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Open Access Publications from the University of California

Scholarly Works (16 results)

  • Thesis
  • Peer Reviewed
UC Berkeley Electronic Theses and Dissertations (2010)

The production of dinitrogen (N2) and emission to the atmosphere returns reactive nitrogen (N) species to the unreactive form, completing the N cycle. Soil N2 emissions are the most poorly understood portion of the terrestrial N cycle because soil N2 fluxes are difficult to measure against the high atmospheric background N2 concentration. For my dissertation, I developed two new methods for quantifying soil N2 production in soils and described a new pathway for N2 production in the terrestrial N cycling. I also explored controls on soil N cycling at a regional scale relevant for policymakers. In laboratory experiments, I demonstrated that the N2/Ar technique can be used to accurately measure surface soil N2 fluxes when solubility and water vapor fractionation effects on the N2/Ar ratio are taken into account. Currently the detection limit of the method is 100 mg N m2 d-1, but proposed modifications to the sampling and analytical protocols can lower the detection limit as well as increase sample throughput. I also developed the 15N-nitrous oxide (N2O) pool dilution technique in a peatland pasture and showed that it can be used to measure gross N2O production and consumption rates without changing soil N2O emissions (i.e., net N2O production). Vertical diffusion modeling suggested that the 15N2O tracer was able to diffuse through the vadose zone to the water table at 60 cm depth during the sampling period, but additional modeling is necessary to evaluate the impact of lateral tracer movement on vertical tracer penetration into the soil profile. Nitrous oxide emissions ranged from 0.05 to 77.4 mg N m-2 d-1 across four micro-topographic zones and the proportion of gross N2O production released to the atmosphere was 0.84 ± 0.03. Mineral N concentrations and denitrifying enzyme activity together best predicted gross N2O production rates (R2 = 0.73). When the four landforms were grouped by soil moisture content, soil oxygen concentrations explained over 64% of the variability in N2O consumption rates. Denitrification is currently thought to be the only N2 production pathway in terrestrial soils, but I showed that, in a humid tropical forest soil, iron reduction coupled to anaerobic ammonium (NH4+) oxidation (Feammox) can lead to N2 production both directly and indirectly (via denitrification of Feammox-generated nitrite). Anaerobic ammonium oxidation rates were comparable to denitrification rates for this forest, suggesting the potential importance of this pathway. Lastly, I found that a small suite of soil properties could reliably predict internal N cycling processes in soils from deserts, forests, grasslands, shrublands, and wetlands in California. Microbial biomass N, soil organic carbon (C) concentration, and soil NH4+ concentrations together explained 80 % of the variability in gross mineralization rates whereas soil nitrate (NO3-) concentration and soil C:N ratios together explained 59 % of the variability in gross nitrification rates. Dissimilatory NO3- reduction to NH4+ occurred in all soils and rates were best predicted by the combination of gross nitrification rates and soil NH4+ concentrations (R2 = 0.83). These results will support modeling efforts at the regional scale that are important for setting land use and N emissions policies. Overall, my dissertation has moved the field closer to understanding soil N2 emissions and suggests that the controls on soil N cycling can be modeled at a regional scale incorporating many different ecosystem types.

    Cover page: Quantification of and Controls on Dinitrogen and Nitrous Oxide Fluxes from Terrestrial Ecosystems
    • Article
    • Peer Reviewed
    UC Berkeley Previously Published Works (2016)
    Sea level rise will change inundation regimes in salt marshes, altering redox dynamics that control nitrification - a potential source of the potent greenhouse gas, nitrous oxide (N2 O) - and denitrification, a major nitrogen (N) loss pathway in coastal ecosystems and both a source and sink of N2 O. Measurements of net N2 O fluxes alone yield little insight into the different effects of redox conditions on N2 O production and consumption. We used in situ measurements of gross N2 O fluxes across a salt marsh elevation gradient to determine how soil N2 O emissions in coastal ecosystems may respond to future sea level rise. Soil redox declined as marsh elevation decreased, with lower soil nitrate and higher ferrous iron in the low marsh compared to the mid and high marshes (P < 0.001 for both). In addition, soil oxygen concentrations were lower in the low and mid-marshes relative to the high marsh (P < 0.001). Net N2 O fluxes differed significantly among marsh zones (P = 0.009), averaging 9.8 ± 5.4 μg N m(-2)  h(-1) , -2.2 ± 0.9 μg N m(-2)  h(-1) , and 0.67 ± 0.57 μg N m(-2)  h(-1) in the low, mid, and high marshes, respectively. Both net N2 O release and uptake were observed in the low and high marshes, but the mid-marsh was consistently a net N2 O sink. Gross N2 O production was highest in the low marsh and lowest in the mid-marsh (P = 0.02), whereas gross N2 O consumption did not differ among marsh zones. Thus, variability in gross N2 O production rates drove the differences in net N2 O flux among marsh zones. Our results suggest that future studies should focus on elucidating controls on the processes producing, rather than consuming, N2 O in salt marshes to improve our predictions of changes in net N2 O fluxes caused by future sea level rise.
      Cover page: Gross nitrous oxide production drives net nitrous oxide fluxes across a salt marsh landscape
      • Article
      • Peer Reviewed
      UC Berkeley Previously Published Works (2019)
      Invasive plants can increase soil nitrogen (N) pools and accelerate soil N cycling rates, but their effect on gross N cycling and nitrous oxide (N2 O) emissions has rarely been studied. We hypothesized that perennial pepperweed (Lepidium latifolium) invasion would increase rates of N cycling and gaseous N loss, thereby depleting ecosystem N and causing a negative feedback on invasion. We measured a suite of gross N cycling rates and net N2 O fluxes in invaded and uninvaded areas of an annual grassland in the Sacramento-San Joaquin River Delta region of northern California. During the growing season, pepperweed-invaded soils had lower microbial biomass N, gross N mineralization, dissimilatory nitrate reduction to ammonium (DNRA), and denitrification-derived net N2 O fluxes (P < 0.02 for all). During pepperweed dormancy, gross N mineralization, DNRA, and denitrification-derived net N2 O fluxes were stimulated in pepperweed-invaded plots, presumably by N-rich litter inputs and decreased competition between microbes and plants for N (P < 0.04 for all). Soil organic carbon and total N concentrations, which reflect pepperweed effects integrated over longer time scales, were lower in pepperweed-invaded soils (P < 0.001 and P = 0.04, respectively). Overall, pepperweed invasion had a net negative effect on ecosystem N status, depleting soil total N to potentially cause a negative feedback to invasion in the long term.
        Cover page: Invasive perennial forb effects on gross soil nitrogen cycling and nitrous oxide fluxes depend on phenology
        • Article
        • Peer Reviewed
        UC Berkeley Previously Published Works (2015)
        Salt marshes currently play an important role as filters for upslope nitrogen (N) inputs. This could change in the future with sea level rise, warming and eutrophication, which are expected to favor monocultures over diverse plant communities. We explored patterns in gross N cycling, dissimilatory nitrate (NO3-) reduction to ammonium (NH4+) (DNRA), and denitrification in a salt marsh soil under two typical redox conditions (aerobic and anaerobic), and in soils under plant communities manipulated to simulate potential future composition (forb and graminoid monocultures). Natural salt marsh soils exhibited high potential gross N mineralization rates. Averaging 50.4 6 5.7 lg N g-1 d-1 under aerobic conditions; rates declined to 23.6 6 3.4 lg N g-1 d-1 under an N2 headspace. Microbial NH4+ uptake and gross nitrification together accounted for only 14 % of gross N mineralization. Nitrogen retention via DNRA and microbial uptake greatly exceeded N losses via denitrification. Gross nitrification rates were greater in the forb and graminoid monocultures than in the control. This effect may be mediated by the lower plant biomass in the monocultures than in the control, which may have reduced competition between plants and nitrifiers for NH4+. Soil NO3- concentrations and net nitrous oxide (N2O) fluxes were greatest for the forb monoculture, likely due to higher soil oxygen (O2) concentrations in these plots. Our results suggest that salt marsh soils with a diverse plant community have high potential rates of N mineralization and microbial N retention, and the establishment of forb monocultures could lead to greater ecosystem N losses.
          • Article
          • Peer Reviewed
          UC San Francisco Previously Published Works (2011)
          Progress in the functional studies of human olfactory receptors has been largely hampered by the lack of a reliable experimental model system. Although transgenic approaches in mice could characterize the function of individual olfactory receptors, the presence of over 300 functional genes in the human genome becomes a daunting task. Thus, the characterization of individuals with a genetic susceptibility to altered olfaction coupled with the absence of particular olfactory receptor genes will allow phenotype/genotype correlations and vindicate the function of specific olfactory receptors with their cognate ligands. We characterized a 118 kb β-globin deletion and found that its 3' end breakpoint extends to the neighboring olfactory receptor region downstream of the β-globin gene cluster. This deletion encompasses six contiguous olfactory receptor genes (OR51V1, OR52Z1, OR51A1P, OR52A1, OR52A5, and OR52A4) all of which are expressed in the brain. Topology analysis of the encoded proteins from these olfactory receptor genes revealed that OR52Z1, OR52A1, OR52A5, and OR52A4 are predicted to be functional receptors as they display integral characteristics of G-proteins coupled receptors. Individuals homozygous for the 118 kb β-globin deletion are afflicted with β-thalassemia due to a homozygous deletion of the β-globin gene and have no alleles for the above mentioned olfactory receptors genes. This is the first example of a homozygous deletion of olfactory receptor genes in human. Although altered olfaction remains to be ascertained in these individuals, such a study can be carried out in β-thalassemia patients from Malaysia, Indonesia and the Philippines where this mutation is common. Furthermore, OR52A1 contains a γ-globin enhancer, which was previously shown to confer continuous expression of the fetal γ-globin genes. Thus, the hypothesis that β-thalassemia individuals, who are homozygous for the 118 kb deletion, may also have an exacerbation of their anemia due to the deletion of two copies of the γ-globin enhancer element is worthy of consideration.
            Cover page: Homozygous Deletion of Six Olfactory Receptor Genes in a Subset of Individuals with Beta-Thalassemia
            • Article
            • Peer Reviewed
            UC Merced Previously Published Works (2017)
            Microbial transformations of nitrogen (N) largely determine whether N is retained in ecosystems via net primary productivity or lost via gaseous emissions and leaching. The controls on soil N cycling are often studied at single locales, making it difficult to predict N cycling at regional to global scales. We hypothesized that contemporary soil properties exhibit consistent relationships with instantaneous gross N cycling rates across diverse biomes that create a continuum in these properties. We measured ex situ gross N cycling rates and soil properties at 33 study sites representing five biome classifications in California including deserts, grasslands, shrublands, forest, and wetlands. Desert soils had significantly lower total N, organic carbon (C), microbial biomass N, and soil moisture as well as higher pH than all other biomes, whereas forests and wetlands had significantly lower soil nitrate (NO3−) concentrations (P < 0.001 for all). Gross mineralization rates were best predicted by the combination of soil moisture and soil C:N ratios (R2 = 0.46), which exerted positive and negative controls, respectively. Grasslands exhibited marginally higher gross mineralization than all other biomes, whereas deserts had the lowest rates due to low soil moisture (P = 0.09). Gross nitrification rates were positively correlated to soil NO3− concentrations (R2 = 0.34) and negatively correlated to soil C:N ratios (R2 = 0.31). The negative relationship between gross nitrification and soil C:N ratios was driven by forest soils, which had significantly higher C:N ratios and lower gross nitrification than all other biomes (P < 0.05). Dissimilatory NO3− reduction to NH4+ (DNRA) occurred in soils from all biomes. The strong positive correlation between DNRA rates and soil NO3− (R2 = 0.41) suggests NO3− limitation of DNRA. Predictable patterns in gross N cycling across biomes in California suggest that contemporary soil properties are important drivers of instantaneous soil N cycling rates that integrate over differences in vegetation type, atmospheric N deposition rates, and local climate.
              Cover page: Cross-biome assessment of gross soil nitrogen cycling in California ecosystems
              • Article
              • Peer Reviewed
              UC Berkeley Previously Published Works (2020)

              Objective

              To assess the association between clinical integration and financial integration, quality-focused care delivery processes, and beneficiary utilization and outcomes.

              Data sources

              Multiphysician practices in the 2017-2018 National Survey of Healthcare Organizations and Systems (response rate 47%) and 2017 Medicare claims data.

              Study design

              Cross-sectional study of Medicare beneficiaries attributed to physician practices, focusing on two domains of integration: clinical (coordination of patient services, use of protocols, individual clinician measures, access to information) and financial (financial management and planning across operating units). We examined the association between integration domains, the adoption of quality-focused care delivery processes, beneficiary utilization and health-related outcomes, and price-adjusted spending using linear regression adjusting for practice and beneficiary characteristics, weighting to account for sampling and nonresponse.

              Data collection/extraction methods

              1 604 580 fee-for-service Medicare beneficiaries aged 66 or older attributed to 2113 practices. Of these, 414 209 beneficiaries were considered clinically complex (frailty or 2 + chronic conditions).

              Principal findings

              Financial integration and clinical integration were weakly correlated (correlation coefficient = 0.19). Clinical integration was associated with significantly greater adoption of quality-focused care delivery processes, while financial integration was associated with lower adoption of these processes. Integration was not generally associated with reduced utilization or better beneficiary-level health-related outcomes, but both clinical integration and financial integration were associated with lower spending in both the complex and noncomplex cohorts: (clinical complex cohort: -$2518, [95% CI: -3324, -1712]; clinical noncomplex cohort: -$255 [95% CI: -413, -97]; financial complex cohort: -$997 [95% CI: -$1320, -$679]; and financial noncomplex cohort: -$143 [95% CI: -210, -$76]).

              Conclusions

              Higher levels of financial integration were not associated with improved care delivery or with better health-related beneficiary outcomes. Nonfinancial forms of integration deserve greater attention, as practices scoring high in clinical integration are more likely to adopt quality-focused care delivery processes and have greater associated reductions in spending in complex patients.
                Cover page: Organizational integration, practice capabilities, and outcomes in clinically complex medicare beneficiaries
                • Article
                • Peer Reviewed
                UC Berkeley Previously Published Works (2017)
                Methane (CH4) is a potent greenhouse gas that is both produced and consumed in soils by microbially mediated processes sensitive to soil redox. We evaluated the classical conceptual model of peatland CH4 dynamics—in which the water table position determines the vertical distribution of methanogenesis and methanotrophy—versus an emerging model in which methanogenesis and methanotrophy can both occur throughout the soil profile due to spatially heterogeneous redox and anaerobic CH4 oxidation. We simultaneously measured gross CH4 production and oxidation in situ across a microtopographical gradient in a drained temperate peatland and ex situ along the soil profile, giving us novel insight into the component fluxes of landscape-level net CH4 fluxes. Net CH4 fluxes varied among landforms (p < 0.001), ranging from 180.3 ± 81.2 mg C m−2 d−1 in drainage ditches to −0.7 ± 1.2 mg C m−2 d−1 in the highest landform. Contrary to prediction by the classical conceptual model, variability in methanogenesis alone drove the landscape-level net CH4 flux patterns. Consistent with the emerging model, freshly collected soils from above the water table produced CH4 within anaerobic microsites. Even in soil from beneath the water table, gross CH4 production was best predicted by the methanogenic fraction of carbon mineralization, an index of highly reducing microsites. We measured low rates of anaerobic CH4 oxidation, which may have been limited by relatively low in situ CH4 concentrations in the hummock/hollow soil profile. Our study revealed complex CH4 dynamics better represented by the emerging heterogeneous conceptual model than the classical model based on redox strata.
                  Cover page: Evaluating the Classical Versus an Emerging Conceptual Model of Peatland Methane Dynamics
                  • Article
                  • Peer Reviewed
                  UC San Francisco Previously Published Works (2024)

                  Purpose

                  To investigate sex-based differences in inflammation-related biomarkers on spectral-domain OCT.

                  Design

                  Cross-sectional study.

                  Participants

                  Patients with diabetic macular edema (DME) between February 1, 2019, and March 31, 2023, without intravitreal anti-VEGF injection within the previous 6 months.

                  Methods

                  We reviewed each patient's medical record for age, biological sex, race and ethnicity, most recent glycated hemoglobin A1c (HbA1c) level, visual acuity (VA), and central macular thickness (CMT). OCT biomarkers that have been found in literature to be associated with inflammation, including disorganization of retinal inner layers (DRIL), retinal hyperreflective retinal foci (HRFs), hyperreflective choroidal foci (HCFs), subfoveal neuroretinal detachment (SND), and perturbation in retinal nerve fiber layer thickness, ganglion cell layer thickness, and inner nuclear layer (INL) thickness were evaluated by graders masked to the clinical characteristics of the patients. We performed multivariable regression analyses with the OCT biomarkers as the outcome variables and sex, age, HbA1c, and CMT as independent variables.

                  Main outcome measures

                  OCT inflammation-related biomarkers, as listed above.

                  Results

                  Female patients were, on average, 2 years older than male patients (P = 0.041). There were no significant differences in race and ethnicity, HbA1c, VA, or CMT between male and female patients. After controlling for age, HbA1c, and CMT, we found male sex to be associated with more HRF (incidence rate ratio [IRR] = 1.19; 95% confidence interval [CI] = 1.10-1.29), more HCF (odds ratio = 2.01; 95% CI = 1.12-3.64), and thicker INL (7 μm thicker in males; 95% CI = 2-12). Sex was not a significant predictor for either DRIL or SND in the multivariable regression models. Patients with higher HbA1c were more likely to have more HRF (IRR = 1.02 per 1 point increase; 95% CI = 1.00-1.04) after controlling for other factors.

                  Conclusions

                  Male sex was correlated with more inflammation-related biomarkers on OCT including more HRF, more HCF, and thicker INL, after accounting for age, glycemic control, and amount of DME. Further studies are needed to evaluate the potential implications of these sex-based differences for individualized treatment.

                  Financial disclosures

                  Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.
                    Cover page: Sex Differences in Inflammation-Related Biomarkers Detected with OCT in Patients with Diabetic Macular Edema
                    • Article
                    • Peer Reviewed
                    UCLA Previously Published Works (2016)
                    Fibrotic disorders involve replacement of normal parenchyma with myofibroblasts, which deposit connective tissue, leading to obliteration of the function of the underlying organ. The treatment options are inadequate and reflect the fact that signaling targets in myofibroblasts are unknown. Here we identify the hyperactive Lyn signaling in myofibroblasts of patients with chronic pancreatitis-induced fibrosis. Lyn activation coexpress with markers of activated myofibroblasts, and is increased ~11-fold in chronic pancreatitis compared to normal tissue. Inhibition of Lyn with siRNA or INNO-406 leads to the substantial decrease of migration and proliferation of human chronic pancreatitis myofibroblasts in vitro, while leaving migration and proliferation of normal myofibroblasts only slightly affected. Furthermore, inhibition of Lyn prevents synthesis of procollagen and collagen in myofibroblasts in a mouse model of chronic pancreatitis-induced fibrosis. We conclude that Lyn, as a positive regulator of myofibroblast migration, proliferation, and collagen production, is a key target for preventing fibrosis.
                      Cover page: Essential Role of Lyn in Fibrosis
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