ALBERT

Beschreibung: We have performed an extended palaeomagnetic study of the Oslo Graben volcanics, compared to the study of half a century ago by van Everdingen, using modern techniques and a four times larger amount of sites, plus additional rock magnetic experiments. We conclude that the average direction ( D = 204.0, I = –37.9, k = 46.9, α 95 = 2.0) and associated palaeomagnetic pole ( = 48.3, = 155.5, K = 52.2, A 95 = 1.9) of the Krokskogen and Vestfold volcanics together are statistically identical to those of the earlier study. This gives confidence in the fact that older palaeomagnetic studies can be reliable and robust, even though methods have improved. Our larger number of samples, and better age constraints, enable us to separate the data into two major intervals: the younger, on average, Krokskogen area and the older Vestfold area. The results show firstly that palaeolatitudes are slightly higher than predicted by the latest apparent polar wander path (APWP) for Eurasia by Torsvik et al. These data support an early Permian Pangaea A configuration and do not necessitate a Pangaea B configuration. The larger data set also allows us to assess the distribution of the characteristic remanent magnetization directions of the Oslo Graben in terms of geomagnetic field behaviour, which were acquired during a long period of dominantly single polarity the Permo-Carboniferous Reversed Superchron (PCRS). The distributions show a significantly lower virtual geomagnetic pole (VGP) scatter at the observed (low) latitudes than expected from a compilation from lavas of the last 5 Myr. The data do however show excellent agreement with the scatter observed both during the Cretaceous Normal Superchron and the PCRS. A comparison of the directional distributions in terms of elongation is less discriminating, since the large errors in all cases allow a fit to the predicted elongation/inclination behaviour of the TK03.GAD model.

Beschreibung: Lake sediments are excellent sources of palaeoenvironmental and palaeoclimatic information because they provide continuous and high-resolution records. South America is of particular interest because it is the only landmass that stretches southward into the Pacific and Atlantic Oceans towards Antarctica. The aim of this study is to explore the relationship of magnetic parameters with elemental and palaeobiological data of Laguna Potrok Aike to develop a model of lake-level changes and related hydrological and climatic fluctuations. Magnetic measurements were performed on subsamples from 15 500 cal. BP to the present, and associated rock magnetic parameters were calculated to infer magnetic mineralogy, concentration and grain size. According to the model, parameters dependent on magnetic concentration and grain size are directly related to lake-level changes. During dry periods, the remanent coercivity displays high values, whereas the proportion of magnetite is relatively low. Low percentages of greigite are observed, indicating that the water of the lake was stratified at least four times during the studied period, at approximately 10 300, 8900, 8500 and 8300 cal. BP. The preservation of greigite by inhibiting its complete transformation into pyrite is associated with a rapid burial that occurs with high sedimentation rates. Thermal stratification could be caused by a slight cooling in the area triggered by a weakening of the Westerlies and/or low activity of the sun, sum to the effect of a flood of melt water in the North Atlantic.

Beschreibung: Systematic analysis of the RNA-protein interactome requires robust and scalable methods. We here show the combination of two completely orthogonal, generic techniques to identify RNA-protein interactions: PAR-CLIP reveals a collection of RNAs bound to a protein whereas SILAC-based RNA pull-downs identify a group of proteins bound to an RNA. We investigated binding sites for five different proteins (IGF2BP1-3, QKI and PUM2) exhibiting different binding patterns. We report near perfect agreement between the two approaches. Nevertheless, they are non-redundant, and ideally complement each other to map the RNA-protein interaction network.

Beschreibung: Mirtrons are a recently described category of microRNA (miRNA) relying on splicing rather than processing by the microprocessor complex to generate pre-miRNA precursors of the RNA interference (RNAi) pathway. Their discovery and subsequent verification provides important information about a distinct class of miRNA and inherent advantages that could be exploited to silence genes of interest. These include micro-processor-independent biogenesis, pol-II-dependent transcription, accurate species generation and the delivery of multiple artificial mirtrons as introns within a single host transcript. Here we determined the sequence motifs required for correct processing of the mmu-miR-1224 mirtron and incorporated these into artificial mirtrons targeting Parkinson’s disease-associated LRRK2 and α-synuclein genes. By incorporating these rules associated with processing and splicing, artificial mirtrons could be designed and made to silence complementary targets either at the mRNA or protein level. We further demonstrate with a LRRK2 targeting artificial mirtron that neuronal-specific silencing can be directed under the control of the human synapsin promoter. Finally, multiple mirtrons were co-delivered within a single host transcript, an eGFP reporter, to allow simultaneous targeting of two or more targets in a combinatorial approach. Thus, the unique characteristics of artificial mirtrons make this an attractive approach for future RNAi applications.

Beschreibung: Despite the many advantages of Caenorhabditis elegans , biochemical approaches to study tissue-specific gene expression in post-embryonic stages are challenging. Here, we report a novel experimental approach for efficient determination of tissue-specific transcriptomes involving the rapid release and purification of nuclei from major tissues of post-embryonic animals by f luorescence- a ctivated n uclei s orting (FANS), followed by deep sequencing of linearly amplified 3'-end regions of transcripts (3'-end-seq). We employed these approaches to compile the transcriptome of the developed C. elegans intestine and used this to analyse tissue-specific cleavage and polyadenylation. In agreement with intestinal-specific gene expression, highly expressed genes have enriched GATA-elements in their promoter regions and their functional properties are associated with processes that are characteristic for the intestine. We systematically mapped pre-mRNA cleavage and polyadenylation sites, or polyA sites, including more than 3000 sites that have previously not been identified. The detailed analysis of the 3'-ends of the nuclear mRNA revealed widespread alternative polyA site use (APA) in intestinally expressed genes. Importantly, we found that intestinal polyA sites that undergo APA tend to have U-rich and/or A-rich upstream auxiliary elements that may contribute to the regulation of 3'-end formation in the intestine.

Beschreibung: A novel biosensing approach for the label-free detection of nucleic acid sequences of short and large lengths has been implemented, with special emphasis on targeting RNA sequences with secondary structures. The approach is based on selecting 8-aminoadenine-modified parallel-stranded DNA tail-clamps as affinity bioreceptors. These receptors have the ability of creating a stable triplex-stranded helix at neutral pH upon hybridization with the nucleic acid target. A surface plasmon resonance biosensor has been used for the detection. With this strategy, we have detected short DNA sequences (32-mer) and purified RNA (103-mer) at the femtomol level in a few minutes in an easy and level-free way. This approach is particularly suitable for the detection of RNA molecules with predicted secondary structures, reaching a limit of detection of 50 fmol without any label or amplification steps. Our methodology has shown a marked enhancement for the detection (18% for short DNA and 54% for RNA), when compared with the conventional duplex approach, highlighting the large difficulty of the duplex approach to detect nucleic acid sequences, especially those exhibiting stable secondary structures. We believe that our strategy could be of great interest to the RNA field.

Beschreibung: We illustrate a new imaging method to estimate the depth to the sources of potential fields and the structural index. The method consists of applying the Depth from EXtreme Point (DEXP) transformation to the ratio (R) between two different-order partial derivatives of the field. While the scaling function of the potential field depends on the structural index, we show that the scaling function of R merely depends on the difference between the two used orders of differentiation. This allows three main features to be established for the DEXP transformation of R: (1) it is independent from the structural index; (2) the estimation of the source depths is fully automatic, simply consisting in the search of position of the extreme points of the DEXP image and (3) the structural index of each source is finally determined from the scaling function or the extreme points using the estimated depth. Besides the well-known characteristics of the DEXP transformation, such as high-resolution and stability, the DEXP transformation of R enjoys one more relevant feature: it can be applied to multisource cases, yielding simultaneously correct estimations of structural index and depth for each source in the same image. However, while the DEXP transformation is a linear transformation of the field, the DEXP transformation of R is non-linear, and a procedure is described to circumvent the non-linear effects. The method is tested with synthetic examples and the estimated source parameters show a good agreement with the true values. The method was applied also to real magnetic data from the Pima copper mine, Arizona, USA, Hamrawien area, Egypt and Cataldere, Bala district of Turkey. The results are consistent with the known information about the causative sources.

Beschreibung: This paper presents new directional archeomagnetic data from nine Meso-/Neolithic fireplaces, sampled in a cave shelter, at Arconciel, in western Switzerland. Rock magnetic measurements indicate a homogenous magnetic mineralogy in all fireplaces, with magnetite as the main magnetic carrier. The remanent magnetization is stable and generally shows one characteristic directional component. Nine new directions, which were obtained from Arconciel, are combined with 356 other archeomagnetic data from a circular area with a radius of 700 km around this site, to obtain a penalized least square spline fit for the past 9000 yr. We found in general good agreement with other local compilations, such as the Balkan curve, the regional SCHA.DIF.8k model and with lake sediments from UK, Fennoscandia and Switzerland. Nevertheless, a time lag of several centuries is observed for a declination maximum between the archeomagnetic spline fit and the other European data records around 5900 BC. This time lag is also observed in the Swiss lake sediment record; therefore we interpret this shift as a local feature of the Earth's magnetic field.

Beschreibung: Reconstructions of the Holocene geomagnetic field and how it varies on millennial timescales are important for understanding processes in the core but may also be used to study long-term solar-terrestrial relationships and as relative dating tools for geological and archaeological archives. Here, we present a new family of spherical harmonic geomagnetic field models spanning the past 9000 yr based on magnetic field directions and intensity stored in archaeological artefacts, igneous rocks and sediment records. A new modelling strategy introduces alternative data treatments with a focus on extracting more information from sedimentary data. To reduce the influence of a few individual records all sedimentary data are resampled in 50-yr bins, which also means that more weight is given to archaeomagnetic data during the inversion. The sedimentary declination data are treated as relative values and adjusted iteratively based on prior information. Finally, an alternative way of treating the sediment data chronologies has enabled us to both assess the likely range of age uncertainties, often up to and possibly exceeding 500 yr and adjust the timescale of each record based on comparisons with predictions from a preliminary model. As a result of the data adjustments, power has been shifted from quadrupole and octupole to higher degrees compared with previous Holocene geomagnetic field models. We find evidence for dominantly westward drift of northern high latitude high intensity flux patches at the core mantle boundary for the last 4000 yr. The new models also show intermittent occurrence of reversed flux at the edge of or inside the inner core tangent cylinder, possibly originating from the equator.

Beschreibung: Compared to transcriptional activation, other mechanisms of gene regulation have not been widely exploited for the control of transgenes. One barrier to the general use and application of alternative splicing is that splicing-regulated transgenes have not been shown to be reliably and simply designed. Here, we demonstrate that a cassette bearing a suicide exon can be inserted into a variety of open reading frames (ORFs), generating transgenes whose expression is activated by exon skipping in response to a specific protein inducer. The surprisingly minimal sequence requirements for the maintenance of splicing fidelity and regulation indicate that this splicing cassette can be used to regulate any ORF containing one of the amino acids Glu, Gln or Lys. Furthermore, a single copy of the splicing cassette was optimized by rational design to confer robust gene activation with no background expression in plants. Thus, conditional splicing has the potential to be generally useful for transgene regulation.