Chemical State Mapping of p/n-Controlled SrB6 Bulk Specimens by Soft X-ray Emission Electron Microscope

Elemental and chemical state maps of p/n-controlled SrB6 bulk specimens are presented by using a soft X-ray emission spectroscopy electron microscope. Those bulk specimens were obtained by sintering powder specimens, prepared by the molten-salt method with different compositions of initial materials. A Sr-map, a chemical shift map of B K-emission, and the spectra of characteristic regions of those materials were compared. It was observed that a local Sr deficiency caused a local hole-doped region, confirmed by a chemical shift in the B K-emission spectrum. n-type SrB6 was rather homogeneous. On the other hand, the p-type SrB6 bulk specimen was a mixture of two different p-type regions. This mixed nature originated, presumably, from an uneven Sr content of SrB6 particles prepared by the molten-salt method using a Sr-deficient starting material. A separation process of the two types of materials will realize a high-quality homogeneous p-type SrB6 bulk specimens.

Cyclic Deformation of Microcantilevers Using In-Situ Micromanipulation

Background The trend in miniaturisation of structural components and continuous development of more advanced crystal plasticity models point towards the need for understanding cyclic properties of engineering materials at the microscale. Though the technology of focused ion beam milling enables the preparation of micron-sized samples for mechanical testing using nanoindenters, much of the focus has been on monotonic testing since the limited 1D motion of nanoindenters imposes restrictions on both sample preparation and cyclic testing. Objective/Methods In this work, we present an approach for cyclic microcantilever bending using a micromanipulator setup having three degrees of freedom, thereby offering more flexibility. Results The method has been demonstrated and validated by cyclic bending of Alloy 718plus microcantilevers prepared on a bulk specimen. The experiments reveal that this method is reliable and produces results that are comparable to a nanoindenter setup. Conclusions Due to the flexibility of the method, it offers straightforward testing of cantilevers manufactured at arbitrary position on bulk samples with fully reversed plastic deformation. Specific microstructural features, e.g., selected orientations, grain boundaries, phase boundaries etc., can therefore be easily targeted.

OTME-7. Cancer - immune cell interactions drive transitions to mesenchymal-like state in glioblastoma

Communication between cancer cells and immune cells is a key determinant of the glioblastoma ecosystem and its response to therapies, but remains poorly understood. Here we leveraged single-cell RNA-sequencing (scRNA-seq) of human samples and mouse models, deconvolution analysis of bulk specimen from The Cancer Genome Atlas (TCGA) and functional approaches, to dissect cellular cross-talks in glioblastoma. We demonstrate that macrophages induce a transition of glioblastoma cells into mesenchymal-like (MES-like) states. This effect is mediated, both in vitro and in vivo, by macrophage-derived Oncostatin M (OSM) and its cognate receptor OSMR on glioblastoma cells. We show that MES-like glioblastoma states are also associated with increased expression of a mesenchymal program in macrophages and with increased cytotoxicity of T cells, highlighting extensive alterations of the immune microenvironment with potential therapeutic implications.

Strategies for sample labelling and library preparation in DNA metabarcoding studies

Metabarcoding of DNA extracted from environmental or bulk specimen samples is increasingly used to detect plant and animal taxa in basic and applied biodiversity research because of its targeted nature that allows sequencing of genetic markers from many samples in parallel. To achieve this, PCR amplification is carried out with primers designed to target a taxonomically informative marker within a taxonomic group, and sample-specific nucleotide identifiers are added to the amplicons prior to sequencing. This enables assignment of the sequences back to the samples they originated from. Nucleotide identifiers can be added during the metabarcoding PCR and/or during ‘library preparation’, i.e. when amplicons are prepared for sequencing. Different strategies to achieve this labelling exist. All have advantages, challenges and limitations, some of which can lead to misleading results, and in the worst case compromise the fidelity of the metabarcoding data. Given the range of questions addressed using metabarcoding, the importance of ensuring that data generation is robust and fit for purpose should be at the forefront of practitioners seeking to employ metabarcoding for biodiversity assessments. Here, we present an overview of the three main workflows for sample-specific labelling and library preparation in metabarcoding studies on Illumina sequencing platforms. Further, we distil the key considerations for researchers seeking to select an appropriate metabarcoding strategy for their specific study. Ultimately, by gaining insights into the consequences of different metabarcoding workflows, we hope to further consolidate the power of metabarcoding as a tool to assess biodiversity across a range of applications.

Labelling strategies in metabarcoding studies & how to ensure that nucleotide tags stay in place

Labelling strategies in metabarcoding studies & how to ensure that nucleotide tags stay in place Metabarcoding of environmental DNA (eDNA) and DNA extracted from bulk specimen samples is a powerful tool in studies of ecological interactions, diet and biodiversity, as its labelling of amplicons allows high-throughput sequencing of taxonomically informative DNA sequences from many samples in parallel. The backbone of metabarcoding is the addition of sample-specific nucleotide identifiers to amplicons and then following sequencing using these to assign metabarcoding sequences to the samples they originated from. This allows the pooling of hundreds to thousands of samples before sequencing and thereby full utilisation of the capacity of high-throughput sequencing platforms. The nucleotide identifiers can be added both during the metabarcoding PCR and during library preparation, i.e. when amplicons are prepared for sequencing. There are three main strategies with which to achieve nucleotide labelling in metabarcoding studies. One commonly used strategy is the so-called tagged PCR approach in which DNA extracts are individually amplified with metabarcoding primers that carry sample-specific nucleotide tags at the 5’ end. The uniquely tagged products are then pooled and a library prepared on the pool of amplicons. However, tag‐jumps have been documented in this commonly used metabarcoding approach (Schnell et al. 2015). Tag-jumps cause nucleotide tags to switch between amplicons, resulting in occurrence of amplicons that carry different tags than originally applied. Sequences in the sequencing output that carry tag combinations not used in the study design are easily identified and excluded. However, sequences carrying incorrect, but already used, tag combinations will cause incorrect assignments of sequences to samples. This can - much to the detriment of metabarcoding studies - lead to false positives and artificial inflation of diversity in the samples (Schnell et al. 2015). The occurrence of tag-jumps has led to recommendations to only carry out metabarcoding PCR amplifications with primers carrying twin-tags to ensure that tag‐jumps cannot result in false assignments of sequences to samples (Schnell et al. 2015). However, this increases both cost and workload of metabarcoding studies. In a recently published article, we demonstrate a tag-jump free single-tube library preparation protocol for Illumina sequencing specifically designed for 5’ nucleotide tagged amplicons, the Tagsteady protocol (Carøe & Bohmann 2020). We designed the Tagsteady protocol to circumvent the two steps during library preparation of pools of 5ʹ nucleotide-tagged amplicons that had previously been suggested to cause tag-jumps; i) T4 DNA polymerase blunt-ending in the end-repair step, and ii) post-ligation PCR amplification of amplicon libraries. We used pools of twin‐tagged amplicons to investigate the effect of these two steps on the occurrence of tag‐jumps. Doing this, we demonstrated that blunt‐ending and post-ligation PCR, alone or together, can result in high proportions of tag-jumps, in our study up to ca. 49% of total sequences. The Tagsteady protocol where both these steps were left out resulted in tag‐jump levels comparable to background contamination (Carøe & Bohmann 2020). In our study, we encourage practitioners to avoid using T4 DNA polymerase blunt‐ending and post-ligation PCR in library preparation of 5’ nucleotide tagged amplicon pools, for example by using the Tagsteady protocol (Carøe & Bohmann 2020). This will enable efficient and cost-effective generation of metabarcoding data with correct assignment of sequences to samples. References Carøe C, Bohmann K (2020) Tagsteady: A metabarcoding library preparation protocol to avoid false assignment of sequences to samples. Molecular Ecology Resources, 20, 1620–1631. Schnell IB, Bohmann K, Gilbert MTP (2015) Tag jumps illuminated - reducing sequence-to-sample misidentifications in metabarcoding studies. Molecular Ecology Resources, 15, 1289–1303.

Advanced analytics of elastic adhesive bonds by means of in situ computed tomography

This paper addresses optimization of parameters and measuring setups for in situ computed tomography measurements on marker particle-filled adhesives. The focus of this work was to increase the detail detectability and discriminability between used marker particles and surrounding adhesive compound even for materials with a high X-ray attenuation. Therefore, it is necessary to reduce the effects of artifacts like scattered X-rays and beam hardening, respectively. A key benefit of being able to distinguish different materials clearly improves the correct interpretation of the reconstructed three-dimensional volume significantly, while a reduction of artificial disturbances enhances the possibility to visualize previously overlaid undetected details, e.g. air voids. Performing in situ computed tomography measurements by applying the optimized parameter setups, cavitation formation was observed investigating the particle behavior of specimens modified with glass beads as marker particles under applied load. An achieved bonding enhancement by using a coupling agent as pre-treatment for glass beads was also proven by means of in situ computed tomography. Furthermore, the parameter setups optimized for bulk specimen could be adapted on material combinations, e.g. single-lap shear specimen, by adjusting a few parameters. Additional experiments demonstrate that computed tomography measurements can also be used for analytical purposes, for instance to evaluate the mixing quality of the so-called QUADRO™ or 2C mixers for two-component adhesives.

Tagsteady: a metabarcoding library preparation protocol to avoid false assignment of sequences to samples

Metabarcoding of environmental DNA (eDNA) and DNA extracted from bulk specimen samples is a powerful tool in studies of biodiversity, diet and ecological interactions as its inherent labelling of amplicons allows sequencing of taxonomically informative genetic markers from many samples in parallel. However, the occurrence of so-called ‘tag-jumps’ can cause incorrect assignment of sequences to samples and artificially inflate diversity. Two steps during library preparation of pools of 5’ nucleotide-tagged amplicons have been suggested to cause tag-jumps; i) T4 DNA polymerase blunt-ending in the end-repair step and ii) post-ligation PCR amplification of amplicon libraries. The discovery of tag-jumps has led to recommendations to only carry out metabarcoding PCR amplifications with primers carrying twin-tags to ensure that tag-jumps cannot result in false assignments of sequences to samples. As this increases both cost and workload, a metabarcoding library preparation protocol which circumvents the two steps that causes tag-jumps is needed. Here, we demonstrate Tagsteady, a metabarcoding Illumina library preparation protocol for pools of nucleotide-tagged amplicons that enables efficient and cost-effective generation of metabarcoding data with virtually no tag-jumps. We use pools of twin-tagged amplicons to investigate the effect of T4 DNA polymerase blunt-ending and post-ligation PCR on the occurrence of tag-jumps. We demonstrate that both blunt-ending and post-ligation PCR, alone or together, can result in detrimental amounts of tag-jumps (here, up to ca. 49% of total sequences), while leaving both steps out (the Tagsteady protocol) results in amounts of sequences carrying new combinations of used tags (tag-jumps) comparable to background contamination.

Tuneable Magneto-Resistance by Severe Plastic Deformation

Bulk metallic samples were synthesized from different binary powder mixtures consisting of elemental Cu, Co, and Fe using severe plastic deformation. Small particles of the ferromagnetic phase originate in the conductive Cu phase, either by incomplete dissolution or by segregation phenomena during the deformation process. These small particles are known to give rise to granular giant magneto-resistance. Taking advantage of the simple production process, it is possible to perform a systematic study on the influence of processing parameters and material compositions on the magneto-resistance. Furthermore, it is feasible to tune the magneto-resistive behavior as a function of the specimens’ chemical composition. It was found that specimens of low ferromagnetic content show an almost isotropic drop in resistance in a magnetic field. With increasing ferromagnetic content, percolating ferromagnetic phases cause an anisotropy of the magneto-resistance. By changing the parameters of the high pressure torsion process, i.e., sample size, deformation temperature, and strain rate, it is possible to tailor the magnitude of giant magneto-resistance. A decrease in room temperature resistivity of ~3.5% was found for a bulk specimen containing an approximately equiatomic fraction of Co and Cu.

In Situ Macroscopic Tensile Testing in SEM and Electron Channeling Contrast Imaging: Pencil Glide Evidenced in a Bulk β-Ti21S Polycrystal

In this paper, we report the successful combination of macroscopic uniaxial tensile testing of bulk specimen combined with In situ dislocation-scale observations of the evolution of deformation microstructures during loading at several stress states. The dislocation-scale observations were performed by Accurate Electron Channeling Contrast Imaging in order to follow the defects evolution and their interactions with grain boundaries for several regions of interest during macroscopic loading. With this novel in situ procedure, the slip systems governing the deformation in polycrystalline bulk β-Ti21S are tracked during the macroscopic uniaxial tensile test. For instance, curved slip lines that are associated with “pencil glide” phenomenon and tangled dislocation networks are evidenced.