ALBERT

Description: A spatially averaged mean-field model for fully or partially ordered members of the ilmenite–hematite solid solution series is rigorously derived from the Heisenberg Hamiltonian by first assuming no temporal correlation of atomic spins, and then by spatially averaging over spins at equivalent atomic positions. The model is based on the geometry of exchange interactions between nearest and next-nearest neighbours and predicts magnetization curves in homogenous solid solutions with variable degree of order. While the general framework presented can also be applied to atomic scale models, and to other solid solution series, here the symmetries of the ilmenite–hematite lattice are exploited to show that four different sublattice magnetizations and six independent combinations of exchange constants determine the temperature variation of the magnetization curves. Comparing measured Curie temperatures T C and M s ( T ) curves to model predictions results in accurate constraints for these combinations. It is also possible to calculate predictions for high-field magnetization slopes HF , which not only improve accurate experimental determination of the Curie temperature but also provide a new magnetic method to estimate the order parameter for ilmenite–hematite solid solution samples.

Description: RNA sequencing (RNAseq) has become the method of choice for transcriptome analysis, yet no consensus exists as to the most appropriate pipeline for its analysis, with current benchmarks suffering important limitations. Here, we address these challenges through a rich benchmarking resource harnessing (i) two RNAseq datasets including ERCC ExFold spike-ins; (ii) Nanostring measurements of a panel of 150 genes on the same samples; (iii) a set of internal, genetically-determined controls; (iv) a reanalysis of the SEQC dataset; and (v) a focus on relative quantification (i.e. across-samples). We use this resource to compare different approaches to each step of RNAseq analysis, from alignment to differential expression testing. We show that methods providing the best absolute quantification do not necessarily provide good relative quantification across samples, that count-based methods are superior for gene-level relative quantification, and that the new generation of pseudo-alignment-based software performs as well as established methods, at a fraction of the computing time. We also assess the impact of library type and size on quantification and differential expression analysis. Finally, we have created a R package and a web platform to enable the simple and streamlined application of this resource to the benchmarking of future methods.

Description: MicroRNAs (miRNAs), small non-coding RNA molecules, are important biomarkers for research and medical purposes. Here, we describe the development of a fast and simple method using highly fluorescent oligonucleotide-silver nanocluster probes (DNA/AgNCs) to efficiently detect specific miRNAs. Due to the great sequence diversity of miRNAs in humans and other organisms, a uniform strategy for miRNA detection is attractive. The concept presented is an oligonucleotide-based locking-to-unlocking system that can be endowed with miRNA complementarity while maintaining the same secondary structure. The locking-to-unlocking system is based on fold-back anchored DNA templates that consist of a cytosine-rich loop for AgNCs stabilization, an miRNA recognition site and an overlap region for hairpin stabilization. When an miRNA is recognized, fluorescence in the visible region is specifically extinguished in a concentration-dependent manner. Here, the exact composition of the fold-back anchor for the locking-to-unlocking system has been systematically optimized, balancing propensity for loop-structure formation, encapsulation of emissive AgNCs and target sensitivity. It is demonstrated that the applied strategy successfully can detect a number of cancer related miRNAs in RNA extracts from human cancer cell lines.

Description: Cap analysis of gene expression (CAGE) is a high-throughput method for transcriptome analysis that provides a single base-pair resolution map of transcription start sites (TSS) and their relative usage. Despite their high resolution and functional significance, published CAGE data are still underused in promoter analysis due to the absence of tools that enable its efficient manipulation and integration with other genome data types. Here we present CAGEr , an R implementation of novel methods for the analysis of differential TSS usage and promoter dynamics, integrated with CAGE data processing and promoterome mining into a first comprehensive CAGE toolbox on a common analysis platform. Crucially, we provide collections of TSSs derived from most published CAGE datasets, as well as direct access to FANTOM5 resource of TSSs for numerous human and mouse cell/tissue types from within R, greatly increasing the accessibility of precise context-specific TSS data for integrative analyses. The CAGEr package is freely available from Bioconductor at http://www.bioconductor.org/packages/release/bioc/html/CAGEr.html .

Description: The sedimentary sequence deposited during the deglaciation phase following the last glacial maximum in the Storfjorden trough, on the northwestern Barents Sea south of Svalbard, was sampled with 10 piston and gravity cores during the SVAIS and EGLACOM cruises. Three cores (SV-02, SV-03 and SV-05) collected on the upper continental slope are characterized by a thin (20–40 cm) Holocene interval and a thick (up to 4.5 m in core SV-03) late Pleistocene sequence of finely laminated fine-grained sediments that have been interpreted as plumites deposited during the Melt Water Pulse 1a (MWP-1a). Radiocarbon ages obtained at the top and bottom of this stratigraphic interval revealed that deposition occurred during less than two centuries at around 15 ka ago, with a very high sedimentary rate exceeding 3 cm a –1 . We studied the palaeomagnetic and rock magnetic properties of this interval, by taking magnetic measurements at 1 cm spacing on u-channel samples collected from the three cores. The data show that this sequence is characterized by good palaeomagnetic properties and the palaeomagnetic and rock magnetic trends may be correlated at high resolution from core to core. The obtained palaeomagnetic data therefore offer the unique opportunity to investigate in detail the rate of geomagnetic palaeosecular variation (PSV) in the high northern latitudes at a decadal scale. Notwithstanding the palaeomagnetic trends of the three cores may be closely matched, the amplitude of directional PSV and the consequent virtual geomagnetic pole (VGP) scatter (S) is distinctly higher in one core (SV-05) than in the other two cores (SV-02 and SV-03). This might result from a variable proportion of two distinct populations of magnetic minerals in core SV-05, as suggested by the variable tendency to acquire a gyromagnetic remanent magnetization at high fields during the AF demagnetization treatment. For the plumite interval of cores SV-02 and SV-03, where the magnetic mineralogy is uniform and magnetite is the main magnetic carrier, a S value of about 9° is obtained. We consider this value as a reliable approximation of palaeomagnetic secular variation at a latitude of 75°N over a time interval spanning a couple of centuries around 15 ka ago.

Description: A recent study of the Matuyama–Brunhes (M-B) geomagnetic field reversal recorded in exposed lacustrine sediments from the Sulmona Basin (Italy) provided a continuous, high-resolution record indicating that the reversal of the field direction at the terminus of the M-B boundary (MBB) occurred in less than a century, about 786 ka ago. In the sediment, thin (4–6 cm) remagnetized horizons were recognized above two distinct tephra layers—SUL2-19 and SUL2-20—that occur ~25 and ~35 cm below the MBB, respectively. Also, a faint, millimetre-thick tephra (SUL2-18) occurs 2–3 cm above the MBB. With the aim of improving the temporal resolution of the previous Sulmona MBB record and understanding the possible influence of cryptotephra on the M-B record in the Sulmona Basin, we performed more detailed sampling and analyses of overlapping standard and smaller samples from a 50 cm-long block that spans the MBB. The new data indicate that (i) the MBB is even sharper than previously reported and occurs ~2.5 cm below tephra SUL2-18, in agreement with the previous study; (ii) the MBB coincides with the rise of an intensity peak of the natural remanent magnetization (NRM) intensity, which extends across SUL2-18; (iii) except for a 2-cm-thick interval just above tephra SUL2-18, the rock magnetic parameters ( k , ARM, M r , M s , B c , B cr ) indicate exactly the same magnetic mineralogy throughout the sampled sequence. We conclude that either SUL2-18 resulted in the remagnetization of an interval of about 6 cm (i.e. during the NRM intensity peak spanning ~260 ± 110 yr, according to the estimated local sedimentation rate), and thus the detailed MBB record is lost because it is overprinted, or the MBB is well recorded, occurred abruptly about 2.5 cm below SUL2-18 and lasted less than 13 ± 6 yr. Both hypotheses challenge our understanding of the geomagnetic field behaviour during a polarity transition and/or of the NRM acquisition process in the Sulmona lacustrine sediment.

Description: The variability and complexity of the transcription initiation process was examined by adapting RNA ligase-mediated rapid amplification of 5' cDNA ends (5'-RACE) to Next-Generation Sequencing (NGS). We oligo-labelled 5'-m 7 G-capped mRNA from two genes, the simple mono-exonic Beta-2-Adrenoceptor (ADRB2R) and the complex multi-exonic Glucocorticoid Receptor (GR, NR3C1) , and detected a variability in TSS location that has received little attention up to now. Transcription was not initiated at a fixed TSS, but from loci of 4 to 10 adjacent nucleotides. Individual TSSs had frequencies from 〈0.001% to 38.5% of the total gene-specific 5' m 7 G-capped transcripts. ADRB2R used a single locus consisting of 4 adjacent TSSs. Unstimulated, the GR used a total of 358 TSSs distributed throughout 38 loci, that were principally in the 5' UTRs and were spliced using established donor and acceptor sites. Complete demethylation of the epigenetically sensitive GR promoter with 5-azacytidine induced one new locus and 127 TSSs, 12 of which were unique. We induced GR transcription with dexamethasone and Interferon-, adding one new locus and 185 additional TSSs distributed throughout the promoter region. In-vitro the TSS microvariability regulated mRNA translation efficiency and the relative abundance of the different GR N-terminal protein isoform levels.

Description: Was the Yukon-Tanana Terrane (YTT), a California-sized part of south-central Yukon, an autochthonous or para-autochthonous part of northern British Columbia in the Early Cretaceous or was it part of a proposed allochthonous ‘Baja B.C.’ continent offshore of southern California? To answer this fundamental question, a paleomagnetic study has been completed on 347 specimens from 24 sites in the 114.7 ± 1.1 Ma Quiet Lake batholith. This 1300 km 2 pluton is composed mostly of massive medium-to-coarse grained biotite quartz monzonite that exhibits no evidence of either deformation or metamorphism, and that intrudes metamorphosed pre-Cretaceous basement rocks of the YTT in southern Yukon. The paleomagnetic analysis utilized thermal and alternating field step demagnetization, and saturation isothermal remanence methods. A well-defined characteristic remanent magnetization (ChRM) direction was isolated throughout the 500–585 °C temperature range at Decl. = 340.6°, Incl. = 77.4° ( N = 14 sites, k = 51.2, A 95 = 5.6°). The ChRM resides in magnetite with a low titanium content and is interpreted to be a primary thermoremanent magnetization. After correction for 490 km of geologically demonstrable dextral displacement on the inboard Tintina fault zone, the Quiet Lake batholith's paleopole is not significantly different at 95 per cent confidence from the co-eval 115 Ma reference paleopole for North America, giving non-significant translation and rotation estimates of 1.4° ± 5.1° (1) northwestwards and 10° ± 13° (1) clockwise, respectively. Thus, this is the first Early Cretaceous paleopole to show clearly that the YTT in Yukon is a para-autochthon that was part of North America's continental margin at that time. Further, after correction for Tintina fault displacement, the eight available Mesozoic YTT paleopoles agree closely with the North American apparent polar wander path (APWP). In contrast, the 22 paleopoles from the Intermontane Belt show the expected behaviour of an allochthonous thin-skin of terranes (i.e. ‘Baja B.C.’ behaviour) and record ~8° of northward translation and ~50° of clockwise rotation relative to both the YTT and North American APWPs during the Mesozoic and Paleogene.

Description: We derive scaling relationships for planetary dynamos based on a balance between energy production and Joule dissipation, and between the curl of the buoyancy and Coriolis forces. These scaling relationships are deduced for the particular case of dynamos driven by helical waves, but are shown to have a much broader applicability. They are consistent with the evidence of the numerical dynamos, yielding predictions consistent with published empirical scaling laws and also with the observed transition from dipolar to multipolar dynamos. A direct comparison with the observational evidence for the planets is hampered by the fact that we do not know what sets the smallest scale of the motion in the planets. Nevertheless, we use our scaling relationships to show that the traditional assumption that the Elsasser number is of order unity is inconsistent with the observation that the gas-giant dynamos are dipolar dynamos, as is the more recent suggestion that the strength of the dipole is independent of rotation rate and controlled by the buoyancy flux alone. On the other hand, we show that the observational data is consistent with the hypothesis that a dipolar dynamo saturates at the lowest permissible magnetic energy compatible with a given buoyancy flux.

Description: In most numerical simulations of the Earth's core the dynamo resides outside the tangent cylinder and may be crudely classified as being of the α 2 type. In this region the flow comprises a sea of thin columnar vortices aligned with the rotation axis, taking the form of alternating cyclones and anticyclones. The dynamo is thought to be driven by these columnar vortices within which the flow is observed to be highly helical, helicity being a crucial ingredient of planetary dynamos. As noted in Davidson, one of the mysteries of this dynamo cartoon is the origin of the helicity, which is observed to be positive in the south and negative in the north. While Ekman pumping at the mantle can induce helicity in some of the overly viscous numerical simulations, it is extremely unlikely to be a significant source within planets. In this paper we return to the suggestion of Davidson that the helicity observed in the less viscous simulations owes its existence to helical wave packets, launched in and around the equatorial plane where the buoyancy flux is observed to be strong. Here we show that such wave packets act as a potent source of planetary helicity, constituting a simple, robust mechanism that yields the correct sign for h north and south of the equator. Since such a mechanism does not rely on the presence of a mantle, it can operate within both the Earth and the gas giants. Moreover, our numerical simulations show that helical wave packets dispersing from the equator produce a random sea of thin, columnar cyclone/anticyclone pairs, very like those observed in the more strongly forced dynamo simulations. We examine the local dynamics of helical wave packets dispersing from the equatorial regions, as well as the overall nature of an α 2 -dynamo driven by such wave packets. Our local analysis predicts the mean emf induced by helical waves, an analysis that rests on a number of simple approximations which are consistent with our numerical experiments, while our global analysis yields exact integral relationships between the mean emf induced by the wave packets and the large-scale dipole and azimuthal field. Combining these local and integral equations yields a kinematic model for an α 2 -dynamo driven by helical waves. Order-of-magnitude estimates based on these equations suggest that such a dynamo is indeed feasible.