CHE.496/2008/Assignments: Difference between revisions
From OpenWetWare
Jump to navigationJump to search
GMcArthurIV (talk | contribs) No edit summary |
GMcArthurIV (talk | contribs) No edit summary |
||
Line 48: | Line 48: | ||
<font color=green> | <font color=green> | ||
# '''Designing biological systems | # '''Designing biological systems | ||
# '''Biology by design: Reduction and synthesis of cellular components and behavior | # '''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>] | ||
</font> | </font> | ||
====Assignment 10: Minimal genomes==== | ====Assignment 10: Minimal genomes==== | ||
Line 62: | Line 62: | ||
====Assignment 12: Genetic circuit engineering==== | ====Assignment 12: Genetic circuit engineering==== | ||
<font color=green> | <font color=green> | ||
# '''A synthetic oscillatory network of transcriptional regulators | # '''A synthetic oscillatory network of transcriptional regulators [http://www.nature.com/nature/journal/v403/n6767/abs/403335a0.html] | ||
# '''Construction of a genetic toggle switch in ''Escherichia coli'' | # '''Construction of a genetic toggle switch in ''Escherichia coli'' [http://www.nature.com/nature/journal/v403/n6767/abs/403339a0.html] | ||
</font> | </font> | ||
====Assignment 13: Genetic circuit engineering==== | ====Assignment 13: Genetic circuit engineering==== | ||
Line 83: | Line 83: | ||
====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 | # '''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 ] | ||
# '''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 | ||
Line 113: | Line 113: | ||
# '''Synthetic biology through the prism of scenarios | # '''Synthetic biology through the prism of scenarios | ||
</font> | </font> | ||
* 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 10:48, 3 January 2008
Assigned Readings
Assignment 1: Synthetic biology overview
Assignment 2: Foundational technologies
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
- Codon bias and heterologous protein expression
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
- The promises and perils of synthetic biology
- DNA synthesis and biological security
Assignment 8: Engineering biology
- A partnership between biology and engineering link
- Fast, cheap and somewhat in control
Assignment 9: Biological machines
- Designing biological systems
- Biology by design: Reduction and synthesis of cellular components and behavior [*Biology by Design
Assignment 10: Minimal genomes
- Essential genes of a minimal bacterium
- Leaner and meaner genomes in E. coli
Assignment 11: Minimal cells
- Toward synthesis of a minimal cell
- Rebuilding microbial genomes
Assignment 12: Genetic circuit engineering
- A synthetic oscillatory network of transcriptional regulators [1]
- Construction of a genetic toggle switch in Escherichia coli [2]
Assignment 13: Genetic circuit engineering
- Environmentally controlled invasion of cancer cells by engineered bacteria
- Environmental signal integration by a modular AND gate
Assignment 14: Metabolic pathway engineering
- Production of isoprenoid pharmaceuticals by engineered microbes
- Balancing a heterologous mevalonate pathway for improved isoprenoid production in Escherichia coli
Assignment 15: Systems biology
- The evolution of molecular biology into systems biology
- Integrating 'omic information: A bridge between genomics and systems biology
- Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles
Assignment 16: Systems biology and synthetic biology
- Systems biology as a foundation for genome-scale synthetic biology [3]
- From systems biology to synthetic biology
- Modular approaches to expanding the functions of living matter
Assignment 17: Computational Biology
- Modelling cellular behaviour
- Bioinformatics analysis for genome design and synthetic biology
Assignment 18: Biological networks
- Biological networks
- Programming and engineering biological networks
Assignment 19: Metabolic modeling
- 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
Assignment 20: RNA synthetic biology
- RNA synthetic biology
- RNA and RNP as new molecular parts in synthetic biology
Assignment 21: The future of synthetic biology
- Synthetic biology: Navigating the challenges ahead
- Synthetic biology through the prism of scenarios
- by Tom Knight
- Foundations for engineering biology by Drew Endy
Current Research
- Production of isoprenoid pharmaceuticals by engineered microbes by Jay Keasling et al
- Balancing a heterologous mevalonate pathway for improved isoprenoid production in Escherichia coli by Jay Keasling et al
- Environmentally Controlled Invasion of Cancer Cells by Engineered Bacteria by Chris Voigt et al