Surface salinity under transitioning ice cover in the Canada Basin: Climate model biases linked to vertical distribution of fresh water

The Canada Basin has exhibited a significant trend toward a fresher surface layer and thus a more stratified upper-ocean over the past three decades. State-of-the-art ice-ocean models, by contrast, tend to simulate a surface layer that is saltier and less stratified than observed. Here, we examine decadal changes to seasonal processes that may contribute to this wide-reaching model bias using climate model simulations from the Community Earth System Model and below-ice observations from the Arctic Ice Dynamics Joint Experiment in 1975 and Ice Tethered Profilers in 2006-2012. In contrast to the observations, the models simulate salinity profiles that show relatively little variation between 1975 and 2012. We demonstrate that this bias can be mainly attributed to unrealistically deep vertical mixing in the model, creating a surface layer that is saltier than observed. The results provide insight for climate model improvement with broad implications for Arctic sea ice and ecosystem dynamics

HIRDLS poster

A poster supporting the HIRDLS data held at the BADC (High Resolution Dynamics Limb Sounder (HIRDLS) instrument)

Pre-launch calibration of the HIRDLS instrument

Report about the aims for the calibration of the HIRDLS instrument

The response of the Antarctic Circumpolar Current to recent climate change

Observations show a significant intensification of the Southern Hemisphere westerlies, the prevailing winds between the latitudes of 30° and 60° S, over the past decades. A continuation of this intensification trend is projected by climate scenarios for the twenty-first century. The response of the Antarctic Circumpolar Current and the carbon sink in the Southern Ocean to changes in wind stress and surface buoyancy fluxes is under debate. Here we analyse the Argo network of profiling floats and historical oceanographic data to detect coherent hemispheric-scale warming and freshening trends that extend to depths of more than 1,000 m. The warming and freshening is partly related to changes in the properties of the water masses that make up the Antarctic Circumpolar Current, which are consistent with the anthropogenic changes in heat and freshwater fluxes suggested by climate models. However, we detect no increase in the tilt of the surfaces of equal density across the Antarctic Circumpolar Current, in contrast to coarse-resolution model studies. Our results imply that the transport in the Antarctic Circumpolar Current and meridional overturning in the Southern Ocean are insensitive to decadal changes in wind stress

Phagocytosis and digestion of pH-sensitive fluorescent dye (Eos-FP) transfected E. coli in whole blood assays from patients with severe sepsis and septic shock

The function of phagocytic and antigen presenting cells is of crucial importance to sustain immune competence against infectious agents as well as malignancies. We here describe a reproducible procedure for the quantification of phagocytosis by leukocytes in whole blood. For this, a pH-sensitive green-fluorescent protein- (GFP) like dye (Eos-FP) is transfected into infectious microroganisms. After UV-irradiation, the transfected bacteria emit green (≈5160 nm) and red (≈581 nm) fluorescent light at 490 nm excitation. Since the red fluorescent light is sensitive to acidic pH, the phagocytosed bacteria stop emitting red fluorescent light as soon as the phagosomes fuse with lysosomes. The green fluorescence is maintained in the phagolysosome until pathogen degradation is completed. Fluorescence emission can be followed by flow cytometry with filter settings documenting fluorescence 1 (FL 1, FITC) and fluorescence 2 (FL 2, phycoerythrin, PE). Eos-FP transfected bacteria can also be traced within phagocytes using microscopical techniques. A standardized assay has been developed which is suitable for clinical studies by providing clinicians with syringes pre-filled with fixed and appropriately UV-irradiated Eos-FP E. coli (TruCulture™). After adding blood or body fluids to these containers and starting the incubation at 37°C, phagocytosis by granulocytes proceeds over time. Cultures can be terminated at a given time by lysing red blood cells followed by flow cytometry. A pilot study demonstrated that Eos-FP E. coli phagocytosis and digestion was up-regulated in the majority of patients with either severe sepsis or septic shock as compared to healthy donors (p < 0.0001 after o/n incubation). Following treatment with recombinant human granulocyte colony-stimulating factor (rhG-CSF) in selected patients with sepsis, phagolysosome fusion appeared to be accelerated

A computational model of liver iron metabolism

Iron is essential for all known life due to its redox properties; however, these same properties can also lead to its toxicity in overload through the production of reactive oxygen species. Robust systemic and cellular control are required to maintain safe levels of iron, and the liver seems to be where this regulation is mainly located. Iron misregulation is implicated in many diseases, and as our understanding of iron metabolism improves, the list of iron-related disorders grows. Recent developments have resulted in greater knowledge of the fate of iron in the body and have led to a detailed map of its metabolism; however, a quantitative understanding at the systems level of how its components interact to produce tight regulation remains elusive. A mechanistic computational model of human liver iron metabolism, which includes the core regulatory components, is presented here. It was constructed based on known mechanisms of regulation and on their kinetic properties, obtained from several publications. The model was then quantitatively validated by comparing its results with previously published physiological data, and it is able to reproduce multiple experimental findings. A time course simulation following an oral dose of iron was compared to a clinical time course study and the simulation was found to recreate the dynamics and time scale of the systems response to iron challenge. A disease state simulation of haemochromatosis was created by altering a single reaction parameter that mimics a human haemochromatosis gene (HFE) mutation. The simulation provides a quantitative understanding of the liver iron overload that arises in this disease. This model supports and supplements understanding of the role of the liver as an iron sensor and provides a framework for further modelling, including simulations to identify valuable drug targets and design of experiments to improve further our knowledge of this system

Global Analysis of Proline-Rich Tandem Repeat Proteins Reveals Broad Phylogenetic Diversity in Plant Secretomes

Cell walls, constructed by precisely choreographed changes in the plant secretome, play critical roles in plant cell physiology and development. Along with structural polysaccharides, secreted proline-rich Tandem Repeat Proteins (TRPs) are important for cell wall function, yet the evolutionary diversity of these structural TRPs remains virtually unexplored. Using a systems-level computational approach to analyze taxonomically diverse plant sequence data, we identified 31 distinct Pro-rich TRP classes targeted for secretion. This analysis expands upon the known phylogenetic diversity of extensins, the most widely studied class of wall structural proteins, and demonstrates that extensins evolved before plant vascularization. Our results also show that most Pro-rich TRP classes have unexpectedly restricted evolutionary distributions, revealing considerable differences in plant secretome signatures that define unexplored diversity