Identification of human pathogens isolated from blood using microarray hybridisation and signal pattern recognition

<p>Abstract</p> <p>Background</p> <p>Pathogen identification in clinical routine is based on the cultivation of microbes with subsequent morphological and physiological characterisation lasting at least 24 hours. However, early and accurate identification is a crucial requisite for fast and optimally targeted antimicrobial treatment. Molecular biology based techniques allow fast identification, however discrimination of very closely related species remains still difficult.</p> <p>Results</p> <p>A molecular approach is presented for the rapid identification of pathogens combining PCR amplification with microarray detection. The DNA chip comprises oligonucleotide capture probes for 25 different pathogens including Gram positive cocci, the most frequently encountered genera of <it>Enterobacteriaceae</it>, non-fermenter and clinical relevant <it>Candida </it>species. The observed detection limits varied from 10 cells (e.g. <it>E. coli</it>) to 10⁵cells (<it>S. aureus</it>) per mL artificially spiked blood. Thus the current low sensitivity for some species still represents a barrier for clinical application. Successful discrimination of closely related species was achieved by a signal pattern recognition approach based on the k-nearest-neighbour method. A prototype software providing this statistical evaluation was developed, allowing correct identification in 100 % of the cases at the genus and in 96.7 % at the species level (n = 241).</p> <p>Conclusion</p> <p>The newly developed molecular assay can be carried out within 6 hours in a research laboratory from pathogen isolation to species identification. From our results we conclude that DNA microarrays can be a useful tool for rapid identification of closely related pathogens particularly when the protocols are adapted to the special clinical scenarios.</p

Magnetic anisotropy in antiferromagnetic hexagonal MnTe

Antiferromagnetic hexagonal MnTe is a promising material for spintronic devices relying on the control of antiferromagnetic domain orientations. Here we report on neutron diffraction, magnetotransport, and magnetometry experiments on semiconducting epitaxial MnTe thin films together with density functional theory (DFT) calculations of the magnetic anisotropies. The easy axes of the magnetic moments within the hexagonal basal plane are determined to be along ⟨1¯100⟩ directions. The spin-flop transition and concomitant repopulation of domains in strong magnetic fields is observed. Using epitaxially induced strain the onset of the spin-flop transition changes from ∼2 to ∼0.5 T for films grown on InP and SrF2 substrates, respectively

Band structure of CuMnAs probed by optical and photoemission spectroscopy

The tetragonal phase of CuMnAs progressively appears as one of the key materials for antiferromagnetic spintronics due to efficient current-induced spin-torques whose existence can be directly inferred from crystal symmetry. Theoretical understanding of spintronic phenomena in this material, however, relies on the detailed knowledge of electronic structure (band structure and corresponding wave functions) which has so far been tested only to a limited extent. We show that AC permittivity (obtained from ellipsometry) and UV photoelectron spectra agree with density functional calculations. Together with the x-ray diffraction and precession electron diffraction tomography, our analysis confirms recent theoretical claim [Phys. Rev. B 96, 094406 (2017)] that copper atoms occupy lattice positions in the basal plane of the tetragonal unit cell

Molecular beam epitaxy of CuMnAs

We present a detailed study of the growth of the tetragonal polymorph of antiferromagnetic CuMnAs by the molecular beam epitaxy technique. We explore the parameter space of growth conditions and their effect on the microstructural and transport properties of the material. We identify its typical structural defects and compare the properties of epitaxial CuMnAs layers grown on GaP, GaAs and Si substrates. Finally, we investigate the correlation between the crystalline quality of CuMnAs and its performance in terms of electrically induced resistance switching.Comment: 10 pages, 8 figures and supplementary materia

Symmetry and topology in antiferromagnetic spintronics

Antiferromagnetic spintronics focuses on investigating and using antiferromagnets as active elements in spintronics structures. Last decade advances in relativistic spintronics led to the discovery of the staggered, current-induced field in antiferromagnets. The corresponding N\'{e}el spin-orbit torque allowed for efficient electrical switching of antiferromagnetic moments and, in combination with electrical readout, for the demonstration of experimental antiferromagnetic memory devices. In parallel, the anomalous Hall effect was predicted and subsequently observed in antiferromagnets. A new field of spintronics based on antiferromagnets has emerged. We will focus here on the introduction into the most significant discoveries which shaped the field together with a more recent spin-off focusing on combining antiferromagnetic spintronics with topological effects, such as antiferromagnetic topological semimetals and insulators, and the interplay of antiferromagnetism, topology, and superconductivity in heterostructures.Comment: Book chapte

MethCancerDB – aberrant DNA methylation in human cancer

Early detection, classification and prognosis of human cancers by analysis of CpG methylation carry huge diagnostic potential. MethCancerDB collects and annotates genes and sequences from the abundance of published methylation studies and interlinks them to all methylation-relevant bioinformatical resources. MethCancerDB starts with 4720 entries from 348 sources and is freely accessible at http://www.methcancerdb.net