The Atlantic salmon genome provides insights into rediploidization

The whole-genome duplication 80 million years ago of the common ancestor of salmonids (salmonid-specific fourth vertebrate whole-genome duplication, Ss4R) provides unique opportunities to learn about the evolutionary fate of a duplicated vertebrate genome in 70 extant lineages. Here we present a high-quality genome assembly for Atlantic salmon (Salmo salar), and show that large genomic reorganizations, coinciding with bursts of transposon-mediated repeat expansions, were crucial for the post-Ss4R rediploidization process. Comparisons of duplicate gene expression patterns across a wide range of tissues with orthologous genes from a pre-Ss4R outgroup unexpectedly demonstrate far more instances of neofunctionalization than subfunctionalization. Surprisingly, we find that genes that were retained as duplicates after the teleost-specific whole-genome duplication 320 million years ago were not more likely to be retained after the Ss4R, and that the duplicate retention was not influenced to a great extent by the nature of the predicted protein interactions of the gene products. Finally, we demonstrate that the Atlantic salmon assembly can serve as a reference sequence for the study of other salmonids for a range of purposes.publishedVersio

Dissemination of Cephalosporin Resistance Genes between Escherichia coli Strains from Farm Animals and Humans by Specific Plasmid Lineages

Third-generation cephalosporins are a class of β-lactam antibiotics that are often used for the treatment of human infections caused by Gram-negative bacteria, especially Escherichia coli. Worryingly, the incidence of human infections caused by third-generation cephalosporin-resistant E. coli is increasing worldwide. Recent studies have suggested that these E. coli strains, and their antibiotic resistance genes, can spread from food-producing animals, via the food-chain, to humans. However, these studies used traditional typing methods, which may not have provided sufficient resolution to reliably assess the relatedness of these strains. We therefore used whole-genome sequencing (WGS) to study the relatedness of cephalosporin-resistant E. coli from humans, chicken meat, poultry and pigs. One strain collection included pairs of human and poultry-associated strains that had previously been considered to be identical based on Multi-Locus Sequence Typing, plasmid typing and antibiotic resistance gene sequencing. The second collection included isolates from farmers and their pigs. WGS analysis revealed considerable heterogeneity between human and poultry-associated isolates. The most closely related pairs of strains from both sources carried 1263 Single-Nucleotide Polymorphisms (SNPs) per Mbp core genome. In contrast, epidemiologically linked strains from humans and pigs differed by only 1.8 SNPs per Mbp core genome. WGS-based plasmid reconstructions revealed three distinct plasmid lineages (IncI1- and IncK-type) that carried cephalosporin resistance genes of the Extended-Spectrum Beta-Lactamase (ESBL)- and AmpC-types. The plasmid backbones within each lineage were virtually identical and were shared by genetically unrelated human and animal isolates. Plasmid reconstructions from short-read sequencing data were validated by long-read DNA sequencing for two strains. Our findings failed to demonstrate evidence for recent clonal transmission of cephalosporin-resistant E. coli strains from poultry to humans, as has been suggested based on traditional, low-resolution typing methods. Instead, our data suggest that cephalosporin resistance genes are mainly disseminated in animals and humans via distinct plasmids

Genome Evolution of a Tertiary Dinoflagellate Plastid

The dinoflagellates have repeatedly replaced their ancestral peridinin-plastid by plastids derived from a variety of algal lineages ranging from green algae to diatoms. Here, we have characterized the genome of a dinoflagellate plastid of tertiary origin in order to understand the evolutionary processes that have shaped the organelle since it was acquired as a symbiont cell. To address this, the genome of the haptophyte-derived plastid in Karlodinium veneficum was analyzed by Sanger sequencing of library clones and 454 pyrosequencing of plastid enriched DNA fractions. The sequences were assembled into a single contig of 143 kb, encoding 70 proteins, 3 rRNAs and a nearly full set of tRNAs. Comparative genomics revealed massive rearrangements and gene losses compared to the haptophyte plastid; only a small fraction of the gene clusters usually found in haptophytes as well as other types of plastids are present in K. veneficum. Despite the reduced number of genes, the K. veneficum plastid genome has retained a large size due to expanded intergenic regions. Some of the plastid genes are highly diverged and may be pseudogenes or subject to RNA editing. Gene losses and rearrangements are also features of the genomes of the peridinin-containing plastids, apicomplexa and Chromera, suggesting that the evolutionary processes that once shaped these plastids have occurred at multiple independent occasions over the history of the Alveolata

A control method for increasing the heat usage efficiency of nearly-zero-energy buildings with heat pumps

In the retrofitting of older buildings with central heating into nearly zero-energy buildings more and more air to water heat pumps are used. These heat pumps are normally connected to heating systems, producing heat only on demand. The greatest demand for heat occurs when the outside temperature and therefore the COP of the pump is lowest. Outside temperature varies during the day, meaning it is possible to save energy by producing and storing heat in a situation where the COP is higher. To determine the periods with higher COP values weather forecast data and COP curves are used. The data enables to rank and select time periods for heat production. This in conjunction with the heat demand curve of the building enables to create an operation schedule for the heat pump. The aim of the study is to develop heat pump control methods for renovated buildings to comply with nearly zero energy building codes. Dependant on the heat pump and weather conditions, up to 10% of the electricity demand for heating can be decreased.Peer reviewe

Responses of the antennal bimodal hygroreceptor neurons to innocuous and noxious high temperatures in the carabid beetle, Pterostichus oblongopunctatus

Electrophysiological responses of thermo- and hygroreceptor neurons from antennal dome-shaped sen- 32 silla of the carabid beetle Pterostichus oblongopunctatus to different levels of steady temperature ranging 33 from 20 to 35 C and rapid step-changes in it were measured and analysed at both constant relative and 34 absolute ambient air humidity conditions. It appeared that both hygroreceptor neurons respond to tem- 35 perature which means that they are bimodal. For the first time in arthropods, the ability of antennal dry 36 and moist neurons to produce high temperature induced spike bursts is documented. Burstiness of the 37 spike trains is temperature dependent and increases with temperature increase. Threshold temperatures 38 at which the two neurons switch from regular spiking to spike bursting are lower compared to that of the 39 cold neuron, differ and approximately coincide with the upper limit of preferred temperatures of the spe- 40 cies. We emphasise that, in contrast to various sensory systems studied, the hygroreceptor neurons of P. 41 oblongopunctatus have stable and continuous burst trains, no temporal information is encoded in the tim- 42 ing of the bursts. We hypothesise that temperature dependent spike bursts produced by the antennal 43 thermo- and hygroreceptor neurons may be responsible for detection of noxious high temperatures 44 important in behavioural thermoregulation of carabid beetles