Vegetation and climate controls on potential CO2, DOC and DON production in northern latitude soils

Climatic change may influence decomposition dynamics in arctic and boreal ecosystems, affecting both atmospheric CO₂ levels, and the flux of dissolved organic carbon (DOC) and dissolved organic nitrogen (DON) to aquatic systems. In this study, we investigated landscape‐scale controls on potential production of these compounds using a one‐year laboratory incubation at two temperatures (10° and 30 °C). We measured the release of CO₂, DOC and DON from tundra soils collected from a variety of vegetation types and climatic regimes: tussock tundra at four sites along a latitudinal gradient from the interior to the north slope of Alaska, and soils from additional vegetation types at two of those sites (upland spruce at Fairbanks, and wet sedge and shrub tundra at Toolik Lake in northern Alaska). Vegetation type strongly influenced carbon fluxes. The highest CO₂ and DOC release at the high incubation temperature occurred in the soils of shrub tundra communities. Tussock tundra soils exhibited the next highest DOC fluxes followed by spruce and wet sedge tundra soils, respectively. Of the fluxes, CO₂ showed the greatest sensitivity to incubation temperatures and vegetation type, followed by DOC. DON fluxes were less variable. Total CO₂ and total DOC release were positively correlated, with DOC fluxes approximately 10% of total CO₂ fluxes. The ratio of CO₂ production to DOC release varied significantly across vegetation types with Tussock soils producing an average of four times as much CO₂ per unit DOC released compared to Spruce soils from the Fairbanks site. Sites in this study released 80–370 mg CO₂‐C g soil C^?1 and 5–46 mg DOC g soil C^?1 at high temperatures. The magnitude of these fluxes indicates that arctic carbon pools contain a large proportion of labile carbon that could be easily decomposed given optimal conditions. The size of this labile pool ranged between 9 and 41% of soil carbon on a g soil C basis, with most variation related to vegetation type rather than climate.     

A billion-fold range in acidity for the solvent-exposed amides of Pyrococcus furiosus rubredoxin

The exchange rates of the static solvent-accessible amide hydrogens of Pyrococcus furiosus rubredoxin range from near the diffusion-limited rate to a billion-fold slower for the non-hydrogen-bonded Val 38 (eubacterial numbering). Hydrogen exchange directly monitors the kinetic acidity of the peptide nitrogen. Electrostatic solvation free energies were calculated by Poisson-Boltzmann methods for the individual peptide anions that form during the hydroxide-catalyzed exchange reaction to examine how well the predicted thermodynamic acidities match the experimentally determined kinetic acidities. With the exception of the Ile 12 amide, the differential exchange rate constant for each solvent-exposed amide proton that is not hydrogen bonded to a backbone carbonyl can be predicted within a factor of 6 (10 (0.78)) root-mean-square deviation (rmsd) using the CHARMM22 electrostatic parameter set and an internal dielectric value of 3. Under equivalent conditions, the PARSE parameter set yields a larger rmsd value of 1.28 pH units, while the AMBER parm99 parameter set resulted in a considerably poorer correlation. Either increasing the internal dielectric value to 4 or reducing it to a value of 2 significantly degrades the quality of the prediction. Assigning the excess charge of the peptide anion equally between the peptide nitrogen and the carbonyl oxygen also reduces the correlation to the experimental data. These continuum electrostatic calculations were further analyzed to characterize the specific structural elements that appear to be responsible for the wide range of peptide acidities observed for these solvent-exposed amides. The striking heterogeneity in the potential at sites along the protein-solvent interface should prove germane to the ongoing challenge of quantifying the contribution that electrostatic interactions make to the catalytic acceleration achieved by enzymes.     

Mosquito transgenesis: what is the fitness cost?

The generation of transgenic mosquitoes with a minimal fitness load is a prerequisite for the success of strategies for controlling mosquito-borne diseases using transgenic insects. It is important to assemble as much information as possible on this subject because realistic estimates of transgene fitness costs are essential for modeling and planning release strategies. Transgenic mosquitoes must have minimal fitness costs, because such costs would reduce the effectiveness of the genetic drive mechanisms that are used to introduce the transgenes into field mosquito populations. Several factors affect fitness of transgenic mosquitoes, including the potential negative effect of transgene products and insertional mutagenesis. Studies to assess fitness of transgenic mosquitoes in the field (as opposed to the laboratory) are still needed.     

Ku and DNA-dependent Protein Kinase Dynamic Conformations and Assembly Regulate DNA Binding and the Initial Non-homologous End Joining Complex

DNA double strand break (DSB) repair by non-homologous end joining (NHEJ) is initiated by DSB detection by Ku70/80 (Ku) and DNA-dependent protein kinase catalytic subunit (DNA-PKcs) recruitment, which promotes pathway progression through poorly defined mechanisms. Here, Ku and DNA-PKcs solution structures alone and in complex with DNA, defined by x-ray scattering, reveal major structural reorganizations that choreograph NHEJ initiation. The Ku80 C-terminal region forms a flexible arm that extends from the DNA-binding core to recruit and retain DNA-PKcs at DSBs. Furthermore, Ku- and DNA-promoted assembly of a DNA-PKcs dimer facilitates trans-autophosphorylation at the DSB. The resulting site-specific autophosphorylation induces a large conformational change that opens DNA-PKcs and promotes its release from DNA ends. These results show how protein and DNA interactions initiate large Ku and DNA-PKcs rearrangements to control DNA-PK biological functions as a macromolecular machine orchestrating assembly and disassembly of the initial NHEJ complex on DNA.     

Effects of fine sediment inputs from a logging road on stream insect communities:a large-scale experimental approach in a Canadian headwater stream

A forest headwater stream was manipulated (logging road-crossing amended) to induce fine sediment inputs. Benthic inorganic sediment concentrations .particles 1.5–250 μm increased from a 2-year pre-disturbance average of about 800 g m^–2 to over 5000 g m^–2 that persisted for 3 years. Aquatic insect communities were examined over the 5-year study period in the manipulated and nearby reference streams. Overall, the effects of the fine sediment increases on aquatic insect communities were minimal. There were no significant effects of sedimentation on total aquatic insect abundance or biomass. An index of multivariate dispersion gave no evidence of community stress at the manipulated site. Multivariate ordination plots and time trends among univariate community metrics indicated only subtle changes in community structure. Among the univariate metrics (16 time series analyses in total), six gave evidence of a sediment impact on aquatic insect communities. Of those, the clearest indications of an effect were small reductions in diversity and richness of spring communities. These resulted from a significant decline in the proportion of spring shredders, accompanied by a significant increase in the percent Chironomidae. This large-scale experimental approach integrated the realism of a whole-stream study with the control of a manipulative study by including pre-manipulation measurements and excluding other confounding catchment disturbances. In this regard, it may provide a more realistic measure of benthic community level responses to sedimentation in streams at a magnitude associated with logging activity than many previous studies.     

1alpha,25(OH)2D3 regulates chondrocyte matrix vesicle protein kinase C (PKC) directly via G-protein-dependent mechanisms and indirectly via incorporation of PKC during matrix vesicle biogenesis.

Matrix vesicles are extracellular organelles involved in mineral formation that are regulated by 1alpha,25(OH)(2)D(3). Prior studies have shown that protein kinase C (PKC) activity is involved in mediating the effects of 1alpha,25(OH)(2)D(3) in both matrix vesicles and plasma membranes. Here, we examined the regulation of matrix vesicle PKC by 1alpha,25(OH)(2)D(3) during biogenesis and after deposition in the matrix. When growth zone costochondral chondrocytes were treated for 9 min with 1alpha,25(OH)(2)D(3), PKCzeta in matrix vesicles was inhibited, while PKCalpha in plasma membranes was increased. In contrast, after treatment for 12 or 24 h, PKCzeta in matrix vesicles was increased, while PKCalpha in plasma membranes was unchanged. The effect of 1alpha,25(OH)(2)D(3) was stereospecific and metabolite-specific. Monensin blocked the increase in matrix vesicle PKC after 24 h, suggesting the secosteroid-regulated packaging of PKC. In addition, the 1alpha,25(OH)(2)D(3) membrane vitamin D receptor (1,25-mVDR) was involved, since a specific antibody blocked the 1alpha,25(OH)(2)D(3)-dependent changes in PKC after both long and short treatment times. In contrast, antibodies to annexin II had no effect, and there was no evidence for the presence of the nuclear VDR on Western blots. To investigate the signaling pathways involved in regulating matrix vesicle PKC activity after biosynthesis, matrix vesicles were isolated and then treated for 9 min with 1alpha,25(OH)(2)D(3) in the presence and absence of specific inhibitors. Inhibition of phosphatidylinositol-phospholipase C, phospholipase D, or G(i)/G(s) had no effect. However, inhibition of G(q) blocked the effect of 1alpha,25(OH)(2)D(3). The rapid effect of 1alpha,25(OH)(2)D(3) also involved the 1,25-mVDR. Moreover, arachidonic acid was found to stimulate PKC when added directly to isolated matrix vesicles. These results indicate that matrix vesicle PKC is regulated by 1alpha,25(OH)(2)D(3) at three levels: 1) during matrix vesicle biogenesis; 2) through direct action on the membrane; and 3) through production of other factors such as arachidonic acid.