Studies on Survival of Bacteria: Rhythmic Response of Microorganisms to Freeze-Drying Additives

Various materials were mixed with suspensions of Serratia marcescens and other organisms. Samples were removed and frozen at intervals after mixing; the number of cells that survived both freeze-drying and exposure to air varied rhythmically as a function of time between mixing and freezing. When assayed before or immediately after drying there were essentially no fluctuations. The response was evident only when these dried samples were exposed to air. In a typical experiment, the number of cells surviving in the sample frozen 30 sec after adding propyl gallate was at least 10 times that in samples frozen either 20 sec earlier or 20 sec later. Other "peaks" in survival were observed at approximately 125 and 450 sec, but the times at which the peaks were observed were not consistent from one experiment to the next. Although we have been unable to control or predict the time at which maxima in resistance occur, we have shown that the phenomenon does occur with Escherichia coli and Saccharomyces cerevisiae as well as with S. marcescens. Furthermore, a rhythmic response also was obtained after a change in pH or cell concentration. It appears that microorganisms respond physiologically and synchronously to changes in their environment, and some of these responses have survival value.     

The biogeochemistry of a north-temperate grassland with native ungulates: Nitrogen dynamics in Yellowstone National Park

Nutrient dynamics of large grassland ecosystems possessing abundant migratory grazers are poorly understood. We examined N cycling on the northern winter range of Yellowstone National Park, home for large herds of free-roaming elk (Cervus elaphus) and bison (Bison bison). Plant and soil N, net N mineralization, and the deposition of ungulate fecal-N were measured at five sites, a ridgetop, mid-slope bench, steep slope, valley-bottom bench, and riparian area, within a watershed from May, 1991 to April, 1992.Results indicated similarities between biogeochemical properties of Yellowstone grassland and other grassland ecosystems: (1) landscape position and soil water affected nutrient dynamics, (2) annual mineralization was positively related to soil N content, and (3) the proportion of soil N mineralized during the year was negatively related to soil C/N.Grazers were a particularly important component of the N budget of this grassland. Estimated rates of N flow from ungulates to the soil ranged from 8.1 to 45.6 kg/ha/yr at the sites (average = 27.0 kg/ha/yr), approximately 4.5 times the amount of N in senescent plants. Rates of nitrogen mineralization for Yellowstone northern range grassland were higher than those measured in other temperate grassland ecosystems, possibly due to grazers promoting N cycling in Yellowstone.     

Mechanisms for oscillation and frequency control in reciprocally inhibitory model neural networks

We describe four different mechanisms that lead to oscillations in a network of two reciprocally inhibitory cells. In two cases (intrinsic release and intrinsic escape) the frequency of the network oscillation is insensitive to the threshold voltage of the synaptic potentials. In the other two cases (synaptic release and synaptic escape) the network frequency is strongly determined by the threshold voltage of the synaptic connections. The distinction between the different mechanisms blurs as the function describing synaptic activation becomes less steep and as the model neurons are removed from the relaxation regime. These mechanisms provide insight into the parameters that control network frequency in motor systems that depend on reciprocal inhibition.     

Constructed floating wetlands: a “safe-to-fail” study with multi-sector participation

The Duwamish River Floating Wetlands project designed, built, and deployed constructed floating wetlands in the estuary of the urban Duwamish River in Seattle, Washington, during the 2019 and 2020 outmigration seasons for juvenile salmon. Using a “safe-to-fail” methodology and adaptive management strategies, these innovative floating wetland prototypes were custom designed to provide the native plants, invertebrates and slow water habitat that juvenile salmon require during their transition from fresh to salt water, and were monitored for these outcomes. This paper will provide insight into the prototype designs, adaptive management strategies and plant performance, and unique public-private-academic-community partnerships that supported 2 years of design and research.     

Recombination-deficient mutants of Salmonella typhimurium are avirulent and sensitive to the oxidative burst of macrophages

Mutations in the genes recA and recBC were constructed in the virulent Salmonella typhimurium strain 14028s. Both the recA and recBC mutants were attenuated in mice. The mutants were also sensitive to killing by macrophages in vitro. The recombination mutants were no longer macrophage sensitive in a variant line of J774 macrophage-like cells that fail to generate superoxide. This suggests that repair of DNA damage by Salmonella is necessary for full virulence in vivo and that the oxidative burst of phagocytes is one source of such DNA damage.     

Design considerations for two-stage enrichment clinical trials

When there is a predictive biomarker, enrichment can focus the clinical trial on a benefiting subpopulation. We describe a two-stage enrichment design, in which the first stage is designed to efficiently estimate a threshold and the second stage is a “phase III-like” trial on the enriched population. The goal of this paper is to explore design issues: sample size in Stages 1 and 2, and re-estimation of the Stage 2 sample size following Stage 1. By treating these as separate trials, we can gain insight into how the predictive nature of the biomarker specifically impacts the sample size. We also show that failure to adequately estimate the threshold can have disastrous consequences in the second stage. While any bivariate model could be used, we assume a continuous outcome and continuous biomarker, described by a bivariate normal model. The correlation coefficient between the outcome and biomarker is the key to understanding the behavior of the design, both for predictive and prognostic biomarkers. Through a series of simulations we illustrate the impact of model misspecification, consequences of poor threshold estimation, and requisite sample sizes that depend on the predictive nature of the biomarker. Such insight should be helpful in understanding and designing enrichment trials.