Characterization of an activity from the strict anaerobe Roseburia cecicola that degrades DNA when exposed to air

Roseburia spp.: a marker of health?

The genus Roseburia consists of obligate Gram-positive anaerobic bacteria that are slightly curved, rod-shaped and motile by means of multiple subterminal flagella. It includes five species: Roseburia intestinalis, R. hominis, R. inulinivorans, R. faecis and R. cecicola. Gut Roseburia spp. metabolize dietary components that stimulate their proliferation and metabolic activities. They are part of commensal bacteria producing short-chain fatty acids, especially butyrate, affecting colonic motility, immunity maintenance and anti-inflammatory properties. Modification in Roseburia spp. representation may affect various metabolic pathways and is associated with several diseases (including irritable bowel syndrome, obesity, Type 2 diabetes, nervous system conditions and allergies). Roseburia spp. could also serve as biomarkers for symptomatic pathologies (e.g., gallstone formation) or as probiotics for restoration of beneficial flora.

Composting: A Potentially Safe Process for Disposal of Genetically Modified Organisms

The widespread use of genetically modified organisms (GMOs) may result in the release of GMOs into the environment. The potential risks regarding their use and implementation of disposal methods, especially the possibility of novel genes from GMOs being transferred to natural organisms, need to be evaluated and better understood. There is an increasingly accepted public view that GMO products introduced into the environment should be degradable and should disappear after a limited period of time. Due to the risk of possible horizontal gene transfer, disposal methods for GMOs need to address destruction of both the organism and the genetic material. During the last two decades, we have developed a greater understanding of the biochemical, microbiological and molecular concepts of the composting process, such that maximum decomposition may be achieved in the shortest time with minimal negative impacts to the environment. The conditions created in a properly managed composting process environment may help in destroying GMOs and their genes, thereby reducing the risk of the spread of genetic material. When considering composting as a potential method for the disposal of GMOs, the establishment of controlled conditions providing an essentially homogenous environment appears to be an important requirement. An evaluation of composting as a safe option for disposal of GMOs is provided in this review.

Bovine articular chondrocyte function in vitro depends upon oxygen tension

Articular cartilage is a physiologically hypoxic tissue with a proposed gradient of oxygen tension ranging from about 10% oxygen at the cartilage surface to less than 1% in the deepest layers. The position of the chondrocyte within this gradient may modulate the cell's behavior and phenotype. Moreover, the oxygen gradient is likely to be disturbed during joint diseases in which the pO(2)of the synovial fluid declines which may cause changes in chondrocyte behavior and gene expression. Thus, there is a need to understand the chondrocyte's response to different oxygen tensions. We compared the behavior of bovine articular chondrocytes cultured in alginate beads for 7 days in medium maintained at <0.1, 5, 10 or 20% oxygen. The chondrocytes' survival, differentiation, cell division, viability and matrix production were assessed at each oxygen tension and rRNA and mRNA abundance was measured. Chondrocytes were able to survive under all oxygen tensions for at least 7 days but cells cultured under anoxic conditions were metabolically less active than cells maintained in higher oxygen tensions; this was associated with a decrease in matrix production. In <0.1% oxygen there was a marked decrease in rRNA and mRNA abundance in the cells. There were no differences in cell division or differentiation between any oxygen tensions. These findings indicate that articular chondrocytes can be cultured successfully in the pO(2)range in which they are thought to exist in vivo (5-10% pO(2)) and are fully active under these conditions. Under anoxic conditions (<0.1% pO(2)) function is severely compromised.

Identification and characterization of nuclease activities in anaerobic environmental samples

DNA-degrading activity from anaerobic samples of bovine ruminal fluid, primary anaerobic digestor wastewater, freshwater sediments, and marine sediments was observed in the presence of 5 mM EDTA. Nuclease activity experiments involved exposing salmon chromosomal DNA to the environmental samples in 50 mM pH 7.2 buffer, incubating at 37°C, and subjecting the products to electrophoresis. The same stock and concentration of EDTA used in these assays (5 mM) completely inhibited commercial grade DNase. Nuclease activity in two of the samples, ruminal fluid and wastewater, was further characterized. DNA degradation in the ruminal sample was significantly reduced when EDTA or citrate concentrations were increased to 50 mM or above. DNA degradation activity in ruminal fluid was associated with material that passed through a 0.22-µm filter, but wastewater activity was associated with material retained by a 3-µm filter. Degradation activity in the wastewater was resistant to heat pretreatment, whereas the rumen activity was heat-labile (70°C, 60 min). These results demonstrated the biochemical complexity of these two environments and that high molecular weight DNA has a short half-life in these anaerobic environments.Key words: nucleic acid degradation, ruminal fluid, wastewater.

Desiccation tolerance of prokaryotes

The removal of cell-bound water through air drying and the addition of water to air-dried cells are forces that have played a pivotal role in the evolution of the prokaryotes. In bacterial cells that have been subjected to air drying, the evaporation of free cytoplasmic water (Vf) can be instantaneous, and an equilibrium between cell-bound water (Vb) and the environmental water (vapor) potential (psi wv) may be achieved rapidly. In the air-dried state some bacteria survive only for seconds whereas others can tolerate desiccation for thousands, perhaps millions, of years. The desiccated (anhydrobiotic) cell is characterized by its singular lack of water--with contents as low as 0.02 g of H2O g (dry weight)-1. At these levels the monolayer coverage by water of macromolecules, including DNA and proteins, is disturbed. As a consequence the mechanisms that confer desiccation tolerance upon air-dried bacteria are markedly different from those, such as the mechanism of preferential exclusion of compatible solutes, that preserve the integrity of salt-, osmotically, and freeze-thaw-stressed cells. Desiccation tolerance reflects a complex array of interactions at the structural, physiological, and molecular levels. Many of the mechanisms remain cryptic, but it is clear that they involve interactions, such as those between proteins and co-solvents, that derive from the unique properties of the water molecule. A water replacement hypothesis accounts for how the nonreducing disaccharides trehalose and sucrose preserve the integrity of membranes and proteins. Nevertheless, we have virtually no insight into the state of the cytoplasm of an air-dried cell. There is no evidence for any obvious adaptations of proteins that can counter the effects of air drying or for the occurrence of any proteins that provide a direct and a tangible contribution to cell stability. Among the prokaryotes that can exist as anhydrobiotic cells, the cyanobacteria have a marked capacity to do so. One form, Nostoc commune, encompasses a number of the features that appear to be critical to the withstanding of a long-term water deficit, including the elaboration of a conspicuous extracellular glycan, synthesis of abundant UV-absorbing pigments, and maintenance of protein stability and structural integrity. There are indications of a growing technology for air-dried cells and enzymes. Paradoxically, desiccation tolerance of bacteria has virtually been ignored for the past quarter century. The present review considers what is known, and what is not known, about desiccation, a phenomenon that impinges upon every facet of the distributions and activities of prokaryotic cells.

Desiccation tolerance of prokaryotes

The removal of cell-bound water through air drying and the addition of water to air-dried cells are forces that have played a pivotal role in the evolution of the prokaryotes. In bacterial cells that have been subjected to air drying, the evaporation of free cytoplasmic water (Vf) can be instantaneous, and an equilibrium between cell-bound water (Vb) and the environmental water (vapor) potential (psi wv) may be achieved rapidly. In the air-dried state some bacteria survive only for seconds whereas others can tolerate desiccation for thousands, perhaps millions, of years. The desiccated (anhydrobiotic) cell is characterized by its singular lack of water--with contents as low as 0.02 g of H2O g (dry weight)-1. At these levels the monolayer coverage by water of macromolecules, including DNA and proteins, is disturbed. As a consequence the mechanisms that confer desiccation tolerance upon air-dried bacteria are markedly different from those, such as the mechanism of preferential exclusion of compatible solutes, that preserve the integrity of salt-, osmotically, and freeze-thaw-stressed cells. Desiccation tolerance reflects a complex array of interactions at the structural, physiological, and molecular levels. Many of the mechanisms remain cryptic, but it is clear that they involve interactions, such as those between proteins and co-solvents, that derive from the unique properties of the water molecule. A water replacement hypothesis accounts for how the nonreducing disaccharides trehalose and sucrose preserve the integrity of membranes and proteins. Nevertheless, we have virtually no insight into the state of the cytoplasm of an air-dried cell. There is no evidence for any obvious adaptations of proteins that can counter the effects of air drying or for the occurrence of any proteins that provide a direct and a tangible contribution to cell stability. Among the prokaryotes that can exist as anhydrobiotic cells, the cyanobacteria have a marked capacity to do so. One form, Nostoc commune, encompasses a number of the features that appear to be critical to the withstanding of a long-term water deficit, including the elaboration of a conspicuous extracellular glycan, synthesis of abundant UV-absorbing pigments, and maintenance of protein stability and structural integrity. There are indications of a growing technology for air-dried cells and enzymes. Paradoxically, desiccation tolerance of bacteria has virtually been ignored for the past quarter century. The present review considers what is known, and what is not known, about desiccation, a phenomenon that impinges upon every facet of the distributions and activities of prokaryotic cells.