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

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.

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

Characterization of distinct subpopulations of hepatic macrophages in HFD/obese mice.

The current dogma is that obesity-associated hepatic inflammation is due to increased Kupffer cell (KC) activation. However, recruited hepatic macrophages (RHMs) were recently shown to represent a sizable liver macrophage population in the context of obesity. Therefore, we assessed whether KCs and RHMs, or both, represent the major liver inflammatory cell type in obesity. We used a combination of in vivo macrophage tracking methodologies and adoptive transfer techniques in which KCs and RHMs are differentially labeled with fluorescent markers. With these approaches, the inflammatory phenotype of these distinct macrophage populations was determined under lean and obese conditions. In vivo macrophage tracking revealed an approximately sixfold higher number of RHMs in obese mice than in lean mice, whereas the number of KCs was comparable. In addition, RHMs comprised smaller size and immature, monocyte-derived cells compared with KCs. Furthermore, RHMs from obese mice were more inflamed and expressed higher levels of tumor necrosis factor-α and interleukin-6 than RHMs from lean mice. A comparison of the MCP-1/C-C chemokine receptor type 2 (CCR2) chemokine system between the two cell types showed that the ligand (MCP-1) is more highly expressed in KCs than in RHMs, whereas CCR2 expression is approximately fivefold greater in RHMs. We conclude that KCs can participate in obesity-induced inflammation by causing the recruitment of RHMs, which are distinct from KCs and are not precursors to KCs. These RHMs then enhance the severity of obesity-induced inflammation and hepatic insulin resistance

Using Rasch modeling to investigate the construct of motor competence in early childhood

Purpose: The present study investigated the dimensionality and homogeneity of motor competence, which is defined as the ability that underlies the performance of a wide variety of motor skills, in early childhood using a large set of items. Method: A total of 1467 children (aged 3-6 years) were measured with the Motor Proficiency Test for 4- to 6-Year-old Children (Motoriktest für vier-bis sechsjährige Kinder [MOT 4-6]), which consists of 17 items. Results: Analyses using the Partial Credit Model and mixed Rasch model revealed a one-dimensional structure (CR = 1.964, pCR = .06; P-χ2 = -.227, pp-χ2=.24). Due to unordered threshold parameters, five items were excluded. These items have a scoring system that counts the amount of successful trials (0-2). Conclusion: The study shows item and person homogeneity within a validated motor score, using 12 items of the MOT 4-6. Thus, it provides evidence of a single latent construct (i.e., motor competence), which underlies the performance of motor skills in early childhood. Furthermore, it shows that counting the number of successful trails may be less suitable as a scoring system in motor competence assessment. Present findings also support the use of validated composite scores in motor assessment