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The Chlamydia suis Genome Exhibits High Levels of Diversity, Plasticity, and Mobile Antibiotic Resistance: Comparative Genomics of a Recent Livestock Cohort Shows Influence of Treatment Regimes
(2017)Genome Biology and EvolutionChlamydia suis is an endemic pig pathogen, belonging to a fascinating genus of obligate intracellular pathogens. Of particular interest, this is the only chlamydial species to have naturally acquired genes encoding for tetracycline resistance. To date, the distribution and mobility of the Tet-island are not well understood. Our study focused on whole genome sequencing of 29 C. suis isolates from a recent porcine cohort within Switzerland, ...Journal Article -
Comparative analyses of the thermodynamic RNA binding signatures of different types of RNA recognition motifs
(2017)Nucleic Acids ResearchRNA recognition motifs (RRMs) are structurally versatile domains important in regulation of alternative splicing. Structural mechanisms of sequence-specific recognition of single-stranded RNAs (ssRNAs) by RRMs are well understood. The thermodynamic strategies are however unclear. Therefore, we utilized microcalorimetry and semi-empirical analyses to comparatively analyze the cognate ssRNA binding thermodynamics of four different RRM ...Journal Article -
Population Heterogeneity in Mutation Rate Increases the Frequency of Higher-Order Mutants and Reduces Long-Term Mutational Load
(2017)Molecular Biology and EvolutionMutation rate is a crucial evolutionary parameter that has typically been treated as a constant in population genetic analyses. However, the propensity to mutate is likely to vary among co-existing individuals within a population, due to genetic polymorphisms, heterogeneous environmental influences, and random physiological fluctuations. We review the evidence for mutation rate heterogeneity and explore its consequences by extending classic ...Journal Article -
Distinct Trajectories of Massive Recent Gene Gains and Losses in Populations of a Microbial Eukaryotic Pathogen
(2017)Molecular Biology and EvolutionDifferences in gene content are a significant source of variability within species and have an impact on phenotypic traits. However, little is known about the mechanisms responsible for the most recent gene gains and losses. We screened the genomes of 123 worldwide isolates of the major pathogen of wheat Zymoseptoria tritici for robust evidence of gene copy number variation. Based on orthology relationships in three closely related fungi, ...Journal Article -
The Structured Coalescent and Its Approximations
(2017)Molecular Biology and EvolutionPhylogeographic methods can help reveal the movement of genes between populations of organisms. This has been widely done to quantify pathogen movement between different host populations, the migration history of humans, and the geographic spread of languages or gene flow between species using the location or state of samples alongside sequence data. Phylogenies therefore offer insights into migration processes not available from classic ...Journal Article -
Active Pacific meridional overturning circulation (PMOC) during the warm Pliocene
(2017)Science AdvancesAn essential element of modern ocean circulation and climate is the Atlantic meridional overturning circulation (AMOC), which includes deep-water formation in the subarctic North Atlantic. However, a comparable overturning circulation is absent in the Pacific, theworld's largest ocean, where relatively fresh surface waters inhibitNorth Pacific deep convection. We present complementary measurement and modeling evidence that the warm, similar ...Journal Article -
Ribonucleotide incorporation by human DNA polymerase eta impacts translesion synthesis and RNase H2 activity
(2017)Nucleic Acids ResearchRibonucleotides (rNs) incorporated in the genome by DNA polymerases (Pols) are removed by RNase H2. Cytidine and guanosine preferentially accumulate over the other rNs. Here we show that human Pol η can incorporate cytidine monophosphate (rCMP) opposite guanine, 8-oxo-7,8-dihydroguanine, 8-methyl-2΄-deoxyguanosine and a cisplatin intrastrand guanine crosslink (cis-PtGG), while it cannot bypass a 3-methylcytidine or an abasic site with rNs ...Journal Article -
What Is Trust? Ethics and Risk Governance in Precision Medicine and Predictive Analytics
(2017)OmicsTrust is a ubiquitous term used in emerging technology (e.g., Big Data, precision medicine), innovation policy, and governance literatures in particular. But what exactly is trust? Even though trust is considered a critical requirement for the successful deployment of precision medicine initiatives, nonetheless, there is a need for further conceptualization with regard to what qualifies as trust, and what factors might establish and sustain ...Journal Article -
Ventral striatum and amygdala activity as convergence sites for early adversity and conduct disorder
(2017)Social Cognitive and Affective NeuroscienceChildhood family adversity (CFA) increases the risk for conduct disorder (CD) and has been associated with alterations in regions of affective processing like ventral striatum (VS) and amygdala. However, no study so far has demonstrated neural converging effects of CFA and CD in the same sample. At age 25 years, functional MRI data during two affective tasks, i.e. a reward (N = 171) and a face-matching paradigm (N = 181) and anatomical ...Journal Article -
A framework for modeling adaptive forest management and decision making under climate change
(2017)Ecology and SocietyAdapting the management of forest resources to climate change involves addressing several crucial aspects to provide a valid basis for decision making. These include the knowledge and belief of decision makers, the mapping of management options for the current as well as anticipated future bioclimatic and socioeconomic conditions, and the ways decisions are evaluated and made. We investigate the adaptive management process and develop a ...Journal Article