INMdok (Leibniz Institute for New Materials)
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A high-throughput 3D kinetic killing assay
Get PDFIn vivo, immune killer cells must infiltrate into tissues and search for their cognate target cells in 3D environments. To investigate the cytotoxic function of immune killer cells, there is currently a significant need for an in vitro kinetic assay that resembles 3D in vivo features. Our work presents a high-throughput kinetic killing assay in 3D that is a robust and powerful tool for evaluating the killing efficiency of immune killer cells, as well as the viability of tumor cells under in vivo-like conditions. This assay holds particular value for assessing primary human CTLs and NK cells and can also be applied to primary murine killer cells. By utilizing collagen concentrations to mimic healthy tissue, soft tumors, and stiff tumors, this assay enables the evaluation of cell function and behavior in physiologically and pathologically relevant scenarios, particularly in the context of solid tumors. Furthermore, this assay shows promise as a personalized strategy for selecting more effective drugs/treatments against tumors, using primary immune cells for individual patients to achieve improved clinical outcomes
Novel genetic modules encoding high-level antibiotic-free protein expression in probiotic lactobacilli
Get PDFLactobacilli are ubiquitous in nature, often beneficially associated with animals as commensals and probiotics, and are extensively used in food fermentation. Due to this close-knit association, there is considerable interest to engineer them for healthcare applications in both humans and animals, for which high-performance and versatile genetic parts are greatly desired. For the first time, we describe two genetic modules in Lactiplantibacillus plantarum that achieve high-level gene expression using plasmids that can be retained without antibiotics, bacteriocins or genomic manipulations. These include (i) a promoter, PtlpA, from a phylogenetically distant bacterium, Salmonella typhimurium, which drives up to 5-fold higher level of gene expression compared to previously reported promoters and (ii) multiple toxin-antitoxin systems as a self-contained and easy-to-implement plasmid retention strategy that facilitates the engineering of tuneable transient genetically modified organisms. These modules and the fundamental factors underlying their functionality that are described in this work will greatly contribute to expanding the genetic programmability of lactobacilli for healthcare applications
Selective Pb2+ removal and electrochemical regeneration of fresh and recycled FeOOH
Get PDFHeavy metal pollution is a key environmental problem. Selectively extracting heavy metals could accomplish water purification and resource recycling simultaneously. Adsorption is a promising approach with a facile process, adaptability for the broad concentration of feed water, and high selectivity. However, the adsorption method faces challenges in synthesizing high-performance sorbents and regenerating adsorbents effectively. FeOOH is an environmentally friendly sorbent with low-cost production on a large scale. Nevertheless, the selectivity behavior and regeneration of FeOOH are seldom studied. Therefore, we investigated the selectivity of FeOOH in a mixed solution of Co2+, Ni2+, and Pb2+ and proposed to enhance the capacity of FeOOH and regenerate it by using external charges. Without charge, the FeOOH electrode shows a Pb2+ uptake capacity of 20 mg/g. After applying a voltage of −0.2/+0.8 V, the uptake capacity increases to a maximum of 42 mg/g and the desorption ratio is 70%–80%. In 35 cycles, FeOOH shows a superior selectivity towards Pb2+ compared with Co2+ and Ni2+, with a purity of 97% ± 3% in the extracts. The high selectivity is attributed to the lower activation energy for Pb2+ sorption. The capacity retentions at the 5th and the 35th cycles are ca. 80% and ca. 50%, respectively, comparable to the chemical regeneration method. With industrially exhausted granular ferric hydroxide as the electrode material, the system exhibits a Pb2+ uptake capacity of 37.4 mg/g with high selectivity. Our work demonstrates the feasibility of regenerating FeOOH by charge and provides a new approach for recycling and upcycling FeOOH sorbent
Ageing-associated small RNA cargo of extracellular vesicles
Get PDFPrevious work on murine models and humans demonstrated global as well as tissue-specific molecular ageing trajectories of RNAs. Extracellular vesicles (EVs) are membrane vesicles mediating the horizontal transfer of genetic information between different tissues. We sequenced small regulatory RNAs (sncRNAs) in two mouse plasma fractions at five time points across the lifespan from 2–18 months: (1) sncRNAs that are free-circulating (fc-RNA) and (2) sncRNAs bound outside or inside EVs (EV-RNA). Different sncRNA classes exhibit unique ageing patterns that vary between the fcRNA and EV-RNA fractions. While tRNAs showed the highest correlation with ageing in both fractions, rRNAs exhibited inverse correlation trajectories between the EV- and fc-fractions. For miRNAs, the EV-RNA fraction was exceptionally strongly associated with ageing, especially the miR-29 family in adipose tissues. Sequencing of sncRNAs and coding genes in fat tissue of an independent cohort of aged mice up to 27 months highlighted the pivotal role of miR-29a-3p and miR-29b-3p in ageing-related gene regulation that we validated in a third cohort by RT-qPCR
Transcriptional Response to Standard AML Drugs Identifies Synergistic Combinations
Get PDFUnlike genomic alterations, gene expression profiles have not been widely used to refine cancer therapies. We analyzed transcriptional changes in acute myeloid leukemia (AML) cell lines in response to standard first-line AML drugs cytarabine and daunorubicin by means of RNA sequencing. Those changes were highly cell- and treatment-specific. By comparing the changes unique to treatment-sensitive and treatment-resistant AML cells, we enriched for treatment-relevant genes. Those genes were associated with drug response-specific pathways, including calcium ion-dependent exocytosis and chromatin remodeling. Pharmacological mimicking of those changes using EGFR and MEK inhibitors enhanced the response to daunorubicin with minimum standalone cytotoxicity. The synergistic response was observed even in the cell lines beyond those used for the discovery, including a primary AML sample. Additionally, publicly available cytotoxicity data confirmed the synergistic effect of EGFR inhibitors in combination with daunorubicin in all 60 investigated cancer cell lines. In conclusion, we demonstrate the utility of treatment-evoked gene expression changes to formulate rational drug combinations. This approach could improve the standard AML therapy, especially in older patients
Real-time monitoring of cell surface protein arrival with split luciferases
Get PDFEach cell in a multicellular organism permanently adjusts the concentration of its cell surface proteins. In particular, epithelial cells tightly control the number of carriers, transporters and cell adhesion proteins at their plasma membrane. However, sensitively measuring the cell surface concentration of a particular protein of interest in live cells and in real time represents a considerable challenge. Here, we introduce a novel approach based on split luciferases, which uses one luciferase fragment as a tag on the protein of interest and the second fragment as a supplement to the extra-cellular medium. Once the protein of interest arrives at the cell surface, the luciferase fragments complement and generate luminescence. We compared the performance of split Gaussia luciferase and split Nanoluciferase by using a system to synchronize biosynthetic trafficking with conditional aggregation domains. The best results were achieved with split Nanoluciferase, for which luminescence increased more than 6000-fold upon recombination. Furthermore, we showed that our approach can separately detect and quantify the arrival of membrane proteins at the apical and basolateral plasma membrane in single polarized epithelial cells by detecting theluminescence signals with a microscope, thus opening novel avenues for characterizing the variations in trafficking in individual epithelial cells
Application of machine learning to object manipulation with bio-inspired microstructures
Get PDFBioinspired fibrillar adhesives have been proposed for novel gripping systems with enhanced scalability and resource efficiency. Here, we propose an in-situ optical monitoring system of the contact signatures, coupled with image processing and machine learning. Visual features were extracted from the contact signature images recorded at maximum compressive preload and after lifting a glass object. The algorithm was trained to cope with several degrees of misalignment and with unbalanced weight distributions by off-center gripping. The system allowed an assessment of the picking process for objects of various mass (200, 300, and 400 g). Several classifiers showed a high accuracy of about 90 % for successful prediction of attachment, depending on the mass of the object. The results promise improved reliability of handling objects, even in difficult situations
Topotaxis of Active Particles Induced by Spatially Heterogeneous Sliding along Obstacles
Get PDFMany biological active agents respond to gradients of environmental cues by redirecting their motion. Besides the well-studied prominent examples such as photo- and chemotaxis, there has been considerable recent interest in topotaxis, i.e.\ the ability to sense and follow topographic environmental cues. We numerically investigate the topotaxis of active agents moving in regular arrays of circular pillars. While a trivial topotaxis is achievable through a spatial gradient of obstacle density, here we show that imposing a gradient in the characteristics of agent-obstacle interaction can lead to an effective topotaxis in an environment with a spatially uniform density of obstacles. As a proof of concept, we demonstrate how a gradient in the angle of sliding around pillars -- as e.g.\ observed in bacterial dynamics near surfaces -- breaks the spatial symmetry and biases the direction of motion. We provide an explanation for this phenomenon based on effective reflection at the imaginary interface between pillars with different sliding angles. Our results are of technological importance for design of efficient taxis devices
Cracking and associated volumetric expansion of NMC811 secondary particles
Get PDFSecondary particles comprising a large number of nickel-rich single crystal primary particles are extensively used as storage particles in cathodes of lithium-ion batteries. It is well-established that crack formation in secondary particles is an important degradation mode that contributes to decline in battery performance. Recent X-ray tomographic observations suggest that, at very low C-rates, concentration gradients of lithium within an NMC811 secondary particle are negligible yet cracking still occurs. Additionally, during delithiation the primary particles shrink yet a volumetric expansion of the secondary particle occurs. These observations are explained by a numerical model of distributed cracking due to the extreme anisotropy of lithiation strain of primary particles. The incompatible deformation from grain to grain induces large self-stresses even in the absence of spatial gradients in the lithium concentration. The stress state is sufficient to drive a dynamic catastrophic fracture event, and the associated kinetic energy acquired by the primary particles moves them apart (akin to an explosive event) with the carbon and binder domain surrounding each secondary particle restricting the outward motion of the primary particles. It is predicted that a volume expansion of the secondary particles on the order of 20 % accompanies cracking, in agreement with recently reported observations
A tandem of GC-MS and electroanalysis for a rapid chemical profiling of bacterial extracellular matrix
Get PDFHerein an assay toward a rapid and reliable profiling of extracellular matrix of Escherichia coli (E. coli) utilizing a tandem of GC-MS as a tool for definition of the exact chemical nature of low molecular weight compounds and cyclic voltammetry for their high throughput detection is presented. Briefly, during a set of investigations the formation of glycerol in the extracellular matrix (ECM) of E. coli at physiological relevant conditions of cells was revealed. Based on the obtained knowledge, the electrochemical protocol allowing both qualitative and quantitative analyses of glycerol in E. coli ECMs at palladium ink-modified screen printed electrodes with precision values (RSD) <10 % and recovery rates ranged from 98 % to 102 % was proposed. The provided protocol for a rapid electrochemical profiling of the bacterial ECMs can readily be used as a guideline for the controlled electroanalysis of target electroactive signaling analytes in complex biological samples