Placing environmental next-generation sequencing amplicons from microbial eukaryotes into a phylogenetic context.

Nucleotide positions in the hypervariable V4 and V9 regions of the small subunit (SSU)-rDNA locus are normally difficult to align and are usually removed before standard phylogenetic analyses. Yet, with next-generation sequencing data, amplicons of these regions are all that are available to answer ecological and evolutionary questions that rely on phylogenetic inferences. With ciliates, we asked how inclusion of the V4 or V9 regions, regardless of alignment quality, affects tree topologies using distinct phylogenetic methods (including PairDist that is introduced here). Results show that the best approach is to place V4 amplicons into an alignment of full-length Sanger SSU-rDNA sequences and to infer the phylogenetic tree with RAxML. A sliding window algorithm as implemented in RAxML shows, though, that not all nucleotide positions in the V4 region are better than V9 at inferring the ciliate tree. With this approach and an ancestral-state reconstruction, we use V4 amplicons from European nearshore sampling sites to infer that rather than being primarily terrestrial and freshwater, colpodean ciliates may have repeatedly transitioned from terrestrial/freshwater to marine environments.

Oligonucleotide microarray chip for the quantification of MS2, ΦX174, and adenoviruses on the multiplex analysis platform MCR 3.

Pathogenic viruses are emerging contaminants in water which should be analyzed for water safety to preserve public health. A strategy was developed to quantify RNA and DNA viruses in parallel on chemiluminescence flow-through oligonucleotide microarrays. In order to show the proof of principle, bacteriophage MS2, ΦX174, and the human pathogenic adenovirus type 2 (hAdV2) were analyzed in spiked tap water samples on the analysis platform MCR 3. The chemiluminescence microarray imaging unit was equipped with a Peltier heater for a controlled heating of the flow cell. The efficiency and selectivity of DNA hybridization could be increased resulting in higher signal intensities and lower cross-reactivities of polymerase chain reaction (PCR) products from other viruses. The total analysis time for DNA/RNA extraction, cDNA synthesis for RNA viruses, polymerase chain reaction, single-strand separation, and oligonucleotide microarray analysis was performed in 4-4.5 h. The parallel quantification was possible in a concentration range of 9.6 × 10(5)-1.4 × 10(10) genomic units (GU)/mL for bacteriophage MS2, 1.4 × 10(5)-3.7 × 10(8) GU/mL for bacteriophage ΦX174, and 6.5 × 10(3)-1.2 × 10(5) for hAdV2, respectively, by using a measuring temperature of 40 °C. Detection limits could be calculated to 6.6 × 10(5) GU/mL for MS2, 5.3 × 10(3) GU/mL for ΦX174, and 1.5 × 10(2) GU/mL for hAdV2, respectively. Real samples of surface water and treated wastewater were tested. Generally, found concentrations of hAdV2, bacteriophage MS2, and ΦX174 were at the detection limit. Nevertheless, bacteriophages could be identified with similar results by means of quantitative PCR and oligonucleotide microarray analysis on the MCR 3.

Separation of Damage Mechanisms in Full Forward Rod Extruded Case-Hardening Steel 16MnCrS5 Using 3D Image Segmentation.

In general, formed components are lightweight as well as highly economic and resource efficient. However, forming-induced ductile damage, which particularly affects the formation and growth of pores, has not been considered in the design of components so far. Therefore, an evaluation of forming-induced ductile damage would enable an improved design and take better advantage of the lightweight nature as it affects the static and dynamic mechanical material properties. To quantify the amount, morphology and distribution of the pores, advanced scanning electron microscopy (SEM) methods such as scanning transmission electron microscopy (STEM) and electron channeling contrast imaging (ECCI) were used. Image segmentation using a deep learning algorithm was applied to reproducibly separate the pores from inclusions such as manganese sulfide inclusions. This was achieved via layer-by-layer ablation of the case-hardened steel 16MnCrS5 (DIN 1.7139, AISI/SAE 5115) with a focused ion beam (FIB). The resulting images were reconstructed in a 3D model to gain a mechanism-based understanding beyond the previous 2D investigations.

Ultrafast element-resolved magneto-optics using a fiber-laser-driven extreme ultraviolet light source.

We present a novel setup to measure the transverse magneto-optical Kerr effect in the extreme ultraviolet spectral range based on a fiber laser amplifier system with a repetition rate between 100 and 300 kHz, which we use to measure element-resolved demagnetization dynamics. The setup is equipped with a strong electromagnet and a cryostat, allowing measurements between 10 and 420 K using magnetic fields up to 0.86 T. The performance of our setup is demonstrated by a set of temperature- and time-dependent magnetization measurements with elemental resolution.

Microstructure and Defect-Based Fatigue Mechanism Evaluation of Brazed Coaxial Ti/Al2O3 Joints for Enhanced Endoprosthesis Design.

Alumina-based ceramic hip endoprosthesis heads have excellent tribological properties, such as low wear rates. However, stress peaks can occur at the point of contact with the prosthesis stem, increasing the probability of fracture. This risk should be minimized, especially for younger and active patients. Metal elevations at the stem taper after revision surgery without removal of a well-fixed stem are also known to increase the risk of fracture. A solution that also eliminates the need for an adapter sleeve could be a fixed titanium insert in the ceramic ball head, which would be suitable as a damping element to reduce the occurrence of stress peaks. A viable method for producing such a permanent titanium-ceramic joint is brazing. Therefore, a brazing method was developed for coaxial samples, and two modifications were made to the ceramic surface to braze a joint that could withstand high cyclic loading. This cyclic loading was applied in multiple amplitude tests in a self-developed test setup, followed by fractographic studies. Computed tomography and microstructural analyses-such as energy dispersive X-ray spectroscopy-were also used to characterize the process-structure-property relationships. It was found that the cyclic loading capacity can be significantly increased by modification of the surface structure of the ceramic.

Biodegradation of chloro- and bromobenzoic acids: effect of milieu conditions and microbial community analysis.

Monohalogenated benzoic acids often appear in industrial wastewaters where biodegradation can be hampered by complex mixtures of pollutants and prevailing extreme milieu conditions. In this study, the biodegradation of chlorinated and brominated benzoic acids was conducted at a pH range of 5.0-9.0, at elevated salt concentrations and with pollutant mixtures including fluorinated and iodinated compounds. In mixtures of the isomers, the degradation order was primarily 4-substituted followed by 3-substituted and then 2-substituted halogenated benzoic acids. If the pH and salt concentration were altered simultaneously, long adaptation periods were required. Community analyses were conducted in liquid batch cultures and after immobilization on sand columns. The Alphaproteobacteria represented an important fraction in all of the enrichment cultures. On the genus level, Afipia sp. was detected most frequently. In particular, Bacteroidetes were detected in high numbers with chlorinated benzoic acids.