A genomic analysis using RNA-Seq to investigate the adaptation of the psychrophilic diatom Fragilariopsis cylindrus to the polar environment

Diatoms are unicellular photosynthetic eukaryotes with a silicate cell wall. They often dominate polar marine ecosystems, driving the major biogeochemical cycles in these areas. The obligate psychrophilic diatom Fragilariopsis cylindrus is a keystone species in the Southern Ocean. It thrives both in open waters and sea ice and has become a model for studying eukaryotic microalgal adaptations to polar marine conditions. The aim of this thesis was to identify how the genome of F. cylindrus has evolved to cope with marine environmental conditions of the Southern Ocean. To identify key genes, comparative genomics, high-throughput transcriptome sequencing and reverse genetics were applied. Comparative genomics with the sequenced mesophilic diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana was combined with genome-wide RNA-Seq transcriptome analysis, leading to the discovery a new bacteria-like rhodopsin not present in other sequenced diatoms. The characterisation of a bacteria-like rhodopsin in F. cylindrus was conducted by applying reverse genetics tools. The genome was characterised by a low G+C content, which affected codon usage. High sequence polymorphism resulted in pronounced unequal expression of putative heterozygous allelic gene copies in response to six different conditions. RNA-Seq detected transcriptional activity for 95% of the 27,137 predicted genes and > 4 fold expression changes between 55% of putative alleles. The most significant transcriptional changes were detected during prolonged darkness affecting 70% of genes and 30% of RNA-Seq reads mapped to unannotated regions of the genome. Two rhodopsin alleles showed unequal bi-allelic expression in response to iron starvation and heterologous expression in Xenopus laevis oocytes experimentally confirmed light-driven proton pumping for the iron-induced rhodopsin allele, suggesting significance for the adaptation of F. cylindrus to environmental conditions of the Southern Ocean. These data show how the polar environment can shape the genome of a eukaryotic phytoplankton in unprecedented detail. High numbers of species-specific genes resulting in expansion of gene and protein families, low G+C likely enabling efficient translation at low temperatures and a high degree of heterozygosity combined with unequal bi-allelic expression, may provide an adaptive strategy to polar conditions by conferring metabolic flexibility and capacity to adapt to a rapidly changing environment

Greenhouse gas production potential and associated degradation of organic carbon in warming permafrost – an incubation experiment coupled to biomarker analyses from drained lake basin sediments on the Yukon Coastal Plain, Canada

Permafrost carbon pools are vulnerable to a warming climate and bear the potential to alter the terrestrial carbon cycle. In the extensive drained lake basin wetlands that cover Arctic lowlands, enhanced degradation of organic-rich deposits upon permafrost thaw could lead to greenhouse gas emissions to the atmosphere. This study investigates processes and intensity of organic matter decomposition and associated potential greenhouse gas production in thawed sediment from drained lake basins on the Yukon Coastal Plain in the western Canadian Arctic. We conducted three-month low temperature (4 °C) incubation experiments, assessing the greenhouse gas production potential in the active layer, transition layer, and permafrost of sediment cores from two adjacent drained lake basins under aerobic and anaerobic conditons. The study was supplemented by comprehensive geochemical and biomarker analyses before and after the incubation experiments. Our findings revealed a higher carbon turnover of up to 2.7 % of the available organic carbon to CO2 under aerobic conditions. Carbon loss from mineral permafrost layers matched that of surface peat samples, whereas nitrogen limitation constrained short term carbon mineralization in pioneer peat layers that accumulated shortly after lake drainage. The GHG production under anaerobic conditions exhibited a high depth-dependency, with permafrost layer samples deviating from the otherwise observed high methanogenesis in active and transition layer samples within the short incubation period. High contributions of the potent greenhouse gas methane of up to 94 % enhanced the climate forcing effect of anaerobic emissions. Consequently, the determined relative climate forcing is higher under anaerobic compared to aerobic conditions in active and transition layers, suggesting that waterlogged conditions within drained lake basins are more unfavorable in the short term. While established degradation proxies C:N, δ13C and CPI did not distinctly trace significant degradation of terrestrial organic matter, we observed major shifts in lipid composition, reflected in increasing concentrations of n-alkanols and n-alkanes

Separate assessment of gluteus medius and minimus: B-mode or M-mode ultrasound?

The hip abductors gluteus medius (Gmed) and minimus (Gmin) differ slightly in function and how they are affected by hip joint pathology. A separate assessment of Gmed and Gmin is feasible by ultrasound (US) imaging. B-mode and M-mode US can be used to measure muscle thickness. Two B- and two M-mode scans of Gmed and Gmin thickness were taken in relaxation on 16 asymptomatic volunteers, repeated within 4 days on 11 subjects. Three types of intra-rater reliability of muscle thickness measurements were examined: (1) within-session reliability comparing two scans from the same session, (2) between-days reliability comparing thickness from two scanning occasion within 4 days and (3) reliability of taking thickness measurements by re-measuring the same US scans after 1 week. Thickness measurements on B- and M-mode images provided ICC3,1 >0.96 for within-session reliability. ICC3,k >0.89 for between-days reliability and ICC3,1 >0.85 for re-reading the same scans were estimated. Minimal detectable changes >1.0 mm within-session, >2.4 mm between-days and >1.7 mm for re-reading scans indicated that small thickness changes are not detectable. The investigation suggests a slight advantage for fascia recognition in B-mode and the advantage of visual control of muscle relaxation in M-mode

The Quest for Stability: the macro view

On September 3-4, 2009 SUERF and Utrecht University School of Economicsorganized the Colloquium "The Quest for Stability" in Utrecht, the Netherlands. The papers included in this SUERF Study are based on contributions to the Colloquium.asset prices, bubbles, financial institutions, global recession, interest rates, liquidity, monetary policy, regulation, stability, supervision.

Power to all or few People? An Exploration of Power Dynamics in Holocrazy

Power is key to all organizing. It allows actors to perform actions, make decisions and assign tasks to others. In bureaucratic organizations power is mainly associated with the position that the actor holds. Because actors compete for power, change their position within an organization or leave an organization, power is dynamically changing. We refer to these changes in power as power dynamics. Many New Forms of Organizing, such as Holacracy, claim that individuals have more decision-making capacity, i.e., that power is more equally distributed within the organization. In this paper, we use a unique dataset from a holacratic organization to empirically examine how power dynamics in Holacracy evolve over time. In particular, we use temporal network analysis to reconstruct and contrast two related networks that capture information on how decisions in Holacracy are made. Our findings indicate that also in Holacracy power is not equally distributed, but that few individuals hold most power

Muscle thickness measurements to estimate gluteus mediusand minimus activity levels

The clinical assessment of gluteus medius and minimus force sharing requires non-invasive measurements of individual activity levels. Do ultrasound measurements of change of muscle thickness substitute invasive electromyography (EMG)? Isometric hip abduction in 20–80% maximal voluntary isometric contraction (MVIC) was measured using dynamometry, M-mode ultrasound for gluteus medius and minimus thickness and EMG using (1) surface electrodes on gluteus medius, n = 15, (2) fine-wire electrodes in deep gluteus medius and minimus, n = 6. Gluteus medius thickened by 5.0 (SD 2.5) mm at 80% MVIC while gluteus minimus thickness was constant in the surface EMG study and decreased by 1.6 (SD 1.6) mm at the more ventral location in the fine-wire EMG study. Thickness change of gluteus medius enabled prediction of torque (r2 0.66) and of surface EMG amplitude (r2 0.57). Surface EMG enabled higher torque prediction (r2 0.84) than thickness change. Thickness change of gluteus minimus did not enable a practically relevant estimation of torque production. Ultrasound examination revealed a differential thickening behaviour of gluteus medius and minimus which enabled estimation of isometric torque production only for gluteus medius but with lower precision than surface EMG

Novel Behavioral and Developmental Defects Associated with Drosophila single-minded

In Drosophila, the development of the midline cells of the embryonic ventral nerve cord depends on the function of the bHLH-PAS transcription factor Single-minded (Sim). The expression domain of sim, however, is also found anterior and posterior to the developing ventral cord throughout the germ band. Indeed, mutations in sim were identified based on their characteristic cuticle phenotype. Eight abdominal segments (A1–A8) can be easily seen in the larval cuticle, while three more can be identified during embryogenesis. Cells located in A8–A10 give rise to the formation of the genital imaginal discs, and a highly modified A11 segment gives rise to the anal pads that flank the anus. sim is expressed in all these segments and is required for the formation of both the anal pads and the genital imaginal discs. A new temperature-sensitive sim allele allowed an assessment of possible postembryonic function(s) of sim. Reduction of sim function below a 50% threshold leads to sterile flies with marked behavioral deficits. Most mutant sim flies were only able to walk in circles. Further analyses indicated that this phenotype is likely due to defects in the brain central complex. This brain region, which has previously been implicated in the control of walking behavior, expresses high levels of nuclear Sim protein in three clusters of neurons in each central brain hemisphere. Additional Sim localization in the medullary and laminar neurons of the optic lobes may correlate with the presence of ectopic axon bundles observed in the optic lobes of sim mutant flies

Building a locally diploid genome and transcriptome of the diatom Fragilariopsis cylindrus

The genome of the cold-adapted diatom Fragilariopsis cylindrus is characterized by highly diverged haplotypes that intersperse its homozygous genome. Here, we describe how a combination of PacBio DNA and Illumina RNA sequencing can be used to resolve this complex genomic landscape locally into the highly diverged haplotypes, and how to map various environmentally controlled transcripts onto individual haplotypes. We assembled PacBio sequence data with the FALCON assembler and created a haplotype resolved annotation of the assembly using annotations of a Sanger sequenced F. cylindrus genome. RNA-seq datasets from six different growth conditions were used to resolve allele-specifc gene expression in F. cylindrus. This approach enables to study differential expression of alleles in a complex genomic landscape and provides a useful tool to study how diverged haplotypes in diploid organisms are used for adaptation and evolution to highly variable environments

Optimizing a Rodent Model of Parkinson's Disease for Exploring the Effects and Mechanisms of Deep Brain Stimulation

Deep brain stimulation (DBS) has become a treatment for a growing number of neurological and psychiatric disorders, especially for therapy-refractory Parkinson's disease (PD). However, not all of the symptoms of PD are sufficiently improved in all patients, and side effects may occur. Further progress depends on a deeper insight into the mechanisms of action of DBS in the context of disturbed brain circuits. For this, optimized animal models have to be developed. We review not only charge transfer mechanisms at the electrode/tissue interface and strategies to increase the stimulation's energy-efficiency but also the electrochemical, electrophysiological, biochemical and functional effects of DBS. We introduce a hemi-Parkinsonian rat model for long-term experiments with chronically instrumented rats carrying a backpack stimulator and implanted platinum/iridium electrodes. This model is suitable for (1) elucidating the electrochemical processes at the electrode/tissue interface, (2) analyzing the molecular, cellular and behavioral stimulation effects, (3) testing new target regions for DBS, (4) screening for potential neuroprotective DBS effects, and (5) improving the efficacy and safety of the method. An outlook is given on further developments of experimental DBS, including the use of transgenic animals and the testing of closed-loop systems for the direct on-demand application of electric stimulation