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1.
  • Fernandez, Yuri A. Diaz, 1978, et al. (författare)
  • The conquest of middle-earth: combining top-down and bottom-up nanofabrication for constructing nanoparticle based devices
  • 2014
  • Ingår i: Nanoscale. - 2040-3364. ; 6:24, s. 14605-14616
  • Tidskriftsartikel (refereegranskat)abstract
    • The development of top-down nanofabrication techniques has opened many possibilities for the design and realization of complex devices based on single molecule phenomena such as e. g. single molecule electronic devices. These impressive achievements have been complemented by the fundamental understanding of self-assembly phenomena, leading to bottom-up strategies to obtain hybrid nanomaterials that can be used as building blocks for more complex structures. In this feature article we highlight some relevant published work as well as present new experimental results, illustrating the versatility of self-assembly methods combined with top-down fabrication techniques for solving relevant challenges in modern nanotechnology. We present recent developments on the use of hierarchical self-assembly methods to bridge the gap between sub-nanometer and micrometer length scales. By the use of non-covalent self-assembly methods, we show that we are able to control the positioning of nanoparticles on surfaces, and to address the deterministic assembly of nano-devices with potential applications in plasmonic sensing and single-molecule electronics experiments.
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2.
  • Gschneidtner, Tina, 1985, et al. (författare)
  • A Versatile Self-Assembly Strategy for the Synthesis of Shape-Selected Colloidal Noble Metal Nanoparticle Heterodimers
  • 2014
  • Ingår i: Langmuir. - 1520-5827 .- 0743-7463. ; 30:11, s. 3041-3050
  • Tidskriftsartikel (refereegranskat)abstract
    • The self-assembly of individual nanoparticles into-dimers so-called heterodimers-is relevant for a broad range of applications, in particular in the vibrant field of nano-plasmonics and nanooptics. In this paper we report the synthesis and characterization of material- and shape-selected nanoparticle heterodimers assembled from individual particles via electrostatic interaction. The versatility of the synthetic strategy is shown by assembling combinations of metal particles of different shapes, sizes, and metal compositions like a gold sphere (90 nm) with either a gold cube (35 nm), gold rhombic dodecahedron (50 nm), palladium truncated cube (120 nm), palladium rhombic dodecahedron (110 nm), palladium octahedron (130 nm), or palladium cubes (25 and 70 nm) as well as a silver sphere (90 nm) with palladium cubes (25 and 70 nm). The obtained heterodimer combinations are characterized by transmission electron microscopy (TEM), scanning electron microscopy (SEM), scanning transmission electron microscopy energy dispersive X-ray spectroscopy (STEM-EDX), dynamic light scattering (DLS), and zeta-potential measurements. We describe the optimal experimental conditions to achieve the highest yield of heterodimers compared to other aggregates. The experimental results have been rationalized using theoretical modeling. A proof-of-principle experiment where individual Au-Pd heterodimers are exploited for indirect plasmonic sensing of hydrogen finally illustrates the potential of these structures to probe catalytic processes at the single particle level.
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3.
  • Lubart, Quentin, 1989, et al. (författare)
  • High throughput size-determination and multiplexed fluorescence analysis of single biological particles in a nanofluidic device
  • 2019
  • Ingår i: 23rd International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2019. ; , s. 1420-1421
  • Konferensbidrag (refereegranskat)abstract
    • Biological nanoparticles, such as exosomes and viruses, are responsible for a multitude of important functions, but methods to characterize them on the single particle level are rare. We here present a nanofluidic platform for multi-parametric characterization of biological nanoparticles with high throughput. The device consists of feeding microchannels and an array of ~100 nanochannels where the nanoparticles can be characterized. We determine the size by analyzing the Brownian motion of the particles and quantify their content based on fluorescence imaging of up to three different colors. We successfully benchmark our method against existing techniques, such as Nanoparticle Tracking Analysis (NTA).
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4.
  • Singh, V., et al. (författare)
  • Quantifying DNA damage induced by ionizing radiation and hyperthermia using single DNA molecule imaging
  • 2020
  • Ingår i: Translational Oncology. - 1936-5233. ; 13:10
  • Tidskriftsartikel (refereegranskat)abstract
    • Ionizing radiation (IR) is a common mode of cancer therapy, where DNA damage is the major reason of cell death. Here, we use an assay based on fluorescence imaging of single damaged DNA molecules isolated from radiated lymphocytes, to quantify IR induced DNA damage. The assay uses a cocktail of DNA-repair enzymes that recognizes and excises DNA lesions and then a polymerase and a ligase incorporate fluorescent nucleotides at the damage sites, resulting in a fluorescent “spot” at each site. The individual fluorescent spots can then be counted along single stretched DNA molecules and the global level of DNA damage can be quantified. Our results demonstrate that inclusion of the human apurinic/apyrimidinic endonuclease 1 (APE1) in the enzyme cocktail increases the sensitivity of the assay for detection of IR induced damage significantly. This optimized assay also allowed detection of a cooperative increase in DNA damage when IR was combined with mild hyperthermia, which is sometimes used as an adjuvant in IR therapy. Finally, we discuss how the method may be used to identify patients that are sensitive to IR and other types of DNA damaging agents. © 2020 The Authors
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5.
  • Singh, V., et al. (författare)
  • Shining light on single-strand lesions caused by the chemotherapy drug bleomycin
  • 2021
  • Ingår i: DNA Repair. - 1568-7864. ; 105
  • Tidskriftsartikel (refereegranskat)abstract
    • Quantification of the DNA damage induced by chemotherapy in patient cells may aid in personalization of the dose used. However, assays to evaluate individual patient response to chemotherapy are not available today. Here, we present an assay that quantifies single-stranded lesions caused by the chemotherapeutic drug Bleomycin (BLM) in peripheral blood mononuclear cells (PBMCs) isolated from healthy individuals. We use base excision repair (BER) enzymes to process the DNA damage induced by BLM and then extend the processed sites with fluorescent nucleotides using a DNA polymerase. The fluorescent patches are quantified on single DNA molecules using fluorescence microscopy. Using the assay, we observe a significant variation in the in vitro induced BLM damage and its repair for different individuals. Treatment of the cells with the BER inhibitor CRT0044876 leads to a lower level of repair of BLM-induced damage, indicating the ability of the assay to detect a compromised DNA repair in patients. Overall, the data suggest that our assay could be used to sensitively detect the variation in BLM-induced DNA damage and repair in patients and can potentially be able to aid in personalizing patient doses.
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6.
  • Syrenova, Svetlana, 1987, et al. (författare)
  • Hydride formation thermodynamics and hysteresis in individual Pd nanocrystals with different size and shape
  • 2015
  • Ingår i: Nature Materials. - 1476-4660 .- 1476-1122. ; 14:12, s. 1236-1244
  • Tidskriftsartikel (refereegranskat)abstract
    • Physicochemical properties of nanoparticles may depend on their size and shape and are traditionally assessed in ensemble-level experiments, which accordingly may be plagued by averaging effects. These effects can be eliminated in single-nanoparticle experiments. Using plasmonic nanospectroscopy, we present a comprehensive study of hydride formation thermodynamics in individual Pd nanocrystals of different size and shape, and find corresponding enthalpies and entropies to be nearly size- and shape-independent. The hysteresis observed is significantly wider than in bulk, with details depending on the specifics of individual nanoparticles. Generally, the absorption branch of the hysteresis loop is size-dependent in the sub-30 nm regime, whereas desorption is size- and shape-independent. The former is consistent with a coherent phase transition during hydride formation, influenced kinetically by the specifics of nucleation, whereas the latter implies that hydride decomposition either occurs incoherently or via different kinetic pathways.
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7.
  • Friedrich, R., et al. (författare)
  • A nano flow cytometer for single lipid vesicle analysis
  • 2017
  • Ingår i: Lab on a Chip - Miniaturisation for Chemistry and Biology. - 1473-0189 .- 1473-0197. ; 17:5, s. 830-841
  • Tidskriftsartikel (refereegranskat)abstract
    • We present a nanofluidic device for fluorescence-based detection and characterization of small lipid vesicles on a single particle basis. The device works like a nano flow cytometer where individual vesicles are visualized by fluorescence microscopy while passing through parallel nanochannels in a pressure-driven flow. An experiment requires less than 20 mu l sample volume to quantify both the vesicle content and the fluorescence signals emitted by individual vesicles. We show that the device can be used to accurately count the number of fluorescent synthetic lipid vesicles down to a vesicle concentration of 170 fM. We also show that the size-distribution of the vesicles can be resolved from their fluorescence intensity distribution after calibration. We demonstrate the applicability of the assay in two different examples. In the first, we use the nanofluidic device to determine the particle concentration in a sample containing cell-derived extracellular vesicles labelled with a lipophilic dye. In the second, we demonstrate that dual-color detection can be used to probe peptide binding to synthetic lipid vesicles; we identify a positive membrane-curvature sensing behavior of an arginine enriched version of the Antennapedia homeodomain peptide penetratin. Altogether, these results illustrate the potential of this nanofluidic-based methodology for characterization and quantification of small biological vesicles and their interactors without ensemble averaging. The device is therefore likely to find use as a quantitative analytical tool in a variety of fields ranging from diagnostics to fundamental biology research. Moreover, our results have potential to facilitate further development of automated lab-on-a-chip devices for vesicle analysis.
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8.
  • Johnning, Anna, 1985, et al. (författare)
  • The resistomes of six carbapenem-resistant pathogens - a critical genotype-phenotype analysis
  • 2018
  • Ingår i: Microbial Genomics. - : Microbiology Society. - 2057-5858. ; 4:11
  • Tidskriftsartikel (refereegranskat)abstract
    • Carbapenem resistance is a rapidly growing threat to our ability to treat refractory bacterial infections. To understand how carbapenem resistance is mobilized and spread between pathogens, it is important to study the genetic context of the underlying resistance mechanisms. In this study, the resistomes of six clinical carbapenem-resistant isolates of five different species - Acinetobacter baumannii, Escherichia colt, two Klebsiella pneumoniae, Proteus mirabilis and Pseudomonas aeruginosa - were characterized using whole genome sequencing. All Enterobacteriaceae isolates and the A. baumannii isolate had acquired a large number of antimicrobial resistance genes (7-18 different genes per isolate), including the following encoding carbapenemases: bla(KPC-2), bla(OXA-48), bla(OXA-72), bla(NDM-1), bla(NDm-7) and bla(VIM-1). In addition, a novel version of bla(SHv) was discovered. Four new resistance plasmids were identified and their fully assembled sequences were verified using optical DNA mapping. Most of the resistance genes were colocalized on these and other plasmids, suggesting a risk for coselection. In contrast, five out of six carbapenemase genes were present on plasmids with no or few other resistance genes. The expected level of resistance - based on acquired resistance determinants - was concordant with measured levels in most cases. There were, however, several important discrepancies for four of the six isolates concerning multiple classes of antibiotics. In conclusion, our results further elucidate the diversity of carbapenemases, their mechanisms of horizontal transfer and possible patterns of co-selection. The study also emphasizes the difficulty of using whole genome sequencing for antimicrobial susceptibility testing of pathogens with complex genotypes.
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9.
  • Karami, N., et al. (författare)
  • Identity of bla ctx-m carrying plasmids in sequential esbl-e. Coli isolates from patients with recurrent urinary tract infections
  • 2021
  • Ingår i: Microorganisms. - 2076-2607. ; 9:6
  • Tidskriftsartikel (refereegranskat)abstract
    • Plasmid-mediated multidrug resistance in E. coli is becoming increasingly prevalent. Considering this global threat to human health, it is important to understand how plasmid-mediated resistance spreads. From a cohort of 123 patients with recurrent urinary tract infections (RUTI) due to extended spectrum beta-lactamase (ESBL)-producing Escherichia coli (ESBL E. coli), only five events with a change of ESBL E. coli strain between RUTI episodes were identified. Their blaCTX-M encoding plasmids were compared within each pair of isolates using optical DNA mapping (ODM) and PCR-based replicon typing. Despite similar blaCTX-M genes and replicon types, ODM detected only one case with identical plasmids in the sequential ESBL E. coli strains, indicating that plasmid transfer could have occurred. For comparison, plasmids from seven patients with the same ESBL E. coli strain reoccurring in both episodes were analyzed. These plasmids (encoding blaCTX-M-3, blaCTX-M-14, and blaCTX-M-15 ) were unaltered for up to six months between recurrent infections. Thus, transmission of blaCTX-M plasmids appears to be a rare event during the course of RUTI. Despite the limited number (n = 23) of plasmids investigated, similar blaCTX-M-15 plasmids in unrelated isolates from different patients were detected, suggesting that some successful plasmids could be associated with specific strains, or are more easily transmitted.
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10.
  • Kesarimangalam, Sriram, 1983, et al. (författare)
  • A parallelized nanofluidic device for high-throughput optical dna mapping of bacterial plasmids
  • 2021
  • Ingår i: Micromachines. - 2072-666X. ; 12:10
  • Tidskriftsartikel (refereegranskat)abstract
    • Optical DNA mapping (ODM) has developed into an important technique for DNA anal-ysis, where single DNA molecules are sequence-specifically labeled and stretched, for example, in nanofluidic channels. We have developed an ODM assay to analyze bacterial plasmids—circular extrachromosomal DNA that often carry genes that make bacteria resistant to antibiotics. As for most techniques, the next important step is to increase throughput and automation. In this work, we designed and fabricated a nanofluidic device that, together with a simple automation routine, allows parallel analysis of up to 10 samples at the same time. Using plasmids encoding extended-spectrum beta-lactamases (ESBL), isolated from Escherichia coli and Klebsiella pneumoniae, we demon-strate the multiplexing capabilities of the device when it comes to both many samples in parallel and different resistance genes. As a final example, we combined the device with a novel protocol for rapid cultivation and extraction of plasmids from fecal samples collected from patients. This combined protocol will make it possible to analyze many patient samples in one device already on the day the sample is collected, which is an important step forward for the ODM analysis of plas-mids in clinical diagnostics.
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