CHE.496/2008/Assignments: Difference between revisions

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{{Template:CHE.496/2008}}
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==Assigned Readings==
==Assigned Readings==
====Assignment 1: Synthetic biology overview====
====Assignment 1: Synthetic biology overview====
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# '''Designing biological systems
# '''Designing biological systems
# '''Biology by design: Reduction and synthesis of cellular components and behavior [*[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17251159&ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum <font color="#000000">Biology by Design</font>]
# '''Biology by design: Reduction and synthesis of cellular components and behavior [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17251159&ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum link]
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====Assignment 10: Minimal genomes====
====Assignment 10: Minimal genomes====
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====Assignment 12: Genetic circuit engineering====
====Assignment 12: Genetic circuit engineering====
<font color=green>
<font color=green>
# '''A synthetic oscillatory network of transcriptional regulators [http://www.nature.com/nature/journal/v403/n6767/abs/403335a0.html]
# '''A synthetic oscillatory network of transcriptional regulators [http://www.nature.com/nature/journal/v403/n6767/abs/403335a0.html link]
# '''Construction of a genetic toggle switch in ''Escherichia coli'' [http://www.nature.com/nature/journal/v403/n6767/abs/403339a0.html]
# '''Construction of a genetic toggle switch in ''Escherichia coli'' [http://www.nature.com/nature/journal/v403/n6767/abs/403339a0.html link]
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====Assignment 13: Genetic circuit engineering====
====Assignment 13: Genetic circuit engineering====
<font color=green>
<font color=green>
# '''Environmentally controlled invasion of cancer cells by engineered bacteria
# '''Environmentally controlled invasion of cancer cells by engineered bacteria [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-4HJRXGD-4&_user=709071&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000039638&_version=1&_urlVersion=0&_userid=709071&md5=cac1dbad4022f85af3724a9ba787d3dd  link]
# '''Environmental signal integration by a modular AND gate
# '''Environmental signal integration by a modular AND gate
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====Assignment 14: Metabolic pathway engineering====
====Assignment 14: Metabolic pathway engineering====
<font color=green>
<font color=green>
# '''Production of isoprenoid pharmaceuticals by engineered microbes
# '''Production of isoprenoid pharmaceuticals by engineered microbes [http://www.nature.com/nchembio/journal/v2/n12/abs/nchembio836.html;jsessionid=EFAF8B58DDCC1CB3D2EB61B11223039B  link]
# '''Balancing a heterologous mevalonate pathway for improved isoprenoid production in Escherichia coli
# '''Balancing a heterologous mevalonate pathway for improved isoprenoid production in Escherichia coli [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17239639&ordinalpos=12&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum link]
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====Assignment 15: Systems biology====
====Assignment 15: Systems biology====
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====Assignment 16: Systems biology and synthetic biology====
====Assignment 16: Systems biology and synthetic biology====
<font color=red>
<font color=red>
# '''Systems biology as a foundation for genome-scale synthetic biology [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VRV-4KPX8RY-1&_user=709071&_coverDate=10%2F31%2F2006&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000039638&_version=1&_urlVersion=0&_userid=709071&md5=7a316893fbee50cab2742cc3b6de73b4 ]
# '''Systems biology as a foundation for genome-scale synthetic biology [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VRV-4KPX8RY-1&_user=709071&_coverDate=10%2F31%2F2006&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000039638&_version=1&_urlVersion=0&_userid=709071&md5=7a316893fbee50cab2742cc3b6de73b4 link]
# '''From systems biology to synthetic biology
# '''From systems biology to synthetic biology
# '''Modular approaches to expanding the functions of living matter
# '''Modular approaches to expanding the functions of living matter
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# '''Synthetic biology through the prism of scenarios
# '''Synthetic biology through the prism of scenarios
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* by Tom Knight
*[http://www.nature.com/nature/journal/v438/n7067/abs/nature04342.html;jsessionid=3E7E09FF4E647671DF79F2A37BC3632F <font color="#000000">Foundations for engineering biology</font>] by Drew Endy
===Current Research===
*[http://www.nature.com/nchembio/journal/v2/n12/abs/nchembio836.html;jsessionid=EFAF8B58DDCC1CB3D2EB61B11223039B <font color="#000000">Production of isoprenoid pharmaceuticals by engineered microbes</font>] by Jay Keasling ''et al''
*[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17239639&ordinalpos=12&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum<font color="#000000">Balancing a heterologous mevalonate pathway for improved isoprenoid production in Escherichia coli</font>] by Jay Keasling ''et al''
*[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-4HJRXGD-4&_user=709071&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000039638&_version=1&_urlVersion=0&_userid=709071&md5=cac1dbad4022f85af3724a9ba787d3dd <font color="#000000">Environmentally Controlled Invasion of Cancer Cells by Engineered Bacteria</font>] by Chris Voigt ''et al''
===Implications===
*[http://www.nature.com/nbt/journal/v25/n6/pdf/nbt0607-627.pdf<font color="#000000">DNA synthesis and biological security</font>]

Revision as of 11:15, 3 January 2008

CHE.496: Biological Systems Design Seminar

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Assigned Readings

Assignment 1: Synthetic biology overview

  1. Intelligent Life link
  2. Extreme genetic engineering: an introduction to synthetic biology link

Assignment 2: Foundational technologies

  1. Foundations for engineering biology link
  2. Economics of synthetic biology link

Assignment 3: Engineering principles

  1. Synthetic biology - putting engineering into biology link
  2. Synthetic biology: new engineering rules for an emerging discipline link

Assignment 4: Genetic programming

  1. Idempotent vector design for standard assembly of biobricks link
  2. Genetic parts to program bacteria link

Assignment 5: Natural biological parts

  1. Another side of genomics: Synthetic biology as a means for the exploitation of whole-genome sequence information
  2. Codon bias and heterologous protein expression

Assignment 6: Practical applications

  1. Advances in synthetic biology: on the path from prototypes to applications link
  2. Molecular switches for cellular sensors link

Assignment 7: Social implications

  1. The promises and perils of synthetic biology
  2. DNA synthesis and biological security

Assignment 8: Engineering biology

  1. A partnership between biology and engineering link
  2. Fast, cheap and somewhat in control

Assignment 9: Biological machines

  1. Designing biological systems
  2. Biology by design: Reduction and synthesis of cellular components and behavior link

Assignment 10: Minimal genomes

  1. Essential genes of a minimal bacterium
  2. Leaner and meaner genomes in E. coli

Assignment 11: Minimal cells

  1. Toward synthesis of a minimal cell
  2. Rebuilding microbial genomes

Assignment 12: Genetic circuit engineering

  1. A synthetic oscillatory network of transcriptional regulators link
  2. Construction of a genetic toggle switch in Escherichia coli link

Assignment 13: Genetic circuit engineering

  1. Environmentally controlled invasion of cancer cells by engineered bacteria link
  2. Environmental signal integration by a modular AND gate

Assignment 14: Metabolic pathway engineering

  1. Production of isoprenoid pharmaceuticals by engineered microbes link
  2. Balancing a heterologous mevalonate pathway for improved isoprenoid production in Escherichia coli link

Assignment 15: Systems biology

  1. The evolution of molecular biology into systems biology
  2. Integrating 'omic information: A bridge between genomics and systems biology
  3. Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles

Assignment 16: Systems biology and synthetic biology

  1. Systems biology as a foundation for genome-scale synthetic biology link
  2. From systems biology to synthetic biology
  3. Modular approaches to expanding the functions of living matter

Assignment 17: Computational Biology

  1. Modelling cellular behaviour
  2. Bioinformatics analysis for genome design and synthetic biology

Assignment 18: Biological networks

  1. Biological networks
  2. Programming and engineering biological networks

Assignment 19: Metabolic modeling

  1. Use of genome-scale microbial models for metabolic engineering
  2. Global physiological understanding and metabolic engineering of microorganisms based on omics studies
  3. Microbial regulatory and metabolic networks

Assignment 20: RNA synthetic biology

  1. RNA synthetic biology
  2. RNA and RNP as new molecular parts in synthetic biology

Assignment 21: The future of synthetic biology

  1. Synthetic biology: Navigating the challenges ahead
  2. Synthetic biology through the prism of scenarios

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