Divergent roles of CprK paralogues from Desulfitobacterium hafniense in activating gene expression

Gene duplication and horizontal gene transfer play an important role in the evolution of prokaryotic genomes. We have investigated the role of three CprK paralogues from the cAMP receptor protein-fumarate and nitrate reduction regulator (CRP-FNR) family of transcriptional regulators that are encoded in the genome of Desulfitobacterium hafniense DCB-2 and possibly regulate expression of genes involved in the energy-conserving terminal reduction of organohalides (halorespiration). The results from in vivo and in vitro promoter probe assays show that two regulators (CprK1 and CprK2) have an at least partially overlapping effector specificity, with preference for ortho-chlorophenols, while meta-chlorophenols proved to be effectors for CprK4. The presence of a potential transposase-encoding gene in the vicinity of the cprK genes indicates that their redundancy is probably caused by mobile genetic elements. The CprK paralogues activated transcription from promoters containing a 14 bp inverted repeat (dehalobox) that closely resembles the FNR-box. We found a strong negative correlation between the rate of transcriptional activation and the number of nuclecitide changes from the optimal dehalobox sequence (TTAAT-N-4-ATTAA). Transcription was initiated by CprK4 from a promoter that is situated upstream of a gene encoding a methyl-accepting chemotaxis protein. This might be the first indication of taxis of an anaerobic bacterium to halogenated aromatic compounds

Are Medieval Mya arenaria (Mollusca; Bivalvia) in the Netherlands also clams before Columbus?

During the Pleistocene, the coastal marine bivalve mollusc Mya arenaria became extinct in northwest Europe. The species remained present in North America. Datings of Mya shells found in northern Denmark and the southern Baltic Sea suggest that repopulation of northwest European coasts already occurred before Columbus' discovery of America (1492), possibly facilitated by Viking (Norse) settlers at Greenland and northeast North America. In this paper we report on findings of M. arenaria at five locations in the coastal landscape of the Netherlands: polders reclaimed from the Wadden Sea and the former estuaries of Oer-IJ and Old Rhine. The shells from four of these locations also date before 1492 AD

Error estimates for solid-state density-functional theory predictions: an overview by means of the ground-state elemental crystals

Predictions of observable properties by density-functional theory calculations (DFT) are used increasingly often in experimental condensed-matter physics and materials engineering as data. These predictions are used to analyze recent measurements, or to plan future experiments. Increasingly more experimental scientists in these fields therefore face the natural question: what is the expected error for such an ab initio prediction? Information and experience about this question is scattered over two decades of literature. The present review aims to summarize and quantify this implicit knowledge. This leads to a practical protocol that allows any scientist - experimental or theoretical - to determine justifiable error estimates for many basic property predictions, without having to perform additional DFT calculations. A central role is played by a large and diverse test set of crystalline solids, containing all ground-state elemental crystals (except most lanthanides). For several properties of each crystal, the difference between DFT results and experimental values is assessed. We discuss trends in these deviations and review explanations suggested in the literature. A prerequisite for such an error analysis is that different implementations of the same first-principles formalism provide the same predictions. Therefore, the reproducibility of predictions across several mainstream methods and codes is discussed too. A quality factor Delta expresses the spread in predictions from two distinct DFT implementations by a single number. To compare the PAW method to the highly accurate APW+lo approach, a code assessment of VASP and GPAW with respect to WIEN2k yields Delta values of 1.9 and 3.3 meV/atom, respectively. These differences are an order of magnitude smaller than the typical difference with experiment, and therefore predictions by APW+lo and PAW are for practical purposes identical.Comment: 27 pages, 20 figures, supplementary material available (v5 contains updated supplementary material

Natural vs anthropogenic streams in Europe: History, ecology and implications for restoration, river-rewilding and riverine ecosystem services

This is the author accepted manuscript. The final version is available from Elsevier via the DOI in this recordIn Europe and North America the prevailing model of “natural” lowland streams is incised-meandering channels with silt-clay floodplains, and this is the typical template for stream restoration. Using both published and new unpublished geological and historical data from Europe we critically review this model, show how it is inappropriate for the European context, and examine the implications for carbon sequestration and Riverine Ecosystem Services (RES) including river rewilding. This paper brings together for the first time, all the pertinent strands of evidence we now have on the long-term trajectories of floodplain system from sediment-based dating to sedaDNA. Floodplain chronostratigraphy shows that early Holocene streams were predominantly multi-channel (anabranching) systems, often choked with vegetation and relatively rarely single-channel actively meandering systems. Floodplains were either non-existent or limited to adjacent organic-filled palaeochannels, spring/valley mires and flushes. This applied to many, if not most, small to medium rivers but also major sections of the larger rivers such as the Thames, Seine, Rhône, Lower Rhine, Vistula and Danube. As shown by radiocarbon and optically stimulated luminescence (OSL) dating during the mid-late Holocene c. 4–2 ka BP, overbank silt-clay deposition transformed European floodplains, covering former wetlands and silting-up secondary channels. This was followed by direct intervention in the Medieval period incorporating weir and mill-based systems – part of a deep engagement with rivers and floodplains which is even reflected in river and floodplain settlement place names. The final transformation was the “industrialisation of channels” through hard-engineering – part of the Anthropocene great acceleration. The primary causative factor in transforming pristine floodplains was accelerated soil erosion caused by deforestation and arable farming, but with effective sediment delivery also reflecting climatic fluctuations. Later floodplain modifications built on these transformed floodplain topographies. So, unlike North America where channel-floodplain transformation was rapid, the transformation of European streams occurred over a much longer time-period with considerable spatial diversity regarding timing and kind of modification. This has had implications for the evolution of RES including reduced carbon sequestration over the past millennia. Due to the multi-faceted combination of catchment controls, ecological change and cultural legacy, it is impractical, if not impossible, to identify an originally natural condition and thus restore European rivers to their pre-transformation state (naturalisation). Nevertheless, attempts to restore to historical (pre-industrial) states allowing for natural floodplain processes can have both ecological and carbon offset benefits, as well as additional abiotic benefits such as flood attenuation and water quality improvements. This includes rewilding using beaver reintroduction which has overall positive benefits on river corridor ecology. New developments, particularly biomolecular methods offer the potential of unifying modern ecological monitoring with the reconstruction of past ecosystems and their trajectories. The sustainable restoration of rivers and floodplains designed to maximise desirable RES and natural capital must be predicated on the awareness that Anthropocene rivers are still largely imprisoned in the banks of their history and this requires acceptance of an increased complexity for the achievement and maintenance of desirable restoration goals.OSL dating from the Severn-Wye Basin was undertaken at the Geochronology Laboratories, University of Gloucestershire under grants from the EU Leader+ Programme (administered by English Heritage) and the Leverhulme Flood and Flow Project (RPG-2016-004)

The interdisciplinary nature of SOIL

The holistic study of soils requires an interdisciplinary approach involving biologists, chemists, geologists, and physicists, amongst others, something that has been true from the earliest days of the field. In more recent years this list has grown to include anthropologists, economists, engineers, medical professionals, military professionals, sociologists, and even artists. This approach has been strengthened and reinforced as current research continues to use experts trained in both soil science and related fields and by the wide array of issues impacting the world that require an in-depth understanding of soils. Of fundamental importance amongst these issues are biodiversity, biofuels/energy security, climate change, ecosystem services, food security, human health, land degradation, and water security, each representing a critical challenge for research. In order to establish a benchmark for the type of research that we seek to publish in each issue of SOIL, we have outlined the interdisciplinary nature of soil science research we are looking for. This includes a focus on the myriad ways soil science can be used to expand investigation into a more holistic and therefore richer approach to soil research. In addition, a selection of invited review papers are published in this first issue of SOIL that address the study of soils and the ways in which soil investigations are essential to other related fields. We hope that both this editorial and the papers in the first issue will serve as examples of the kinds of topics we would like to see published in SOIL and will stimulate excitement among our readers and authors to participate in this new venture

Structural basis for CRISPR RNA-guided DNA recognition by Cascade

The CRISPR (clustered regularly interspaced short palindromic repeats) immune system in prokaryotes uses small guide RNAs to neutralize invading viruses and plasmids. In Escherichia coli, immunity depends on a ribonucleoprotein complex called Cascade. Here we present the composition and low-resolution structure of Cascade and show how it recognizes double-stranded DNA (dsDNA) targets in a sequence-specific manner. Cascade is a 405-kDa complex comprising five functionally essential CRISPR-associated (Cas) proteins (CasA1B2C6D1E1) and a 61-nucleotide CRISPR RNA (crRNA) with 5′-hydroxyl and 2′,3′-cyclic phosphate termini. The crRNA guides Cascade to dsDNA target sequences by forming base pairs with the complementary DNA strand while displacing the noncomplementary strand to form an R-loop. Cascade recognizes target DNA without consuming ATP, which suggests that continuous invader DNA surveillance takes place without energy investment. The structure of Cascade shows an unusual seahorse shape that undergoes conformational changes when it binds target DNA.