A new method for mapping mutations in the Salmonella typhimurium chromosome is described and applied to the localization of novel regulatory mutations affecting expression of the nirB (nitrite reductase) gene. The mapping technique'is also illustrated by the mapping of mutations in genes affecting carbohydrate catabolism and biosynthetic pathways. The new mapping method involves use of the hybrid phage MudP and MudQ (together referred to as Mud-P22), originally constructed by Youderian et al. (Genetics 118:581-592, 1988). This report describes a set of Mud-P22 lysogens, each member of the set containing a different Mud-P22 insertion. The insertions are scattered along the entire Salmonella genome. These lysogens, when induced by mitomycin C, generate transducing lysates that are enriched (45-to 1,400-fold over the background, generalized transducing particle population) for transducing particles containing bacterial DNA that flanks one side of the insertion. We demonstrate that within the set of lysogens there can be found at least one Mud-P22 insertion that enriches for any particular region of the Salmonella chromosome and that, therefore, all regions of the chromosome are discretely enriched and represented by the collection as a whole. We describe a technique that allows the rapid and facile determination of which lysate contains enriched sequences for the repair of a mutant locus, thereby allowing the determination of the map position of the locus. This technique is applicable to those mutations for which the wild-type allele is selectable. We also describe a procedure whereby any TnlO insertion can be mapped by selecting for the loss of Tetr. Transduction refers to the transfer of genetic information (DNA) from one bacterium to another via a phage particle. Generalized transduction refers to the ability of the transducing mechanism to transfer information from all parts of the donor genome. P22 is one of several phage that mediate generalized transduction in salmonellae (21). The mechanism whereby P22 mediates generalized transduction is understood at a general level, although some of the specific molecular details require further elucidation (for a review of P22 molecular genetics, see references 25 and 31).P22 packages its genome by processive packaging of 43. 4-kb (+0.75 kb [3]) fragments derived from a doublestranded, linear, concatemeric DNA molecule. Gene 3 is believed to code for a nuclease which recognizes a specific nucleotide sequence within the gene 3 coding sequence called the pac site (4,20,26). Once the pac site is recognized, a cut is made near the pac site (3, 17) and unidirectional packaging of the concatemer into phage heads begins. The direction of packaging is from gene 3, towards the late genes and the immunity I region. Continuous filling of heads from one concatemer may continue for 3 to 8 headfuls, depending on the genotype of the virus (1).Lysates made from wild-type P22 are found to contain small amounts of host rather than viral DNA (approximately 3% of the plaque-forming particl...

We describe a non-invasive approach for recovering RNA from the surface of skin via a simple tape stripping procedure that permits a direct quantitative and qualitative assessment of pathologic and physiologic biomarkers. Using semi-quantitative RT-PCR we show that tape-harvested RNA is comparable in quality and utility to RNA recovered by biopsy. It is likely that tape-harvested RNA is derived from epidermal cells residing close to the surface and includes adnexal structures and present data showing that tape and biopsy likely recover different cell populations. We report the successful amplification of tape-harvested RNA for hybridization to DNA microarrays. These experiments showed no significant gene expression level differences between replicate sites on a subject and minimal differences between a male and female subject. We also compared the array generated RNA profiles between normal and 24 h 1% SLS-occluded skin and observed that SLS treatment resulted in statistically significant changes in the expression levels of more than 1,700 genes. These data establish the utility of tape harvesting as a non-invasive method for capturing RNA from human skin and support the hypothesis that tape harvesting is an efficient method for sampling the epidermis and identifying select differentially regulated epidermal biomarkers.

Dimerization of lambda cI repressor monomers is required for high-affinity binding to bacteriophage lambda operator DNA and is known to involve protein-protein contacts between C-terminal domains of the repressor monomers. In order to address the importance of the C-terminal domain in mediating the oligomeric properties of dimerization and cooperative binding to operator DNA, eight single-site mutant repressors were screened for possible deficiencies in cooperative interactions; all but one of the amino acid substitutions are located within the C-terminal domain. As a prelude to binding studies and the complete characterization of cooperativity mutants of lambda cI repressor (Burz, D. S., & Ackers, G. K. (1994) Biochemistry 33, 8406-8416), the thermodynamics of self-assembly of seven of these mutants was examined from 10(-11) to 10(-5) M total repressor using analytical gel chromatography. Results show that the structural perturbation accompanying single amino acid replacement does not significantly affect the monomer-dimer equilibrium with the exception of that accompanying replacements of serine 228; mutations at that site weaken, by 2-4 kcal/mol, the protein-protein interactions responsible for self-association. An additional mutant repressor, Pro158-->Thr, was also examined and found to associate reversibly from monomers to a species with stoichiometry greater than 2. All mutations increase the apparent Stokes radius of the monomeric form by 2-4.5 A and that of dimers by 1 or 3 A.

We report the use of non-invasive tape stripping to sample psoriatic lesional and non-lesional skin in 96 patients. The procedure was well tolerated with any discomfort described as mild; we did not observe any cases of Koebner phenomena at any non-lesional tape-stripped sites. Tape-harvested epidermis was extracted for RNA, which was profiled by semiquantitative reverse transcriptase-PCR. This analysis revealed that mRNAs for tumor necrosis factor alpha, IFNgamma, Krt-16, CD2, IL-23A, IL-12B, and vascular endothelial growth factor are overexpressed in the "average" psoriatic lesion in a majority of patients. In addition, 10 of these patients were biopsied at lesional and non-lesional sites and the expression data compared to tape-stripping data. This comparison shows that five of seven mRNA are more highly expressed in cells captured by tape stripping than biopsy, suggesting that the upper aspect of a lesion contains cells very active in the disease. The tape-harvesting data reveal that approximately 46% of lesions have at least one pathogenic mRNA within non-lesional skin limits. Data demonstrate that tape stripping reveals mRNA markers not detected in biopsy samples and thus the method may be a useful supplement to biopsy.

Bacteriophage lambda repressor binds co-operatively to adjacent pairs of DNA target sites. A novel combination of positive genetic selections, involving two different operon fusions derived from P22 challenge phages, was used to isolate mutant lambda repressors that have lost the ability to bind co-operatively to tandem sites yet retain the ability to bind a strong, single site. These cb (co-operative binding) mutations result in 10 different amino acid changes, which define eight residues in the carboxyl-terminus of repressor. Because challenge phage derivatives may be applied to study essentially any specific protein-DNA interaction, analogous combinations of genetic selections may be used to explore the ways that a variety of proteins interact to assemble regulatory complexes.