOSC 1280 MICROBIAL GENETIC ENGINEERING SPRING TERM 2017 SYLLABUS AND COURSE POLICIES LECTURERS: Dr. Karen Arndt Dr. Graham Hatfull A316 Langley Hall 378 Crawford Hall Office hours: by appointment Office hours: by appointment Phone: 624-6963 Phone: 624-4350 email: [email protected] email: [email protected] LECTURES: Mon., Wed., Fri. 11:00 – 11:50 a.m. Langley Hall, Room A214 COURSE DESCRIPTION Microbes – both prokaryotic and eukaryotic – are critical to our understanding of the fundamentals of biology at the molecular level as well as for understanding human diseases. Microbes such as bacteria and yeast are advantageous in that they can be grown to very large numbers in small volumes, making them ideal for genetic approaches that require the isolation of mutants with informative phenotypes and for understanding the roles that genes perform. In this course we will discuss fundamental aspects of microbial genetics in bacteria and yeast and how this information can be used to understand pathogenic and inherent human diseases. LEARNING OBJECTIVES Upon completing this course, you will be able to apply the theories of classical and modern molecular genetic analysis of prokaryotic and eukaryotic microorganisms to current problems in microbial genetics. PREREQUISITES Completion of BioSc1850 Microbiology, with a grade of C or better. Please consult with the instructors if you have not satisfied this requirement or the prerequisites for BioSc1850. TEXTBOOKS Required Molecular Genetics of Bacteria, fourth edition (2013), by Larry Snyder, Joseph Peters, Tina Henkin and Wendy Champness. Published by ASM Press, Washington D.C. This textbook contains readings and problems that are required for successful completion of the prokaryotic section of the course. -
Biosensors with Built-In Biomolecular Logic Gates for Practical Applications
Biosensors 2014, 4, 273-300; doi:10.3390/bios4030273 OPEN ACCESS biosensors ISSN 2079-6374 www.mdpi.com/journal/biosensors/ Review Biosensors with Built-In Biomolecular Logic Gates for Practical Applications Yu-Hsuan Lai, Sin-Cih Sun and Min-Chieh Chuang * Department of Chemistry, Tunghai University, Taichung 40704, Taiwan; E-Mails: [email protected] (Y.-H.L.); [email protected] (S.-C.S.) * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +886-4-2359-0248 (ext. 205); Fax: +886-4-2359-0426. Received: 3 July 2014; in revised form: 15 August 2014 / Accepted: 22 August 2014 / Published: 27 August 2014 Abstract: Molecular logic gates, designs constructed with biological and chemical molecules, have emerged as an alternative computing approach to silicon-based logic operations. These molecular computers are capable of receiving and integrating multiple stimuli of biochemical significance to generate a definitive output, opening a new research avenue to advanced diagnostics and therapeutics which demand handling of complex factors and precise control. In molecularly gated devices, Boolean logic computations can be activated by specific inputs and accurately processed via bio-recognition, bio-catalysis, and selective chemical reactions. In this review, we survey recent advances of the molecular logic approaches to practical applications of biosensors, including designs constructed with proteins, enzymes, nucleic acids, nanomaterials, and organic compounds, as well as the research avenues for future development of digitally operating “sense and act” schemes that logically process biochemical signals through networked circuits to implement intelligent control systems. Keywords: biosensor; molecular computing; logic gate; biomedical application 1. Introduction A biosensor, a device that responds to a particular analyte in a selective way, incorporates “biological recognition” as sensing elements connected to a “transducer”. -
Plant & Microbial Biology
Plant & Microbial Biology 1 PLANTBI 200A Plant Developmental Genetics Plant & Microbial 1.5 Unit Terms offered: Fall 2021, Fall 2020, Fall 2019 Biology The students will be provided with both the basic framework and current topics of plant developmental genetics. Overview Plant Developmental Genetics: Read More [+] Rules & Requirements The Department of Plant and Microbial Biology consists of the Division of Plant Biology and the Division of Microbial Biology. Programs at both the Prerequisites: Consent of instructor undergraduate and graduate levels have been designed to offer students maximum flexibility in defining their own areas of interest. In addition to Hours & Format departmental resources that are available in Koshland Hall, the facilities Fall and/or spring: 5 weeks - 4 hours of lecture and 2 hours of of the College of Natural Resources Biological Imaging Facility and the discussion per week United States Department of Agriculture Plant Gene Expression Center are available for the programs of the department. Additional Details The Division of Plant Biology Subject/Course Level: Plant and Microbial Biology/Graduate The Division of Plant Biology program emphasizes basic research and its Grading: Letter grade. application to plants and promotes the design of plant biotechnologies. With an increasing awareness of environmental problems, global Instructor: Hake changes, and emerging food needs, plants are a focal point for new research initiatives and educational training programs. Understanding the Plant Developmental Genetics: Read Less [-] biology of plants, their development, their responses to the environment, and the impact of human activities on the plant biosphere are many of PLANTBI 200B Genomics and Computational the challenges that will continue to fuel the expansion of plant biology Biology 1.5 Unit research well into the twenty-first century.