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Rebuttal: Adaptive Point Mutation (Rosenberg and Hastings). John R. Roth, 2004. Genomic Analyses of Anaerobically Induced Genes in Saccharomyces cerevisiae: Functional Roles of Rox1 and Other Factors in Mediating the Anoxic Response. Kurt E. Kwast, 2002.DNA arrays were used to investigate the functional role of Rox1 in mediating acclimatization to anaerobic conditions in Saccharomyces cerevisiae . Multiple growth conditions for wild-type and rox1 null strains were used to identify open reading frames with a statistically robust response to this repressor . These results were compared to those obtained for a wild-type strain in response to oxygen availability . Transcripts of nearly one-sixth of the genome were differentially expressed (P < 0.05) with respect to oxygen availability, the majority (>65%) being down-regulated under anoxia . Of the anaerobically induced genes, about one-third (106) contain putative Rox1-binding sites in their promoters and were significantly (P < 0.05) up-regulated in the rox1 null strains under aerobiosis . Additional promoter searches revealed that nearly one-third of the anaerobically induced genes contain an AR1 site(s) for the Upc2 transcription factor, suggesting that Upc2 and Rox1 regulate the majority of anaerobically induced genes in S . cerevisiae . Functional analyses indicate that a large fraction of the anaerobically induced genes are involved in cell stress (  1/3), cell wall maintenance (1/8), carbohydrate metabolism (1/10), and lipid metabolism (1/12), with both Rox1 and Upc2 predominating in the regulation of this latter group and Upc2 predominating in cell wall maintenance . Mapping the changes in expression of functional regulons onto metabolic pathways has provided novel insight into the role of Rox1 and other trans-acting factors in mediating the physiological response of S . cerevisiae to anaerobic conditions .
Role of Rhodobacter sp . Strain PS9, a Purple Non-Sulfur Photosynthetic Bacterium Isolated from an Anaerobic Swine Waste Lagoon, in Odor Remediation. Young S. Do, 2003.Temporal pigmentation changes resulting from the development of a purple color in anaerobic swine waste lagoons were investigated during a 4-year period . The major purple photosynthetic bacterium responsible for these color changes and the corresponding reductions in odor was isolated from nine photosynthetic lagoons . By using morphological, physiological, and phylogenetic characterization methods we identified the predominant photosynthetic bacterium as a new strain of Rhodobacter, designated Rhodobacter sp . strain PS9 . Rhodobacter sp . strain PS9 is capable of photoorganotrophic growth on a variety of organic compounds, including all of the characteristic volatile organic compounds (VOC) responsible for the odor associated with swine production facilities (J . A . Zahn, A . A . DiSpirito, Y . S . Do, B . E . Brooks, E . E . Copper, and J . L . Hatfield, J . Environ . Qual . 30:624-634, 2001) . The seasonal variations in airborne VOC emitted from waste lagoons showed that there was a 80 to 93% decrease in the concentration of VOC during a photosynthetic bloom . During the height of a bloom, the Rhodobacter sp . strain PS9 population accounted for 10% of the total community and up to 27% of the eubacterial community based on 16S ribosomal DNA signals . Additional observations based on seasonal variations in meteorological, biological, and chemical parameters suggested that the photosynthetic blooms of Rhodobacter sp . strain PS9 were correlated with lagoon water temperature and with the concentrations of sulfate and phosphate . In addition, the photosynthetic blooms of Rhodobacter sp . strain PS9 were inversely correlated with the concentrations of protein and fluoride .
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