Effects of poisons and preservatives on the composition of organic matter in a sediment trap experiment

Fluxes and molecular compositions of a group of major biochemical classes (lipids, lignin, pigments, amino acids, and carbohydrates) were compared among sediment traps treated with different poisons and preservatives and deployed for 1–2 months in a coastal marine environment. Fluxes and compositions of biochemicals were significantly more variable than bulk particle fluxes and elemental compositions. This observation was attributed to a greater influence of dead zooplankton “swimmers” in treated traps rather than differences in microbial decomposition due to the various treatments. Molecular compositions, especially of lipids, confirm the influence of zooplankton swimmers on the biochemical composition of the particulate material in treated traps compared to untreated controls even when large swimmers had been removed. An inventory of the major biochemicals we measured accounted for 25–45% of the organic carbon in our samples, with amino acids and sugars making up the bulk (80–90%) of the identified carbon

Droplet digital PCR quantification suggests that higher viral load correlates with improved survival in HPV-positive oropharyngeal tumours

Background: Although HPV-positive oropharyngeal cancer (OPC) patients have improved prognosis compared to HPV negative patients; there remains an HPV-positive group who have poor outcomes. Biomarkers to stratify discrete patient outcomes are thus desirable. Our objective was to analyse viral load (VL) by droplet digital PCR (ddPCR), in HPV-positive patients with OPC on whom clinical outcome data were available. Methods: In a cohort of patients that had previously tested HPV positive via conventional PCR, VL was determined using ddPCR assays for HPV16 L1 and E6 genes. VL was classed as “medium/high” if more than 5.57 copies or 8.68 copies of the HPV 16 L1 or E6 gene were detected respectively. Effect of VL on overall survival and hazard of death & disease progression was performed with adjustments made for sex, age, deprivation, smoking, alcohol consumption and stage. Results: L1 VL ranged from 0.0014–304 gene copies per cell with a mean of 30.9; comparatively E6 VL ranged from 0.0012–356 copies per cell with a mean of 37.9. Univariate analysis showed those with a medium/high VL had a lower hazard of death; this was significant for L1 (p = 0.02) but not for E6 (p = 0.67). The ratio of E6 to L1 deviated from n = 1 in most samples but had no influence on clinical outcomes. Conclusions: HPV viral load may be informative for the further stratification of clinical outcomes in HPV positive OPC patient

A prospective cohort study of human papillomavirus-driven oropharyngeal cancers: implications for prognosis and immunisation

Aims: Oropharyngeal cancer (OPC) is increasing on a global scale, including the component driven by high-risk human papillomavirus (HR-HPV); contemporary data that provides insight into the prognosis of this disease in addition to the fraction attributable to HR-HPV are essential to inform primary and secondary disease management strategies. Materials and methods: A population-based cohort of 235 patients diagnosed with OPC between 2013 and 2015 in Scotland was assessed for HPV status using molecular genotyping. Associations between HR-HPV status and key clinical and demographic variables were estimated using the Pearson chi-squared test. Rates of overall survival and progression-free survival were estimated and visualised using Kaplan–Meier curves. Results: HPV DNA (largely HPV 16) was identified in 60% of cases. After adjustment for age, gender, deprivation, smoking, alcohol consumption and tumour stage, patients with HR-HPV-positive OPC had an 89% reduction in the risk of death (hazard ratio = 0.11, 95% confidence interval 0.05–0.25) and an 85% reduction in the risk of disease progression (hazard ratio = 0.15, 95% confidence interval 0.07–0.30). HPV positivity was not associated with age, deprivation or smoking status, whereas those who reported excess alcohol consumption were less likely to be positive for HR-HPV. Conclusions: The prevalence of HR-HPV-associated OPC is high in Scotland and strongly associated with dramatically improved clinical outcomes, including survival. Demographic/behavioural variables did not reliably predict HPV positivity in this cohort, which underlines the importance of laboratory confirmation. Finally, the dominance of HPV 16 in OPC indicates the significant impact of prophylactic immunisation on this disease

Editorial: Current Topics in Marine Organic Biogeochemical Research

Complex and incompletely understood chemical, biological and physical processes affect the delivery, transport, and storage of organic matter (OM) in the ocean. Atmospheric and climate-relevant gases, primarily carbon dioxide, are closely linked to the production and flux of organic matter within the ocean via the biological pump. Marine and continental OM is transformed in the water column, some is transported to the sediments where a fraction is stored over geological time, and some marine OM is released to the atmosphere. These functions are intimately linked to global nutrient cycles and ecosystem processes. Perhaps indicative of how the field has matured, the multidisciplinary nature of ocean carbon studies and the importance of biological processes in organic carbon cycling has resulted in a morphing of “marine organic geochemistry” into “marine organic biogeochemistry.” Marine organic biogeochemistry now provides a molecular-level window onto the functioning and scale of processes that control the behavior of OM in the ocean. New sampling tools, analytical methods, and data handling capabilities have been applied to marine chemistry since the 1970s; and in tandem with coordinated, international and interdisciplinary research programs, this has led to explosive growth of marine organic biogeochemistry