CHE.496/2008/Assignments

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==Assigned Readings==
==Assigned Readings==
====Assignment 1: Synthetic biology overview====
====Assignment 1: Synthetic biology overview====
<font color=blue>
<font color=blue>
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# '''Extreme genetic engineering: An introduction to synthetic biology
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# '''Intelligent Design [http://sciencereview.berkeley.edu/articles.php?issue=8&article=synthbio link]
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# '''Intelligent Life
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# '''Extreme genetic engineering: an introduction to synthetic biology [http://www.etcgroup.org/en/materials/publications.html?pub_id=602 link]
</font>
</font>
====Assignment 2: Foundational technologies====
====Assignment 2: Foundational technologies====
<font color=blue>
<font color=blue>
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# '''Foundations for engineering biology
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# '''Foundations for engineering biology [http://www.nature.com/nature/journal/v438/n7067/abs/nature04342.html link]
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# '''Economics of synthetic biology
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# '''Synthetic biology: promises and challenges [http://www.nature.com/doifinder/10.1038/msb4100202 link]
 +
# '''The iGEM competition: building with biology [http://ieeexplore.ieee.org/Xplore/login.jsp?url=/iel5/4290605/4290606/04290608.pdf link]
</font>
</font>
====Assignment 3: Engineering principles====
====Assignment 3: Engineering principles====
<font color=blue>
<font color=blue>
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# '''Synthetic biology - putting engineering into biology
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# '''Synthetic biology - putting engineering into biology [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/22/2790 link]
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# '''Synthetic biology: New engineering rules for an emerging discipline
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# '''Synthetic biology: new engineering rules for an emerging discipline [http://www.nature.com/msb/journal/v2/n1/full/msb4100073.html link]
</font>
</font>
====Assignment 4: Genetic programming====
====Assignment 4: Genetic programming====
<font color=blue>
<font color=blue>
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# '''Idempotent vector design for standard assembly of biobricks
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# '''Idempotent vector design for standard assembly of biobricks [http://web.mit.edu/synbio/release/docs/biobricks.pdf link]
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# '''Genetic parts to program bacteria
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# '''Genetic parts to program bacteria [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VRV-4KWTFBB-3&_user=10&_coverDate=10%2F31%2F2006&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=af25b842448fbeab46cb6869a684d7b4 link]
</font>
</font>
====Assignment 5: Natural biological parts====
====Assignment 5: Natural biological parts====
<font color=blue>
<font color=blue>
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# '''Another side of genomics: Synthetic biology as a means for the exploitation of whole-genome sequence information
+
# '''Another side of genomics: Synthetic biology as a means for the exploitation of whole-genome sequence information [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T3C-4J3WG6G-2&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=991e2e60d1fea5abc67784f073c716dd link]
-
# '''Codon bias and heterologous protein expression
+
# '''Codon bias and heterologous protein expression [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TCW-4C8NKCY-3&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=45ad088ad31ff6fef31fa219d8f4099d link]
</font>
</font>
====Assignment 6: Practical applications====
====Assignment 6: Practical applications====
<font color=blue>
<font color=blue>
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# '''Advances in synthetic biology: on the path from prototypes to applications
+
# '''Advances in synthetic biology: on the path from prototypes to applications [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VRV-4GM45W4-2&_user=10&_coverDate=08%2F31%2F2005&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=a52006fd41df553f10c641cf1bd30272 link]
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# '''Molecular switches for cellular sensors
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# '''Molecular switches for cellular sensors [http://eands.caltech.edu/articles/LXVII4/Smolke%20Feature.pdf link]
</font>
</font>
====Assignment 7: Social implications====
====Assignment 7: Social implications====
<font color=blue>
<font color=blue>
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# '''The promises and perils of synthetic biology
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# '''The promises and perils of synthetic biology [http://www.thenewatlantis.com/archive/12/tuckerzilinskas.htm link]
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# '''DNA synthesis and biological security
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# '''DNA synthesis and biological security [http://cstsp.aaas.org/files/DNA_synthesis_NGP2007.pdf link]
</font>
</font>
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<font color=green>
 
====Assignment 8: Engineering biology====
====Assignment 8: Engineering biology====
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# '''A partnership between biology and engineering
 
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# '''Fast, cheap and somewhat in control
 
-
====Assignment 9: Biological machines====
 
<font color=green>
<font color=green>
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# '''Designing biological systems
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# '''A partnership between biology and engineering [http://www.nature.com/nbt/journal/v22/n10/full/nbt1004-1211.html link]
-
# '''Biology by design: Reduction and synthesis of cellular components and behavior
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# '''Fast, cheap and somewhat in control [http://genomics.lbl.gov/Stuff/Arkin_FastCheapGenomeBiology.pdf link]
</font>
</font>
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====Assignment 10: Minimal genomes====
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====Assignment 9: Biological machines====
<font color=green>
<font color=green>
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# '''Essential genes of a minimal bacterium
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# '''Designing biological systems [http://www.genesdev.org/cgi/content/abstract/21/3/242 link]
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# '''Leaner and meaner genomes in ''E. coli''
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# '''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]
</font>
</font>
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====Assignment 11: Minimal cells====
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====Assignment 10: Genetic circuit engineering (part 1)====
<font color=green>
<font color=green>
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# '''Toward synthesis of a minimal cell
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# '''A synthetic oscillatory network of transcriptional regulators [http://www.nature.com/nature/journal/v403/n6767/abs/403335a0.html link]
-
# '''Rebuilding microbial genomes
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# '''Construction of a genetic toggle switch in ''Escherichia coli'' [http://www.nature.com/nature/journal/v403/n6767/abs/403339a0.html link]
</font>
</font>
-
====Assignment 12: Genetic circuit engineering====
+
====Assignment 11: Genetic circuit engineering (part 2)====
<font color=green>
<font color=green>
-
# '''A synthetic oscillatory network of transcriptional regulators
+
# '''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]
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# '''Construction of a genetic toggle switch in ''Escherichia coli''
+
# '''Environmental signal integration by a modular AND gate [http://www.nature.com/msb/journal/v3/n1/synopsis/msb4100173.html link]
</font>
</font>
-
====Assignment 13: Genetic circuit engineering====
+
====Assignment 12: Metabolic pathway engineering====
<font color=green>
<font color=green>
-
# '''Environmentally controlled invasion of cancer cells by engineered bacteria
+
# '''Bioengineering novel in vitro metabolic pathways using synthetic biology [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VS2-4NWNF66-2&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=7914d28255c54bd144ea8516409bb86a  link]
-
# '''Environmental signal integration by a modular AND gate
+
# '''Synthetic biology for synthetic chemistry [http://pubs.acs.org/cgi-bin/sample.cgi/acbcct/2008/3/i01/pdf/cb7002434.pdf link]
</font>
</font>
-
====Assignment 14: Metabolic pathway engineering====
+
====Assignment 13: Systems biology and synthetic biology====
-
<font color=green>
+
-
# '''Production of isoprenoid pharmaceuticals by engineered microbes
+
-
# '''Balancing a heterologous mevalonate pathway for improved isoprenoid production in Escherichia coli
+
-
</font>
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-
 
+
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<font color=red>
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-
====Assignment 15: Systems biology and synthetic biology====
+
-
# '''The evolution of molecular biology into systems biology
+
-
# '''Integrating 'omic information: A bridge between genomics and systems biology
+
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<font color=red>
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====Assignment 16: Systems biology and synthetic biology====
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# '''Systems biology as a foundation for genome-scale synthetic biology
+
-
# '''From systems biology to synthetic biology
+
-
<font color=red>
+
-
====Assignment 17: Systems biology and synthetic biology====
+
-
# '''Biological networks
+
-
# '''Programming and engineering biological networks
+
-
<font color=red>
+
-
====Assignment 18: Computational Biology====
+
<font color=red>
<font color=red>
-
# '''From molecular to modular cell biology
+
# '''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]
-
# '''Modelling cellular behaviour
+
# '''Modular approaches to expanding the functions of living matter [http://www.nature.com/nchembio/journal/v2/n6/abs/nchembio789.html link]
</font>
</font>
-
====Assignment 19: Computational biology====
+
====Assignment 14: Biological networks====
<font color=red>
<font color=red>
-
# '''Bioinformatics analysis for genome design and synthetic biology
+
# '''Biological networks [http://www.ecs.umass.edu/~mettu/ece697s/papers/systems%20biology/biological%20networks.pdf link]
-
# '''Large-scale mapping and validation of ''Escherichia coli'' transcriptional regulation from a compendium of expression profiles
+
# '''Programming and engineering biological networks [http://lib.bioinfo.pl/pmid:16842994 link]
-
# '''Use of genome-scale microbial models for metabolic engineering
+
-
# '''Global physiological understanding and metabolic engineering of microorganisms based on omics studies
+
-
# '''Microbial regulatory and metabolic networks
+
-
# '''Modular approaches to expanding the functions of living matter
+
</font>
</font>
-
====Assignment 20: RNA synthetic biology====
+
====Assignment 15: RNA synthetic biology====
<font color=red>
<font color=red>
-
# '''RNA synthetic biology
+
# '''RNA synthetic biology [http://www.bu.edu/abl/files/naturebiotech_isaacs.pdf link]
-
# '''RNA and RNP as new molecular parts in synthetic biology
+
# '''RNA and RNP as new molecular parts in synthetic biology [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T3C-4PCGRPV-1&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=59ffbe8c79641a38cdf9d39750e8a7ae link]
</font>
</font>
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====Assignment 21: Systems biotechnology====
 
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<font color=red>
 
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# '''Synthetic biology: Navigating the challenges ahead
 
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# '''Synthetic biology through the prism of scenarios
 

Current revision

CHE.496: Biological Systems Design Seminar

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Assigned Readings

Assignment 1: Synthetic biology overview

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

Assignment 2: Foundational technologies

  1. Foundations for engineering biology link
  2. Synthetic biology: promises and challenges link
  3. The iGEM competition: building with 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 link
  2. Codon bias and heterologous protein expression link

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 link
  2. DNA synthesis and biological security link

Assignment 8: Engineering biology

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

Assignment 9: Biological machines

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

Assignment 10: Genetic circuit engineering (part 1)

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

Assignment 11: Genetic circuit engineering (part 2)

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

Assignment 12: Metabolic pathway engineering

  1. Bioengineering novel in vitro metabolic pathways using synthetic biology link
  2. Synthetic biology for synthetic chemistry link

Assignment 13: Systems biology and synthetic biology

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

Assignment 14: Biological networks

  1. Biological networks link
  2. Programming and engineering biological networks link

Assignment 15: RNA synthetic biology

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