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Vertical profiles of salinity, and isotopic abundance ratios of hydrogen (δ2H) and oxygen (δ18O) of 18 landfast ice cores, collected along the northeast coast of James Bay in March 2019, and one ice core collected in Belcher Islands, were used to obtain the winter timeseries of the spatiotemporal evolution of the under-ice plume of La Grande River (LGR), the dominant river in the area. Variability in the isotopic composition and salinity of the ice cores indicated changes to the water source composition at the ice–water interface when the ice layers formed. The increased presence of river water beneath the ice during January–March was marked by more negative isotopic ratios in the lower portion of the ice as river discharge was increased for hydroelectric production. River water was the source of ∼43% of the ice in our ice core samples (n = 320) with the interquartile range from 16% to 71%. The river water fractions incorporated into the ice indicate that LGR under-ice plume extended more than 75 km north and at least 30 km south of the river mouth for ∼3 months. These findings correspond well with more challenging to obtain hydrographic observations. End-of-winter ice core sampling and analysis for isotopic abundance has potential as a tool to monitor dispersal of LGR discharge into the ice-covered coastal environment.

IntroductionER aminopeptidase 1 (ERAP1) is a polymorphic intracellular aminopeptidase with key roles in antigen presentation and adaptive immune responses. ERAP1 allotype 10 is highly protective toward developing some forms of autoimmunity and displays unusual functional properties, including very low activity versus some substrates.MethodsTo understand the molecular mechanisms that underlie the biology of allotype 10, we studied its enzymatic and biophysical properties focusing on its unique polymorphisms V349M and Q725R.ResultsCompared to ancestral allotype 1, allotype 10 is much less effective in trimming small substrates but presents allosteric kinetics that ameliorate activity differences at high substrate concentrations. Furthermore, it is inhibited by a transition-state analogue via a non-competitive mechanism and is much less responsive to an allosteric small-molecule modulator. It also presents opposite enthalpy, entropy, and heat capacity of activation compared to allotype 1, and its catalytic rate is highly dependent on viscosity. Polymorphisms V349M and Q725R significantly contribute to the lower enzymatic activity of allotype 10 for small substrates, especially at high substrate concentrations, influence the cooperation between the regulatory and active sites, and regulate viscosity dependence, likely by limiting product release.ConclusionsOverall, our results suggest that allotype 10 is not just an inactive variant of ERAP1 but rather carries distinct enzymatic properties that largely stem from changes at positions 349 and 725. These changes affect kinetic and thermodynamic parameters that likely control rate-limiting steps in the catalytic cycle, resulting in an enzyme optimized for sparing small substrates and contributing to the homeostasis of antigenic epitopes in the ER.

Herein, we present the structure-based design, synthesis and biological evaluation of novel mono- and di-carboxylic 3,4-dihydroquinoxalin-2(1H)-one derivatives as potential heme-independent activators of soluble guanylate cyclase (sGC). Docking calculations of several known sGC agonists by utilizing both a homology model of human sGC β1 Η-ΝΟΧ domain and a recent cryo-EM structure of the same domain guided the structural optimization of various designed compounds. Among these, mono- and di-carboxylic 3,4-dihydroquinoxalin-2(1H)-one derivatives arose as promising candidate sGC activators. A series of such compounds was synthesized and assessed for their effect on sGC activity. None of them was able to trigger any detectable activation of native sGC in prostate cancer (LnCaP) or rat aortic smooth muscle (A7r5) cells, even after loss of heme by treatment with the heme oxidant ODQ. Furthermore, selected derivatives did not exhibit any antagonistic effect against the known heme-independent sGC activator BAY 60-2770 nor any additive or synergistic effect with the heme-dependent NO donor sodium nitroprusside (SNP) on heme-associated sGC in A7r5 cells. However, when tested in vitro using purified recombinant sGC enzyme, the dicarboxylic 3,4-dihydroquinoxalin-2(1H)-one derivative 30d was able to increase the enzymatic activity of both the wild-type α1/β1 sGC dimer (by 4.4-fold, EC50 = 0.77 μΜ) as well as the heme-free α1/β1 His105Ala mutant sGC (by 4.8-fold, EC50 = 1.8 μΜ). Notably, the activity of compound 30d towards the mutant α1/β1 Η105A enzyme was comparable with that previously reported by us for the bona fide activator BAY 60-2770, using the functionally equivalent wild-type sGC preparation treated with ODQ. These results indicate that compound 30d can indeed act as a promising sGC activator and may serve as a basic structure in the design of novel, optimized analogues with enhanced sGC agonistic activity and improved efficiency in cell-based and in vivo systems.

Abstract Processing of N-terminally elongated antigenic peptide precursors by Endoplasmic Reticulum Aminopeptidase 1 (ERAP1) is a key step in antigen presentation and the adaptive immune response. Although ERAP1 can efficiently process long peptides in solution, it has been proposed that it can also process peptides bound onto Major Histocompatibility Complex I molecules (MHCI). In a previous study, we suggested that the occasionally observed “ontο MHCI” trimming by ERAP1 is likely due to fast peptide dissociation followed by solution trimming, rather than direct action of ERAP1 onto the MHCI complex. However, other groups have proposed that ERAP1 can trim peptides covalently bound onto MHCI, which would preclude peptide dissociation. To explore this interaction, we constructed disulfide-linked MHCI-peptide complexes using HLA-B*08 and a 12mer kinetically labile peptide, or a 16mer carrying a phosphinic transition-state analogue N-terminus with high-affinity for ERAP1. Kinetic and biochemical analyses suggested that while both peptides could access the ERAP1 active site when free in solution, they were unable to do so when tethered in the MHCI binding groove. Our results suggest that MHCI binding protects, rather than promotes, antigenic peptide precursor trimming by ERAP1 and thus solution trimming is the more likely model of antigenic peptide processing.

The MALINA oceanographic campaign was conducted during summer 2009 to investigate the carbon stocks and the processes controlling the carbon fluxes in the Mackenzie River estuary and the Beaufort Sea. During the campaign, an extensive suite of physical, chemical and biological variables were measured across seven shelf–basin transects (south–north) to capture the meridional gradient between the estuary and the open ocean. Key variables such as temperature, absolute salinity, radiance, irradiance, nutrient concentrations, chlorophyll a concentration, bacteria, phytoplankton and zooplankton abundance and taxonomy, and carbon stocks and fluxes were routinely measured onboard the Canadian research icebreaker CCGS Amundsen and from a barge in shallow coastal areas or for sampling within broken ice fields. Here, we present the results of a joint effort to compile and standardize the collected data sets that will facilitate their reuse in further studies of the changing Arctic Ocean. The data set is available at https://doi.org/10.17882/75345 (Massicotte et al., 2020).

Endoplasmic reticulum aminopeptidases 1 and 2 (ERAP1 and ERAP2) play important roles in the generation of antigenic peptides presented by Major Histocompatibility Class I (MHCI) molecules and indirectly regulate adaptive immune responses. Although the discrete function of these enzymes has been extensively characterized, recent reports have suggested that they can also form heterodimers with functional consequences. However, lack of structural characterization of a putative ERAP1/ERAP2 dimer has limited our understanding of its biological role and significance. To address this, we employed computational molecular dynamics calculations to explore the topology of interactions between these two, based on experimentally determined homo-dimerization interfaces observed in crystal structures of ERAP2 or homologous enzymes. Our analysis of 8 possible dimerization models, suggested that the most likely ERAP1/ERAP2 heterodimerization topology involves the exon 10 loop, a non-conserved loop previously implicated in interactions between ERAP1 and the disulfide-bond shuffling chaperone ERp44. This dimerization topology allows access to the active site of both enzymes and is consistent with a previously reported construct in which ERAP1 and ERAP2 were linked by Fos/Jun zipper tags. The proposed model constitutes a tentative structural template to help understand the physiological role and significance of ERAP1/ERAP2 molecular interactions.

An amendment to this paper has been published and can be accessed via the original article.

Members of the oxytocinase subfamily of M1 aminopeptidases (ERAP1, ERAP2, and IRAP) play important roles in both the adaptive and innate human immune responses. Their enzymatic activity can contribute to the pathogenesis of several major human diseases ranging from viral and parasitic infections to autoimmunity and cancer. We have previously demonstrated that diaminobenzoic acid derivatives show promise as selective inhibitors for this group of aminopeptidases. In this study, we have thoroughly explored a series of 3,4-diaminobenzoic acid derivatives as inhibitors of this class of enzymes, achieving submicromolar inhibitors for ERAP2 (IC50 = 237 nM) and IRAP (IC50 = 105 nM). Cell-based analysis indicated that the lead compounds can be effective in downregulating macrophage activation induced by lipopolysaccharide and interferon-γ as well as cross-presentation by bone marrow-derived dendritic cells. Our results indicate that this class of inhibitors may be useful for the targeted downregulation of immune responses.

Riboswitches are structured non-coding RNAs found in the 5′ UTR of important genes for bacterial metabolism, virulence and survival. Upon the binding of specific ligands that can vary from simple ions to complex molecules such as nucleotides and tRNAs, riboswitches change their local and global mRNA conformations to affect downstream transcription or translation. Due to their dynamic nature and central regulatory role in bacterial metabolism, riboswitches have been exploited as novel RNA-based targets for the development of new generation antibacterials that can overcome drug-resistance problems. During recent years, several important riboswitch structures from many bacterial representatives, including several prominent human pathogens, have shown that riboswitches are ideal RNA targets for new compounds that can interfere with their structure and function, exhibiting much reduced resistance over time. Most interestingly, mainstream antibiotics that target the ribosome have been shown to effectively modulate the regulatory behavior and capacity of several riboswitches, both in vivo and in vitro, emphasizing the need for more in-depth studies and biological evaluation of new antibiotics. Herein, we summarize the currently known compounds that target several main riboswitches and discuss the role of mainstream antibiotics as modulators of T-box riboswitches, in the dawn of an era of novel inhibitors that target important bacterial regulatory RNAs.

The β3 subunit of nicotinic acetylcholine receptors (nAChRs) participates in heteropentameric assemblies with some α and other β neuronal subunits forming a plethora of various subtypes, differing in their electrophysiological and pharmacological properties. While β3 has for several years been considered an accessory subunit without direct participation in the formation of functional binding sites, recent electrophysiology data have disputed this notion and indicated the presence of a functional (+) side on the extracellular domain (ECD) of β3. In this study, we present the 2.4 Å resolution crystal structure of the monomeric β3 ECD, which revealed rather distinctive loop C features as compared to those of α nAChR subunits, leading to intramolecular stereochemical hindrance of the binding site cavity. Vigorous molecular dynamics simulations in the context of full length pentameric β3-containing nAChRs, while not excluding the possibility of a β3 (+) binding site, demonstrate that this site cannot efficiently accommodate the agonist nicotine. From the structural perspective, our results endorse the accessory rather than functional role of the β3 nAChR subunit, in accordance with earlier functional studies on β3-containing nAChRs.

Endoplasmic reticulum aminopeptidases, ERAP1 and ERAP2, as well as Insulin regulated aminopeptidase (IRAP) play key roles in antigen processing, and have recently emerged as biologically important targets for manipulation of antigen presentation. Taking advantage of the available structural and substrate-selectivity data for these enzymes, we have rationally designed a new series of inhibitors that display low micromolar activity. The selectivity profile for these three highly homologous aminopeptidases provides a promising avenue for modulating intracellular antigen processing.

In order to gain a deeper understanding of the recently emerged and highly divergent Omicron variant of concern (VoC), a study of amino acid substitution (AAS) patterns was performed and compared with those of the other four successful variants of concern (Alpha, Beta, Gamma, Delta) and one closely related variant of interest (VoI—Lambda). The Spike ORF consistently emerges as an AAS hotspot in all six lineages, but in Omicron this enrichment is significantly higher. The progenitors of each of these VoC/VoI lineages underwent positive selection in the Spike ORF. However, once they were established, their Spike ORFs have been undergoing purifying selection, despite the application of global vaccination schemes from 2021 onwards. Our analyses reject the hypothesis that the heavily mutated receptor binding domain (RBD) of the Omicron Spike was introduced via recombination from another closely related Sarbecovirus. Thus, successive point mutations appear as the most parsimonious scenario. Intriguingly, in each of the six lineages, we observed a significant number of AAS wherein the new residue is not present at any homologous site among the other known Sarbecoviruses. Such AAS should be further investigated as potential adaptations to the human host. By studying the phylogenetic distribution of AAS shared between the six lineages, we observed that the Omicron (BA.1) lineage had the highest number (8/10) of recurrent mutations.

The source strength and capability of aerosol particles in the Arctic to act as cloud condensation nuclei have important implications for understanding the indirect aerosol–cloud effect within the polar climate system. It has been shown in several Arctic regions that ultrafine particle (UFP) formation and growth is a key contributor to aerosol number concentrations during the summer. This study uses aerosol number size distribution measurements from shipboard expeditions aboard the research icebreaker CCGS Amundsen in the summers of 2014 and 2016 throughout the Canadian Arctic to gain a deeper understanding of the drivers of UFP formation and growth within this marine boundary layer. UFP number concentrations (diameter > 4 nm) in the range of 101–104 cm−3 were observed during the two seasons, with concentrations greater than 103 cm−3 occurring more frequently in 2016. Higher concentrations in 2016 were associated with UFP formation and growth, with events occurring on 41 % of days, while events were only observed on 6 % of days in 2014. Assessment of relevant parameters for aerosol nucleation showed that the median condensation sink in this region was approximately 1.2 h−1 in 2016 and 2.2 h−1 in 2014, which lie at the lower end of ranges observed at even the most remote stations reported in the literature. Apparent growth rates of all observed events in both expeditions averaged 4.3 ± 4.1 nm h−1, in general agreement with other recent studies at similar latitudes. Higher solar radiation, lower cloud fractions, and lower sea ice concentrations combined with differences in the developmental stage and activity of marine microbial communities within the Canadian Arctic were documented and help explain differences between the aerosol measurements made during the 2014 and 2016 expeditions. These findings help to motivate further studies of biosphere–atmosphere interactions within the Arctic marine environment to explain the production of UFP and their growth to sizes relevant for cloud droplet activation.

The enantioselectivity of β-cyclodextrin (β-CD) towards L- and D-N-acetyltryptophan (NAcTrp) has been studied in aqueous solution and the crystalline state. NMR studies in solution show that β-CD forms complexes of very similar but not identical geometry with both L- and D-NAcTrp and exhibits stronger binding with L-NAcTrp. In the crystalline state, only β-CD–L-NAcTrp crystallizes readily from aqueous solutions as a dimeric complex (two hosts enclosing two guest molecules). In contrast, crystals of the complex β-CD–D-NAcTrp were never obtained, although numerous conditions were tried. In aqueous solution, the orientation of the guest in both complexes is different than in the β-CD–L-NAcTrp complex in the crystal. Overall, the study shows that subtle differences observed between the β-CD–L,D-NAcTrp complexes in aqueous solution are magnified at the onset of crystallization, as a consequence of accumulation of many soft host–guest interactions and of the imposed crystallographic order, thus resulting in very dissimilar propensity of each enantiomer to produce crystals with β-CD.

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 Saccharomyces cerevisiae has been analyzed together with two more datasets from the fungal pathogen 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.

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.

Insulin-Regulated aminopeptidase (IRAP) is a zinc-dependent aminopeptidase with several important biological functions and is an emerging pharmaceutical target for cognitive enhancement and immune system regulation. Aiming to discover lead-like IRAP inhibitors with enhanced selectivity versus homologous enzymes, we targeted an allosteric site at the C-terminal domain pocket of IRAP. We compiled a library of 2.5 million commercially available compounds from the ZINC database, and performed molecular docking at the target pocket of IRAP and the corresponding pocket of the homologous endoplasmic reticulum aminopeptidase 1 (ERAP1). Of the top compounds that showed high selectivity, 305 were further analyzed by molecular dynamics simulations and free energy calculations, leading to the selection of 33 compounds for in vitro evaluation. Two orthogonal functional assays were employed: one using a small fluorogenic substrate and one following the degradation of oxytocin, a natural peptidic substrate of IRAP. In vitro evaluation suggested that several of the compounds tested can inhibit IRAP, but the inhibition profile was dependent on substrate size, consistent with the allosteric nature of the targeted site. Overall, our results describe several novel leads as IRAP inhibitors and suggest that the C-terminal domain pocket of IRAP is a promising target for developing highly selective IRAP inhibitors.

The precipitation of ikaite and its fate within sea ice is still poorly understood. We quantify temporal inorganic carbon dynamics in sea ice from initial formation to its melt in a sea ice–seawater mesocosm pool from 11 to 29 January 2013. Based on measurements of total alkalinity (TA) and total dissolved inorganic carbon (TCO2), the main processes affecting inorganic carbon dynamics within sea ice were ikaite precipitation and CO2 exchange with the atmosphere. In the underlying seawater, the dissolution of ikaite was the main process affecting inorganic carbon dynamics. Sea ice acted as an active layer, releasing CO2 to the atmosphere during the growth phase, taking up CO2 as it melted and exporting both ikaite and TCO2 into the underlying seawater during the whole experiment. Ikaite precipitation of up to 167 µmolkg−1 within sea ice was estimated, while its export and dissolution into the underlying seawater was responsible for a TA increase of 64–66 µmolkg−1 in the water column. The export of TCO2 from sea ice to the water column increased the underlying seawater TCO2 by 43.5 µmolkg−1, suggesting that almost all of the TCO2 that left the sea ice was exported to the underlying seawater. The export of ikaite from the ice to the underlying seawater was associated with brine rejection during sea ice growth, increased vertical connectivity in sea ice due to the upward percolation of seawater and meltwater flushing during sea ice melt. Based on the change in TA in the water column around the onset of sea ice melt, more than half of the total ikaite precipitated in the ice during sea ice growth was still contained in the ice when the sea ice began to melt. Ikaite crystal dissolution in the water column kept the seawater pCO2 undersaturated with respect to the atmosphere in spite of increased salinity, TA and TCO2 associated with sea ice growth. Results indicate that ikaite export from sea ice and its dissolution in the underlying seawater can potentially hamper the effect of oceanic acidification on the aragonite saturation state (Ωaragonite) in fall and in winter in ice-covered areas, at the time when Ωaragonite is smallest.

The distributions of carbonate system parameters in Hudson Bay, which not only receives nearly one-third of Canada's river discharge but is also subject to annual cycles of sea-ice formation and melt, indicate that the timing and magnitude of freshwater inputs play an important role in carbon biogeochemistry and acidification in this unique Arctic ecosystem. This study uses basin-wide measurements of dissolved inorganic carbon (DIC) and total alkalinity (TA), as well as stable isotope tracers (δ18O and δ13CDIC), to provide a detailed assessment of carbon cycling processes within the bay. Surface distributions of carbonate parameters reveal the particular importance of freshwater inputs in the southern portion of the bay. Based on TA, we surmise that the deep waters in the Hudson Bay are largely of Pacific origin. Riverine TA end-members vary significantly both regionally and with small changes in near-surface depths, highlighting the importance of careful surface water sampling in highly stratified waters. In an along-shore transect, large increases in subsurface DIC are accompanied by equivalent decreases in δ13CDIC with no discernable change in TA, indicating a respiratory DIC production on the order of 100 µmol kg−1 DIC during deep water circulation around the bay.

Zebrafish has emerged as a powerful model organism for high throughput drug screening. Several morphological criteria, transgenic lines and in situ expression screens have been developed to identify novel bioactive compounds and their mechanism of action. Here, we used the inhibition of melanogenesis during early zebrafish embryo development to identify natural compounds that block melanogenesis. We identified an extract from the Greek hawthorn Crataegus pycnoloba as a potent inhibitor of melanin synthesis and used activity based subfractionation to identify active subfractions and eventually three single compounds of the same family (dibenzofurans). These compounds show reversible inhibition of melanin synthesis and do not act via inhibition of tyrosinase. We also showed that they do not interfere with neural crest differentiation or migration. We identified via in silico modeling that the compounds can bind to the aryl hydrocarbon receptor (AHR) and verified activation of the Ahr signaling pathway showing the induction of the expression of target genes.

Net ecosystem exchange of carbon was measured using eddy covariance for four growing seasons at a subarctic hummocky fen in northern Manitoba, Canada. Over a 115 day measurement period each year, cumulative net ecosystem exchange of carbon ranged from a gain of 49 g C m−2 to a loss of 16 g C m−2 with a mean loss of 6 g C m−2 from the fen, with an uncertainty of about ±34 g C m−2. Ecosystem respiration decreased with higher water tables (r2 = 0.3), especially in one summer when flooding occurred to 0.12 m above the peat surface. Additional methane emissions previously documented for the site of 4–5.7 g C m−2 year−1 added to the carbon loss. Carbon loss was measured from this same fen in the 1990s and it is likely that the carbon gain (peat accumulation) during past centuries has not continued in recent decades. Scaling to annual greenhouse gas emissions as a 100 year global warming potential showed that this fen is currently a source of 192–490 g CO2-equivalents m−2 year−1 based on both carbon dioxide and methane flux measurements, indicating that peat is decomposing.

Eddy covariance observations of CO2 fluxes were conducted during March–April 2012 in a temporally sequential order for 8, 4 and 30 days, respectively, at three locations on fast sea ice and on newly formed polynya ice in a coastal fjord environment in northeast Greenland. CO2 fluxes at the sites characterized by fast sea ice (ICEI and DNB) were found to increasingly reflect periods of strong outgassing in accordance with the progression of springtime warming and the occurrence of strong wind events: FCO2ICE1 = 1.73 ± 5 mmol m−2 day−1 and FCO2DNB = 8.64 ± 39.64 mmol m−2 day−1, while CO2 fluxes at the polynya site (POLYI) were found to generally reflect uptake FCO2POLY1 = −9.97 ± 19.8 mmol m−2 day−1. Values given are the mean and standard deviation, and negative/positive values indicate uptake/outgassing, respectively. A diurnal correlation analysis supports a significant connection between site energetics and CO2 fluxes linked to a number of possible thermally driven processes, which are thought to change the pCO2 gradient at the snow–ice interface. The relative influence of these processes on atmospheric exchanges likely depends on the thickness of the ice. Specifically, the study indicates a predominant influence of brine volume expansion/contraction, brine dissolution/concentration and calcium carbonate formation/dissolution at sites characterized by a thick sea-ice cover, such that surface warming leads to an uptake of CO2 and vice versa, while convective overturning within the sea-ice brines dominate at sites characterized by comparatively thin sea-ice cover, such that nighttime surface cooling leads to an uptake of CO2 to the extent permitted by simultaneous formation of superimposed ice in the lower snow column.

Melt pond formation is a common feature of spring and summer Arctic sea ice, but the role and impact of sea ice melt and pond formation on both the direction and size of CO2 fluxes between air and sea is still unknown. Here we report on the CO2–carbonate chemistry of melting sea ice, melt ponds and the underlying seawater as well as CO2 fluxes at the surface of first-year landfast sea ice in the Resolute Passage, Nunavut, in June 2012. Early in the melt season, the increase in ice temperature and the subsequent decrease in bulk ice salinity promote a strong decrease of the total alkalinity (TA), total dissolved inorganic carbon (TCO2) and partial pressure of CO2 (pCO2) within the bulk sea ice and the brine. As sea ice melt progresses, melt ponds form, mainly from melted snow, leading to a low in situ melt pond pCO2 (36 μatm). The percolation of this low salinity and low pCO2 meltwater into the sea ice matrix decreased the brine salinity, TA and TCO2, and lowered the in situ brine pCO2 (to 20 μatm). This initial low in situ pCO2 observed in brine and melt ponds results in air–ice CO2 fluxes ranging between −0.04 and −5.4 mmol m−2 day−1 (negative sign for fluxes from the atmosphere into the ocean). As melt ponds strive to reach pCO2 equilibrium with the atmosphere, their in situ pCO2 increases (up to 380 μatm) with time and the percolation of this relatively high concentration pCO2 meltwater increases the in situ brine pCO2 within the sea ice matrix as the melt season progresses. As the melt pond pCO2 increases, the uptake of atmospheric CO2 becomes less significant. However, since melt ponds are continuously supplied by meltwater, their in situ pCO2 remains undersaturated with respect to the atmosphere, promoting a continuous but moderate uptake of CO2 (~ −1 mmol m−2 day−1) into the ocean. Considering the Arctic seasonal sea ice extent during the melt period (90 days), we estimate an uptake of atmospheric CO2 of −10.4 Tg of C yr−1. This represents an additional uptake of CO2 associated with Arctic sea ice that needs to be further explored and considered in the estimation of the Arctic Ocean's overall CO2 budget.

Estimating representative surface fluxes using eddy covariance leads invariably to questions concerning inclusion or exclusion of low-frequency flux contributions. For studies where fluxes are linked to local physical parameters and up-scaled through numerical modelling efforts, low-frequency contributions interfere with our ability to isolate local biogeochemical processes of interest, as represented by turbulent fluxes. No method currently exists to disentangle low-frequency contributions on flux estimates. Here, we present a novel comprehensive numerical scheme to identify and separate out low-frequency contributions to vertical turbulent surface fluxes. For high flux rates (|Sensible heat flux| > 40 Wm−2, |latent heat flux|> 20 Wm−2 and |CO2 flux|> 100 mmol m−2 d−1 we found that the average relative difference between fluxes estimated by ogive optimization and the conventional method was low (5–20%) suggesting negligible low-frequency influence and that both methods capture the turbulent fluxes equally well. For flux rates below these thresholds, however, the average relative difference between flux estimates was found to be very high (23–98%) suggesting non-negligible low-frequency influence and that the conventional method fails in separating low-frequency influences from the turbulent fluxes. Hence, the ogive optimization method is an appropriate method of flux analysis, particularly in low-flux environments.

Antigenic peptides presented by the major histocompatibility complex class I (MHC-I) molecules for recognition by cytotoxic T-lymphocytes are processed by members of the oxytocinase sub-family of M1 aminopeptidases ERAP1, ERAP2, and IRAP. These three homologous zinc metallopeptidases trim N-terminally extended precursor antigenic peptides down to the correct length for loading onto the MHC-I but can also destroy some antigenic peptides by over-trimming, therefore, influencing the antigenic peptide repertoire and immunodominance hierarchy. Polymorphic variation has been found to affect their trimming function and predispose to human disease in complex and poorly understood patterns. Structural and biochemical analysis have pointed toward a complicated trimming mechanism that involves a major conformational transition during each catalytic cycle. Here, we provide an overview of current knowledge on the structure and mechanism of action of those enzymes with a focus on the proposed key role of conformational dynamics in their function.

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 CO2 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 −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.

The accelerated decline in Arctic sea ice and an ongoing trend toward more energetic atmospheric and oceanic forcings are modifying carbon cycling in the Arctic Ocean. A critical issue is to understand how net community production (NCP; the balance between gross primary production and community respiration) responds to changes and modulates air–sea CO2 fluxes. Using data collected as part of the ArcticNet–Malina 2009 expedition in the southeastern Beaufort Sea (Arctic Ocean), we synthesize information on sea ice, wind, river, water column properties, metabolism of the planktonic food web, organic carbon fluxes and pools, as well as air–sea CO2 exchange, with the aim of documenting the ecosystem response to environmental changes. Data were analyzed to develop a non-steady-state carbon budget and an assessment of NCP against air–sea CO2 fluxes. During the field campaign, the mean wind field was a mild upwelling-favorable wind (~ 5 km h−1) from the NE. A decaying ice cover (< 80% concentration) was observed beyond the shelf, the latter being fully exposed to the atmosphere. We detected some areas where the surface mixed layer was net autotrophic owing to high rates of primary production (PP), but the ecosystem was overall net heterotrophic. The region acted nonetheless as a sink for atmospheric CO2, with an uptake rate of −2.0 ± 3.3 mmol C m−2 d−1 (mean ± standard deviation associated with spatial variability). We attribute this discrepancy to (1) elevated PP rates (> 600 mg C m−2 d−1) over the shelf prior to our survey, (2) freshwater dilution by river runoff and ice melt, and (3) the presence of cold surface waters offshore. Only the Mackenzie River delta and localized shelf areas directly affected by upwelling were identified as substantial sources of CO2 to the atmosphere (> 10 mmol C m−2 d−1). Daily PP rates were generally < 100 mg C m−2 d−1 and cumulated to a total PP of ~ 437.6 × 103 t C for the region over a 35-day period. This amount was about twice the organic carbon delivery by river inputs (~ 241.2 × 103 t C). Subsurface PP represented 37.4% of total PP for the whole area and as much as ~ 72.0% seaward of the shelf break. In the upper 100 m, bacteria dominated (54%) total community respiration (~ 250 mg C m−2 d−1), whereas protozoans, metazoans, and benthos, contributed to 24, 10, and 12%, respectively. The range of production-to-biomass ratios of bacteria was wide (1–27% d−1), while we estimated a narrower range for protozoans (6–11% d−1) and metazoans (1–3% d−1). Over the shelf, benthic biomass was twofold (~ 5.9 g C m−2) the biomass of pelagic heterotrophs (~ 2.4 g C m−2), in accord with high vertical carbon fluxes on the shelf (956 ± 129 mg C m−2 d−1). Threshold PP (PP at which NCP becomes positive) in the surface layer oscillated from 20 to 152 mg C m−2 d−1, with a pattern from low-to-high values as the distance from the Mackenzie River decreased. We conclude that (1) climate change is exacerbating the already extreme biological gradient across the Beaufort shelf–basin system; (2) the Mackenzie Shelf acts as a weak sink for atmospheric CO2, suggesting that PP might exceed the respiration of terrigenous and marine organic matter in the surface layer; and (3) shelf break upwelling can transfer CO2 to the atmosphere, but CO2 outgassing can be attenuated if nutrients brought also by upwelling support diatom production. Our study underscores that cross-shelf exchange of waters, nutrients and particles is a key mechanism that needs to be properly monitored as the Arctic transits to a new state.

Ecosystem-scale methane (CH4) flux (FCH4) over a subarctic fen at Churchill, Manitoba, Canada was measured to understand the magnitude of emissions during spring and fall shoulder seasons, and the growing season in relation to physical and biological conditions. FCH4 was measured using eddy covariance with a closed-path analyser in four years (2008–2011). Cumulative measured annual FCH4 (shoulder plus growing seasons) ranged from 3.0 to 9.6 g CH4 m−2 yr−1 among the four study years, with a mean of 6.5 to 7.1 g CH4 m−2 yr−1 depending upon gap-filling method. Soil temperatures to depths of 50 cm and air temperature were highly correlated with FCH4, with near-surface soil temperature at 5 cm most correlated across spring, fall, and the shoulder and growing seasons. The response of FCH4 to soil temperature at the 5 cm depth and air temperature was more than double in spring to that of fall. Emission episodes were generally not observed during spring thaw. Growing season emissions also depended upon soil and air temperatures but the water table also exerted influence, with FCH4 highest when water was 2–13 cm below and lowest when it was at or above the mean peat surface.

The precipitation of ikaite (CaCO3 ⋅ 6H2O) in polar sea ice is critical to the efficiency of the sea ice-driven carbon pump and potentially important to the global carbon cycle, yet the spatial and temporal occurrence of ikaite within the ice is poorly known. We report unique observations of ikaite in unmelted ice and vertical profiles of ikaite abundance and concentration in sea ice for the crucial season of winter. Ice was examined from two locations: a 1 m thick land-fast ice site and a 0.3 m thick polynya site, both in the Young Sound area (74° N, 20° W) of NE Greenland. Ikaite crystals, ranging in size from a few μm to 700 μm, were observed to concentrate in the interstices between the ice platelets in both granular and columnar sea ice. In vertical sea ice profiles from both locations, ikaite concentration determined from image analysis, decreased with depth from surface-ice values of 700–900 μmol kg−1 ice (~25 × 106 crystals kg−1) to values of 100–200 μmol kg−1 ice (1–7 × 106 crystals kg−1) near the sea ice–water interface, all of which are much higher (4–10 times) than those reported in the few previous studies. Direct measurements of total alkalinity (TA) in surface layers fell within the same range as ikaite concentration, whereas TA concentrations in the lower half of the sea ice were twice as high. This depth-related discrepancy suggests interior ice processes where ikaite crystals form in surface sea ice layers and partly dissolve in layers below. Melting of sea ice and dissolution of observed concentrations of ikaite would result in meltwater with a pCO2 of 2.

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.

Two of the most successful chemotherapeutic agents used in the treatment of several neoplasias are bleomycin and cisplatin. Both drugs attack the DNA leading to the cancer cells death via different mechanisms. In view of the fact that the combination with each other leads to enhanced activity with less sever side effects, we have undertaken NMR studies on the complexes formed between bleomycin and PtII, PdII, cisplatin and transplatin. Herein we present a brief review of the studies on metallobleomycins which were carried out by our lab and others, as an outline of the results obtained using NMR in combination to circular dichroism spectroscopy. Our data indicate that in most cases and under several conditions studied, both metal ions form similar complexes with BLM, while more than one species are present in the solution. Structural implications and comparisons with other metallobleomycins are being discussed.

Two of the most successful chemotherapeutic agents used in the treatment of several neoplasias are bleomycin and cisplatin. Both drugs attack the DNA leading to the cancer cells death via different mechanisms. In view of the fact that the combination with each other leads to enhanced activity with less sever side effects, we have undertaken NMR studies on the complexes formed between bleomycin and PtII, PdII, cisplatin and transplatin. Herein we present a brief review of the studies on metallobleomycins which were carried out by our lab and others, as an outline of the results obtained using NMR in combination to circular dichroism spectroscopy. Our data indicate that in most cases and under several conditions studied, both metal ions form similar complexes with BLM while more than one species are present in the solution. Structural implications and comparisons with other metallobleomycins are being discussed. .

Glutathione transferases (GSTs) are enzymes that contribute to cellular detoxification by catalysing the nucleophilic attack of glutathione (GSH) on the electrophilic centre of a number of xenobiotic compounds, including several chemotherapeutic drugs. In the present work we investigated the interaction of the chemotherapeutic drug chlorambucil (CBL) with human GSTA1-1 (hGSTA1-1) using kinetic analysis, protein crystallography and molecular dynamics. In the presence of GSH, CBL behaves as an efficient substrate for hGSTA1-1. The rate-limiting step of the catalytic reaction between CBL and GSH is viscosity-dependent and kinetic data suggest that product release is rate-limiting. The crystal structure of the hGSTA1-1/CBL-GSH complex was solved at 2.1 Å resolution by molecular replacement. CBL is bound at the H-site attached to the thiol group of GSH, is partially ordered and exposed to the solvent, making specific interactions with the enzyme. Molecular dynamics simulations based on the crystal structure indicated high mobility of the CBL moiety and stabilization of the C-terminal helix due to the presence of the adduct. In the absence of GSH, CBL is shown to be an alkylating irreversible inhibitor for hGSTA1-1. Inactivation of the enzyme by CBL followed a biphasic pseudo-first-order saturation kinetics with approximately 1 mol of CBL per mol of dimeric enzyme being incorporated. Structural analysis suggested that the modifying residue is Cys112 which is located at the entrance of the H-site. The results are indicative of a structural communication between the subunits on the basis of mutually exclusive modification of Cys112, indicating that the two enzyme active sites are presumably coordinated.