Abstract
The Protein Data Bank in Europe (PDBe), a founding member of the Worldwide Protein Data Bank (wwPDB), actively participates in the deposition, curation, validation, archiving and ...dissemination of macromolecular structure data. PDBe supports diverse research communities in their use of macromolecular structures by enriching the PDB data and by providing advanced tools and services for effective data access, visualization and analysis. This paper details the enrichment of data at PDBe, including mapping of RNA structures to Rfam, and identification of molecules that act as cofactors. PDBe has developed an advanced search facility with ∼100 data categories and sequence searches. New features have been included in the LiteMol viewer at PDBe, with updated visualization of carbohydrates and nucleic acids. Small molecules are now mapped more extensively to external databases and their visual representation has been enhanced. These advances help users to more easily find and interpret macromolecular structure data in order to solve scientific problems.
(See the article by Kalayjian et al, on pages 1796–1805, and the editorial commentary by Dubé and Sattler, on pages 1783–1785.) Background. Human immunodeficiency virus (HIV) replication and immune ...activation may increase inflammation and coagulation biomarkers. Limited data exist comparing such biomarkers in persons with and without HIV infection. Methods. For persons 45–76 years of age, levels of high-sensitivity C-reactive protein (hsCRP), interleukin (IL)-6, D-dimer, and cystatin C were compared in 494 HIV-infected individuals in the Strategies for Management of Anti-Retroviral Therapy (SMART) study and 5386 participants in the Multi-Ethnic Study of Atherosclerosis (MESA) study. For persons 33–44 years of age, hsCRP and IL-6 levels were compared in 287 participants in the SMART study and 3231 participants in the Coronary Artery Development in Young Adults (CARDIA) study. Results. hsCRP and IL-6 levels were 55% (P<.001) and 62% (P<.001) higher among HIV-infected participants than among CARDIA study participants. Compared with levels noted in MESA study participants, hsCRP, IL-6, D-dimer, and cystatin C levels were 50%, 152%, 94%, and 27% higher, respectively (P<.001 , for each), among HIV-infected participants. HIV-infected participants receiving antiretroviral therapy who had HIV RNA levels ≤400 copies/mL had levels higher (by 21% to 60%) (P<.001) than those in the general population, for all biomarkers. Conclusions. hsCRP, IL-6, D-dimer, and cystatin C levels are elevated in persons with HIV infection and remain so even after HIV RNA levels are suppressed with antiretroviral therapy. Additional research is needed on the pathophysiology of HIV-induced activation of inflammatory and coagulation pathways, to guide potential interventions.
In California, water is a perennial concern. As competition for water resources increases due to growth in population, California’s tree nut farmers are committed to improving the efficiency of water ...used for food production. There is an imminent need to have reliable methods that provide information about the temporal and spatial variability of crop water requirements, which allow farmers to make irrigation decisions at field scale. This study focuses on estimating the actual evapotranspiration and crop coefficients of an almond and pistachio orchard located in Central Valley (California) during an entire growing season by combining a simple crop evapotranspiration model with remote sensing data. A dataset of the vegetation index NDVI derived from Landsat-8 was used to facilitate the estimation of the basal crop coefficient (Kcb), or potential crop water use. The soil water evaporation coefficient (Ke) was measured from microlysimeters. The water stress coefficient (Ks) was derived from airborne remotely sensed canopy thermal-based methods, using seasonal regressions between the crop water stress index (CWSI) and stem water potential (Ψstem). These regressions were statistically-significant for both crops, indicating clear seasonal differences in pistachios, but not in almonds. In almonds, the estimated maximum Kcb values ranged between 1.05 to 0.90, while for pistachios, it ranged between 0.89 to 0.80. The model indicated a difference of 97 mm in transpiration over the season between both crops. Soil evaporation accounted for an average of 16% and 13% of the total actual evapotranspiration for almonds and pistachios, respectively. Verification of the model-based daily crop evapotranspiration estimates was done using eddy-covariance and surface renewal data collected in the same orchards, yielding an R2 ≥ 0.7 and average root mean square errors (RMSE) of 0.74 and 0.91 mm·day−1 for almond and pistachio, respectively. It is concluded that the combination of crop evapotranspiration models with remotely-sensed data is helpful for upscaling irrigation information from plant to field scale and thus may be used by farmers for making day-to-day irrigation management decisions.
To determine the rate of grade 4, potentially life-threatening events not attributable to AIDS, cardiovascular disease (CVD), or non-AIDS cancer among participants on antiretroviral therapy and to ...describe associations of these events with interleukin-6 (IL-6) and D-dimer.
Cohort study.
HIV-infected participants on antiretroviral therapy (N = 3568) with an HIV-RNA level ≤ 500 copies/mL were followed for grade 4, AIDS, CVD, non-AIDS cancer, and all-cause mortality events. Grade 4 events were further classified masked to biomarker levels as reflecting chronic inflammation-related disease (ChrIRD) or not (non-ChrIRD). Associations of baseline IL-6 and D-dimer with events were studied using Cox models.
Over a median follow-up of 4.3 years, 339 participants developed a grade 4 event (22.9 per 1000 person-years); 165 participants developed a ChrIRD grade 4 event (10.7 per 1000 person-years). Grade 4 events were more common than AIDS (54 participants), CVD (132), and non-AIDS cancer (80) events, any of which developed in 252 participants (17.1 per 1000 person-years). Grade 4 and AIDS events were associated with similar risks of death. Higher IL-6 hazard ratio (HR) = 1.19 per doubling of biomarker; P = 0.003 and D-dimer (HR = 1.23; P < 0.001) levels were associated with an increased risk of grade 4 events. IL-6 associations were stronger for ChrIRD (HR = 1.38; P < 0.001) than non-ChrIRD grade 4 events (HR = 1.11; P = 0.21).
Morbidity and mortality associated with activation of inflammatory and coagulation pathways include conditions other than AIDS, CVD, and non-AIDS cancer events. Effective inflammation-dampening interventions could greatly affect the health of people with HIV.
Climate change and biodiversity loss are two global challenges that can be addressed simultaneously through reforestation of previously cleared land. However, carbon markets can encourage ...reforestations that focus on maximizing carbon storage, potentially at the expense of biodiversity conservation.
To identify opportunities to optimize reforestation design and management to meet both goals, we examined the forest stand features associated with carbon stocks in biomass and soil, as well as bird abundance and diversity, in remnant and restored riparian forest stands in central California, U.S.A.
Within three decades of reforestation, both planted and naturally regenerating riparian forest stands provided significantly greater carbon storage and avian biodiversity benefits compared to baseline conditions. They were also similar to a remnant riparian forest stand.
We identified a synergy between carbon storage and biodiversity benefits in their positive associations with understorey cover, but we also identified a trade‐off in their relationships to forest stand density. Biomass carbon stocks were strongly positively related to stand density, while bird density and diversity suffered at the highest stand densities.
The variability in understorey cover across forest stands indicates an opportunity for further enhancement of carbon and biodiversity benefits in areas where understorey cover is low, while the variability in stand density suggests an opportunity to re‐examine reforestation goals and consider thinning to achieve those goals.
Synthesis and applications. We identified synergies and trade‐offs between carbon storage and biodiversity in their relationships to forest stand features, indicating opportunities to optimize reforestation design and management to achieve multiple goals. Our approach can be adapted to other reforestation efforts intended to simultaneously address the global challenges of climate change and biodiversity loss.
Foreign Language Resumen
El cambio climatico y la pérdida de biodiversidad son dos problemas globales que se pueden enfrentar con la reforestación de tierras previamente degradadas. Sin embargo, los mercados de carbon promueven reforestaciones enfocadas en maximizar el almacenamiento de carbon, posiblemente a cuestas de la conservación de la biodiversidad.
Para identificar oportunidades de diseño y gestión de programas de reforestación enfocados en estos dos objetivos, evaluamos las características de rodales de bosques que determinan las medias de carbon en la biomasa y en los suelos, y que también determinan la abundancia y diversidad de aves en rodales de bosques riparios remanentes y restaurados en el centro de California, Estados Unidos.
En tres décadas de reforestación, los rodales de bosques riparios sembrados y regenerados naturalmente incrementaron de manera significativa el almacenamiento de carbono y los beneficios para la biodiversidad de aves comparado con condiciones de referencia. Los rodales de bosques riparios también mostraron características similares a un rodal de bosque ripario remanente.
Hemos identificado una sinergia entre el almacenamiento de carbono y beneficios a la biodiversidad porque estan positivamente asociadas con la cobertura del sotobosque, pero también identificamos una compensación con la densidad del rodal de bosque. Las reservas de carbono en la biomasa demostraron una fuerte relación positiva con la densidad del rodal, mientras que la densidad y la diversidad de las aves sufrieron en las densidades más altas del rodal.
La variabilidad en la cobertura del sotobosque en los rodales de bosque indica una oportunidad para augmentar beneficios de carbon y de biodiversidad en áreas donde la coberatura esté baja, mientras que la variabilidad en la densidad de los rodales sugiere una oportunidad para reexaminar las metas de reforestación posiblemente considerando el raleo para alcanzar las metas.
Síntesis y aplicaciones. Identificamos sinergias y compensaciones entre el almacenamiento de carbono y la biodiversidad con las características de rodales de bosque, indicando oportunidades para optimizar el diseño y la gestión de programas de reforestación para lograr objetivos múltiples. Nuestro enfoque se puede adaptar a otros esfuerzos de reforestación dedicados a enfrentar simultáneamente los problemas globales de cambio climatico y la pérdida de biodiversidad.
We identified synergies and trade‐offs between carbon storage and biodiversity in their relationships to forest stand features, indicating opportunities to optimize reforestation design and management to achieve multiple goals. Our approach can be adapted to other reforestation efforts intended to simultaneously address the global challenges of climate change and biodiversity loss.
Active floodplains can putatively store large amounts of organic carbon (SOC) in subsoils originating from catchment erosion processes with subsequent floodplain deposition. Our study focussed on the ...assessment of SOC pools associated with alluvial floodplain soils that are affected by human-induced changes in floodplain deposition and in situ SOC mineralisation due to land use change and drainage. We evaluated depth-dependent SOC contents based on 23 soil cores down to 3 m and 10 drillings down to 7 m in a floodplain area of the lower Cosumnes River. An estimate of 266 Mg C ha−1 or about 59% of the entire SOC stored within the 7 m profiles was found in the upper 2 m. Most profiles (n = 25) contained discrete buried A horizons at depths of approximately 0.8 m. These profiles had up to 130% higher SOC stocks. The mean δ13C of all deep soil profiles clearly indicated that arable land use has already altered the stable isotopic signature in the first meter of the profile. Radiocarbon dating showed that the 14C age in the buried horizon was younger than in overlaying soils indicating a substantial sedimentation phase for the overlaying soils. An additional analysis of total mercury contents in the soil profiles indicated that this sedimentation was associated with upstream hydraulic gold mining after the 1850s. In summary, deep alluvial soils in floodplains store large amounts of SOC not yet accounted for in global carbon models. Historic data give evidence that large amounts of sediment were transported into the floodplains of most rivers of the Central Valley and deposited over organically rich topsoil, which promoted the stabilization of SOC, and needs to be considered to improve our understanding of the human-induced interference with C cycling.
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•Evaluation of depth-dependent SOC contents in a floodplain area of California•About 60% of the entire SOC stored within the 7 m profiles found in the upper 2 m•Radiocarbon dating and mercury analysis showed a substantial sedimentation phase.•This phase was associated with upstream hydraulic gold mining after the 1850s.
Soils account for the largest terrestrial pool of carbon and have the potential for even greater quantities of carbon sequestration. Typical soil carbon (C) stocks used in global carbon models only ...account for the upper 1 meter of soil. Previously unaccounted for deep carbon pools (>1 m) were generally considered to provide a negligible input to total C contents and represent less dynamic C pools. Here we assess deep soil C pools associated with an alluvial floodplain ecosystem transitioning from agricultural production to restoration of native vegetation. We analyzed the soil organic carbon (SOC) concentrations of 87 surface soil samples (0-15 cm) and 23 subsurface boreholes (0-3 m). We evaluated the quantitative importance of the burial process in the sequestration of subsurface C and found our subsurface soils (0-3 m) contained considerably more C than typical C stocks of 0-1 m. This deep unaccounted soil C could have considerable implications for global C accounting. We compared differences in surface soil C related to vegetation and land use history and determined that flooding restoration could promote greater C accumulation in surface soils. We conclude deep floodplain soils may store substantial quantities of C and floodplain restoration should promote active C sequestration.
Abstract
The Protein Data Bank in Europe (PDBe, pdbe.org) is actively engaged in the deposition, annotation, remediation, enrichment and dissemination of macromolecular structure data. This paper ...describes new developments and improvements at PDBe addressing three challenging areas: data enrichment, data dissemination and functional reusability. New features of the PDBe Web site are discussed, including a context dependent menu providing links to raw experimental data and improved presentation of structures solved by hybrid methods. The paper also summarizes the features of the LiteMol suite, which is a set of services enabling fast and interactive 3D visualization of structures, with associated experimental maps, annotations and quality assessment information. We introduce a library of Web components which can be easily reused to port data and functionality available at PDBe to other services. We also introduce updates to the SIFTS resource which maps PDB data to other bioinformatics resources, and the PDBe REST API.
Nitrogen (N) fertilizer use has simultaneously increased global food production and N losses, resulting in degradation of water quality and climate pollution. A better understanding of N application ...rates and crop and environmental response is needed to optimize management of agroecosystems. Here we show an orchard agroecosystem with high N use efficiency promoted substantial gains in carbon (C) storage, thereby lowering net global warming potential (GWP). We conducted a 5-year whole-system analysis comparing reduced (224 kg N ha−1 yr−1) and intensive (309 kg N ha−1 yr−1) fertilizer N rates in a California almond orchard. The intensive rate increased net primary productivity (Mg C ha−1) and significantly increased N productivity (kg N ha−1) and net N mineralization (mg N kg−1 soil d−1). Use of 15N tracers demonstrated short and long-term mechanisms of soil N retention. These low organic matter soils (0.3–0.5%) rapidly immobilized fertilizer nitrate within 36 h of N application and 15N in tree biomass recycled back into soil organic matter over five years. Both fertilizer rates resulted in high crop and total N recovery efficiencies of 90% and 98% for the reduced rate, and 72% and 80% for the intensive rate. However, there was no difference in the proportion of N losses to N inputs due to a significant gain in soil total N (TN) in the intensive rate. Higher soil TN significantly increased net N mineralization and a larger gain in soil organic carbon (SOC) from the intensive rate offset nitrous oxide (N2O) emissions, leading to significantly lower net GWP of −1.64 Mg CO2-eq ha−1 yr−1 compared to −1.22 Mg CO2-eq ha−1 yr−1 for the reduced rate. Our study demonstrates increased N cycling and climate mitigation from intensive fertilizer N use in this orchard agroecosystem, implying a fundamentally different result than seen in conventional annual cropping systems.
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•Orchard intensive N fertilizer use yielded lower net GWP due to soil C increase.•Intensive N fertilizer use increased N uptake and soil N immobilization.•Rapid nitrate immobilization and tree biomass recycling increased soil N retention.•Proportion of N losses did not differ between intensive and reduced fertilizer use.•Outline of climate mitigation and N cycling tradeoffs for intensive orchards.
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