Denitrification Potential in Lake Sediment Increases Across a Gradient of Catchment Agriculture

Intensification of catchment agriculture has increased nutrient loads and accelerated eutrophication in some lakes, often resulting in episodic harmful algal blooms or prolonged periods of anoxia. The influence of catchment agriculture on lake sediment denitrification capacity as a nitrogen (N) removal mechanism in lakes is largely unknown, particularly in contrast to research on denitrification in agricultural streams and rivers. We measured denitrification enzyme activity (DEA) to assess sediment denitrification potential in seven monomictic and three polymictic lakes that range in the proportion of agriculture in the catchment from 3 to 96% to determine if there is a link between agricultural land use in the lake catchment and sediment denitrification potential. We collected sediment cores for DEA measurements over 3 weeks in austral spring 2008 (October–November). Lake Okaro, with 96% catchment agriculture, had approximately 15 times higher DEA than Lake Tikitapu, with 3% catchment agriculture (232.2 ± 55.9 vs. 15.9 ± 4.5 μg N gAFDM⁻¹ h⁻¹, respectively). Additionally, sediment denitrification potential increased with the proportion of catchment in agriculture (R ² = 0.85, P < 0.001). Our data suggest that lakes retain a high capacity to remove excess N via denitrification under increasing N loads from higher proportions of catchment agriculture. However, evidence from the literature suggests that despite a high capacity for denitrification and longer water residence times, lakes with high N loads will still remove a smaller proportion of their N load. Lakes have a denitrification potential that reflects the condition of the lake catchment, but more measurements of in situ denitrification rates across lake catchments is necessary to determine if this capacity translates to high N removal rates.     

Nitrate removal and hydraulic performance of organic carbon for use in denitrification beds

Denitrification beds are a cost-effective technology for removing nitrate from point source discharge. To date, field trials and operational beds have primarily used wood media as the carbon source; however, the use of alternative more labile carbon media could provide for increased removal rate, lower installation costs and reduced bed size. While previous laboratory experiments have investigated the potential of alternative carbon sources, these studies were typically of short duration and small scale and did not necessarily provide reliable information for denitrification bed design purposes. To address this issue, we compared nitrate removal, hydraulic and nutrient leaching characteristics of nine different carbon substrates in 0.2 m³ barrels, at 14 and 23.5 °C over a 23-month period. Mean nitrate removal rates for the period 10–23 months were 19.8 and 15 g N m^?3 d^?1 (maize cobs), 7.8 and 10.5 g N m^?3 d^?1 (green waste), 5.8 and 7.8 g N m^?3 d^?1 (wheat straw), 3.0 and 4.9 g N m^?3 d^?1 (softwood), and 3.3 and 4.4 g N m^?3 d^?1 (hardwood) for the 14 and 23.5 °C treatments, respectively. Maize cobs provided a 3–6.5-fold increase in nitrate removal over wood media, without prohibitive decrease in hydraulic conductivity, but had higher rates of nutrient leaching at start-up. Significant difference in removal rate occurred between the 14 and 23.5 °C treatments, with the mean Q₁₀ temperature coefficient = 1.6 for all media types in the period 10–23 months.     

Mammal use of riparian corridors in semi-arid Sonora,Mexico

Wildlife populations in semi-arid regions are increasingly challenged by human activities and dependent on the connectivity of riparian corridors for access to surface water. The Madrean Archipelago is a biodiversity hotspot along the arid United States–Mexico borderlands that support both Neotropical and Nearctic wildlife. Infrastructure development (e.g., the border wall and the expansion of Mexican Federal Highway 2) in this region inhibits wildlife movement along the transnational mountain archipelago by disconnecting habitat. To explore the relationship between habitat variables and mammal use of riparian corridors in northern Sonora, Mexico, we collected data from 19 motion-sensitive cameras between October 2018 and April 2019 and used single-season occupancy models and Royle-Nichols abundance estimation models to analyze our data. We recorded 21 species of mammals, including the first sighting of jaguar (Panthera onca) in this region in 25 years. River characteristics (distance from river, riparian corridor width, water availability), remoteness (distance from highway, productivity, elevation), and topographic variety (vertical elevation difference) influenced patterns of occupancy probability and estimated abundance of mammals >1 kg, but the strength and direction of these relationships varied by species. Additionally, intermittently wet desert washes were comparable in species richness to the perennial system. These results highlight the importance of examining physical and biological aspects of habitat. This is especially true when identifying corridors where mitigation structures should be placed to improve wildlife connectivity in biodiversity hotspots like the Madrean Archipelago and semi-arid ecosystems worldwide.     

Projecting terrestrial biodiversity intactness with GLOBIO 4

Scenario‐based biodiversity modelling is a powerful approach to evaluate how possible future socio‐economic developments may affect biodiversity. Here, we evaluated the changes in terrestrial biodiversity intactness, expressed by the mean species abundance (MSA) metric, resulting from three of the shared socio‐economic pathways (SSPs) combined with different levels of climate change (according to representative concentration pathways [RCPs]): a future oriented towards sustainability (SSP1xRCP2.6), a future determined by a politically divided world (SSP3xRCP6.0) and a future with continued global dependency on fossil fuels (SSP5xRCP8.5). To this end, we first updated the GLOBIO model, which now runs at a spatial resolution of 10 arc‐seconds (~300 m), contains new modules for downscaling land use and for quantifying impacts of hunting in the tropics, and updated modules to quantify impacts of climate change, land use, habitat fragmentation and nitrogen pollution. We then used the updated model to project terrestrial biodiversity intactness from 2015 to 2050 as a function of land use and climate changes corresponding with the selected scenarios. We estimated a global area‐weighted mean MSA of 0.56 for 2015. Biodiversity intactness declined in all three scenarios, yet the decline was smaller in the sustainability scenario (?0.02) than the regional rivalry and fossil‐fuelled development scenarios (?0.06 and ?0.05 respectively). We further found considerable variation in projected biodiversity change among different world regions, with large future losses particularly for sub‐Saharan Africa. In some scenario‐region combinations, we projected future biodiversity recovery due to reduced demands for agricultural land, yet this recovery was counteracted by increased impacts of other pressures (notably climate change and road disturbance). Effective measures to halt or reverse the decline of terrestrial biodiversity should not only reduce land demand (e.g. by increasing agricultural productivity and dietary changes) but also focus on reducing or mitigating the impacts of other pressures.     

Stereotactic Body Radiation Therapy for Primary and Metastatic Liver Tumors

OBJECTIVES: The full potential of stereotactic body radiation therapy (SBRT), in the treatment of unresectable intrahepatic malignancies, has yet to be realized as our experience is still limited. Thus, we evaluated SBRT outcomes for primary and metastatic liver tumors, with the goal of identifying factors that may aid in optimization of therapy. METHODS: From2005 to 2010, 62 patients with 106 primary and metastatic liver tumors were treated with SBRT to a median biologic effective dose (BED) of 100 Gy (42.6-180). The majority of patients received either three (47%) or five fractions (48%). Median gross tumor volume (GTV) was 8.8 cm³ (0.2-222.4). RESULTS: With a median followup of 18 months (0.46-46.8), freedom from local progression (FFLP) was observed in 97 of 106 treated tumors, with 1- and 2-year FFLP rates of 93% and 82%. Median overall survival (OS) for all patients was 25.2 months, with 1- and 2-year OS of 81%and 52%. Neither BED nor GTV significantly predicted for FFLP. Local failure was associated with a higher risk of death [hazard ratio (HR) = 5.1, P = .0007]. One Child-Pugh Class B patient developed radiationinduced liver disease. There were no other significant toxicities. CONCLUSIONS: SBRT provides excellent local control for both primary and metastatic liver lesions with minimal toxicity. Future studies should focus on appropriate selection of patients and on careful assessment of liver function to maximize both the safety and efficacy of treatment.     

Quantification of epithelial volume by image processing applied to ovarian tumors

This paper describes an image analysis technique for automated estimation of the percentages of epithelium and stroma in (tumor) tissue. The program is evaluated on ovarian tumors of the serous, mucinous, and endometrioid type. From standard paraffin sections, stained with pararosanilin Feulgen and naphthol yellow, a blue-yellow image pair was recorded. The blue image was used for the determination of the total tissue area and the yellow image for the epithelial area. For the latter the image processing method is based on the fact that epithelial nuclei are generally more tightly packed than stromal nuclei. A structural approach was applied, in which the segmentation of the nuclei was based on the image contrast range in the density domain. The method has been tested with 78 image pairs from 19 ovarian tumors with varying degrees of malignancy. The area percentages, as assessed with image processing, were strongly correlated to control percentages, established by interactive morphometry (r = 0.98).     

Metabolomics meets functional assays: coupling LC–MS and microfluidic cell-based receptor-ligand analyses

Introduction

Metabolomics has become a valuable tool in many research areas. However, generating metabolomics-based biochemical profiles without any related bioactivity is only of indirect value in understanding a biological process. Therefore, metabolomics research could greatly benefit from tools that directly determine the bioactivity of the detected compounds.

Objective

We aimed to combine LC–MS metabolomics with a cell based receptor assay. This combination could increase the understanding of biological processes and may provide novel opportunities for functional metabolomics.

Methods

We developed a flow through biosensor with human cells expressing both the TRPV1, a calcium ion channel which responds to capsaicin, and the fluorescent intracellular calcium ion reporter, YC3.6. We have analysed three contrasting Capsicum varieties. Two were selected with contrasting degrees of spiciness for characterization by HPLC coupled to high mass resolution MS. Subsequently, the biosensor was then used to link individual pepper compounds with TRPV1 activity.

Results

Among the compounds in the crude pepper fruit extracts, we confirmed capsaicin and also identified both nordihydrocapsaicin and dihydrocapsaicin as true agonists of the TRPV1 receptor. Furthermore, the biosensor was able to detect receptor activity in extracts of both Capsicum fruits as well as a commercial product. Sensitivity of the biosensor to this commercial product was similar to the sensory threshold of a human sensory panel.

Conclusion

Our results demonstrate that the TRPV1 biosensor is suitable for detecting bioactive metabolites. Novel opportunities may lie in the development of a continuous functional assay, where the biosensor is directly coupled to the LC–MS.

     

Development of a Real-Time PCR for Identification of Brachyspira Species in Human Colonic Biopsies

Background

Brachyspira species are fastidious anaerobic microorganisms, that infect the colon of various animals. The genus contains both important pathogens of livestock as well as commensals. Two species are known to infect humans: B. aalborgi and B. pilosicoli. There is some evidence suggesting that the veterinary pathogenic B. pilosicoli is a potential zoonotic agent, however, since diagnosis in humans is based on histopathology of colon biopsies, species identification is not routinely performed in human materials.

Methods

The study population comprised 57 patients with microscopic evidence of Brachyspira infection and 26 patients with no histopathological evidence of Brachyspira infection. Concomitant faecal samples were available from three infected patients. Based on publically available 16S rDNA gene sequences of all Brachyspira species, species-specific primer sets were designed. DNA was extracted and tested by real-time PCR and 16S rDNA was sequenced.

Results

Sensitivity and specificity for identification of Brachyspira species in colon biopsies was 100% and 87.7% respectively. Sequencing revealed B. pilosicoli in 15.4% of patients, B. aalborgi in 76.9% and a third species, tentatively named “Brachyspira hominis”, in 26.2%. Ten patients (12.3%) had a double and two (3.1%) a triple infection. The presence of Brachyspira pilosicoli was significantly associated with inflammatory changes in the colon-biopsy (p = 0.028).

Conclusions

This newly designed PCR allows for sub-differentiation of Brachyspira species in patient material and thus allows large-scaled surveillance studies to elucidate the pathogenicity of human Brachyspira infections. One-third of affected patients appeared to be infected with a novel species.     

TNFR1 and the TNFα axis as a targetable mediator of liver injury from stereotactic body radiation therapy

IntroductionRadiation therapy for the management of intrahepatic malignancies can adversely affect liver function. Liver damage has been associated with increased levels of inflammatory cytokines, including tumor necrosis factor alpha (TNFα). We hypothesized that an inflammatory state, characterized by increased soluble TNFα receptor (sTNFR1), mediates sensitivity of the liver to radiation.Materials/MethodsPlasma samples collected during 3 trials of liver radiation for liver malignancies were assayed for sTNFR1 level via enzyme-linked immunosorbent assay (ELISA). Univariate and multivariate logistic regression and longitudinal models were used to characterize associations between liver toxicity (defined as a ≥2-point increase in Child-Pugh [CP] score within 6 months of radiation treatment) and sTNFR1 levels, ALBI score, biocorrected mean liver dose (MLD), age, and baseline laboratory values.ResultsSamples from 78 patients given liver stereotactic body radiation therapy [SBRT] (92%) or hypofractionated radiation were examined. There was a significant association between liver toxicity and sTNFR1 levels, and higher values were associated with increased toxicity over a range of mean liver doses. When ALBI score and biocorrected dose were included in the model with sTNFR1, baseline ALBI score and change in ALBI (ΔALBI) were significantly associated with toxicity, but sTNFR1 was not. Baseline aminotransferase levels also predicted toxicity but not independently of ALBI score.ConclusionsElevated plasma sTNFR1 levels are associated with liver injury after liver radiation, suggesting that elevated inflammatory cytokine activity is a predictor of radiation-induced liver dysfunction. Future studies should determine whether administration of agents that decrease inflammation prior to treatment is warranted.