But is it art? Brandeis University 12.07.05. Panel of artists…. and their art… Will the real artist please stand up?

Slides:

Advertisements

Similar presentations

Synthetic Biology Part 1: Introduction Input Output Gene A Gene B Gene C 1.

Advertisements

12.1 DNA Griffith – Questioned how bacteria made people sick/ pneumonia – Smooth strains caused, harmless strains rough – Heat killed; however, heat killed.

Bacterial Genetics. Prokaryotic Cell Circular (and naked) double stranded DNA Bacteria have very short generation spans (ex. E.coli divides every 20 minutes)short.

Lambda phage killing: infection and “parts” N Kuldell for Spring 2009.

PowerPoint Presentation Materials to accompany

Repressilator Presentation contents: The idea Experimental overview. The first attemp. The mathematical model. Determination of the appropiate parameters.

20,000 GENES IN HUMAN GENOME; WHAT WOULD HAPPEN IF ALL THESE GENES WERE EXPRESSED IN EVERY CELL IN YOUR BODY? WHAT WOULD HAPPEN IF THEY WERE EXPRESSED.

Gene Expression AP Biology.

Combinatorial Synthesis of Genetic Networks Guet et. al. Andrew Goodrich Charles Feng.

Lecture 11 Based on Chapter 17 - Regulation of Gene Expression in Bacteria and Bacteriophages Copyright © 2010 Pearson Education Inc.

The Lac Operon Regulation of Prokaryotic Genes. n Scientists investigated a transcriptionally regulation system using the lactose metabolism system in.

Mukund Thattai NCBS Bangalore genetic networks in theory and practice.

Bioinformatics Presented by Frank H. Osborne, Ph. D. © 2005 Bio 2900 Computer Applications in Biology.

1 Molecular genetics of bacteria Emphasis: ways that bacteria differ from eukaryotes DNA structure and function; definitions. DNA replication Transcription.

Promoters and the Lac Operon. Regulation in Prokaryotes Adjust biochemistry quickly as environment changes Jacob and Monod  extensive studies into the.

AP Biology Chapter 18: Gene Regulation. Regulation of Gene Expression Important for cellular control and differentiation. Understanding “expression” is.

Bacterial Operons A model of gene expression regulation Ch 18.4.

Gene Regulation. Levels of Regulation DNA rearrangement –Immune System rearranges DNA Bacteria can change DNA in chromosomes Not as common as other methods.

3.1 An overview of genetic possesses 3.2 The basis of hereditary 3.3 DNA replication 3.4 RNA and protein synthesis 3.5 Gene expression.

Bacteriophage lambda (l)

DNA Science Day 1 Amplifying and Cutting Physical Biology Bootcamp October 2006 Caltech.

23 and 25 October, 2006 Chapter 16 Regulation in Prokaryotes.

Programmed cells: Interfacing natural and engineered gene networks Kobayashi, Kærn, Araki, Chung, Gardner, Cantor & Collins,( PNAS 2004). You, Cox, Weiss.

1 Review Describe the process scientists use to copy DNA Use Analogies How is genetic engineering like computer programming 2 Review What is a transgenic.

Chromosomes, Gene Expression and Epigenetics

Genetic Engineering What is Genetic Engineering? Genetic Engineering = inserting a foreign gene of interest into a host to transcribe and translate a.

Transformation AP Big Idea #3: Genes and Information Transfer connected with AP Big Idea #1 (Evolution) & #2 (Cellular Processes)

Introduction to pGLO lab Bacteria Transformation Please take these notes carefully. You do not need to write anything in RED.

Igor Ulitsky.  “the branch of genetics that studies organisms in terms of their genomes (their full DNA sequences)”  Computational genomics in TAU ◦

A Eukaryotic Transcriptional Activator Bearing the DNA Specificity of a Prokaryotic Repressor By Roger Brent and Mark Ptashne Cell (1985) 43: Presented.

The Programming of a Cell By L Varin and N Kharma Biology and Computer Engineering Departments Concordia University.

Genetically Engineered H 2 Detector Mississippi State University.

SELF-DIFFERENTIATED BACTERIAL ASSEMBLY LINE PEKING 2007 IGEM All ideas and images from Peking 2007 IGEM team unless otherwise noted Allen Lin 1.

Synthetic Biology Risks and opportunities of an emerging field Constructing Life.

A Genetic Differential Amplifier: Design, Simulation, Construction and Testing Seema Nagaraj and Stephen Davies University of Toronto Edward S. Rogers.

Construction of a genetic toggle switch in Escherichia coli Farah and Tom.

Complexities of Gene Expression Cells have regulated, complex systems –Not all genes are expressed in every cell –Many genes are not expressed all of.

Microbial Genetics - DNA Transfer l Review of Information Transfer in Cell l Recombination l Transfer of DNA &Genetic Recombination in Bacteria –Conjugation.

Bacteria Gene Regulation. Compare/Contrast Prokaryotic and Eukaryotic Protein Synthesis.

Manipulating DNA. Scientists use their knowledge of the structure of DNA and its chemical properties to study and change DNA molecules Different techniques.

© 2011 Pearson Education, Inc. Lectures by Stephanie Scher Pandolfi BIOLOGICAL SCIENCE FOURTH EDITION SCOTT FREEMAN 17 Control of Gene Expression in Bacteria.

Controlling Gene Expression. Control Mechanisms Determine when to make more proteins and when to stop making more Cell has mechanisms to control transcription.

GENETIC TOGGLE SWITCH IN E. COLI COLLINS LAB (2000) Allen Lin 1.

DNA TO PROTEIN Biology - 9. Monday, Nov. 25 th  Objective: Students will put the vocabulary of DNA and protein synthesis into context.  Go Over Test.

Combinatorial Synthesis of Genetic Networks Calin C. Guet, Michael B. Elowitz, Weihong Hsing, Stanislas Leibler Amit Meshulam Bioinformatics Seminar Technion,

The lac Operon Laboratory Purpose: Learning to analyze an example of gene expression Example: lac operon Type of control: negative inducible.

Chapter 4 Recombinant DNA Technology

PLASMIDS ...and genetic engineering..

What is Synthetic Biology?

Distributed computation: the new wave of synthetic biology devices

G. GENE CONTROL MECHANISMS

Biotechnology Part 2 Genetics of Bacteria

Controlling Gene Expression

Homework #2 is posted and due 10/17

Chapter 12.5 Gene Regulation.

Why do genetic classes always bring up the lac operon?

@kscornSTEM Seed2stem.org

Daily Warm-Up January 8th

Gene Expression AP Biology.

Self-differentiated Bacterial Assembly Line Peking 2007 IGEM

Place these notes into your Biology Notebook.

Biotechnology Part 2 Genetics of Bacteria

EE 194 Advanced VLSI Spring 2018 Tufts University

Biotechnology Part 2 Genetics of Bacteria

A Tunable Genetic Switch Based on RNAi and Repressor Proteins for Regulating Gene Expression in Mammalian Cells Tara L. Deans, Charles R. Cantor, James.

Biology II Study Guide for Unit Test on Operons and Transformation Lab 2013 You should be able to … 1. describe gene expression by explaining the following:

A Tunable Genetic Switch Based on RNAi and Repressor Proteins for Regulating Gene Expression in Mammalian Cells Tara L. Deans, Charles R. Cantor, James.

Central Dogma Theory and Kinetic Models

Presentation transcript:

But is it art? Brandeis University

Panel of artists…. and their art… Will the real artist please stand up?

Genetically-encoded Oscillator Period is ~120’ (two doublings) Time (minutes)

Electronics 101 Hartley Oscillator Colpitts Oscillator

1. Motivation why engineer biology?

1. Motivation why engineer biology? 2. Plan how to engineer biology?

1. Motivation why engineer biology? 2. Plan how to engineer biology? 3. Execution state of the art (stupid bacteria tricks)

1. Motivation why engineer biology? 2. Plan 3. Execution … because we can … because there’s so much to build … because there’s so much to learn

Genetically-Encoded Digital Logic “transfer function” time at 42°C transcript level 3’ heat shock promoter heat shock response gene

Heat Shock Response:  32 induction Straus, Walter, and Gross Nature (1987) 329: 347

Genetically-Encoded Logic Functions heat shock promoter heat shock response gene

Genetically-Encoded Logic Functions heat shock promoter repressor gene repressible promoter heat shock response gene

Genetically-Encoded Logic Functions heat shock promoter repressor gene repressible promoter heat shock response gene

Genetically-Encoded Logic Functions heat shock promoter repressor gene repressible promoter heat shock response gene X

Logic Functions Inverter inputoutput AND gate a b aboutput

Programming with DNA: hiding the details repressor gene repressible promoter Genetic Inverter Lambda cI, P22 c2, lacI, TetR… P RM, P R, P lac, P tet …

Programming with DNA: hiding the details repressor gene repressible promoter Genetic Inverter Lambda cI, P22 c2, lacI, TetR… P RM, P R, P lac, P tet …

Programming with DNA: hiding the details Genetic Inverter

Nature is source for code “Genetic Parts” Synthetic Biology: programming with DNA Make just about anything Logically combined in a cell

“There is a great satisfaction in building good tools for other people to use.” -Freeman Dyson Biology Engineering

“There is a great satisfaction in building good tools for other people to use.” -Freeman Dyson Biology Engineering “how can we help?”

“There is a great satisfaction in building good tools for other people to use.” -Freeman Dyson Biology Engineering “Cells are tiny machines” “OK then, build me a cell”

1. Motivation why engineer biology? 2. Plan 3. Execution

1. Motivation 2. Plan how to engineer biology? 3. Execution

1. Motivation 2. Plan how to engineer biology? 3. Execution …what foundational technologies are needed? …are safeguards needed?

Works of Art “A good scientist is a person with original ideas. A good engineer is a person who makes a design that works with as few original ideas as possible. There are no prima donnas in engineering.” -Freeman Dyson

well characterized predictable modular insulated stable Attributes for Foundational Technologies

well characterized predictable modular…. insulated stable Attributes for Foundational Technologies

225 basic parts 454 composite parts

Standard Assembly

Broadly consider two sources of risk 1. from the technology itself 2. from the people (hackers) who use it G. Church, “Let us go forth and safely multiply” Nature (2005) 438:423

1. Motivation 2. Plan how to engineer biology? 3. Execution

1. Motivation 2. Plan 3. Execution state of the art

1. Motivation 2. Plan 3. Execution state of the art …SB accomplishments …undergrad. contributions

Nature (2005) 434: 1130

A new kind of biofilm: “coli-roid”

conditionlacZresult lightlowlight color darkhighdark color Light Dependent Gene Expression Phytochromes from Synechocystis Osmoregulation system from E. coli LacZ reporter strain from literature (1979)

Light Dependent Gene Expression

Biofilm v2.0 mRFP conditionmRFPresult lighthighred darklownot red

1. Motivation why engineer biology? 2. Plan how to engineer biology? 3. Execution state of the art

Three comic strips to conclude Worst case scenario: total failure

Three comic strips to conclude Worst case scenario: total failure Best case: total success, are we ready?

Three comic strips to conclude Worst case scenario: total failure Best case: total success, are we ready? Biological Engineers, an oxymoron?

Credits Tom KnightDrew EndyRandy Rettberg

the end