... sequence2.1
This chapter was co-written with Sean Eddy, and appears in Lowe & Eddy, Nucleic Acids Research 25: 955-964, 1997. 
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... Yeast4.1
This chapter was co-written with Sean Eddy, and appears in a shortened version in Lowe & Eddy, Science 283: 1168-1171, 1999. 
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... sequence4.4
Random sequences were generated by a fifth order Markov chain based on 6mer frequencies within the yeast genome. 
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... Genomes5.1
This chapter was co-written with Patrick Dennis as a collaboration between the Eddy and Dennis labs. The paper appears in a shortened version in Omer, Lowe, Russel, Ebhardt, Eddy, & Dennis, Science (2000) (in press). 
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... lab5.4
The Dennis lab at University of British Columbia, Department of Biochemistry and Molecular Biology, includes Patrick Dennis, Arina Omer, Anthony Russell, and Holger Ebhart. As collaborators on this project, the Dennis lab performed all S. acidocaldarius protein biochemistry, immunoprecipitation, and sRNA cloning. 
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... 5.5
A clone containing the aFIB and aNOP56 genes from S. solfataricus was provided by M.A. Ragan and C.W. Sensen. The Dennis lab used Southern hybridization to identify and clone the corresponding genes from S. acidocaldarius. The 16S rRNA sequences from S. acidocaldarius and S. solfataricus are about 90% identical. The aFIB and aNOP proteins from the two organisms are respectively 76 and 66 percent identical. The accession numbers for the S. acidocaldarius aFIB and aNOP genes will be obtained upon submission of the manuscript describing this work 
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... RT-PCR5.6
The primer AO30 (5' CTCGAGATCTGGATCCGGG 3') was 5' end-labeled with T4 polynucleotide kinase and $\gamma-^{32}$P-ATP and blocked at the 3' end using terminal deoxynucleotidyl transferase (Gibco BRL) and dCTP. The modified oligo was then ligated to gel purified sRNA for 16 hrs at 4C. The ligation products were reverse transcribed with Thermoscript RT (Gibco BRL) at 55C for 30 min, using AO31 (5' CCCGGATCCAGATCTCGAG 3') as primer. The RNA template was hydrolyzed with RNase H and the cDNA strand was extended with dATP using terminal deoxynucleotidyl transferase. The extended cDNA strand was used as template for PCR (95C denaturation, 65C hybridization, 72C extension, 30 cycles) using AO30 and AO32 [5' GCGAATTCTGCAG(T)30 3'] as primers. The DNA products were cleaved with PstI and XhoI, ligated between the PstI and XhoI sites of plasmid pSP72 and transformed into E. coli. Plasmids were isolated and their sequences was determined. 
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Todd M. Lowe
2000-03-31