CHE.496/2008/Assignments: Difference between revisions
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__NOTOC__ | __NOTOC__ | ||
{{Template:CHE.496/2008}} | {{Template:CHE.496/2008}} | ||
<div style="padding: 10px; width: | <div style="padding: 10px; width: 750px; border: 5px solid #B3CD4E;"> | ||
==Assigned Readings== | ==Assigned Readings== | ||
====Assignment 1: Synthetic biology overview==== | ====Assignment 1: Synthetic biology overview==== | ||
<font color=blue> | <font color=blue> | ||
# '''Extreme genetic engineering: | # '''Intelligent Design [http://sciencereview.berkeley.edu/articles.php?issue=8&article=synthbio link] | ||
# '''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> | ||
# '''Foundations for engineering biology | # '''Foundations for engineering biology [http://www.nature.com/nature/journal/v438/n7067/abs/nature04342.html link] | ||
# ''' | # '''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> | ||
# '''Synthetic biology - putting engineering into biology | # '''Synthetic biology - putting engineering into biology [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/22/2790 link] | ||
# '''Synthetic biology: | # '''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> | ||
# '''Idempotent vector design for standard assembly of biobricks | # '''Idempotent vector design for standard assembly of biobricks [http://web.mit.edu/synbio/release/docs/biobricks.pdf link] | ||
# '''Genetic parts to program bacteria | # '''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> | ||
# '''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] | |||
# '''Another side of genomics: Synthetic biology as a means for the exploitation of whole-genome sequence information | # '''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] | ||
# '''Codon bias and heterologous protein expression | |||
</font> | </font> | ||
====Assignment 6: Practical applications==== | ====Assignment 6: Practical applications==== | ||
<font color=blue> | <font color=blue> | ||
# '''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] | ||
# '''Molecular switches for cellular sensors | # '''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> | ||
# '''The promises and perils of synthetic biology | # '''The promises and perils of synthetic biology [http://www.thenewatlantis.com/archive/12/tuckerzilinskas.htm link] | ||
# '''DNA synthesis and biological security | # '''DNA synthesis and biological security [http://cstsp.aaas.org/files/DNA_synthesis_NGP2007.pdf link] | ||
</font> | </font> | ||
====Assignment 8: | ====Assignment 8: Engineering biology==== | ||
<font color=green> | <font color=green> | ||
# ''' | # '''A partnership between biology and engineering [http://www.nature.com/nbt/journal/v22/n10/full/nbt1004-1211.html link] | ||
# '''Fast, cheap and somewhat in control [http://genomics.lbl.gov/Stuff/Arkin_FastCheapGenomeBiology.pdf link] | |||
# '''Fast, cheap and somewhat in control | |||
</font> | </font> | ||
====Assignment 9: | ====Assignment 9: Biological machines==== | ||
<font color=green> | <font color=green> | ||
# ''' | # '''Designing biological systems [http://www.genesdev.org/cgi/content/abstract/21/3/242 link] | ||
# ''' | # '''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> | ||
====Assignment 10: | ====Assignment 10: Genetic circuit engineering (part 1)==== | ||
<font color=green> | <font color=green> | ||
# ''' | # '''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 link] | |||
</font> | </font> | ||
====Assignment 11: | ====Assignment 11: Genetic circuit engineering (part 2)==== | ||
<font color=green> | <font color=green> | ||
# ''' | # '''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 [http://www.nature.com/msb/journal/v3/n1/synopsis/msb4100173.html link] | |||
</font> | </font> | ||
====Assignment 12: | ====Assignment 12: Metabolic pathway engineering==== | ||
<font color=green> | <font color=green> | ||
# ''' | # '''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] | ||
# ''' | # '''Synthetic biology for synthetic chemistry [http://pubs.acs.org/cgi-bin/sample.cgi/acbcct/2008/3/i01/pdf/cb7002434.pdf link] | ||
</font> | </font> | ||
====Assignment 13 | ====Assignment 13: 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 link] | |||
# '''Modular approaches to expanding the functions of living matter [http://www.nature.com/nchembio/journal/v2/n6/abs/nchembio789.html link] | |||
</font> | </font> | ||
====Assignment | ====Assignment 14: Biological networks==== | ||
<font color=red> | <font color=red> | ||
# '''Biological networks [http://www.ecs.umass.edu/~mettu/ece697s/papers/systems%20biology/biological%20networks.pdf link] | |||
# '''Programming and engineering biological networks [http://lib.bioinfo.pl/pmid:16842994 link] | |||
</font> | </font> | ||
====Assignment | ====Assignment 15: RNA synthetic biology==== | ||
<font color=red> | <font color=red> | ||
# '''RNA synthetic biology [http://www.bu.edu/abl/files/naturebiotech_isaacs.pdf link] | |||
# '''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> | ||
Latest revision as of 16:42, 12 March 2008
Assigned Readings
Assignment 1: Synthetic biology overview
Assignment 2: Foundational technologies
- Foundations for engineering biology link
- Synthetic biology: promises and challenges link
- The iGEM competition: building with biology link
Assignment 3: Engineering principles
- Synthetic biology - putting engineering into biology link
- Synthetic biology: new engineering rules for an emerging discipline link
Assignment 4: Genetic programming
- Idempotent vector design for standard assembly of biobricks link
- Genetic parts to program bacteria link
Assignment 5: Natural biological parts
- Another side of genomics: Synthetic biology as a means for the exploitation of whole-genome sequence information link
- Codon bias and heterologous protein expression link
Assignment 6: Practical applications
- Advances in synthetic biology: on the path from prototypes to applications link
- Molecular switches for cellular sensors link
Assignment 7: Social implications
Assignment 8: Engineering biology
Assignment 9: Biological machines
- Designing biological systems link
- Biology by design: Reduction and synthesis of cellular components and behavior link
Assignment 10: Genetic circuit engineering (part 1)
- A synthetic oscillatory network of transcriptional regulators link
- Construction of a genetic toggle switch in Escherichia coli link
Assignment 11: Genetic circuit engineering (part 2)
- Environmentally controlled invasion of cancer cells by engineered bacteria link
- Environmental signal integration by a modular AND gate link
Assignment 12: Metabolic pathway engineering
- Bioengineering novel in vitro metabolic pathways using synthetic biology link
- Synthetic biology for synthetic chemistry link
Assignment 13: Systems biology and synthetic biology
- Systems biology as a foundation for genome-scale synthetic biology link
- Modular approaches to expanding the functions of living matter link
Assignment 14: Biological networks
Assignment 15: RNA synthetic biology