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Gene duplications and novel genes have been shown to play a major role in helminth adaptation to a parasitic lifestyle because they provide the novelty necessary for adaptation to a changing environment, such as living in multiple hosts. Here we present the de novo sequenced and annotated genome of the parasitic trematode Atriophallophorus winterbourni and its comparative genomic analysis to other major parasitic trematodes. First, we reconstructed the species phylogeny, and dated the split of A. winterbourni from the Opisthorchiata suborder to approximately 237.4 Ma (±120.4 Myr). We then addressed the question of which expanded gene families and gained genes are potentially involved in adaptation to parasitism. To do this, we used hierarchical orthologous groups to reconstruct three ancestral genomes on the phylogeny leading to A. winterbourni and performed a GO (Gene Ontology) enrichment analysis of the gene composition of each ancestral genome, allowing us to characterize the subsequent genomic changes. Out of the 11,499 genes in the A. winterbourni genome, as much as 24% have arisen through duplication events since the speciation of A. winterbourni from the Opisthorchiata, and as much as 31.9% appear to be novel, that is, newly acquired. We found 13 gene families in A. winterbourni to have had more than ten genes arising through these recent duplications; all of which have functions potentially relating to host behavioral manipulation, host tissue penetration, and hiding from host immunity through antigen presentation. We identified several families with genes evolving under positive selection. Our results provide a valuable resource for future studies on the genomic basis of adaptation to parasitism and point to specific candidate genes putatively involved in antagonistic host–parasite adaptation., Genome Biology and Evolution, 13 (3), ISSN:1759-6653

This thesis reports on the development, optimization and experimental testing of a solar receiver-reactor for the thermochemical splitting of H2O and CO2 to produce H2 and CO (syngas). The solar reactor allows to apply a temperature and pressure swing redox cycle to pure ceria in the form of a reticulated porous ceramic (RPC). In the first, endothermic step, the ceria RPC is directly heated with concentrated solar radiation to around 1500 °C while under vacuum pressure of less than 100 mbar, thereby releasing oxygen from its crystal lattice. In the subsequent, exothermic step, the reactor is repressurized with H2O and/or CO2 as it cools, and at temperatures typically below 1000 °C, the partially reduced ceria is re-oxidized with a flow of H2O and/or CO2 at atmospheric pressure. The produced syngas can be catalytically processed to conventional liquid hydrocarbon fuels. A reactor prototype at the 4 kW scale has been previously designed and tested using a high-flux solar simulator. In this work, the same reactor technology is realized and optimized at the 50 kW scale and tested under realistic conditions using a solar concentrating facility located in Móstoles, Spain. Initial experiments focused on comparing the cycling performance and the mechanical stability of three different ceria cavities made of an interlocking structure of RPC bricks with different porosities, thicknesses and geometries. The performance of the solar reactor for CO2 splitting was experimentally assessed in a high-flux solar simulator. The mechanical strength and stability of the RPCs was assessed with three-point bend testing after fabrication and visually after testing in the solar reactor. The results indicate that lower porosity and higher thickness, both resulting in a higher ceria mass loading, are generally beneficial for the mechanical integrity of the RPC cavity, but the addition of mass without ensuring effective volumetric absorption of the solar radiation and uniform heating of the ceria does not increase the reactor performance. The maximum power of the solar simulator was limited to 32.2 kW delivered at the 16 cm diameter aperture of the solar reactor, which corresponds to a solar concentration ratio of 1602 suns. As a result of the limited power input, a relatively low maximum solar-to-fuel conversion efficiency, defined as the ratio of the heating value of the fuel produced to the input of solar radiative energy and the energy penalties associated with inert gas separation and vacuum pumping, of 3.48±0.08% was measured. Stable operation over multiple cycles without observable degradation was shown with an extended experiment of five consecutive CO2 splitting cycles. To further analyse the performance of the solar reactor and to gain insight into improved design and operation conditions, a transient heat transfer model of the solar reactor was developed. The numerical model couples the incoming concentrated solar radiation using Monte Carlo ray tracing, incorporates the reduction chemistry by assuming thermodynamic equilibrium, and accounts for internal radiation heat transfer inside the porous ceria by applying effective heat transfer properties. The model was experimentally validated using the data acquired in the high-flux solar simulator. The numerical results highlight the potential of the solar reactor to reach high solar-to-fuel energy conversion efficiencies when operated at high power levels. At a solar radiative power input of 50 kW, an efficiency exceeding 6% is predicted. If the RPC macroporosity could be substantially increased to achieve better volumetric absorption of radiation and uniform heating of the ceria, the model predicts efficiencies exceeding 10%. Based on the experimental results acquired in the high-flux solar simulator and the numerical results of the heat transfer model, a new ceria RPC cavity was designed for the operation of the solar reactor with the solar concentrating facility located in Móstoles, Spain. The facility consists of 169 heliostats which concentrate sunlight onto a tower with an optical height of 15 m. The solar reactor, situated on top of the tower, is facing downwards onto the heliostats and features a self-supporting design of the ceria RPC cavity that is adapted for the inclination angle of 40 degrees. With this adjusted solar reactor, a maximum solar-to-fuel energy conversion efficiency of 5.6±1.0% is experimentally demonstrated for CO2 splitting at a solar radiative power input of 55.8±8.2 kW. Simulating the same experiment using the transient heat transfer model reveals how the performance of the reactor could be further improved. At a power input of 55.8 kW, 21.0% of the total solar energy input is lost by reradiation from the hot cavity, but by far the biggest share of energy is used for sensible heating of the ceria and the bulk reactor components, accounting for 58.4% of the solar energy input in total. This energy is mostly lost when the reactor cools down to the oxidation temperature, which highlights the need for implementing heat recovery in order to increase the efficiency of such reactor technology in the future. For the co-splitting of H2O and CO2 in the solar reactor, different measures to adjust the composition of the produced syngas are discussed. At optimal operating conditions, 62 consecutive redox cycles are performed with the same ceria RPC cavity. The produced syngas is collected and stored in a pressurized gas cylinder. Within the European research consortium SUN-to-LIQUID, the accumulated syngas is further processed via Fischer-Tropsch synthesis to produce liquid hydrocarbon fuels on-site. This work demonstrates the technical feasibility of solar thermochemical H2O and CO2 splitting via ceria redox cycling under real-world conditions and at a relevant scale and as such contributes towards the development of a commercial application for the production of solar hydrocarbon fuels.

Experimental evidence shows that synonymous mutations can have important consequences on genetic fitness. Many organisms display codon usage bias (CUB), where synonymous codons that are translated into the same amino acid appear with distinct frequency. Within genomes, CUB is thought to arise from selection for translational efficiency and accuracy, termed the translational efficiency hypothesis (TEH). Indeed, CUB indices correlate with protein expression levels, which is widely interpreted as evidence for translational selection. However, these tests neglect -1 programmed ribosomal frameshifting (-1 PRF), an important translational disruption effect found across all organisms of the tree of life. Genes that contain -1 PRF signals should cost more to express than genes without. Thus, CUB indices that do not consider -1 PRF may overestimate genes’ true adaptation to translational efficiency and accuracy constraints. Here, we first investigate whether -1 PRF signals do indeed carry such translational cost. We then propose two corrections for CUB indices for genes containing -1 PRF signals. We retest the TEH in Saccharomyces cerevisiae under these corrections. We find that the correlation between corrected CUB index and protein expression remains intact for most levels of uniform -1 PRF efficiencies, and tends to increase when these efficiencies decline with protein expression. We conclude that the TEH is strengthened and that -1 PRF events constitute a promising and useful tool to examine the relationships between CUB and selection for translation efficiency and accuracy.

Aims We aimed to identify a novel biomarker involved in the early events leading to an acute coronary syndrome (ACS) and evaluate its role in diagnosis and risk stratification. Methods and results Biomarker identification was based on gene expression profiling. In coronary thrombi of ACS patients, cysteine-rich angiogenic inducer 61 (Cyr61, CCN1) gene transcripts were highly up-regulated compared with peripheral mononuclear cells. In a murine ischaemia–reperfusion model (I/R), myocardial Cyr61 expression was markedly increased compared with the controls. Cyr61 levels were determined in human serum using an enzyme-linked immunosorbent assay. Cohorts of ACS (n = 2168) referred for coronary angiography, stable coronary artery disease (CAD) (n = 53), and hypertrophic obstructive cardiomyopathy (HOCM) patients (n = 15) served to identify and evaluate the diagnostic and prognostic performance of the biomarker. Cyr61 was markedly elevated in ST-elevation myocardial infarction patients compared with non-ST-elevation myocardial infarction/unstable angina or stable CAD patients, irrespective of whether coronary thrombi were present. Cyr61 was rapidly released after occlusion of a septal branch in HOCM patients undergoing transcoronary ablation of septal hypertrophy. Cyr61 improved risk stratification for all-cause mortality when added to the reference GRACE risk score at 30 days (C-statistic 0.88 to 0.89, P = 0.001) and 1 year (C-statistic 0.77 to 0.80, P, European Heart Journal, 38 (47), ISSN:1522-9645, ISSN:0195-668X