Fine-root respiration in a loblolly pine (Pinus taeda L.) forest exposed to elevated CO2 and N fertilization

Forest ecosystems release large amounts of carbon to the atmosphere from fine-root respiration (R(r)), but the control of this flux and its temperature sensitivity (Q(10)) are poorly understood. We attempted to: (1) identify the factors limiting this flux using additions of glucose and an electron transport uncoupler (carbonyl cyanide m-chlorophenylhydrazone); and (2) improve yearly estimates of R(r) by directly measuring its Q(10)in situ using temperature-controlled cuvettes buried around intact, attached roots. The proximal limits of R(r) of loblolly pine (Pinus taeda L.) trees exposed to free-air CO(2) enrichment (FACE) and N fertilization were seasonally variable; enzyme capacity limited R(r) in the winter, and a combination of substrate supply and adenylate availability limited R(r) in summer months. The limiting factors of R(r) were not affected by elevated CO(2) or N fertilization. Elevated CO(2 )increased annual stand-level R(r) by 34% whereas the combination of elevated CO(2) and N fertilization reduced R(r) by 40%. Measurements of in situ R(r) with high temporal resolution detected diel patterns that were correlated with canopy photosynthesis with a lag of 1 d or less as measured by eddy covariance, indicating a dynamic link between canopy photosynthesis and root respiration. These results suggest that R(r) is coupled to daily canopy photosynthesis and increases with carbon allocation below ground.     

CyclinA2-Cyclin-dependent Kinase Regulates SAMHD1 Protein Phosphohydrolase Domain

SAMHD1 is a nuclear deoxyribonucleoside triphosphate triphosphohydrolase that contributes to the control of cellular deoxyribonucleoside triphosphate (dNTP) pool sizes through dNTP hydrolysis and modulates the innate immune response to viruses. CyclinA2-CDK1/2 phosphorylates SAMHD1 at Thr-592, but how this modification controls SAMHD1 functions in proliferating cells is not known. Here, we show that SAMHD1 levels remain relatively unchanged during the cell division cycle in primary human T lymphocytes and in monocytic cell lines. Inactivation of the bipartite cyclinA2-CDK-binding site in the SAMHD1 C terminus described herein abolished SAMHD1 phosphorylation on Thr-592 during S and G₂ phases thus interfering with DNA replication and progression of cells through S phase. The effects exerted by Thr-592 phosphorylation-defective SAMHD1 mutants were associated with activation of DNA damage checkpoint and depletion of dNTP concentrations to levels lower than those seen upon expression of wild type SAMHD1 protein. These disruptive effects were relieved by either mutation of the catalytic residues of the SAMHD1 phosphohydrolase domain or by a Thr-592 phosphomimetic mutation, thus linking the Thr-592 phosphorylation state to the control of SAMHD1 dNTPase activity. Our findings support a model in which phosphorylation of Thr-592 by cyclinA2-CDK down-modulates, but does not inactivate, SAMHD1 dNTPase in S phase, thereby fine-tuning SAMHD1 control of dNTP levels during DNA replication.     

Insect herbivory in an intact forest understory under experimental CO2 enrichment

Human-induced increases in atmospheric CO₂ concentration have the potential to alter the chemical composition of plant tissue, and thereby affect the amount of tissue consumed by herbivorous arthropods. At the Duke Forest free-air concentration enrichment (FACE) facility in North Carolina (FACTS–1 research facility), we measured the amount of leaf tissue damaged by insects and other herbivorous arthropods during two growing seasons in a deciduous forest understory continuously exposed to ambient (360 l l^–1) and elevated (~560 µl l^–1) CO₂ conditions. In 1999, there was a significant interaction between CO₂ and species such that winged elm (Ulmus alata) showed lower herbivory in elevated CO₂ plots, whereas red maple (Acer rubra) and sweetgum (Liquidambar styraciflua) did not. In 2000, our results did not achieve statistical significance but the magnitude of the result was consistent with the 1999 results. In 1999 and 2000, we found a decline (10–46%) in community-level herbivory in elevated CO₂ plots driven primarily by reductions in herbivory on elm. The major contribution to total leaf damage was from missing tissue (66% of the damaged tissue), with galls, skeletonized, and discolored tissue making smaller contributions. It is unclear whether the decline in leaf damage is a result of altered insect populations, altered feeding, or a combination. We were not able to quantify insect populations, and our measurements did not resolve an effect of elevated CO₂ on leaf chemical composition (total nitrogen, carbon, C/N, sugars, phenolics, starch). Despite predictions from a large number of single-species studies that herbivory may increase under elevated CO₂, we have found a decrease in herbivory in a naturally established forest understory exposed to a full suite of insect herbivores and their predators.     

Respiratory oxygen uptake is not decreased by an instantaneous elevation of [CO2], but is increased with long-term growth in the field at elevated [CO2

Averaged across many previous investigations, doubling the CO2 concentration ([CO2]) has frequently been reported to cause an instantaneous reduction of leaf dark respiration measured as CO2 efflux. No known mechanism accounts for this effect, and four recent studies have shown that the measurement of respiratory CO2 efflux is prone to experimental artifacts that could account for the reported response. Here, these artifacts are avoided by use of a high-resolution dual channel oxygen analyzer within an open gas exchange system to measure respiratory O2 uptake in normal air. Leaf O2 uptake was determined in response to instantaneous elevation of [CO2] in nine contrasting species and to long-term elevation in seven species from four field experiments. Over six hundred separate measurements of respiration failed to reveal any decrease in respiratory O2 uptake with an instantaneous increase in [CO2]. Respiration was found insensitive not only to doubling [CO2], but also to a 5-fold increase and to decrease to zero. Using a wide range of species and conditions, we confirm earlier reports that inhibition of respiration by instantaneous elevation of [CO2] is likely an experimental artifact. Instead of the expected decrease in respiration per unit leaf area in response to long-term growth in the field at elevated [CO2], there was a significant increase of 11% and 7% on an area and mass basis, respectively, averaged across all experiments. The findings suggest that leaf dark respiration will increase not decrease as atmospheric [CO2] rises.     

Domain structure of the simian virus 40 core origin of replication.

The simian virus 40 core origin of replication consists of nucleotides 5211 through 31. These 64 base pairs contain three functional domains with strict sequence requirements and two spacer regions with relaxed sequence specificity but precise positional constraints. The early domain extends for 10 contiguous base pairs between nucleotides 5211 and 5220. A 9-base pair spacer from sequences 5221 through 5229 separates the early domain from the 23-base pair central palindrome that directs the binding of T antigen. The late end of the core between nucleotides 12 and 31 also contains spacer and sequence-specific functions that are not yet completely mapped. We propose that the sequence-specific domains are interaction sites for viral and cellular proteins, determinants of DNA conformation, or both. The spacers would position these signals at required distances and rotations relative to one another.     

The adenine-thymine domain of the simian virus 40 core origin directs DNA bending and coordinately regulates DNA replication.

The simian virus 40 origin of replication contains a 20-base-pair adenine-thymine-rich segment with the sequence 5'-TGCATAAATAAAAAAAATTA-3'. The continuous tract of eight adenines is highly conserved among polyomaviruses. We used single-base substitutions to map structural and functional features of this DNA. Mutations in the AAA and AAAAAAAATT sequences significantly reduce DNA replication and thus identify two sequence-specific functional domains or a single domain with two parts. The AAAAAAAATT sequence also determines a DNA conformation that is characteristic of DNA bending. Single-base mutations in this domain change the degree of net bending, presumably by altering the length and location of the bending sequence. Thus, DNA bending in the correct conformation and location may be a structural signal for replication in polyomavirus origins and perhaps in other origins of replication with consecutive runs of adenines. The first five base pairs (TGCAT) of the 20-base-pair segment and the T between the AAA and AAAAAAAATT domains serve a sequence-independent function that may establish proper spacing within the core origin.     

Gap filling strategies and error in estimating annual soil respiration

Soil respiration (R_soil) is one of the largest CO₂ fluxes in the global carbon (C) cycle. Estimation of annual R_soil requires extrapolation of survey measurements or gap filling of automated records to produce a complete time series. Although many gap filling methodologies have been employed, there is no standardized procedure for producing defensible estimates of annual R_soil. Here, we test the reliability of nine different gap filling techniques by inserting artificial gaps into 20 automated R_soil records and comparing gap filling R_soil estimates of each technique to measured values. We show that although the most commonly used techniques do not, on average, produce large systematic biases, gap filling accuracy may be significantly improved through application of the most reliable methods. All methods performed best at lower gap fractions and had relatively high, systematic errors for simulated survey measurements. Overall, the most accurate technique estimated R_soil based on the soil temperature dependence of R_soil by assuming constant temperature sensitivity and linearly interpolating reference respiration (R_soil at 10 °C) across gaps. The linear interpolation method was the second best‐performing method. In contrast, estimating R_soil based on a single annual R_soil – T_soil relationship, which is currently the most commonly used technique, was among the most poorly‐performing methods. Thus, our analysis demonstrates that gap filling accuracy may be improved substantially without sacrificing computational simplicity. Improved and standardized techniques for estimation of annual R_soil will be valuable for understanding the role of R_soil in the global C cycle.     

Ammonia volatilization during drought in perennial C4 grasses of tallgrass prairie

We measured foliar NH₃ volatilization as part of our study of the decrease (up to 40%) in shoot N concentration during drought in three perennial C₄ grasses of tallgrass prairie. Volatilization of recently expanded leaves was quantified using cuvettes and acid traps for Spartina pectinata, Andropogon gerardii, and Schizachyrium scoparium, a mesic, intermediate, and xeric species, respectively. In general, volatilization decreased during drought, approaching zero as stomates closed, and increased with plant N status and drought tolerance. Prior to drought, NH₃ volatilization was greater in xeric than mesic species (179 and 131 vs. 115 ng m^-2 s^-1 for individual leaves of S. scoparium and A. gerardii vs. Sp. pectinata). During a 2–3 week drought, whole-shoot volatile N losses can exceed 5% of total plant N in these species, accounting for 2–10% of the decrease in shoot percent N (again, xeric > mesic). Drought-induced N retranslocation of shoot N to roots and rhizomes is responsible for c. 63% of the decrease in percent N in Sp. pectinata, 28% in A. gerardii, and 8% in S. scoparium. The remainder of the decrease in percent N is attributable to growth dilution of existing shoot N, accounting for 34, 65, and 87% of the decrease in shoot percent N during drought in Sp. pectinata, A. gerardii, and S. scoparium, respectively. Thus, the relative importance of volatilization, retranslocation, and dilution in decreasing foliar percent N during drought in prairie grasses is species dependent and related to drought tolerance.     

UmuD2 Inhibits a Non-covalent Step during DinB-mediated Template Slippage on Homopolymeric Nucleotide Runs

Escherichia coli DinB (DNA polymerase IV) possesses an enzyme architecture resulting in specialized lesion bypass function and the potential for creating −1 frameshifts in homopolymeric nucleotide runs. We have previously shown that the mutagenic potential of DinB is regulated by the DNA damage response protein UmuD₂. In the current study, we employ a pre-steady-state fluorescence approach to gain a mechanistic understanding of DinB regulation by UmuD₂. Our results suggest that DinB, like its mammalian and archaeal orthologs, uses a template slippage mechanism to create single base deletions on homopolymeric runs. With 2-aminopurine as a fluorescent reporter in the DNA substrate, the template slippage reaction results in a prechemistry fluorescence change that is inhibited by UmuD₂. We propose a model in which DNA templates containing homopolymeric nucleotide runs, when bound to DinB, are in an equilibrium between non-slipped and slipped conformations. UmuD₂, when bound to DinB, displaces the equilibrium in favor of the non-slipped conformation, thereby preventing frameshifting and potentially enhancing DinB activity on non-slipped substrates.