Journal: BMC Genomics

Article Title: Transcriptomic and proteomic analyses of Desulfovibrio vulgaris biofilms: Carbon and energy flow contribute to the distinct biofilm growth state

doi: 10.1186/1471-2164-13-138

Figure Lengend Snippet: Correlation matrix for D. vulgaris gene expression that compares biofilm cells to planktonic cells grown with different substrates using a centered Pearson correlation. Cells were grown in a defined S4D medium with sulfate (except for ‘pyruvate only’), and provided with a different carbon and energy source (lactate, pyruvate, hydrogen, or formate). The correlation matrix was generated with MicrobesOnline functional genomics analysis (microbesonline.org).

Article Snippet: Cultures of Desulfovibrio vulgaris ATCC 29579 were acquired from Dr. T.C.

Techniques: Expressing, Generated, Functional Assay

Journal: BMC Genomics

Article Title: Transcriptomic and proteomic analyses of Desulfovibrio vulgaris biofilms: Carbon and energy flow contribute to the distinct biofilm growth state

doi: 10.1186/1471-2164-13-138

Figure Lengend Snippet: Cell-wide depiction of significantly up-expressed transcripts for mature D. vulgaris biofilms compared to both batch and chemostat planktonic cells. The following genes were also detected as significantly up-expressed proteins: SodB, KatA, Hsp20 (DVU2441), Hsp20 (DVU2442), UspA (DVU0423).

Article Snippet: Cultures of Desulfovibrio vulgaris ATCC 29579 were acquired from Dr. T.C.

Techniques:

Journal: BMC Genomics

Article Title: Transcriptomic and proteomic analyses of Desulfovibrio vulgaris biofilms: Carbon and energy flow contribute to the distinct biofilm growth state

doi: 10.1186/1471-2164-13-138

Figure Lengend Snippet: Conceptual model (a) of the transcriptional responses in energy metabolism and pyruvate-acetate metabolic node for a mature D. vulgaris biofilm (red is up-expressed and blue is down-expressed) compared to planktonic cells.

Article Snippet: Cultures of Desulfovibrio vulgaris ATCC 29579 were acquired from Dr. T.C.

Techniques:

Journal: PLoS ONE

Article Title: Similar Gene Estimates from Circular and Linear Standards in Quantitative PCR Analyses Using the Prokaryotic 16S rRNA Gene as a Model

doi: 10.1371/journal.pone.0051931

Figure Lengend Snippet: Expected bacterial 16S rRNA gene copies were calculated based on four and five 16S copies per genome for ( a ) P. aeruginosa and ( b ) D. vulgaris , respectively. Black bars = predicted 16S copies. White bars = estimated 16S copies based on supercoiled plasmid standard. Grey bars = estimated 16S copies based on nicked-circular plasmid standard. Black and white striped bars = estimated 16S copies based on linearized plasmid standard. Black and gray striped bars = estimated 16S copies based on amplicon-based standard. Data are the average (n = 3) and error bars are ±1 standard deviation among replicates.

Article Snippet: Lyophilized genomic DNA samples from Desulfovibrio vulgaris subsp. vulgaris strain Hildenborough (NCIB 8303/ATCC 29579), Pseudomonas aeruginosa strain PAO1-LAC (ATCC 47085), Archaeoglobus fulgidus strain VC16 (DSM 4304/ATCC 49203), and Methanocaldococcus jannaschii strain JAL-1 (DSM 2661/ATCC 43067) were purchased from the American Type Culture Collection (ATCC).

Techniques: Plasmid Preparation, Amplification, Standard Deviation

Journal: PLoS ONE

Article Title: Similar Gene Estimates from Circular and Linear Standards in Quantitative PCR Analyses Using the Prokaryotic 16S rRNA Gene as a Model

doi: 10.1371/journal.pone.0051931

Figure Lengend Snippet: Estimated and expected 16S rRNA gene copies in microbial gDNA samples based on qPCR standard curves.

Article Snippet: Lyophilized genomic DNA samples from Desulfovibrio vulgaris subsp. vulgaris strain Hildenborough (NCIB 8303/ATCC 29579), Pseudomonas aeruginosa strain PAO1-LAC (ATCC 47085), Archaeoglobus fulgidus strain VC16 (DSM 4304/ATCC 49203), and Methanocaldococcus jannaschii strain JAL-1 (DSM 2661/ATCC 43067) were purchased from the American Type Culture Collection (ATCC).

Techniques: Amplification