Tk:Ab hac una re

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Ab hac una re

29 August 2006

Order medium components (Spencer 93)

Sequencing primers for pRML1, pRML2

Construct parts from Left, Right telomere, Left, Right chromosome ends

Construct parts from 1000 bp sequences at MF terminator

17 August 2006

Wood's Hole ISAT TCDB transporter database. Useful in characterizing and searching for transporter protein properties and motifs.

Demo of "cool stuff" minty fresh E. coli and banana smelling E. coli. Discussions with Carl Landweber and Bob Colwell especially imporant. Possible teaming on energy production with SRI / Sandia.

12 August 2006

Sci Foo camp. Jonathan Eisen discussions. Dyson / Danny / Brand

10 August 2006

Peter Karp. Discussons on SRI EcoCyc/Biocyc uses for Mesoplasma florum design and editing.

9 August 2006

Rocha paper on survey of recombination systems in sequenced bacteria. Florum has RecO, RecR, but not RecF in the RecFOR system. RecA present. RecD present. RuvAB present, ruvC not, but replaced with RecU. yqgF gene part of the recomination system. PriA missing. RecBC missing, RecD form is different from the form found in organisms with RecBC also.

Received yeast strains and plasmids from Weiss lab. Confirmed that they cannot PCR through the centromere CDS II region.

Codon usage of the P1014 cassette. CTC codon (Lys) is rare and used 4+ times. CGG is not present in the CDS. Three GATC sequences.

7 August 2006

SMC proteins maintain chromosome condensation. Co-factors scpA and scpB. Me. florum proteins are AAT7589, AAT75908, AAT75907 respectively. B. subtilis homologs: P51834, P35154, P35155. Volkov03. Notarnicola91 reports SMC protein in M. hyorhinis (P115).

Compromise codon usage: multiply codon probabilities for corresponding codons from each organism, then take the square root (geometric mean). Renormalize within each amino acid to establish new relative probabilities.