Transcriptional silencing of nonsense codon-containing immunoglobulin micro genes requires translation of its mRNA

Eukaryotes have evolved quality control mechanisms that prevent the expression of genes in which the protein coding potential is crippled by the presence of a premature translation-termination codon (PTC). In addition to nonsense-mediated mRNA decay (NMD), a well documented posttranscriptional consequence of the presence of a PTC in an mRNA, we recently reported the transcriptional silencing of PTC-containing immunoglobulin (Ig) mu and gamma minigenes when they are stably integrated into the genome of HeLa cells. Here we demonstrate that this transcriptional silencing of PTC-containing Ig-mu constructs requires active translation of the cognate mRNA, as it is not observed under conditions where translation of the PTC-containing mRNA is inhibited through an iron-responsive element in the 5'-untranslated region. Furthermore, RNA interference-mediated depletion of the essential NMD factor Upf1 not only abolishes NMD but also reduces the extent of nonsense-mediated transcriptional gene silencing (NMTGS). Collectively, our data indicate that NMTGS and NMD are linked, relying on the same mechanism for PTC recognition, and that the NMTGS pathway branches from the NMD pathway at a step after Upf1 function.

Surface uplift and climate change - the geomorphic evolution of the western escarpment of the Andes of northern Chile between the Miocene and present

The Western Escarpment of the Andes at 18.30°S (Arica area, northern Chile) is a classical example for a transient state in landscape evolution. This part of the Andes is characterized by the presence of >10,000 km2 plains that formed between the Miocene and the present, and >1500 m deeply incised valleys. Although processes in these valleys scale the rates of landscape evolution, determinations of ages of incision, and more importantly, interpretations of possible controls on valley formation have been controversial. This paper uses morphometric data and observations, stratigraphic information, and estimates of sediment yields for the time interval between ca. 7.5 Ma and present to illustrate that the formation of these valleys was driven by two probably unrelated components. The first component is a phase of base-level lowering with magnitudes of∼300–500 m in the Coastal Cordillera. This period of base-level change in the Arica area, that started at ca. 7.5 Ma according to stratigraphic data, caused the trunk streams to dissect headward into the plains. The headward erosion interpretation is based on the presence of well-defined knickzones in stream profiles and the decrease in valley widths from the coast toward these knickzones. The second component is a change in paleoclimate. This interpretation is based on (1) the increase in the size of the largest alluvial boulders (from dm to m scale) with distal sources during the last 7.5 m.y., and (2) the calculated increase in minimum fluvial incision rates of ∼0.2 mm/yr between ca. 7.5 Ma and 3 Ma to ∼0.3 mm/yr subsequently. These trends suggest an increase in effective water discharge for systems sourced in the Western Cordillera (distal source). During the same time, however, valleys with headwaters in the coastal region (local source) lack any evidence of fluvial incision. This implies that the Coastal Cordillera became hyperarid sometime after 7.5 Ma. Furthermore, between 7.5 Ma and present, the sediment yields have been consistently higher in the catchments with distal sources (∼15 m/m.y.) than in the headwaters of rivers with local sources (<7 m/m.y.). The positive correlation between sediment yields and the altitude of the headwaters (distal versus local sources) seems to reflect the effect of orographic precipitation on surface erosion. It appears that base-level change in the coastal region, in combination with an increase in the orographic effect of precipitation, has controlled the topographic evolution of the northern Chilean Andes.

Late Quaternary paleosols and their paleoenvironmental significance along the Andean piedmont, Eastern Bolivia

The Andean piedmont of eastern Bolivia is situated at the southern margin of Amazonia characterized by an overall humid climate regime with a marked contrast between the rainy and dry seasons. The nearby Subandean foothills deliver abundant sandy sediments to the piedmont, leading to a complex array of sediments and paleosol horizons. Within this setting, the presented study analyzes four profiles of paleosol-sediment-sequences along incised ephemeral streams near Santa Cruz de la Sierra with a focus on past pedogenic variability in the context of the regional late Quaternary geomorphic and environmental evolution. Based on field observations, micromorphological analysis, geochemical and clay mineralogical data five classes of paleosol horizons could be distinguished. The individual paleosol horizons as well as the sediments, in which they developed, were interpreted regarding their paleoenvironmental significance, taking into consideration the various controls on soil formation with particular focus on changes of local environmental conditions through time. Thus, three different pathways of soil formation were established. On the late Quaternary timescale, the results suggest a strong relation between paleoenvironmental conditions (climate, vegetation etc.), soil environment (soil water flow, micro-environment) and the type of paleosol horizons developed in the study area. The formation of “red beds” (Bw horizons) implies very dry soil environments under dominantly dry conditions, which seem to have prevailed in the study area some time before ∼ 18 cal ka BP. Moderately dry but markedly seasonal environmental conditions with a long dry season and strong seasonal contrasts in soil water flow could explain the formation of moderately developed Bwt horizons around ∼ 18 cal ka BP and much of the mid-Holocene. The formation of Bt horizons and/or clay lamellae in relation to intense neoformation of clay and dominant clay illuviation by soil water points to wet conditions similar to today, which have probably prevailed in the study area before ∼ 8 cal ka BP and since ∼ 5 cal ka BP.

Multi-scale micro-structure generation strategy for up-scaling transport in clays

Clays and claystones are used as backfill and barrier materials in the design of waste repositories, because they act as hydraulic barriers and retain contaminants. Transport through such barriers occurs mainly by molecular diffusion. There is thus an interest to relate the diffusion properties of clays to their structural properties. In previous work, we have developed a concept for up-scaling pore-scale molecular diffusion coefficients using a grid-based model for the sample pore structure. Here we present an operational algorithm which can generate such model pore structures of polymineral materials. The obtained pore maps match the rock’s mineralogical components and its macroscopic properties such as porosity, grain and pore size distributions. Representative ensembles of grains in 2D or 3D are created by a lattice Monte Carlo (MC) method, which minimizes the interfacial energy of grains starting from an initial grain distribution. Pores are generated at grain boundaries and/or within grains. The method is general and allows to generate anisotropic structures with grains of approximately predetermined shapes, or with mixtures of different grain types. A specific focus of this study was on the simulation of clay-like materials. The generated clay pore maps were then used to derive upscaled effective diffusion coefficients for non-sorbing tracers using a homogenization technique. The large number of generated maps allowed to check the relations between micro-structural features of clays and their effective transport parameters, as is required to explain and extrapolate experimental diffusion results. As examples, we present a set of 2D and 3D simulations and investigated the effects of nanopores within particles (interlayer pores) and micropores between particles. Archie’s simple power law is followed in systems with only micropores. When nanopores are present, additional parameters are required; the data reveal that effective diffusion coefficients could be described by a sum of two power functions, related to the micro- and nanoporosity. We further used the model to investigate the relationships between particle orientation and effective transport properties of the sample.

In-situ X-ray micro-diffraction studies of heterogeneous interfaces between cementitious materials and geological formations

In the present study the challenge of analyzing complex micro X-ray diffraction (microXRD) patterns from cement–clay interfaces has been addressed. In order to extract the maximum information concerning both the spatial distribution and the crystal structure type associated with each of the many diffracting grains in heterogeneous, polycrystalline samples, an approach has been developed in which microXRD was applied to thin sections which were rotated in the X-ray beam. The data analysis, performed on microXRD patterns collected from a filled vein of a cement–clay interface from the natural analogue in Maqarin (Jordan), and a sample from a two-year-old altered interface between cement and argillaceous rock, demonstrate the potential of this method.

Terrestrial and submarine evidence for the extent and timing of the Last Glacial Maximum and the onset of deglaciation on the maritime-Antarctic and sub-Antarctic islands

This paper is the maritime and sub–Antarctic contribution to the Scientific Committee for Antarctic Research (SCAR) Past Antarctic Ice Sheet Dynamics (PAIS) community Antarctic Ice Sheet reconstruction. The overarching aim for all sectors of Antarctica was to reconstruct the Last Glacial Maximum (LGM) ice sheet extent and thickness, and map the subsequent deglaciation in a series of 5000 year time slices. However, our review of the literature found surprisingly few high quality chronological constraints on changing glacier extents on these timescales in the maritime and sub–Antarctic sector. Therefore, in this paper we focus on an assessment of the terrestrial and offshore evidence for the LGM ice extent, establishing minimum ages for the onset of deglaciation, and separating evidence of deglaciation from LGM limits from those associated with later Holocene glacier fluctuations. Evidence included geomorphological descriptions of glacial landscapes, radiocarbon dated basal peat and lake sediment deposits, cosmogenic isotope ages of glacial features and molecular biological data. We propose a classification of the glacial history of the maritime and sub–Antarctic islands based on this assembled evidence. These include: (Type I) islands which accumulated little or no LGM ice; (Type II) islands with a limited LGM ice extent but evidence of extensive earlier continental shelf glaciations; (Type III) seamounts and volcanoes unlikely to have accumulated significant LGM ice cover; (Type IV) islands on shallow shelves with both terrestrial and submarine evidence of LGM (and/or earlier) ice expansion; (Type V) Islands north of the Antarctic Polar Front with terrestrial evidence of LGM ice expansion; and (Type VI) islands with no data. Finally, we review the climatological and geomorphological settings that separate the glaciological history of the islands within this classification scheme.