Fluids as primary carriers of sulphur and copper in magmatic assimilation

Magmas readily react with their wall-rocks forming metamorphic contact aureoles. Sulphur and possibly metal mobilization within these contact aureoles is essential in the formation of economic magmatic sulphide deposits. We performed heating and partial melting experiments on a black shale sample from the Paleoproterozoic Virginia Formation, which is the main source of sulphur for the world-class Cu-Ni sulphide deposits of the 1.1 Ga Duluth Complex, Minnesota. These experiments show that an autochthonous devolatilization fluid effectively mobilizes carbon, sulphur, and copper in the black shale within subsolidus conditions (≤ 700 °C). Further mobilization occurs when the black shale melts and droplets of Cu-rich sulphide melt and pyrrhotite form at ∼1000 °C. The sulphide droplets attach to bubbles of devolatilization fluid, which promotes buoyancy-driven transportation in silicate melt. Our study shows that devolatilization fluids can supply large proportions of sulphur and copper in mafic–ultramafic layered intrusion-hosted Cu-Ni sulphide deposits.

RNA Helix Thermodynamics: The End Game

Nearest neighbor parameters for estimating the folding stability of RNA secondary structures are in widespread use. For helices, current parameters penalize terminal AU base pairs relative to terminal GC base pairs. We curated an expanded database of helix stabilities determined by optical melting experiments. Analysis of the updated database shows that terminal penalties depend on the sequence identity of the adjacent penultimate base pair. New nearest neighbor parameters that include this additional sequence dependence accurately predict the measured values of 271 helices in an updated database with a correlation coefficient of 0.982. This refined understanding of helix ends facilitates fitting terms for base pair stacks with GU pairs. Prior parameter sets treated 5'GGUC/3'CUGG separately from other 5'GU/3'UG stacks. The improved understanding of helix end stability, however, makes the separate treatment unnecessary. Introduction of the additional terms was tested with three optical melting experiments. The average absolute difference between measured and predicted free energy changes at 37° C for these three duplexes containing terminal adjacent AU and GU pairs improved from 1.38 to 0.27 kcal/mol. This confirms the need for the additional sequence dependence in the model.

Partitioning of Fe2O3 in peridotite partial melting experiments over a range of oxygen fugacities elucidates ferric iron systematics in mid-ocean ridge basalts and ferric iron content of the upper mantle

Basalts and peridotites from mid-ocean ridges record fO2 near the quartz-fayalite-magnetite buffer (QFM), but peridotite partial melting experiments have mostly been performed in graphite capsules (~ QFM-3), precluding evaluation of ferric iron’s behavior during basalt generation. We performed experiments at 1.5 GPa, 1350–1400 °C, and fO2 from about QFM-3 to QFM+3 to investigate the anhydrous partitioning behavior of Fe2O3 between silicate melts and coexisting peridotite mineral phases. We find spinel/melt partitioning of Fe2O3 ($${D}_{\mathrm{Fe}2\mathrm{O}3}^{\mathrm{spl}/\mathrm{melt}}$$ D Fe 2 O 3 spl / melt ) increases as spinel Fe2O3 concentrations increase, independent of increases in fO2, and decreases with temperature, which is consistent with new and previous experiments at 0.1 MPa. We find $${D}_{\mathrm{Fe}2\mathrm{O}3}^{\mathrm{opx}/\mathrm{melt}}$$ D Fe 2 O 3 opx / melt = 0.63 ± 0.10 and $${D}_{\mathrm{Fe}2\mathrm{O}3}^{\mathrm{cpx}/\mathrm{melt}}$$ D Fe 2 O 3 cpx / melt = 0.78 ± 0.30. MORB Fe2O3 and Na2O concentrations are consistent with a modeled MORB source with Fe2O3 = 0.48 ± 0.03 wt% (Fe3+/ΣFe = 0.053 ± 0.003) at potential temperatures (TP) from 1320 to 1440 °C. The temperature-dependence of the $${D}_{\mathrm{Fe}2\mathrm{O}3}^{\mathrm{spl}/\mathrm{melt}}$$ D Fe 2 O 3 spl / melt function alone allows ~ 40% of the variation in MORB compositions. If we allow $${D}_{\mathrm{Fe}2\mathrm{O}3}^{\mathrm{opx}/\mathrm{melt}}$$ D Fe 2 O 3 opx / melt and $${D}_{\mathrm{Fe}2\mathrm{O}3}^{\mathrm{opx}/\mathrm{melt}}$$ D Fe 2 O 3 opx / melt to also vary with temperature by tying them to spinel Fe2O3 through intermineral partitioning, then all the MORB data are within error of the model. Our model Fe2O3 concentration for the MORB source would require that the convecting mantle be more oxidized at a given depth than recorded by continental mantle xenoliths. Our result is supported by thermodynamic models of mantle with Fe3+/ΣFe = 0.03 that predict fO2 of ~ QFM-1 near the garnet-spinel transition, which is inconsistent with fO2 of MORB. Our results support previous suggestions that redox melting may occur between 200 and 250 km depth.

Secondary Structure Prediction for RNA Sequences Including N6-methyladenosine

There is increasing interest in the roles played by covalently modified nucleotides in mRNAs and non-coding RNAs. New high-throughput sequencing technologies localize these modifications to exact nucleotide positions. There has been, however, and inability to account for these modifications in secondary structure prediction because of a lack of software tools for handling modifications and a lack of thermodynamic parameters for modifications. Here, we report that we solved these issues for N6-methyladenosine (m6A), for the first time allowing secondary structure prediction for a nucleotide alphabet of A, C, G, U, and m6A. We revised the RNAstructure software package to work with any user-defined alphabet of nucleotides. We also developed a set of nearest neighbor parameters for helices and loops containing m6A, using a set of 45 optical melting experiments. Interestingly, N6-methylation decreases the folding stability of structures with adenosines in the middle of a helix, has little effect on the folding stability of adenosines at the ends of helices, and stabilizes the folding stability for structures with unpaired adenosines stacked on the end of a helix. The parameters were tested against an additional two melting experiments, including a consensus sequence for methylation and an m6A dangling end. The utility of the new software was tested using predictions of the structure of a molecular switch in the MALAT1 lncRNA, for which a conformation change is triggered by methylation. Additionally, human transcriptome-wide calculations for the effect of N6-methylation on the probability of an adenosine being buried in a helix compare favorably with PARS structure mapping data. Now users of RNAstructure are able to develop hypothesis for structure-function relationships for RNAs with m6A, including conformational switching triggered by methylation.

Locking up the AS1411 Aptamer with a Flanking Duplex: Towards an Improved Nucleolin-Targeting

We have designed AS1411-N6, a derivative of the nucleolin (NCL)-binding aptamer AS1411, by adding six nucleotides to the 5′-end that are complementary to nucleotides at the 3′-end forcing it into a stem-loop structure. We evaluated by several biophysical techniques if AS1411-N6 can adopt one or more conformations, one of which allows NCL binding. We found a decrease of polymorphism of G-quadruplex (G4)-forming sequences comparing to AS1411 and the G4 formation in presence of K+ promotes the duplex folding. We also studied the binding properties of ligands TMPyP4, PhenDC3, PDS, 360A, and BRACO-19 in terms of stability, binding, topology maintenance of AS1411-N6, and NCL recognition. The melting experiments revealed promising stabilizer effects of PhenDC3, 360A, and TMPyP4, and the affinity calculations showed that 360A is the most prominent affinity ligand for AS1411-N6 and AS1411. The affinity determined between AS1411-N6 and NCL denoting a strong interaction and complex formation was assessed by PAGE in which the electrophoretic profile of AS1411-N6 showed bands of the dimeric form in the presence of the ligands and NCL.