Project description:Investigation of whole genome gene expression AdnA in Pseudomonas fluorescens, an ortholog of FleQ in P. aeruginosa, regulates both motility and flagella-mediated attachment to various surfaces. A whole genome microarray determined the AdnA transcriptome by comparing the gene expression pattern of wild-type Pf0-1 to that of Pf0-2x (adnA-) in broth culture. In the absence of AdnA, expression of 92 genes was decreased, while 11 genes showed increased expression. Analysis of 16 of these genes fused to lacZ confirmed the microarray results. Several genes were further evaluated for their role in motility and biofilm formation. Two genes, Pfl01_1508 and Pfl01_1517, affected motility and had different effects on biofilm formation in Pf0-1. These two genes are predicted to encode proteins similar to the glycosyl transferases FgtA1 and FgtA2, which have been shown to be involved in virulence and motility in P. syringae. Three other genes, Pfl01_1516, Pfl01_1572, and Pfl01_1573, not previously associated with motility and biofilm formation in Pseudomonas had similar affects on biofilm formation in Pf0-1. Deletion of each of these genes led to different motility defects. Our data revealed an additional level of complexity in the control of flagella function beyond the core genes known to be required, and may yield insights into processes important for environmental persistence of P. fluorescens Pf0-1.
Project description:Investigation of whole genome gene expression AdnA in Pseudomonas fluorescens, an ortholog of FleQ in P. aeruginosa, regulates both motility and flagella-mediated attachment to various surfaces. A whole genome microarray determined the AdnA transcriptome by comparing the gene expression pattern of wild-type Pf0-1 to that of Pf0-2x (adnA-) in broth culture. In the absence of AdnA, expression of 92 genes was decreased, while 11 genes showed increased expression. Analysis of 16 of these genes fused to lacZ confirmed the microarray results. Several genes were further evaluated for their role in motility and biofilm formation. Two genes, Pfl01_1508 and Pfl01_1517, affected motility and had different effects on biofilm formation in Pf0-1. These two genes are predicted to encode proteins similar to the glycosyl transferases FgtA1 and FgtA2, which have been shown to be involved in virulence and motility in P. syringae. Three other genes, Pfl01_1516, Pfl01_1572, and Pfl01_1573, not previously associated with motility and biofilm formation in Pseudomonas had similar affects on biofilm formation in Pf0-1. Deletion of each of these genes led to different motility defects. Our data revealed an additional level of complexity in the control of flagella function beyond the core genes known to be required, and may yield insights into processes important for environmental persistence of P. fluorescens Pf0-1. Catalog design for Pseudomonas fluorescens Pf0-1 (Taxonomy Id: 205922) covering NC_007492. Probes selected for 5736/5736 sequences. Median number of probes/sequence is 13 with an average of 13.00. Each probe will be replicated 5 times on the chip. Probes are randomly distributed over the surface of the array. Unused features have been filled with randomly generated probes of comparable GC content.
Project description:Archaeological remains covered with concretions, including human bones, are commonly found in certain areas and time periods of interest for understanding the past, but have yet to be investigated for potential ancient DNA (aDNA) and protein content. We extracted aDNA and proteins in tandem from human dental remains and the concretions surrounding them and compared them to non-concreted human dental remains from the same site. Concretions appeared homogeneous in colour and texture, consisting of a hard dark grey sediment adhered to the bone surfaces, presumably as a result of cyclical waterlogging of the burial deposits as well as postcranial human remains from a contemporary site. Concretions were found to contain human oral microbiome genomic and proteomic leached from the original skeletal source, as well as environmental and human proteins. Despite this, both the original element and concretions lacked endogenous human aDNA, indicating that the use of this type of material in future molecular archaeological applications is limited.