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Eric A Davidson

Publications and source records attributed to Eric A Davidson.

9 recordsLinked to original sources
PubMed2007

Synthetic RNA circuits.

Natural and engineered RNA 'parts' can perform a variety of functions, including hybridizing to targets, binding ligands and undergoing programmed conformational changes, and catalyzing reactions. These RNA parts can in turn be assembled into synthetic genetic circuits that regulate gene expression by acting either in cis or in trans on mRNAs. As more parts are discovered and engineered, it should be increasingly possible to create synthetic RNA circuits that are able to carry out complex logical operations in cells, either superimposed on or autonomous to extant gene regulation.

Catalysis↗
PubMed2006

Temperature sensitivity of soil carbon decomposition and feedbacks to climate change.

Significantly more carbon is stored in the world's soils--including peatlands, wetlands and permafrost--than is present in the atmosphere. Disagreement exists, however, regarding the effects of climate change on global soil carbon stocks. If carbon stored belowground is transferred to the atmosphere by a warming-induced acceleration of its decomposition, a positive feedback to climate change would occur. Conversely, if increases of plant-derived carbon inputs to soils exceed increases in decomposition, the feedback would be negative. Despite much research, a consensus has not yet emerged on the temperature sensitivity of soil carbon decomposition. Unravelling the feedback effect is particularly difficult, because the diverse soil organic compounds exhibit a wide range of kinetic properties, which determine the intrinsic temperature sensitivity of their decomposition. Moreover, several environmental constraints obscure the intrinsic temperature sensitivity of substrate decomposition, causing lower observed 'apparent' temperature sensitivity, and these constraints may, themselves, be sensitive to climate.

Carbon↗
PubMed2006

The enigma of progress in denitrification research.

Humans have dramatically increased the amount of reactive nitrogen (primarily ammonium, nitrogen oxides, and organically bound N) circulating in the biosphere and atmosphere, creating a wide array of desirable products (e.g., food production) and undesirable consequences (e.g., eutrophication of aquatic ecosystems and air pollution). Only when this reactive N is converted back to the chemically unreactive dinitrogen (N2) form, do these cascading effects of elevated reactive N cease to be of concern. Among the quantitatively most important processes for converting reactive N to N2 gas is the biological process of classical denitrification, in which oxides of nitrogen are used as terminal electron acceptors in anaerobic respiration. This Invited Feature on denitrification includes a series of papers that integrate our current state of knowledge across terrestrial, freshwater, and marine systems on denitrification rates, controlling factors, and methodologies for measuring and modeling denitrification. In this paper, we present an overview of the role of denitrification within the broader N cycle, the environmental and health concerns that have resulted from human alteration of the N cycle, and a brief historical perspective on why denitrification has been so difficult to study. Despite over a century of research on denitrification and numerous recent technological advances, we still lack a comprehensive, quantitative understanding of denitrification rates and controlling factors across ecosystems. Inherent problems of measuring spatially and temporally heterogeneous N2 production under an N2-rich atmosphere account for much of this slow progress, but lack of interdisciplinary communication of research results and methodological developments has also impeded denitrification research. An integrated multidisciplinary approach to denitrification research, from upland terrestrial ecosystems, to small streams, river systems, estuaries, and continental shelf ecosystems, and to the open ocean, may yield new insights into denitrification across landscapes and waterscapes.

Environmental Pollutants↗
PubMed2005

Synthetic biology: engineering Escherichia coli to see light.

We have designed a bacterial system that is switched between different states by red light. The system consists of a synthetic sensor kinase that allows a lawn of bacteria to function as a biological film, such that the projection of a pattern of light on to the bacteria produces a high-definition (about 100 megapixels per square inch), two-dimensional chemical image. This spatial control of bacterial gene expression could be used to 'print' complex biological materials, for example, and to investigate signalling pathways through precise spatial and temporal control of their phosphorylation steps.

Agar↗
PubMed2005

Engineering regulatory RNAs.

RNA has long been a favoured medium for in vitro evolution and engineering. Functional RNAs produced in vitro can bind small molecules (aptamers), possess catalytic activity (ribozymes) or do both (aptazymes). A plethora of recent work has shown similar strategies used naturally for gene regulation in bacteria. Interest in these natural systems has inspired an effort to engineer and evolve this activity in vivo. A recent paper by Isaacs et al. describes the engineering and in vivo activity of a small RNA that removes translation inhibition by binding the 5' untranslated region of its target mRNA and making the ribosome-binding site accessible.

Animals↗
PubMed2003

A comparison of manual and automated systems for soil CO2 flux measurements: trade-offs between spatial and temporal resolution.

Soil respiration is affected by distributions of roots and soil carbon substrates and by temperature and soil water content, all of which vary spatially and temporally. The objective of this paper was to compare a manual system for measuring soil respiration in a temperate forest, which had a greater spatial distribution of measurements (n=12), but poorer temporal resolution (once per week), with an automated system which had poorer spatial distribution (n=3) but superior temporal frequency of measurements (hourly). Soil respiration was measured between 18 June and 21 August, 2002, at the Harvard Forest in central Massachusetts, USA. The fluxes measured within 1 h of each other by these systems were not significantly different. However, extrapolations of the mid-morning manual measurements to daily flux values were consistently lower (averaging 13% lower) than the daily estimates obtained from summing the 24 hourly measurements of the automated system. On the other hand, seasonal flux estimates obtained by interpolating between weekly manual sampling dates or by summing the hourly automated measurements were nearly identical. Underestimates by interpolated weekly manual measurements during some periods were cancelled by overestimates during other periods. Hence, a weekly sampling schedule may be sufficient to capture the most important variation of seasonal efflux of CO(2) from the soil. The larger number of chambers that could be measured with the manual system (larger n) resulted in a smaller 95% confidence interval for characterizing spatial variability within the study area on most dates. However, the greater sampling frequency of the automated system revealed rapid responses of soil respiration to wetting events, which permitted better empirical modelling of the effects of soil temperature and moisture on soil respiration than could have been achieved with the manual sampling system. Most of the positive residuals of a function that predicts soil respiration based on temperature were from fluxes measured within 12 h of a rain event, and the residuals were positively correlated with water content of the O horizon. The automated system also demonstrated that Q(10) values calculated for diel variation in soil temperature over a few days were not significantly different than Q(10) values for the entire 3 month summer sampling period. In summary, a manual system of numerous, spatially well-distributed flux chambers measured on a weekly basis may be adequate for measuring seasonal fluxes and may maximize confidence in the characterization of spatial variance. The high temporal frequency of measurements afforded by automation greatly improves the ability to measure and model the effects of rapidly varying water content and temperature. When the two approaches can be combined, the temporal representativeness of the manual measurements can be tested with the automated measurements and the spatial representativeness of the automated measurements can be tested by the manual measurements.

Carbon Dioxide↗
PubMed2002

Automated acquisition of aptamer sequences.

While the in vitro selection of nucleic acid binding species (aptamers) requires numerous liquid-handling steps, these steps are relatively straightforward and the overall process is therefore amenable to automation. Here we demonstrate that automated selection techniques are capable of generating aptamers against a number of diverse protein targets. Automated selection techniques can be integrated with automated analytical methods, including sequencing, determination of binding constants, and structural analysis. The methods that have so far been developed can be further multiplexed, and it should soon be possible to attempt the selection of aptamers against organismal proteomes or metabolomes.

Automation↗