Tk:Ab hac una re

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Ab hac una re

2 September 2006

Established role of protein AAT75660, previously unknown function, now clearly yggJ or rsmE (Basturea06, PMID: 16431987). Methyltransferase modifying the 16S base at location U1498. E value match 2E-16 with the E. coli gene.

No evidence for tusBDC complex in MF.

ksgA (rsmA), another 16S ribosomal RNA modifying protein is AAT75361. VanBuul85 rsmB is AAT75553 (5-methyl cytosine transferase for tRNA and rRNA) Tscherne99 rsmC appears to be missing.

1 September 2006

design and order fluorescent primers for debugging construction plasmid PCR, cutting and ligation. Pacific blue and Alexa Fluor 488 appear to work well with UV excitation. Prefix-R and Suffix-F ordered.

Miniprep of pRML1, pRML2, pYAC4. Design and order sequencing primers and half of the needed construction primers for YAC left and right arms. Remainder awaiting sequencing results.

29 August 2006

Order medium components (Spencer 93)

Sequencing primers for pRML1, pRML2

  • pBluescript II SK+
  • pCGS966
  • URA3
  • TRP
  • ARS1
  • ARSH4
  • CEN4

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.