High-throughput chromatin accessibility profiling at single-cell resolution.

Here we develop a high-throughput single-cell ATAC-seq (assay for transposition of accessible chromatin) method to measure physical access to DNA in whole cells. Our approach integrates fluorescence imaging and addressable reagent deposition across a massively parallel (5184) nano-well array, yielding a nearly 20-fold improvement in throughput (up to ~1800 cells/chip, 4-5 h on-chip processing time) and library preparation cost (~81¢ per cell) compared to prior microfluidic implementations. We apply this method to measure regulatory variation in peripheral blood mononuclear cells (PBMCs) and show robust, de novo clustering of single cells by hematopoietic cell type

In situ characterization of the functional degradation of a [001] orientated Fe–Mn–Al–Ni single crystal under compression using acoustic emission measurements

Acoustic emission (AE) measurements were conducted in situ during cyclic compressive loading on an [ 00 1 over line ] orientated single crystal of Fe-Mn-Al-Ni shape memory alloy to study functional degradation of its superelastic response. The acoustic investigations were corroborated by optical microscopy, employing video imaging, and transmission electron microscopy. The analysis of acoustic emissions recorded during repeated loading and unloading sessions revealed two categories of AE signals that are differed by their characteristics in time and frequency domains. These two distinct types of AE signals were related to two underlying mechanisms: (i) the nucleation and reverse transformation of stress-induced (twinned) martensite, and (ii) the lateral growth and shrinkage of one dominant martensite variant and related dislocation activities, respectively. In addition, an asymmetry in the AE activity during forward and reverse transformation during mechanical loading and unloading was detected. In particular, an unexpected high AE activity was observed during the superelastic unloading of martensitic microstructure from the point of maximum load/strain. This effect was attributed to the reverse transformation of small, tiny areas of martensite as well as to unpinning and annihilation effects related to dislocations. (c) 2021 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved

The spatial arrangement of ORC binding modules determines the functionality of replication origins in budding yeast

In the quest to define autonomously replicating sequences (ARSs) in eukaryotic cells, an ARS consensus sequence (ACS) has emerged for budding yeast. This ACS is recognized by the replication initiator, the origin recognition complex (ORC). However, not every match to the ACS constitutes a replication origin. Here, we investigated the requirements for ORC binding to origins that carry multiple, redundant ACSs, such as ARS603. Previous studies raised the possibility that these ACSs function as individual ORC binding sites. Detailed mutational analysis of the two ACSs in ARS603 revealed that they function in concert and give rise to an initiation pattern compatible with a single bipartite ORC binding site. Consistent with this notion, deletion of one base pair between the ACS matches abolished ORC binding at ARS603. Importantly, loss of ORC binding in vitro correlated with the loss of ARS activity in vivo. Our results argue that replication origins in yeast are in general comprised of bipartite ORC binding sites that cannot function in random alignment but must conform to a configuration that permits ORC binding. These requirements help to explain why only a limited number of ACS matches in the yeast genome qualify as ORC binding sites

Aβ Mediated Diminution of MTT Reduction—An Artefact of Single Cell Culture?

The 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-tetrazoliumbromide (MTT) reduction assay is a frequently used and easily reproducible method to measure beta-amyloid (Aβ) toxicity in different types of single cell culture. To our knowledge, the influence of Aβ on MTT reduction has never been tested in more complex tissue. Initially, we reproduced the disturbed MTT reduction in neuron and astroglia primary cell cultures from rats as well as in the BV2 microglia cell line, utilizing four different Aβ species, namely freshly dissolved Aβ (25-35), fibrillar Aβ (1-40), oligomeric Aβ (1-42) and oligomeric Aβ (1-40). In contrast to the findings in single cell cultures, none of these Aβ species altered MTT reduction in rat organotypic hippocampal slice cultures (OHC). Moreover, application of Aβ to acutely isolated hippocampal slices from adult rats and in vivo intracerebroventricular injection of Aβ also did not influence the MTT reduction in the respective tissue. Failure of Aβ penetration into the tissue cannot explain the differences between single cells and the more complex brain tissue. Thus electrophysiological investigations disclosed an impairment of long-term potentiation (LTP) in the CA1 region of hippocampal slices from rat by application of oligomeric Aβ (1-40), but not by freshly dissolved Aβ (25-35) or fibrillar Aβ (1-40). In conclusion, the experiments revealed a glaring discrepancy between single cell cultures and complex brain tissue regarding the effect of different Aβ species on MTT reduction. Particularly, the differential effect of oligomeric versus other Aβ forms on LTP was not reflected in the MTT reduction assay. This may indicate that the Aβ oligomer effect on synaptic function reflected by LTP impairment precedes changes in formazane formation rate or that cells embedded in a more natural environment in the tissue are less susceptible to damage by Aβ, raising cautions against the consideration of single cell MTT reduction activity as a reliable assay in Alzheimer's drug discovery studies

Thymus-Derived Regulatory T Cells Are Positively Selected on Natural Self-Antigen through Cognate Interactions of High Functional Avidity

Regulatory T (Treg) cells expressing Foxp3 transcripton factor are essential for immune homeostasis. They arise in the thymus as a separate lineage from conventional CD4(+)Foxp3(-) T (Tconv) cells. Here, we show that the thymic development of Treg cells depends on the expression of their endogenous cognate self-antigen. The formation of these cells was impaired in mice lacking this self-antigen, while Tconv cell development was not negatively affected. Thymus-derived Treg cells were selected by self-antigens in a specific manner, while autoreactive Tconv cells were produced through degenerate recognition of distinct antigens. These distinct modes of development were associated with the expression of T cell receptor of higher functional avidity for self-antigen by Treg cells than Tconv cells, a difference subsequently essential for the control of autoimmunity. Our study documents how self-antigens define the repertoire of thymus-derived Treg cells to subsequently endow this cell type with the capacity to undermine autoimmune attack

Investigations on the Microstructure of an Aluminium Nitride Layer and Its Interface with the Aluminium Substrate (Part I)

In principle, the plasma nitriding of Al based substrates is a well-known process, though it remains extremely challenging from both the technological point of view and the aspect of stress loading conditions. In order to improve the latter, a duplex treatment consisting of plasma nitriding and subsequent surface remelting using electron beam technology was employed. The focus of this paper (part I) was on the characterisation of the initial microstructure after plasma nitriding. This should create the basis for a better understanding of the processes taking place or changes in the subsequent duplex treatment. This was done with the help of high-resolution imaging and analysis tools in the scanning and transmission electron microscope as well as XPS analyses. Special attention was paid to the nitriding mechanism at the interface as a function of the local microstructural constituents of the hypereutectic Al alloy substrate (Al solid solution, primary silicon, and intermetallic phases). While the main part of the nitride layer formed consisted of AlN and small fractions of pure Al in the diffusion paths, other nitrides and oxides could also be detected in the area of the interface

High-throughput chromatin accessibility profiling at single-cell resolution.

Here we develop a high-throughput single-cell ATAC-seq (assay for transposition of accessible chromatin) method to measure physical access to DNA in whole cells. Our approach integrates fluorescence imaging and addressable reagent deposition across a massively parallel (5184) nano-well array, yielding a nearly 20-fold improvement in throughput (up to ~1800 cells/chip, 4-5 h on-chip processing time) and library preparation cost (~81¢ per cell) compared to prior microfluidic implementations. We apply this method to measure regulatory variation in peripheral blood mononuclear cells (PBMCs) and show robust, de novo clustering of single cells by hematopoietic cell type