Handouts

• Syllabus
• General Overview

Protocols

1. Quikchange site-directed kit
2. NEB Impact Intein manual

Powerpoint Slides

• Lecture 1
• Lecture 2
• Lecture 3
• Lecture 4
• Lecture 5
• Lecture 6
• Lecture 7 & 8
• Lecture 9 (large file)
• Lecture 10 & 11 (large file)
• Lecture 12, 13 & 14 (large file)

Readings, not required but cited in class

• Cohen et al.
• Sanger et al.
• Watson and Crick

Arabidopsis branching papers

1. Regulation of Carotenoid Composition and Shoot Branching in Arabidopsis by a Chromatin Modifying Histone Methyltransferase, SDG8
2. Phytochrome Regulation of Branching in Arabidopsis
3. Inhibition of shoot branching by new terpenoid plant hormones

Quicktime Movies

• Dye Terminator Sequencing Reaction Mixture

Lab Websites

• OligoPerfect Designer for RT-PCR primers (From Invitrogen)
• To translate a DNA sequence use "orf finder" at http://www.ncbi.nlm.nih.gov/projects/gorf/
• INVITROGEN: Zero Blunt TOPO manual.pdf
• The TIGR Comprehensive Microbial Resource Database
  http://cmr.tigr.org/tigr-scripts/CMR/CmrHomePage.cgi
• DNA Sequence Manipulation Tool
  http://www.vivo.colostate.edu/molkit/manip/
• NEB Cutter
  http://tools.neb.com/NEBcutter2/index.php
• NCBI
  http://www.ncbi.nlm.nih.gov/
• Encyclopedia of Escherichia coli K-12 Genes and Metabolism
  www.ecocyc.org
• EcoGene
  www.ecogene.org
• Integrated DNA Technologies
  www.idtdna.com
• Clustal W Sequence Aligner
  http://www.ebi.ac.uk/Tools/clustalw/index.html
• TAIR
  http://www.arabidopsis.org/
• ENTREZ Genome Projects: from NCBI-- al completed and unfinished genome
  sequences: http://www.ncbi.nlm.nih.gov/genomes/static/gpstat.html
• Microbial genome links, including the KEGG metabolic and gene databases:
  http://www.ncbi.nlm.nih.gov/genomes/MICROBES/collaborators.html
• The website for all enzymes & nomenclature: The International Union of
  Biochemistry and Molecular Biology. (IUBMB) :
  http://www.chem.qmul.ac.uk/iubmb/
• MOLECULAR EVOLUTIONARY GENETICS ANALYSIS (MEGA). Free software for conducting automatic and manual sequence alignment, inferring phylogenetic trees, mining web-based databases, estimating rates of molecular evolution, inferring ancestral sequences, and testing evolutionary hypotheses: http://www.megasoftware.net/