Q/R site interactions with the M3 helix in GluK2 kainate receptor channels revealed by thermodynamic mutant cycles

RNA editing at the Q/R site near the apex of the pore loop of AMPA and kainate receptors controls a diverse array of channel properties, including ion selectivity and unitary conductance and susceptibility to inhibition by polyamines and cis-unsaturated fatty acids, as well as subunit assembly into tetramers and regulation by auxiliary subunits. How these different aspects of channel function are all determined by a single amino acid substitution remains poorly understood; however, several lines of evidence suggest that interaction between the pore helix (M2) and adjacent segments of the transmembrane inner (M3) and outer (M1) helices may be involved. In the present study, we have used double mutant cycle analysis to test for energetic coupling between the Q/R site residue and amino acid side chains along the M3 helix. Our results demonstrate interaction with several M3 locations and particularly strong coupling to substitution for L614 at the level of the central cavity. In this location, replacement with smaller side chains completely and selectively reverses the effect of fatty acids on gating of edited channels, converting strong inhibition of wild-type GluK2(R) to nearly 10-fold potentiation of GluK2(R) L614A.     

Nutrient mobilization and processing in Sonoran desert riparian soils following artificial re-wetting

Research in river-floodplain systems has emphasized the importance of nutrient delivery by floodwaters, but the mechanisms by which floods make nutrients available are rarely evaluated. Using a laboratory re-wetting experiment, we evaluated the alternative hypotheses that increased nutrient concentrations in riparian groundwater during flash floods are due to (H1) elevated nutrient concentrations in surface floodwaters entering the riparian zone or (H2) re-mobilization of nutrients from riparian soils. We sampled soils from the riparian zone of a 400m reach of Sycamore Creek, AZ. Two sub-samples from each soil were re-wetted with a solution that mimicked the chemistry of floodwaters, with one sub-sample simultaneously treated with a biocide. We also measured structural characteristics of soils (texture, organic matter, moisture, and extractable nutrients) to investigate relationships between these characteristics and response to re-wetting. Riparian soils exhibited considerable variation in physical and chemical structure. Soil organic matter, moisture, and texture co-varied among samples. Re-wetting increased concentrations of nitrate and ammonium, and decreased SRP, relative to initial concentrations. Live soils were significantly lower in NO3-and SRP than biocide-treated samples. Extractable DIN pools were the best predictors of mobilization, and soil organic matter was strongly correlated with nitrate losses, probably via its relationship with microbial uptake. Nutrient mobilization and processing also varied considerably with depth, lateral position, and among plots. We estimate that 70–80% of N in riparian groundwater during flash floods is re-mobilized from riparian soils, but are unable to reject the hypothesis that flood inputs may be important sources of nutrients to riparian soils over longer time scales.     

Transport of Carbon and Nitrogen Between Litter and Soil Organic Matter in a Northern Hardwood Forest

We used sugar maple litter double-labeled with ¹³C and ¹⁵N to quantify fluxes of carbon (C) and nitrogen (N) between litter and soil in a northern hardwood forest and the retention of litter C and N in soil. Two cohorts of litter were compared, one in which the label was preferentially incorporated into non-structural tissue and the other structural tissue. Loss of ¹³C from this litter generally followed dry mass and total C loss whereas loss of ¹⁵N (20–30% in 1 year) was accompanied by large increases of total N content of this decaying litter (26–32%). Enrichment of ¹³C and ¹⁵N was detected in soil down to 10–15 cm depth. After 6 months of decay (November–May) 36–43% of the ¹³C released from the litter was recovered in the soil, with no differences between the structural and non-structural labeled litter. By October the percentage recovery of litter ¹³C in soil was much lower (16%). The C released from litter and remaining in soil organic matter (SOM) after 1 year represented over 30 g C m⁻² y⁻¹ of SOM accumulation. Recovery of litter ¹⁵N in soil was much higher than for C (over 90%) and in May ¹⁵N was mostly in organic horizons whereas by October it was mostly in 0–10 cm mineral soil. A small proportion of this N was recovered as inorganic N (2–6%). Recovery of ¹⁵N in microbial biomass was higher in May (13–15%) than in October (about 5%). The C:N ratio of the SOM and microbial biomass derived from the labeled litter was much higher for the structural than the non-structural litter and for the forest floor than mineral SOM, illustrating the interactive role of substrates and microbial activity in regulating the C:N stoichiometry of forest SOM formation. These results for a forest ecosystem long exposed to chronically high atmospheric N deposition (ca. 10 kg N ha⁻¹ y⁻¹) suggest possible mechanisms of N retention in soil: increased organic N leaching from fresh litter and reduced fungal transport of N from soil to decaying litter may promote N stabilization in mineral SOM even at a relatively low C:N ratio.     

Calcium Additions and Microbial Nitrogen Cycle Processes in a Northern Hardwood Forest

Evaluating, and possibly ameliorating, the effects of base cation depletion in forest soils caused by acid deposition is an important topic in the northeastern United States. We added 850 kg Ca ha⁻¹ as wollastonite (CaSiO₃) to an 11.8-ha watershed at the Hubbard Brook Experimental Forest (HBEF), a northern hardwood forest in New Hampshire, USA, in fall 1999 to replace calcium (Ca) leached from the ecosystem by acid deposition over the past 6 decades. Soil microbial biomass carbon (C) and nitrogen (N) concentrations, gross and potential net N mineralization and nitrification rates, soil solution and stream chemistry, soil:atmosphere trace gas (CO₂, N₂O, CH₄) fluxes, and foliar N concentrations have been monitored in the treated watershed and in reference areas at the HBEF before and since the Ca addition. We expected that rates of microbial C and N cycle processes would increase in response to the treatment. By 2000, soil pH was increased by a full unit in the Oie soil horizon, and by 2002 it was increased by nearly 0.5 units in the Oa soil horizon. However, there were declines in the N content of the microbial biomass, potential net and gross N mineralization rates, and soil inorganic N pools in the Oie horizon of the treated watershed. Stream, soil solution, and foliar concentrations of N showed no response to treatment. The lack of stimulation of N cycling by Ca addition suggests that microbes may not be stimulated by increased pH and Ca levels in the naturally acidic soils at the HBEF, or that other factors (for example, phosphorus, or Ca binding of labile organic matter) may constrain the capacity of microbes to respond to increased pH in the treated watershed. Possible fates for the approximately 10 kg N ha⁻¹ decline in microbial and soil inorganic pools include components of the plant community that we did not measure (for example, seedlings, understory shrubs), increased fluxes of N₂ and/or N storage in soil organic matter. These results raise questions about the factors regulating microbial biomass and activity in northern hardwood forests that should be considered in the context of proposals to mitigate the depletion of nutrient cations in soil.     

Drainage Size, Stream Intermittency, and Ecosystem Function in a Sonoran Desert Landscape

Understanding the interactions between terrestrial and aquatic ecosystems remains an important research focus in ecology. In arid landscapes, catchments are drained by a channel continuum that represents a potentially important driver of ecological pattern and process in the surrounding terrestrial environment. To better understand the role of drainage networks in arid landscapes, we determined how stream size influences the structure and productivity of riparian vegetation, and the accumulation of organic matter (OM) in soils beneath plants in an upper Sonoran Desert basin. Canopy volume of velvet mesquite (Prosopis velutina), as well as overall plant cover, increased along lateral upland–riparian gradients, and among riparian zones adjacent to increasingly larger streams. Foliar δ¹³C signatures for P. velutina suggested that landscape patterns in vegetation structure reflect increases in water availability along this arid stream continuum. Leaf litter and annual grass biomass production both increased with canopy volume, and total aboveground litter production ranged from 137 g m⁻² y⁻¹ in upland habitat to 446 g m⁻² y⁻¹ in the riparian zone of the perennial stream. OM accumulation in soils beneath P. velutina increased with canopy volume across a broad range of drainage sizes; however, in the riparian zone of larger streams, flooding further modified patterns of OM storage. Drainage networks represent important determinants of vegetation structure and function in upper Sonoran Desert basins, and the extent to which streams act as sources of plant-available water and/or agents of fluvial disturbance has implications for material storage in arid soils.     

Microarray analysis of Bacillus cereus group virulence factors

Bacillus cereus, B. thuringiensis and B. anthracis are closely related medically and economically important bacterial species that belong to the B. cereus group. Members of the B. cereus group carry genes encoding several important virulence factors, including enterotoxins, phospholipases and exotoxins. Since it is difficult to differentiate among B. cereus group members, and because Bacillus virulence factors are very important for pathogenesis, we explored the use of microarray-based detection of virulence factor genes as a tool for strain identification and for determining virulence. Our method requires an initial multiplex PCR amplification step, followed by identification of the PCR amplicons by hybridization to an oligonucleotide microarray containing genes for all three types of Bacillus virulence factors including B. anthracis virulence factors. The DNA chip described here contains 21 identical arrays used for analysis of seven samples in triplicates. Using the arrays, we found that virulence factors are present in several combinations in the strains analyzed. This work also demonstrates the potential of oligonucleotide microarrays for medical, food safety and biodefense analysis of microbial pathogens.     

Relationships between land use, spatial scale and stream macroinvertebrate communities

1. The structure of lotic macroinvertebrate communities may be strongly influenced by land‐use practices within catchments. However, the relative magnitude of influence on the benthos may depend upon the spatial arrangement of different land uses in the catchment. 2. We examined the influence of land‐cover patterns on in‐stream physico‐chemical features and macroinvertebrate assemblages in nine southern Appalachian headwater basins characterized by a mixture of land‐use practices. Using a geographical information system (GIS)/remote sensing approach, we quantified land‐cover at five spatial scales; the entire catchment, the riparian corridor, and three riparian ‘sub‐corridors’ extending 200, 1000 and 2000 m upstream of sampling reaches. 3. Stream water chemistry was generally related to features at the catchment scale. Conversely, stream temperature and substratum characteristics were strongly influenced by land‐cover patterns at the riparian corridor and sub‐corridor scales. 4. Macroinvertebrate assemblage structure was quantified using the slope of rank‐abundance plots, and further described using diversity and evenness indices. Taxon richness ranged from 24 to 54 among sites, and the analysis of rank‐abundance curves defined three distinct groups with high, medium and low diversity. In general, other macroinvertebrate indices were in accord with rank‐abundance groups, with richness and evenness decreasing among sites with maximum stream temperature. 5. Macroinvertebrate indices were most closely related to land‐cover patterns evaluated at the 200 m sub‐corridor scale, suggesting that local, streamside development effectively alters assemblage structure. 6. Results suggest that differences in macroinvertebrate assemblage structure can be explained by land‐cover patterns when appropriate spatial scales are employed. In addition, the influence of riparian forest patches on in‐stream habitat features (e.g. the thermal regime) may be critical to the distribution of many taxa in headwater streams draining catchments with mixed land‐use practices.     

Microbial biomass and nitrogen cycling responses to fertilization and litter removal in young northern hardwood forests

The influence of site fertility on soil microbial biomass and activity is not well understood but is likely to be complex because of interactions with plant responses to nutrient availability. We examined the effects of long-term (8 yr) fertilization and litter removal on forest floor microbial biomass and N and C transformations to test the hypothesis that higher soil resource availability stimulates microbial activity. Microbial biomass and respiration decreased by 20–30 % in response to fertilization. Microbial C averaged 3.8 mg C/g soil in fertilized, 5.8 mg C/g in control, and 5.5 mg C/g in litter removal plots. Microbial respiration was 200 µg CO₂-C g^–1 d^–1 in fertilized plots, compared to 270 µg CO₂-C g^–1 d^–1 in controls. Gross N mineralization and N immobilization did not differ among treatments, despite higher litter nutrient concentrations in fertilized plots and the removal of substantial quantities of C and N in litter removal plots. Net N mineralization was significantly reduced by fertilization. Gross nitrification and NO₃ ^– immobilization both were increased by fertilization. Nitrate thus became a more important part of microbial N cycling in fertilized plots even though NH₄ ⁺ availability was not stimulated by fertilization.Soil microorganisms did not mineralize more C or N in response to fertilization and higher litter quality; instead, results suggest a difference in the physiological status of microbial biomass in fertilized plots that influenced N transformations. Respiration quotients (qCO₂, respiration per unit biomass) were higher in fertilized plots (56 µg CO₂-C mg C^–1 d^–1) than control (48 µg CO₂-C mg C^–1 d ^–1) or litter removal (45 µg CO₂-C mg C^–1 d^–1), corresponding to higher microbial growth efficiency, higher proportions of gross mineralization immobilized, and lower net N mineralization in fertilized plots. While microbial biomass is an important labile nutrient pool, patterns of microbial growth and turnover were distinct from this pool and were more important to microbial function in nitrogen cycling.     

Interfacial Effects of Tin Oxide Atomic Layer Deposition in Metal Halide Perovskite Photovoltaics

Metal halide perovskites offer a wide and tunable bandgap, making them promising candidates for top‐cell absorbers in tandem photovoltaics. In this work, the authors aim to understand the atomic layer deposition (ALD) precursor–perovskite interactions of the tin oxide ALD system and the role of organic fullerenes at the perovskite–tin oxide interface while establishing a framework for developing alternative perovskite‐compatible ALD processes in the future. It is shown, in the case of tin oxide ALD growth with tetrakis(dimethylamino)tin(IV) and water on FA_0.83Cs_0.17Pb(I_0.83Br_0.17)₃ perovskite, that perovskite stability is most sensitive to metal–organic exposure at elevated temperatures with an onset near 110 °C, resulting in removal of the formamidinium cation. Transitioning from ALD to pulsed‐chemical vapor deposition tin oxide growth can minimize the degradation effects. Investigation of fullerenes at the perovskite interface shows that thin fullerene layers offer minor improvements to perovskite stability under ALD conditions, but significant enhancement in carrier extraction. Fullerene materials are undesirable due to fabrication cost and poor mechanical stability. Compositional tuning of the perovskite material can improve the fullerene‐free device performance. This method is demonstrated with a bromine‐rich perovskite phase to enable an 8.2% efficient perovskite device with all‐inorganic extraction layers.