Sea ice biogeochemistry and material transport across the frozen interface

Author Posting. © Oceanography Society, 2011. This article is posted here by permission of Oceanography Society for personal use, not for redistribution. The definitive version was published in Oceanography 24 no. 3 (2011): 202–218, doi:10.5670/oceanog.2011.72.The porous nature of sea ice not only provides a habitat for ice algae but also opens a pathway for exchanges of organic matter, nutrients, and gases with the seawater below and the atmosphere above. These constituents permeate the ice cover through air-ice gas exchange, brine drainage, seawater entrainment into the ice, and air-sea gas exchange within leads and polynyas. The central goal in sea ice biogeochemistry since the 1980s has been to discover the physical, biological, and chemical rates and pathways by which sea ice affects the distribution and storage of biogenic gases (namely CO2, O2, and dimethyl sulfide) between the ocean and the atmosphere. Historically, sea ice held the fascination of scientists for its role in the ocean heat budget, and the resulting view of sea ice as a barrier to heat and mass transport became its canonical representation. However, the recognition that sea ice contains a vibrant community of ice-tolerant organisms and strategic reserves of carbon has brought forward a more nuanced view of the "barrier" as an active participant in polar biogeochemical cycles. In this context, the organisms and their habitat of brine and salt crystals drive material fluxes into and out of the ice, regulated by liquid and gas permeability. Today, scientists who study sea ice are acutely focused on determining the flux pathways of inorganic carbon, particulate organics, climate-active gases, excess carbonate alkalinity, and ultimately, the role of all of these constituents in the climate system. Thomas and Dieckmann (2010) recently reviewed sea ice biogeochemistry, and so we do not attempt a comprehensive review here. Instead, our goal is to provide a historical perspective, along with some recent discoveries and observations to highlight the most outstanding questions and possibly useful avenues for future research

Positioning resilience science more centrally in affirming LGBTIQA+ persons and communities

Historically, in psychology, there was a tendency towards focusing on the individual and intrapsychic pathologisation of LGBTIQA+ persons. Despite a recent shift to affirmative, systemic, interpersonal, and contextual stances, too much emphasis in South African LGBTIQA+ scholarly work remains on adversity. Adversity derived from historical tensions may have accelerated adaptive problem-solving capabilities and solution-focused behaviours in some LGBTIQA+ populations. Certain solutions have generated creative resilience responses inexorably situated in race, ethnicity, culture, religion, gender, history, political oppression, and social class. Resilience science that has similarly evolved from the individual trait conceptualisation may have an important complementary contribution to make in affirming LGBTIQA+ persons and communities and enhancing the understanding of their resilience. Exploring resilience for wellbeing and survival addresses the infinite streams of human experiences of vulnerability and sustainable adaptive solutions. The multisystemic resilience perspective in this article endeavours to summarise current thinking in resilience science and position its applicability to future South African LGBTIQA+ scholarly work, building on existing systematic and critical reviews relating to the resilience of LGBTIQA+ persons. The aim of this position piece, suggesting the expansion of a ‘resilience’ frame, is to offer an important intervention in the overarching ways in which South African scholars and psychology professionals theorise and conduct research; to inform therapeutic and other psychological services to LGBTIQA+ persons and provide an important counterweight to the more general focus in South African LGBTIQA+ scholarship and psychological practice on adversity.College of Human Science

The Pivotal Role of Protein Phosphorylation in the Control of Yeast Central Metabolism

Protein phosphorylation is the most frequent eukaryotic post-translational modification and can act as either a molecular switch or rheostat for protein functions. The deliberate manipulation of protein phosphorylation has great potential for regulating specific protein functions with surgical precision, rather than the gross effects gained by the over/underexpression or complete deletion of a protein-encoding gene. In order to assess the impact of phosphorylation on central metabolism, and thus its potential for biotechnological and medical exploitation, a compendium of highly confident protein phosphorylation sites (p-sites) for the model organism $\textit{Saccharomyces cerevisiae}$ has been analyzed together with two more datasets from the fungal pathogen $\textit{Candida albicans}$. Our analysis highlights the global properties of the regulation of yeast central metabolism by protein phosphorylation, where almost half of the enzymes involved are subject to this sort of post-translational modification. These phosphorylated enzymes, compared to the nonphosphorylated ones, are more abundant, regulate more reactions, have more protein–protein interactions, and a higher fraction of them are ubiquitinated. The p-sites of metabolic enzymes are also more conserved than the background p-sites, and hundreds of them have the potential for regulating metabolite production. All this integrated information has allowed us to prioritize thousands of p-sites in terms of their potential phenotypic impact. This multi-source compendium should enable the design of future high-throughput (HTP) mutation studies to identify key molecular switches/rheostats for the manipulation of not only the metabolism of yeast, but also that of many other biotechnologically and medically important fungi and eukaryotes.G.D.A. acknowledges financial support from the “ARISTEIA II” Action of the “Operational Programme Education and Lifelong Learning” that is cofunded by the European Social Fund and National Resources (code 4288 to G.D.A.). S.G.O. acknowledges the University of Cambridge for the award of sabbatical leave that allowed him to work with G.D.A. at the University of Thessaly, Greece

Micrometeorological and Thermal Control of Frost Flower Growth and Decay on Young Sea Ice

Frost flowers are transient crystal structures that form on new and young sea ice surfaces. They have been implicated in a variety of biological, chemical, and physical processes and interactions with the atmosphere at the sea ice surface. We describe the atmospheric and radiative conditions and the physical and thermal properties of the sea ice and atmosphere that form, decay, and destroy frost flowers on young sea ice. Frost flower formation occurred during a high-pressure system that caused air temperatures to drop to −30˚C, with relative humidity of 70% (an undersaturated atmosphere), and very calm wind conditions. The sea ice surface temperature at the time of frost flower initiation was 10˚–13˚C warmer than the air temperature. Frost flowers grew on nodules raised above the mean surface height by 5 mm, which were 4˚–6˚C colder than the bare, brine-wetted, highly saline sea ice surface that provided the necessary moisture. The cold nodules created potential water vapour supersaturation zones above them with respect to air over the brine skim. Frost flowers formed and grew overnight in the absence of shortwave radiation, while the net longwave radiation was negative and dominated the net all-wave radiation balance at the surface. The observed crystal habits of the frost flowers were long needles, betraying their origin from the vapour phase at temperatures between −20˚C and −30˚C. After a night of growth, frost flowers decayed in association with increased solar radiation, a net surface radiation balance of 0 W m-2, increased air and surface temperatures, increased wind speed, and decreased relative humidity. We hypothesize that these conditions increased vertical mixing, which eroded near-surface water vapour saturation and initiated sublimation. The frost flowers finally were rapidly destroyed by snowfall.Les fleurs de glace sont des structures cristallines transitoires qui se forment sur des surfaces de glace de mer nouvelles et jeunes. Elles découlent de divers processus et interactions biologiques, chimiques et physiques avec l’atmosphère, à la surface de la glace de mer. Nous décrivons les conditions atmosphériques et radiatives de même que les propriétés physiques et thermiques de la glace de mer qui forment, détériorent et détruisent les fleurs de glace sur la jeune glace de mer. La formation de fleurs de glace s’est produite lorsqu’un système de haute pression a fait baisser les températures de l’air à −30 ˚C, avec une humidité relative de 70 % (atmosphère sous-saturée) et un régime des vents très calme. À l’amorçage des fleurs de glace, la température à la surface de la glace de mer était de 10˚ à 13 ˚C plus chaude que la température de l’air. Les fleurs de glace se sont formées sur des nodules élevés au-dessus de la hauteur moyenne de la surface dans une mesure de 5 mm, ce qui était entre 4˚ et 6 ˚C plus froid que la surface de glace de mer brute, saumurée et fortement saline qui a fourni l’humidité nécessaire. En ce qui a trait à l’air au-dessus de l’écume de saumure, les nodules de froid ont créé des zones potentielles de sursaturation de vapeur d’eau au-dessus. Des fleurs de glace se sont formées et ont grossi pendant la nuit, en l’absence de rayonnement de courtes longueurs d’onde, tandis que le rayonnement net de grandes longueurs d’onde était négatif et dominait l’équilibre du rayonnement net de toutes ondes à la surface. L’habitus cristallin observé dans les fleurs de glace prenait la forme de longues aiguilles, trahissant son origine de la phase vapeur à des températures variant de −20 ˚C à −30 ˚C. Après une nuit de croissance, les fleurs de glace se sont détériorées en présence du rayonnement solaire accru, du bilan radiatif de la surface de 0 W m-2, des températures accrues de l’air et de la surface, de la plus grande vitesse du vent et de l’humidité relative réduite. Nous formulons l’hypothèse que ces conditions ont eu pour effet d’augmenter le mélange vertical, ce qui a érodé la saturation de vapeur d’eau près de la surface et déclenché la sublimation. Par la suite, les fleurs de glace ont été rapidement détruites par la chute de neige

Temporal dynamics of ikaite in experimental sea ice

Ikaite (CaCO3 · 6H2O) is a metastable phase of calcium carbonate that normally forms in a cold environment and/or under high pressure. Recently, ikaite crystals have been found in sea ice, and it has been suggested that their precipitation may play an important role in air-sea CO 2 exchange in ice-covered seas. Little is known, however, of the spatial and temporal dynamics of ikaite in sea ice. Here we present evidence for highly dynamic ikaite precipitation and dissolution in sea ice grown at an outdoor pool of the Sea-ice Environmental Research Facility (SERF) in Manitoba, Canada. During the experiment, ikaite precipitated in sea ice when temperatures were below -4 °C, creating three distinct zones of ikaite concentrations: (1) a millimeter-to-centimeter-thin surface layer containing frost flowers and brine skim with bulk ikaite concentrations of >2000 μmol kg-1, (2) an internal layer with ikaite concentrations of 200-400 μmol kg -1, and (3) a bottom layer with ikaite concentrations of <100 μmol kg-1. Snowfall events caused the sea ice to warm and ikaite crystals to dissolve. Manual removal of the snow cover allowed the sea ice to cool and brine salinities to increase, resulting in rapid ikaite precipitation. The observed ikaite concentrations were on the same order of magnitude as modeled by FREZCHEM, which further supports the notion that ikaite concentration in sea ice increases with decreasing temperature. Thus, varying snow conditions may play a key role in ikaite precipitation and dissolution in sea ice. This could have a major implication for CO2 exchange with the atmosphere and ocean that has not been accounted for previously

Barium and Carbon fluxes in the Canadian Arctic Archipelago

Seasonal and spatial variability of dissolved Barium (Ba) in Amundsen Gulf, southeastern Beaufort Sea, was monitored over a full year from September 2007 to September 2008. Dissolved Ba displays a nutrient-type behavior: the maximum water column concentration is located below the surface layer. Highest Ba concentrations are typically observed at river mouths, the lowest concentrations are found in water masses of Atlantic origin. Barium concentrations decrease eastward through the Canadian Arctic Archipelago. Barite (BaSO4) saturation is reached at the maximum concentrations of dissolved Ba in the subsurface layer, whereas the remaining water column is undersaturated. A three end-member mixing model comprising freshwater from sea-ice melt and rivers, as well as upper halocline water, was used to establish their relative contributions to the Ba concentrations in the upper water column of the Amundsen Gulf. Based on water column and riverine Ba contributions, we assess the depletion of dissolved Ba by formation and concomitant sinking of biologically bound Ba (bio-Ba), from which we derive an estimate of the carbon export production. In the upper 50 m of the water column of Amundsen Gulf, riverine Ba accounts for up to 15% of the available dissolved Ba inventory, of which up to 20% is depleted by bio-Ba formation and export. Since riverine inputs and Ba export occur concurrently, the seasonal variability of dissolved Ba in the upper water column is moderate. Assuming a fixed organic carbon to bio-Ba flux ratio, carbon export out of the surface layer is estimated at 1.8{plus minus}0.45 mol C m‑2 yr‑1. We propose a climatological carbon budget for the Amundsen Gulf

The Internal Sequence of the Peptide-Substrate Determines Its N-Terminus Trimming by ERAP1

Background: Endoplasmic reticulum aminopeptidase 1 (ERAP1) trims N-terminally extended antigenic peptide precursors down to mature antigenic peptides for presentation by major histocompatibility complex (MHC) class I molecules. ERAP1 has unique properties for an aminopeptidase being able to trim peptides in vitro based on their length and the nature of their C-termini. Methodology/Principal Findings: In an effort to better understand the molecular mechanism that ERAP1 uses to trim peptides, we systematically analyzed the enzyme's substrate preferences using collections of peptide substrates. We discovered strong internal sequence preferences of peptide N-terminus trimming by ERAP1. Preferences were only found for positively charged or hydrophobic residues resulting to trimming rate changes by up to 100 fold for single residue substitutions and more than 40,000 fold for multiple residue substitutions for peptides with identical N-termini. Molecular modelling of ERAP1 revealed a large internal cavity that carries a strong negative electrostatic potential and is large enough to accommodate peptides adjacent to the enzyme's active site. This model can readily account for the strong preference for positively charged side chains. Conclusions/Significance: To our knowledge no other aminopeptidase has been described to have such strong preferences for internal residues so distal to the N-terminus. Overall, our findings indicate that the internal sequence of the peptide can affect its trimming by ERAP1 as much as the peptide's length and C-terminus. We therefore propose that ERAP1 recognizes the full length of its peptide-substrate and not just the N- and C- termini. It is possible that ERAP1 trimming preferences influence the rate of generation and the composition of antigenic peptides in vivo

Crystal Structure of the Monomeric Extracellular Domain of α9 Nicotinic Receptor Subunit in Complex With α-Conotoxin RgIA: Molecular Dynamics Insights Into RgIA Binding to α9α10 Nicotinic Receptors

The α9 subunit of nicotinic acetylcholine receptors (nAChRs) exists mainly in heteropentameric assemblies with α10. Accumulating data indicate the presence of three different binding sites in α9α10 nAChRs: the α9(+)/α9(−), the α9(+)/α10(−), and the α10(+)/α9(−). The major role of the principal (+) side of the extracellular domain (ECD) of α9 subunit in binding of the antagonists methyllylcaconitine and α-bungarotoxin was shown previously by the crystal structures of the monomeric α9-ECD with these molecules. Here we present the 2.26-Å resolution crystal structure of α9-ECD in complex with α-conotoxin (α-Ctx) RgIA, a potential drug for chronic pain, the first structure reported for a complex between an nAChR domain and an α-Ctx. Superposition of this structure with those of other α-Ctxs bound to the homologous pentameric acetylcholine binding proteins revealed significant similarities in the orientation of bound conotoxins, despite the monomeric state of the α9-ECD. In addition, ligand-binding studies calculated a binding affinity of RgIA to the α9-ECD at the low micromolar range. Given the high identity between α9 and α10 ECDs, particularly at their (+) sides, the presented structure was used as template for molecular dynamics simulations of the ECDs of the human α9α10 nAChR in pentameric assemblies. Our results support a favorable binding of RgIA at α9(+)/α9(−) or α10(+)/α9(−) rather than the α9(+)/α10(−) interface, in accordance with previous mutational and functional data

The structure-function relationship of oncogenic LMTK3

Elucidating signaling driven by lemur tyrosine kinase 3 (LMTK3) could help drug development. Here, we solve the crystal structure of LMTK3 kinase domain to 2.1Å resolution, determine its consensus motif and phosphoproteome, unveiling in vitro and in vivo LMTK3 substrates. Via high-throughput homogeneous time-resolved fluorescence screen coupled with biochemical, cellular, and biophysical assays, we identify a potent LMTK3 small-molecule inhibitor (C28). Functional and mechanistic studies reveal LMTK3 is a heat shock protein 90 (HSP90) client protein, requiring HSP90 for folding and stability, while C28 promotes proteasome-mediated degradation of LMTK3. Pharmacologic inhibition of LMTK3 decreases proliferation of cancer cell lines in the NCI-60 panel, with a concomitant increase in apoptosis in breast cancer cells, recapitulating effects of LMTK3 gene silencing. Furthermore, LMTK3 inhibition reduces growth of xenograft and transgenic breast cancer mouse models without displaying systemic toxicity at effective doses. Our data reinforce LMTK3 as a druggable target for cancer therap