Simple staining method for differentiating live and dead marine zooplankton in field samples

We describe and evaluate a method for the use of neutral red staining to differentiate live and dead zooplankton in marine field samples. The protocol can be easily incorporated into shipboard zooplankton sampling. The use of neutral red in laboratory studies is common, but its application for quantifying natural live/dead zooplankton composition under field conditions has not been evaluated in detail. We tested the accuracy and precision of the method for a range of salinities and temperatures, and for common estuarine zooplankton groups. Detailed descriptions of staining intensities and patterns are provided. In addition, we evaluated potential artifact mortality due to collection and sample handling. The method produced accurate results under conditions tested, and artifact mortality was negligible using the recommended protocol. Neutral red staining is ideal for quantification of zooplankton carcasses in field samples, which will allow for more systematic study of in situ zooplankton mortality and related processes

Dead in the water: The fate of copepod carcasses in the York River estuary, Virginia

Using laboratory and field experiments we investigated three fates of copepod carcass organic matter in the York River estuary, Virginia: ingestion by planktivores (necrophagy), microbial decomposition, and removal by gravitational settling in the presence of turbulence (sinking). The ctenophore Mnemiopsis leidyi ingested live copepods and carcasses indiscriminately in feeding experiments. Microbial decomposition led to ca. 50% of carcass dry weight loss within 8 h after death. Carcass settling velocities in still water were ca. 0.1 cm s(-1), implying short residence time (hours) in the shallow estuary. However, turbulent mixing kept carcasses in suspension much of the time, reducing sinking losses. Rates of carcass organic matter removal were combined in a simple mathematical model predicting the fate of estuarine copepod carcasses. When sinking was considered, it removed a large fraction of carcass organic matter (\u3e= 58% for copepodites, \u3e= 35% for nauplii), with most of the remainder being removed by microbial decomposition. In the absence of sinking losses, necrophagy became proportionally more important in removing carcass organic matter (\u3e= 49%, except in summer)

Survival and recovery of Phaeocystis antarctica (Prymnesiophyceae) from prolonged darkness and freezing

The colony-forming haptophyte Phaeocystis antarctica is an important primary producer in the Ross Sea, and must survive long periods of darkness and freezing temperature in this extreme environment. We conducted experiments on the responses of P. antarctica-dominated phytoplankton assemblages to prolonged periods of darkness and freezing. Chlorophyll and photosynthetic capacity of the alga declined nonlinearly and independently of each other in the dark, and darkness alone would potentially reduce photosynthetic capacity by only 60 per cent over 150 days (approximately the length of the Antarctic winter in the southern Ross Sea). The estimated reduction of colonial mucous carbon is higher than that of colonial cell carbon, suggesting metabolism of the colonial matrix in the dark. The alga quickly resumed growth upon return to light. Phaeocystis antarctica also survived freezing, although longer freezing durations lengthened the lag before growth resumption. Particulate dimethylsulfoniopropionate relative to chlorophyll increased upon freezing and decreased upon darkness. Taken together, the abilities of P. antarctica to survive freezing and initiate growth quickly after darkness may provide it with the capability to survive in both the ice and the water column, and help explain its repeated dominance in austral spring blooms in the Ross Sea and elsewhere in the Southern Ocean

White blood cell count and risk of incident lung cancer in the UK Biobank

Background The contribution of measurable immunological/inflammatory parameters to lung cancer development remains unclear, particularly among never-smokers. We investigated the relationship between total and differential white blood cell (WBC) counts and incident lung cancer risk overall and among subgroups defined by smoking status and sex in the United Kingdom (UK). Methods We evaluated 424,407 adults aged 37-73 years from the UK Biobank. Questionnaires, physical measurements, and blood were administered/collected at baseline in 2006-2010. Complete blood cell counts were measured using standard methods. Lung cancer diagnoses and histological classifications were obtained from cancer registries. Multivariable Cox regression models were used to estimate the hazard ratio (HR) and 95% confidence intervals (CI) of incident lung cancer in relation to quartiles (Q) of total WBC and subtype-specific counts, with Q1 as the reference. Results There were 1,493 incident cases diagnosed over an average 7-year follow-up. Overall, the highest quartile of total WBC count was significantly associated with elevated lung cancer risk (HRQ4=1.67, 95% CI:1.41-1.98). Among women, increased risks were found in current-smokers (ncases/n=244/19,464, HRQ4=2.15, 95% CI:1.46-3.16), former-smokers (ncases/n=280/69,198, HRQ4=1.75, 95% CI:1.24-2.47), and never-smokers without environmental tobacco smoke exposure (ncases/n=108/111,294, HRQ4=1.93, 95% CI:1.11-3.35). Among men, stronger associations were identified in current-smokers (ncases/n=329/22,934, HRQ4=2.95, 95% CI:2.04-4.26) and former-smokers (ncases/n= 358/71,616, HRQ4=2.38, 95% CI:1.74-3.27) but not in never-smokers. Findings were similar for lung adenocarcinoma and squamous cell carcinoma and were driven primarily by elevated neutrophil fractions. Conclusions Elevated WBCs could potentially be one of many important markers for increased lung cancer risk, especially among never-smoking women and ever-smoking men

Issues potentially affecting quality of life arising from long-term medicines use: a qualitative study

Background Polypharmacy is increasing and managing large number of medicines may create a burden for patients. Many patients have negative views of medicines and their use can adversely affect quality of life. No studies have specifically explored the impact of general long-term medicines use on quality of life. Objective To determine the issues which patients taking long-term medicines consider affect their day-to-day lives, including quality of life. Setting Four primary care general practices in North West England Methods Face-to-face interviews with adults living at home, prescribed four or more regular medicines for at least 1 year. Interviewees were identified from primary care medical records and purposively selected to ensure different types of medicines use. Interviews were recorded, transcribed and analysed thematically. Results Twenty-one interviews were conducted and analysed. Patients used an average of 7.8 medicines, 51 % were preventive, 40 % for symptom relief and 9 % treatment. Eight themes emerged: relationships with health professionals, practicalities, information, efficacy, side effects, attitudes, impact and control. Ability to discuss medicines with health professionals varied and many views were coloured by negative experiences, mainly with doctors. All interviewees had developed routines for using multiple medicines, some requiring considerable effort. Few felt able to exert control over medicines routines specified by health professionals. Over half sought additional information about medicines whereas others avoided this, trusting in doctors to guide their medicines use. Patients recognised their inability to assess efficacy for many medicines, notably those used for prophylaxis. All were concerned about possible side effects and some had poor experiences of discussing concerns with doctors. Medicines led to restrictions on social activities and personal life to the extent that, for some, life can revolve around medicines. Conclusion There is a multiplicity and complexity of issues surrounding medicines use, which impact on day-to-day lives for patients with long-term conditions. While most patients adapt to long-term medicines use, others did so at some cost to their quality of life

A population-based analysis of germline BAP1 mutations in melanoma

Germline mutation of the BRCA1 associated protein-1 (BAP1) gene has been linked to uveal melanoma, mesothelioma, meningioma, renal cell carcinoma and basal cell carcinoma. Germline variants have also been found in familial cutaneous melanoma pedigrees, but their contribution to sporadic melanoma has not been fully assessed. We sequenced BAP1 in 1,977 melanoma cases and 754 controls and used deubiquitinase assays, a pedigree analysis, and a histopathological review to assess the consequences of the mutations found. Sequencing revealed 30 BAP1 variants in total, of which 27 were rare (ExAc allele frequency <0.002). Of the 27 rare variants, 22 were present in cases (18 missense, one splice acceptor, one frameshift and two near splice regions) and 5 in controls (all missense). A missense change (S98R) in a case that completely abolished BAP1 deubiquitinase activity was identified. Analysis of cancers in the pedigree of the proband carrying the S98R variant and in two other pedigrees carrying clear loss-of-function alleles showed the presence of BAP1-associated cancers such as renal cell carcinoma, mesothelioma and meningioma, but not uveal melanoma. Two of these three probands carrying BAP1 loss-of-function variants also had melanomas with histopathological features suggestive of a germline BAP1 mutation. The remaining cases with germline mutations, which were predominantly missense mutations, were associated with less typical pedigrees and tumours lacking a characteristic BAP1-associated histopathological appearances, but may still represent less penetrant variants. Germline BAP1 alleles defined as loss-of-function or predicted to be deleterious/damaging are rare in melanoma

Carbon storage and DNA absorption in allophanic soils and paleosols

Andisols and andic paleosols dominated by the nanocrystalline mineral allophane sequester large amounts of carbon (C), attributable mainly to its chemical bonding with charged hydroxyl groups on the surface of allophane together with its physical protection in nanopores within and between allophane nanoaggregates. C near-edge X-ray absorption fine structure (NEXAFS) spectra for a New Zealand Andisol (Tirau series) showed that the organic matter (OM) mainly comprises quinonic, aromatic, aliphatic, and carboxylic C. In different buried horizons from several other Andisols, C contents varied but the C species were similar, attributable to pedogenic processes operating during developmental upbuilding, downward leaching, or both. The presence of OM in natural allophanic soils weakened the adsorption of DNA on clay; an adsorption isotherm experiment involving humic acid (HA) showed that HA-free synthetic allophane adsorbed seven times more DNA than HA-rich synthetic allophane. Phosphorus X-ray absorption near-edge structure (XANES) spectra for salmonsperm DNA and DNA-clay complexes indicated that DNA was bound to the allophane clay through the phosphate group, but it is not clear if DNA was chemically bound to the surface of the allophane or to OM, or both. We plan more experiments to investigate interactions among DNA, allophane (natural and synthetic), and OM. Because DNA shows a high affinity to allophane, we are studying the potential to reconstruct late Quaternary palaeoenvironments by attempting to extract and characterise ancient DNA from allophanic paleosol

Impact of Scottish smoke-free legislation on smoking quit attempts and prevalence

&lt;p&gt;&lt;b&gt;Objectives:&lt;/b&gt; In Scotland, legislation was implemented in March 2006 prohibiting smoking in all wholly or partially enclosed public spaces. We investigated the impact on attempts to quit smoking and smoking prevalence.&lt;/p&gt; &lt;p&gt;&lt;b&gt;Methods:&lt;/b&gt; We performed time series models using Box-Jenkins autoregressive integrated moving averages (ARIMA) on monthly data on the gross ingredient cost of all nicotine replacement therapy (NRT) prescribed in Scotland in 2003–2009, and quarterly data on self-reported smoking prevalence between January 1999 and September 2010 from the Scottish Household Survey.&lt;/p&gt; &lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; NRT prescription costs were significantly higher than expected over the three months prior to implementation of the legislation. Prescription costs peaked at £1.3 million in March 2006; £292,005.9 (95% CI £260,402.3, £323,609, p&#60;0.001) higher than the monthly norm. Following implementation of the legislation, costs fell exponentially by around 26% per month (95% CI 17%, 35%, p&#60;0.001). Twelve months following implementation, the costs were not significantly different to monthly norms. Smoking prevalence fell by 8.0% overall, from 31.3% in January 1999 to 23.7% in July–September 2010. In the quarter prior to implementation of the legislation, smoking prevalence fell by 1.7% (95% CI 2.4%, 1.0%, p&#60;0.001) more than expected from the underlying trend.&lt;/p&gt; &lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; Quit attempts increased in the three months leading up to Scotland's smoke-free legislation, resulting in a fall in smoking prevalence. However, neither has been sustained suggesting the need for additional tobacco control measures and ongoing support.&lt;/p&gt