Segmented flow coil equilibrator coupled to a proton-transfer-reaction mass spectrometer for measurements of a broad range of volatile organic compounds in seawater

We present a technique that utilises a segmented flow coil equilibrator coupled to a proton-transferreaction mass spectrometer to measure a broad range of dissolved volatile organic compounds. Thanks to its relatively large surface area for gas exchange, small internal volume, and smooth headspace-water separation, the equilibrator is highly efficient for gas exchange and has a fast response time (under 1 min). The system allows for both continuous and discrete measurements of volatile organic compounds in seawater due to its low sample water flow (100 cm3 min-1) and the ease of changing sample intake. The equilibrator setup is both relatively inexpensive and compact. Hence, it can be easily reproduced and installed on a variety of oceanic platforms, particularly where space is limited. The internal area of the equilibrator is smooth and unreactive. Thus, the segmented flow coil equilibrator is expected to be less sensitive to biofouling and easier to clean than membrane-based equilibration systems. The equilibrator described here fully equilibrates for gases that are similarly soluble or more soluble than toluene and can easily be modified to fully equilibrate for even less soluble gases. The method has been successfully deployed in the Canadian Arctic. Some example data from underway surface water and Niskin bottle measurements in the sea ice zone are presented to illustrate the efficacy of this measurement system

Underway seawater and atmospheric measurements of volatile organic compounds in the Southern Ocean

Dimethyl sulfide and volatile organic compounds (VOCs) are important for atmospheric chemistry. The emissions of biogenically derived organic gases, including dimethyl sulfide and especially isoprene, are not well constrained in the Southern Ocean. Due to a paucity of measurements, the role of the ocean in the atmospheric budgets of atmospheric methanol, acetone, and acetaldehyde is even more poorly known. In order to quantify the air-sea fluxes of these gases, we measured their seawater concentrations and air mixing ratios in the Atlantic sector of the Southern Ocean, along a ĝˆ1/4 11 000 km long transect at approximately 60ĝˆ S in February-April 2019. Concentrations, oceanic saturations, and estimated fluxes of five simultaneously sampled gases (dimethyl sulfide, isoprene, methanol, acetone, and acetaldehyde) are presented here. Campaign mean (±1σ) surface water concentrations of dimethyl sulfide, isoprene, methanol, acetone, and acetaldehyde were 2.60 (±3.94), 0.0133 (±0.0063), 67 (±35), 5.5 (±2.5), and 2.6 (±2.7) nmol dm-3 respectively. In this dataset, seawater isoprene and methanol concentrations correlated positively. Furthermore, seawater acetone, methanol, and isoprene concentrations were found to correlate negatively with the fugacity of carbon dioxide, possibly due to a common biological origin. Campaign mean (±1σ) air mixing ratios of dimethyl sulfide, isoprene, methanol, acetone, and acetaldehyde were 0.17 (±0.09), 0.053 (±0.034), 0.17 (±0.08), 0.081 (±0.031), and 0.049 (±0.040) ppbv. We observed diel changes in averaged acetaldehyde concentrations in seawater and ambient air (and to a lesser degree also for acetone and isoprene), which suggest light-driven production. Campaign mean (±1σ) fluxes of 4.3 (±7.4) μmol m-2 d-1 DMS and 0.028 (±0.021) μmol m-2 d-1 isoprene are determined where a positive flux indicates from the ocean to the atmosphere. Methanol was largely undersaturated in the surface ocean with a mean (±1σ) net flux of -2.4 (±4.7) μmol m-2 d-1, but it also had a few occasional episodes of outgassing. This section of the Southern Ocean was found to be a source and a sink for acetone and acetaldehyde this time of the year, depending on location, resulting in a mean net flux of -0.55 (±1.14) μmol m-2 d-1 for acetone and -0.28 (±1.22) μmol m-2 d-1 for acetaldehyde. The data collected here will be important for constraining the air-sea exchange, cycling, and atmospheric impact of these gases, especially over the Southern Ocean

Satellites will address critical science priorities for quantifying ocean carbon

The ability to routinely quantify global carbon dioxide (CO2) absorption by the oceans has become crucial: it provides a powerful constraint for establishing global and regional carbon (C) budgets, and enables identification of the ecological impacts and risks of this uptake on the marine environment. Advances in understanding, technology, and international coordination have made it possible to measure CO2 absorption by the oceans to a greater degree of accuracy than is possible in terrestrial landscapes. These advances, combined with new satellite‐based Earth observation capabilities, increasing public availability of data, and cloud computing, provide important opportunities for addressing critical knowledge gaps. Furthermore, Earth observation in synergy with in‐situ monitoring can provide the large‐scale ocean monitoring that is necessary to support policies to protect ocean ecosystems at risk, and motivate societal shifts toward meeting C emissions targets; however, sustained effort will be needed

Rise and Demise of Bioinformatics? Promise and Progress

The field of bioinformatics and computational biology has gone through a number of transformations during the past 15 years, establishing itself as a key component of new biology. This spectacular growth has been challenged by a number of disruptive changes in science and technology. Despite the apparent fatigue of the linguistic use of the term itself, bioinformatics has grown perhaps to a point beyond recognition. We explore both historical aspects and future trends and argue that as the field expands, key questions remain unanswered and acquire new meaning while at the same time the range of applications is widening to cover an ever increasing number of biological disciplines. These trends appear to be pointing to a redefinition of certain objectives, milestones, and possibly the field itself

Accelerating root system phenotyping of seedlings through a computer-assisted processing pipeline

Background: There are numerous systems and techniques to measure the growth of plant roots. However, phenotyping large numbers of plant roots for breeding and genetic analyses remains challenging. One major difficulty is to achieve high throughput and resolution at a reasonable cost per plant sample. Here we describe a cost-effective root phenotyping pipeline, on which we perform time and accuracy benchmarking to identify bottlenecks in such pipelines and strategies for their acceleration. Results: Our root phenotyping pipeline was assembled with custom software and low cost material and equipment. Results show that sample preparation and handling of samples during screening are the most time consuming task in root phenotyping. Algorithms can be used to speed up the extraction of root traits from image data, but when applied to large numbers of images, there is a trade-off between time of processing the data and errors contained in the database. Conclusions: Scaling-up root phenotyping to large numbers of genotypes will require not only automation of sample preparation and sample handling, but also efficient algorithms for error detection for more reliable replacement of manual interventions

Riverine concentrations and export of dissolved silicon, and potential controls on nutrient stoichiometry, across the land–ocean continuum in Great Britain

Silicon (Si) is an essential nutrient element in freshwater and marine ecosystems, and its abundance relative to macro-nutrients (N, P) can impact phytoplankton communities in eutrophic rivers and estuaries. This study is the first national assessment examining (i) the primary sources (geological, biological, landcover) and controls (geomorphological, precipitation) on the transport of terrestrial dissolved silicon across Great Britain to the ocean, and (ii) the current extent and nature of its interactions with macro-nutrients in these catchments in relation to its potential impacts on phytoplankton community structure. It uses results from a year-long survey of 41 rivers along with historical data. Highest concentrations of dissolved Si (4–5.5 mg L-1) were found in rivers of the chalk- and sedimentary sandstone-based catchments of southern Great Britain and the hard sandstone catchments of Scotland. Catchment yield rates for dissolved Si varied between 0.2 and 2.6 t km−2 yr−1, with highest yields found in catchments with higher precipitation and runoff. Analysis of river N:P and dissolved Si:N ratios suggested that the sampled rivers were typically N enriched, and P limited with respect to dissolved Si. Molar dissolved Si:N ratios < 1, an indicator of river eutrophication, were associated with total nitrogen concentrations exceeding 1.8 mg L-1 or greater. The Indicator of Coastal Eutrophication index was used to assess the potential role of dissolved Si in the eutrophication of coastal waters. Negative values indicating limited eutrophication potential to non-siliceous algae were generally found, although some rivers had annual Indicator of Coastal Eutrophication index values exceeding 0, with values as high as 35 kg C km−2 day−1. In many eutrophic rivers, high dissolved Si concentrations derived from catchment lithology, kept the Indicator of Coastal Eutrophication index values below zero. Results have demonstrated that high N and P export have likely shifted most Great Britain rivers and coastal waters beyond the stoichiometric range where diatoms dominate production and into one where non-siliceous algae maybe increasingly present. Thus, future assessments of macro-nutrient management schemes, such as those involving wetlands should include dissolved Si routinely due to its stoichiometric importance

Dissolved inorganic carbon export from rivers of Great Britain: Spatial distribution and potential catchment-scale controls

Dissolved inorganic carbon (DIC) fluxes from the land to ocean have been quantified for many rivers globally. However, CO2 fluxes to the atmosphere from inland waters are quantitatively significant components of the global carbon cycle that are currently poorly constrained. Understanding, the relative contributions of natural and human-impacted processes on the DIC cycle within catchments may provide a basis for developing improved management strategies to mitigate free CO2 concentrations in rivers and subsequent evasion to the atmosphere. Here, a large, internally consistent dataset collected from 41 catchments across Great Britain (GB), accounting for ∼36% of land area (∼83,997 km2) and representative of national land cover, was used to investigate catchment controls on riverine dissolved inorganic carbon (DIC), bicarbonate (HCO3−) and free CO2 concentrations, fluxes to the coastal sea and annual yields per unit area of catchment. Estimated DIC flux to sea for the survey catchments was 647 kt DIC yr−1 which represented 69% of the total dissolved carbon flux from these catchments. Generally, those catchments with large proportions of carbonate and sedimentary sandstone were found to deliver greater DIC and HCO3− to the ocean. The calculated mean free CO2 yield for survey catchments (i.e. potential CO2 emission to the atmosphere) was 0.56 t C km−2 yr−1. Regression models demonstrated that whilst river DIC (R2 = 0.77) and HCO3− (R2 = 0.77) concentrations are largely explained by the geology of the landmass, along with a negative correlation to annual precipitation, free CO2 concentrations were strongly linked to catchment macronutrient status. Overall, DIC dominates dissolved C inputs to coastal waters, meaning that estuarine carbon dynamics are sensitive to underlying geology and therefore are likely to be reasonably constant. In contrast, potential losses of carbon to the atmosphere via dissolved CO2, which likely constitute a significant fraction of net terrestrial ecosystem production and hence the national carbon budget, may be amenable to greater direct management via altering patterns of land use

BHPR research: qualitative1. Complex reasoning determines patients' perception of outcome following foot surgery in rheumatoid arhtritis

Background: Foot surgery is common in patients with RA but research into surgical outcomes is limited and conceptually flawed as current outcome measures lack face validity: to date no one has asked patients what is important to them. This study aimed to determine which factors are important to patients when evaluating the success of foot surgery in RA Methods: Semi structured interviews of RA patients who had undergone foot surgery were conducted and transcribed verbatim. Thematic analysis of interviews was conducted to explore issues that were important to patients. Results: 11 RA patients (9 ♂, mean age 59, dis dur = 22yrs, mean of 3 yrs post op) with mixed experiences of foot surgery were interviewed. Patients interpreted outcome in respect to a multitude of factors, frequently positive change in one aspect contrasted with negative opinions about another. Overall, four major themes emerged. Function: Functional ability & participation in valued activities were very important to patients. Walking ability was a key concern but patients interpreted levels of activity in light of other aspects of their disease, reflecting on change in functional ability more than overall level. Positive feelings of improved mobility were often moderated by negative self perception ("I mean, I still walk like a waddling duck”). Appearance: Appearance was important to almost all patients but perhaps the most complex theme of all. Physical appearance, foot shape, and footwear were closely interlinked, yet patients saw these as distinct separate concepts. Patients need to legitimize these feelings was clear and they frequently entered into a defensive repertoire ("it's not cosmetic surgery; it's something that's more important than that, you know?”). Clinician opinion: Surgeons' post operative evaluation of the procedure was very influential. The impact of this appraisal continued to affect patients' lasting impression irrespective of how the outcome compared to their initial goals ("when he'd done it ... he said that hasn't worked as good as he'd wanted to ... but the pain has gone”). Pain: Whilst pain was important to almost all patients, it appeared to be less important than the other themes. Pain was predominately raised when it influenced other themes, such as function; many still felt the need to legitimize their foot pain in order for health professionals to take it seriously ("in the end I went to my GP because it had happened a few times and I went to an orthopaedic surgeon who was quite dismissive of it, it was like what are you complaining about”). Conclusions: Patients interpret the outcome of foot surgery using a multitude of interrelated factors, particularly functional ability, appearance and surgeons' appraisal of the procedure. While pain was often noted, this appeared less important than other factors in the overall outcome of the surgery. Future research into foot surgery should incorporate the complexity of how patients determine their outcome Disclosure statement: All authors have declared no conflicts of interes

Short-Lived Trace Gases in the Surface Ocean and the Atmosphere

The two-way exchange of trace gases between the ocean and the atmosphere is important for both the chemistry and physics of the atmosphere and the biogeochemistry of the oceans, including the global cycling of elements. Here we review these exchanges and their importance for a range of gases whose lifetimes are generally short compared to the main greenhouse gases and which are, in most cases, more reactive than them. Gases considered include sulphur and related compounds, organohalogens, non-methane hydrocarbons, ozone, ammonia and related compounds, hydrogen and carbon monoxide. Finally, we stress the interactivity of the system, the importance of process understanding for modeling, the need for more extensive field measurements and their better seasonal coverage, the importance of inter-calibration exercises and finally the need to show the importance of air-sea exchanges for global cycling and how the field fits into the broader context of Earth System Science

Constraining the Oceanic Uptake and Fluxes of Greenhouse Gases by Building an Ocean Network of Certified Stations: The Ocean Component of the Integrated Carbon Observation System, ICOS-Oceans

The European Research Infrastructure Consortium “Integrated Carbon Observation System” (ICOS) aims at delivering high quality greenhouse gas (GHG) observations and derived data products (e.g., regional GHG-flux maps) for constraining the GHG balance on a European level, on a sustained long-term basis. The marine domain (ICOS-Oceans) currently consists of 11 Ship of Opportunity lines (SOOP – Ship of Opportunity Program) and 10 Fixed Ocean Stations (FOSs) spread across European waters, including the North Atlantic and Arctic Oceans and the Barents, North, Baltic, and Mediterranean Seas. The stations operate in a harmonized and standardized way based on community-proven protocols and methods for ocean GHG observations, improving operational conformity as well as quality control and assurance of the data. This enables the network to focus on long term research into the marine carbon cycle and the anthropogenic carbon sink, while preparing the network to include other GHG fluxes. ICOS data are processed on a near real-time basis and will be published on the ICOS Carbon Portal (CP), allowing monthly estimates of CO2 air-sea exchange to be quantified for European waters. ICOS establishes transparent operational data management routines following the FAIR (Findable, Accessible, Interoperable, and Reusable) guiding principles allowing amongst others reproducibility, interoperability, and traceability. The ICOS-Oceans network is actively integrating with the atmospheric (e.g., improved atmospheric measurements onboard SOOP lines) and ecosystem (e.g., oceanic direct gas flux measurements) domains of ICOS, and utilizes techniques developed by the ICOS Central Facilities and the CP. There is a strong interaction with the international ocean carbon cycle community to enhance interoperability and harmonize data flow. The future vision of ICOS-Oceans includes ship-based ocean survey sections to obtain a three-dimensional understanding of marine carbon cycle processes and optimize the existing network design