TY - JOUR A1 - Orf, I. A1 - Tenenboim, H. A1 - Omranian, N. A1 - Nikoloski, Z. A1 - Fernie, A. R. A1 - Lisec, Jan A1 - Brotman, Y. A1 - Bromke, M. A. T1 - Transcriptomic and Metabolomic Analysis of a Pseudomonas-Resistant versus a Susceptible Arabidopsis Accession N2 - Accessions of one plant species may show significantly different levels of susceptibility to stresses. The Arabidopsis thaliana accessions Col-0 and C24 differ significantly in their resistance to the pathogen Pseudomonas syringae pv. tomato (Pst). To help unravel the underlying mechanisms contributing to this naturally occurring variance in resistance to Pst, we analyzed changes in transcripts and compounds from primary and secondary metabolism of Col-0 and C24 at different time points after infection with Pst. Our results show that the differences in the resistance of Col-0 and C24 mainly involve mechanisms of salicylic-acid-dependent systemic acquired resistance, while responses of jasmonic-acid-dependent mechanisms are shared between the two accessions. In addition, arginine metabolism and differential activity of the biosynthesis pathways of aliphatic glucosinolates and indole glucosinolates may also contribute to the resistance. Thus, this study highlights the difference in the defense response strategies utilized by different genotypes. KW - Mass Spectrometry KW - Arabidopsis KW - Resistance PY - 2022 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-559549 DO - https://doi.org/10.3390/ijms232012087 VL - 23 IS - 20 SP - 1 EP - 27 PB - MDPI AN - OPUS4-55954 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Jiang, Shan A1 - Wang, T. A1 - Behren, S. A1 - Westerlind, U. A1 - Gawlitza, Kornelia A1 - Persson, J. L. A1 - Rurack, Knut T1 - Sialyl-Tn Antigen-Imprinted Dual Fluorescent Core–Shell Nanoparticles for Ratiometric Sialyl-Tn Antigen Detection and Dual-Color Labeling of Cancer Cells N2 - Sialyl-Tn (STn or sialyl-Thomsen-nouveau) is a carbohydrate antigen expressed by more than 80% of human carcinomas. We here report a strategy for ratiometric STn detection and dual-color cancer cell labeling, particularly, by molecularly imprinted polymers (MIPs). Imprinting was based on spectroscopic studies of a urea-containing green-fluorescent monomer 1 and STn-Thr-Na (sodium salt of Neu5Acα2-6GalNAcα-O-Thr). A few-nanometer-thin green-fluorescent polymer shell, in which STn-Thr-Na was imprinted with 1, other comonomers, and a cross-linker, was synthesized from the surface of red-emissive carbon nanodot (R-CND)-doped silica nanoparticles, resulting in dual fluorescent STn-MIPs. Dual-color labeling of cancer cells was achieved since both red and green emissions were detected in two separate channels of the microscope and an improved accuracy was obtained in comparison with single-signal MIPs. The flow cytometric cell analysis showed that the binding of STn-MIPs was significantly higher (p < 0.001) than that of non-imprinted polymer (NIP) control particles within the same cell line, allowing to distinguish populations. Based on the modularity of the luminescent core–fluorescent MIP shell architecture, the concept can be transferred in a straightforward manner to other target analytes. KW - Cancer KW - Core−shell particles KW - Dual-color labeling glycan KW - Molecular imprinting PY - 2022 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-563106 DO - https://doi.org/10.1021/acsanm.2c03252 SP - 1 EP - 14 PB - ACS Publications AN - OPUS4-56310 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Kubheka, G. A1 - Climent, Estela A1 - Tobias, Charlie A1 - Rurack, Knut A1 - Mack, J. A1 - Nyokong, T. T1 - Multiplexed Detection of Human Papillomavirus Based on AzaBODIPY-Doped Silica-Coated Polystyrene Microparticles N2 - Human papillomavirus (HPV) DNA detection can enable the early diagnosis of high-risk HPV types responsible for cervical cancer. HPV detection is also essential for investigating the clinical behavior and epidemiology of particular HPV types, characterization of study populations in HPV vaccination trials and monitoring the efficacy of HPV vaccines. In this study, two azaBODIPY dyes (1 and 2) were used as references and were doped into polystyrene particles (PS40), while a short HPV DNA single strand was used as a target molecule and was covalently bound to the silica shell. These particles were employed as optical probes in 1:1 hybridization assays, and their potential applicability as a tool for multiplex assays for the detection of different strands of HPV was evaluated using flow cytometry. A good separation in the fluorescence of the four different voncentrations prepared for each dye was observed. To perform the hybridization assays, HPV18, HPV16, HPV11 and HPV6 single strands were attached to the particles through EDC-mediated coupling. The c-DNA-1-PS40 and c-DNA-2-PS40 particles exhibited low limit of detection (LOD) and quantification (LOQ) values for HPV11, and a narrow detection range was obtained. Multiplexed assay experiments were successfully performed for both particles, and the results proved that c-DNA-1-PS40 could potentially be used as a tool for multiplexing assays and merits further in-depth study in this context. KW - Flow cytometry KW - BODIPY dyes KW - Core-shell particles KW - Multiplexed assay KW - Human papillomavirus PY - 2023 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-567358 DO - https://doi.org/10.3390/chemosensors11010001 SN - 2227-9040 VL - 11 IS - 1 SP - 1 EP - 21 PB - MDPI CY - Basel AN - OPUS4-56735 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Burnage, Samual A1 - Bell, Jérémy A1 - Wan, Wei A1 - Kislenko, Evgeniia A1 - Rurack, Knut T1 - Combining a hybrid chip and tube microfluidic system with fluorescent molecularly imprinted polymer (MIP) core–shell particles for the derivatisation, extraction, and detection of peptides with N-terminating phosphorylated tyrosine N2 - The reliable identification and quantitation of phosphorylated amino acids, peptides and proteins is one of the key challenges in contemporary bioanalytical research, an area of particular interest when attempting to diagnose and treat diseases at an early stage. We have developed a synthetic probe for targeting phosphorylated amino acids, based on core–shell submicron-sized particles consisting of a silica core, coated with a molecularly imprinted polymer (MIP) shell. The MIP layer contains a fluorescent probe crosslinker which binds selectively to phosphorylated tyrosine (pY) moieties with a significant imprinting factor (IF) and responds with a "light-up” fluorescence signal. The bead-based ratiometric detection scheme has been successfully transferred to a microfluidic chip format and its applicability to rapid assays has been exemplarily shown by discriminating a pY-terminating oligopeptide against its nonphosphorylated counterpart. Such miniaturised devices could lead to an automated pY or pY N-terminated peptide measurement system in the future. The setup combines a modular microfluidic system for amino acid derivatisation, extraction (by micropillar co-flow) and selective adsorption and detection with the fluorescent MIP core–shell particle probes. A miniaturised optical assembly for low-light fluorescence measurements was also developed, based on miniaturised opto-electronic parts and optical fibres. The emission from the MIP particles upon binding of pY or pY N-terminated peptides could be monitored in real-time. KW - Microfluidics KW - Molecularly imprinted polymers KW - Phosphorylated peptides KW - Fluorescence KW - Core-shell particles PY - 2022 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-569204 DO - https://doi.org/10.1039/d2lc00955b SN - 1473-0197 VL - 23 IS - 3 SP - 466 EP - 474 PB - Royal Society of Chemistry CY - Cambridge AN - OPUS4-56920 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Garrido, E. A1 - Hernández-Sigüenza, G. A1 - Climent, Estela A1 - Marcos, M. D. A1 - Rurack, Knut A1 - Gaviña, P. A1 - Parra, M. A1 - Sancenón, F. A1 - Martí-Centelles, V. A1 - Martínez-Máñez, R. T1 - Strip-based lateral flow-type indicator displacement assay for γ-hydroxybutyric acid (GHB) detection in beverages N2 - The use of gamma-hydroxybutyric acid (GHB) in drug-facilitated sexual assault has increased due to its availability and high solubility in aqueous solutions and alcoholic beverages, necessitating the development of rapid methods for GHB detection. In this respect, portable testing methods for use in the field, based on lateral flow assays (LFAs) and capable of detecting trace concentrations of target analytes, are particularly attractive and hold enormous potential for the detection of illicit drugs. Using this strategy, here we report a rapid, low cost, easy-to-handle strip-based LFA for GHB analysis employing a smartphone for fluorescence readout. At molecular signalling level, the ensemble is based on a Cu2+ complex with a tetradentate ligand and the fluorescent dye coumarin 343, which indicate GHB through an indicator displacement assay (IDA) in aqueous solution. When incorporated in a LFA-based strip test this system shows a detection limit as low as 0.03 μM for GHB in MES buffer solution and is able to detect GHB at concentrations of 0.1 μM in soft drinks and alcoholic beverages in only 1 min. KW - Indicator displacement assay KW - Gamma-hydroxybutyric acid KW - Lateral flow assay KW - Test strip KW - Fluorescent dyes KW - Smartphone readout PY - 2022 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-564631 DO - https://doi.org/10.1016/j.snb.2022.133043 SN - 0925-4005 VL - 377 SP - 1 EP - 7 PB - Elsevier B.V. CY - Amsterdam AN - OPUS4-56463 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Munir, R. A1 - Lisec, Jan A1 - Jaeger, Carsten A1 - Zaidi, N. T1 - Abundance, fatty acid composition and saturation index of neutral lipids in colorectal cancer cell lines N2 - Lipid droplets, the dynamic organelles that store Triglycerides (TG) and cholesterol esters (CE), are highly accumulated in colon cancer cells. This work studies the TG and CE subspecies profile in colon carcinoma cell lines, SW480 derived from primary tumor, and SW620 derived from a metastasis of the same tumor. It was previously reported that the total TG and CE content is dramatically higher in SW620 cells; however, TG and CE subspecies profile has not been investigated in detail. The work presented here confirms that the total TG and CE Content is significantly higher in the SW620 cells. Moreover, the fatty acid (FA) composition of TG is significantly altered in the SW620 cells, with significant decrease in the abundance of saturated triglycerides. This resulted in a significantly decreased TG saturation index in the SW620 cells. The saturation index of CE was also significantly decreased in the SW620 cells. KW - Mass Spectroscopy KW - Metabolomics KW - Cancer PY - 2021 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-533504 DO - https://doi.org/10.18388/abp.2020_5465 VL - 68 IS - 1 SP - 1 EP - 4 PB - ABP Acta Biochimica Polonica AN - OPUS4-53350 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Climent Terol, Estela A1 - Rurack, Knut A1 - Hecht, Mandy T1 - Loading and Release of Charged and Neutral Fluorescent Dyes into and from Mesoporous Materials: A Key Role for Sensing Applications N2 - The aim of this study is to determine the efficiency of loading and release of several zwitterionic, neutral, anionic and cationic dyes into/from mesoporous nanoparticles to find the optimum loading and release conditions for their application in detection protocols. The loading is carried out for MCM-41 type silica supports suspended in phosphate-buffered saline (PBS) buffer (pH 7.4) or in acetonitrile, involving the dyes (rhodamine B chloride, rhodamine 101 chloride, rhodamine 101 perchlorate, rhodamine 101 inner salt, meso-(4-hydroxyphenyl)-boron–dipyrromethene (BODIPY), sulforhodamine B sodium salt and fluorescein 27). As a general trend, rhodamine-based dyes are loaded with higher efficiency, when compared with BODIPY and fluorescein dyes. Between the rhodamine-based dyes, their charge and the solvent in which the loading process is carried out play important roles for the amount of cargo that can be loaded into the materials. The delivery experiments carried out in PBS buffer at pH 7.4 reveal for all the materials that anionic dyes are more efficiently released compared to their neutral or cationic counterparts. The overall best performance is achieved with the negatively charged sulforhodamine B dye in acetonitrile. This material also shows a high delivery degree in PBS buffer. KW - Mesoporous materials KW - Charged dyes KW - Neutral dyes KW - Dye loading optimisation KW - Dye release PY - 2021 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-522596 UR - https://www.mdpi.com/2072-666X/12/3/249 DO - https://doi.org/10.3390/mi12030249 VL - 12 IS - 3 SP - 249 PB - MDPI AN - OPUS4-52259 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Kimani, Martha Wamaitha A1 - Beyer, S. A1 - El-Schich, Z. A1 - Gawlitza, Kornelia A1 - Rurack, Knut A1 - Gjörloff-Wingren, A. T1 - Imprinted Particles for Direct Fluorescence Detection of Sialic Acid in Polar Media and on Cancer Cells with Enhanced Control of Nonspecific Binding N2 - Glycoproteins are abundant on the cell surface of mammals, providing structural support, modulating cell Membrane properties, and acting as signaling agents. Variation of glycosylation patterns has been found to indicate various disease states, including cell malignancy. Sialic acid (SA) is present as a terminating group on cell-surface glycans, and its overexpression has been linked to several types of cancer. Detection of SA on the cell surface is therefore critical for detection of cancer in its early stages. In this work, a fluorescent molecularly imprinted polymer layer targeting SA was synthesized on the surface of silica-coated polystyrene (PS) particles. Compared to previous works, a PS core supplies a lighter, lower-density support for improved suspension stability and scattering properties. Moreover, their smaller size provides a higher surface-area-to-volume ratio for binding. The incorporation of a fluorescent monomer in the MIP shell allowed for simple and rapid determination of binding specificity in polar media due to a deprotonation−reprotonation interaction mechanism between the fluorescent monomer and SA, which led to spectral changes. Upon titration of the MIP particles with SA in suspension, an increase in fluorescence emission of the particles was observed, with the MIP particles binding SA more selectively compared to the nonimprinted polymer (NIP) control particles. In cell staining experiments performed by flow cytometry, the binding behavior of the MIP particles compared favorably with that of SA-binding lectins. NIPs prepared with a “dummy” template served as a better negative control in cell binding assays due to the favorable inward orientation of template-binding functional groups in the polymer shell, which reduced nonspecific binding. The results show that fluorescent MIPs targeting SA are a promising tool for in vitro fluorescence staining of cancerous cells and for future diagnosis of cancer at early stages. KW - Flow cytometry KW - Sialic acid KW - Fluorescence KW - Molecularly imprinted polymers KW - Cancer cells PY - 2021 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-525216 DO - https://doi.org/10.1021/acsapm.0c01353 VL - 3 IS - 5 SP - 2363 EP - 2373 PB - American Chemical Society AN - OPUS4-52521 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Li, Q. A1 - Shinde, S. A1 - Grasso, G. A1 - Caroli, A. A1 - Abouhany, R. A1 - Lanzillotta, M. A1 - Pan, G. A1 - Wan, Wei A1 - Rurack, Knut A1 - Sellergren, B. T1 - Selective detection of phospholipids using molecularly imprinted fluorescent sensory core-shell particles N2 - Sphingosine-1-phosphate (S1P) is a bioactive sphingo-lipid with a broad range of activities coupled to its role in G-protein coupled receptor signalling. Monitoring of both intra and extra cellular levels of this lipid is challenging due to its low abundance and lack of robust affinity assays or sensors. We here report on fluorescent sensory core-shell molecularly imprinted polymer (MIP) particles responsive to near physiologically relevant levels of S1P and the S1P receptor modulator fingolimod phosphate (FP) in spiked human serum samples. Imprinting was achieved using the tetrabutylammonium (TBA) salt of FP or phosphatidic acid (DPPA·Na) as templates in combination with a polymerizable nitrobenzoxadiazole (NBD)-urea monomer with the dual role of capturing the phospho-anion and signalling its presence. The monomers were grafted from ca 300 nm RAFT-modified silica core particles using ethyleneglycol dimethacrylate (EGDMA) as crosslinker resulting in 10–20 nm thick shells displaying selective fluorescence response to the targeted lipids S1P and DPPA in aqueous buffered media. Potential use of the sensory particles for monitoring S1P in serum was demonstrated on spiked serum samples, proving a linear range of 18–60 μM and a detection limit of 5.6 μM, a value in the same range as the plasma concentration of the biomarker. KW - Molecularly imprinted polymers KW - Phospholipids KW - Fluorescence KW - Dye monomers PY - 2020 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-509485 DO - https://doi.org/10.1038/s41598-020-66802-3 SN - 2045-2322 VL - 10 IS - 1 SP - 9924 PB - Nature Research CY - London AN - OPUS4-50948 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Noureen, N. A1 - Shah, F. A. A1 - Lisec, Jan A1 - Usman, H. A1 - Khalid, M. A1 - Munir, R. A1 - Zaidi, N. T1 - Revisiting the association between human leukocyte antigen and end-stage renal disease N2 - Multiple works have studied possible associations between human leukocyte antigen (HLA) alleles and end stage renal disease (ESRD) showing, however, contradictory and inconsistent results. Here, we revisit the association between ESRD and HLA antigens, comparing HLA polymorphism (at HLA-A, -B, -C, -DRB1, -DQB1 and DQA1 loci) in ESRD patients (n = 497) and controls (n = 672). Our data identified several HLA alleles that displayed a significant positive or negative association with ESRD. We also determined whether heterozygosity or homozygosity of the ESRD-associated HLA alleles at different loci could modify the prevalence of the disease. Few HLA allele combinations displayed significant associations with ESRD, among which A*3_26 combination showed the highest strength of association (OR = 4.488, P≤ 0.05) with ESRD. Interestingly, the age of ESRD onset was not affected by HLA allele combinations at different loci. We also performed an extensive literature analysis to determine whether the association of HLA to ESRD can be similar across different ethnic groups. Our analysis showed that at least certain HLA alleles, HLA-A*11, HLA-DRB1*11, and HLA-DRB1*4, display a significant association with ESRD in different ethnic groups. The findings of our study will help in determining possible protective or susceptible roles of various HLA alleles in ESRD. KW - Cancer KW - Human leukocyte antigen (HLA) KW - Renal disease PY - 2020 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-512651 DO - https://doi.org/10.1371/journal.pone.0238878 SN - 1932-6203 VL - 15 IS - 9 SP - e0238878 AN - OPUS4-51265 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER -