Extremofiele micro-organismen: some like it hot

Een duik nemen in de Noordzee op nieuwjaarsdag vinden we behoorlijk stoer. De Russen doen er een schepje bovenop door het begin van de winter te vieren met een duik in ijswater van nul graden. Dat valt best wel mee, zeker wanneer je dit afwisselt met een bezoek aan de sauna met een luchttemperatuur van 90 graden. Hiermee hebben we de extremen die we als mens kunnen trotseren echter wel gehad. Wat te denken van een duik in kokend water, zwemmen in een zwembad gevuld met azijn of ammonia, of kokend zwavelzuur? Wat voor ons onmogelijk is, is voor veel micro-organismen de normaalste zaak van de werel

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

Being a Better Neighbor:A Value-Based Perspective on Negotiating Acceptability of Locally-Owned Wind Projects

We pose that instead of problematizing negative attitudes of local stakeholders, such as citizens and NGOs, wind energy implementers should be more focused on scrutinizing the acceptability of their projects. The emphasis in this study is on the potential for representation of local stakeholders’ values in the project design, including amongst others business model and placement. Informed by value sensitive design literature, we analyzed two contrasting, locally-owned wind projects in the Dutch province of Groningen: the implementation of mini-turbines in a national landscape and a large-scale multi MW wind project in an industrialized area close to a World Heritage nature reserve. The study analyses how the respective farmer-developers and other local stakeholders attempted to resolve or ameliorate inter-and intra-value conflicts regarding livability, economy, landscape, and nature. The value conflicts turned out to be fruitful to identifying key issues and creating more widely shared value conceptualizations and design priorities. Hence, from this study it can be concluded that value conflict can be productive if carefully unpacked and managed. Uneven power distribution among stakeholders in the planning process, overcoming incommensurability of perspectives, and creating intersubjectivity remain challenges

New pathways for community energy and storage

Worldwide, the energy landscape is changing [...

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

Effects of Argonaute on gene expression in Thermus thermophilus.

This is the final version of the article. Available from the publisher via the DOI in this record.BACKGROUND: Eukaryotic Argonaute proteins mediate RNA-guided RNA interference, allowing both regulation of host gene expression and defense against invading mobile genetic elements. Recently, it has become evident that prokaryotic Argonaute homologs mediate DNA-guided DNA interference, and play a role in host defense. Argonaute of the bacterium Thermus thermophilus (TtAgo) targets invading plasmid DNA during and after transformation. Using small interfering DNA guides, TtAgo can cleave single and double stranded DNAs. Although TtAgo additionally has been demonstrated to cleave RNA targets complementary to its DNA guide in vitro, RNA targeting by TtAgo has not been demonstrated in vivo. METHODS: To investigate if TtAgo also has the potential to control RNA levels, we analyzed RNA-seq data derived from cultures of four T. thermophilus strain HB27 variants: wild type, TtAgo knockout (Δago), and either strain transformed with a plasmid. Additionally we determined the effect of TtAgo on expression of plasmid-encoded RNA and plasmid DNA levels. RESULTS: In the absence of exogenous DNA (plasmid), TtAgo presence or absence had no effect on gene expression levels. When plasmid DNA is present, TtAgo reduces plasmid DNA levels 4-fold, and a corresponding reduction of plasmid gene transcript levels was observed. We therefore conclude that TtAgo interferes with plasmid DNA, but not with plasmid-encoded RNA. Interestingly, TtAgo presence stimulates expression of specific endogenous genes, but only when exogenous plasmid DNA was present. Specifically, the presence of TtAgo directly or indirectly stimulates expression of CRISPR loci and associated genes, some of which are involved in CRISPR adaptation. This suggests that TtAgo-mediated interference with plasmid DNA stimulates CRISPR adaptation.Funding: This study was financially supported by a TOP grant from the Netherlands Organisation for Scientific Research (NWO) to John van der Oost (NWO-TOP 854.10.003). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Fidelity in Archaeal Information Processing

A key element during the flow of genetic information in living systems is fidelity. The accuracy of DNA replication influences the genome size as well as the rate of genome evolution. The large amount of energy invested in gene expression implies that fidelity plays a major role in fitness. On the other hand, an increase in fidelity generally coincides with a decrease in velocity. Hence, an important determinant of the evolution of life has been the establishment of a delicate balance between fidelity and variability. This paper reviews the current knowledge on quality control in archaeal information processing. While the majority of these processes are homologous in Archaea, Bacteria, and Eukaryotes, examples are provided of nonorthologous factors and processes operating in the archaeal domain. In some instances, evidence for the existence of certain fidelity mechanisms has been provided, but the factors involved still remain to be identified