| 1. |
- Bernin, Diana, 1979, et al.
(författare)
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Microstructure of polymer hydrogels studied by pulsed field gradient NMR diffusion and TEM methods
- 2011
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Ingår i: Soft Matter. - : Royal Society of Chemistry (RSC). - 1744-683X .- 1744-6848. ; 7:12, s. 5711-5716
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Tidskriftsartikel (refereegranskat)abstract
- The microstructure of various alginate gels have been studied by pulsed field gradient NMR (PFG NMR) and transmission electron microscopy (TEM). The reduced diffusivity of dendrimer diffusion within the gels has been obtained from PFG NMR diffusion experiments. The polymer strand radius, an important microstructural property, has been extracted from various diffusion models. The results agree well with the polymer strand radii obtained from image analysis of the corresponding TEM micrographs.
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| 2. |
- Deschout, H., et al.
(författare)
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Disposable microfluidic chip with integrated light sheet illumination enables diagnostics based on membrane vesicles
- 2014
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Ingår i: 17th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2013; Freiburg; Germany; 27 October 2013 through 31 October 2013. - 9781632666246
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Konferensbidrag (refereegranskat)abstract
- Cell-derived membrane vesicles that are released in body fluids are emerging as potential non-invasive biomarkers for diseases like cancer. Techniques capable of measuring the size and concentration of such membrane vesicles directly in body fluids are urgently needed. Here we report on a microfluidic chip with integrated light sheet illumination, and demonstrate accurate fluorescence Single Particle Tracking measurements of the size and concentration of membrane vesicles in cell culture medium and in interstitial fluid collected from primary human breast tumours.
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| 3. |
- Deschout, Hendrik, et al.
(författare)
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Disposable microfluidic chip with integrated light sheet illumination enables diagnostics based on membrane vesicles
- 2013
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Ingår i: 17th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2013; Freiburg; Germany; 27 October 2013 through 31 October 2013. ; 3, s. 2010-2012
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Konferensbidrag (refereegranskat)abstract
- Cell-derived membrane vesicles that are released in body fluids are emerging as potential non-invasive biomarkers for diseases like cancer. Techniques capable of measuring the size and concentration of such membrane vesicles directly in body fluids are urgently needed. Here we report on a microfluidic chip with integrated light sheet illumination, and demonstrate accurate fluorescence Single Particle Tracking measurements of the size and concentration of membrane vesicles in cell culture medium and in interstitial fluid collected from primary human breast tumours.
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| 4. |
- Deschout, H., et al.
(författare)
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On-chip light sheet illumination enables diagnostic size and concentration measurements of membrane vesicles in biofluids
- 2014
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Ingår i: Nanoscale. - : Royal Society of Chemistry (RSC). - 2040-3364 .- 2040-3372. ; 6:3, s. 1741-1747
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Tidskriftsartikel (refereegranskat)abstract
- Cell-derived membrane vesicles that are released in biofluids, like blood or saliva, are emerging as potential non-invasive biomarkers for diseases, such as cancer. Techniques capable of measuring the size and concentration of membrane vesicles directly in biofluids are urgently needed. Fluorescence single particle tracking microscopy has the potential of doing exactly that by labelling the membrane vesicles with a fluorescent label and analysing their Brownian motion in the biofluid. However, an unbound dye in the biofluid can cause high background intensity that strongly biases the fluorescence single particle tracking size and concentration measurements. While such background intensity can be avoided with light sheet illumination, current set-ups require specialty sample holders that are not compatible with high-throughput diagnostics. Here, a microfluidic chip with integrated light sheet illumination is reported, and accurate fluorescence single particle tracking size and concentration measurements of membrane vesicles in cell culture medium and in interstitial fluid collected from primary human breast tumours are demonstrated.
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| 5. |
- Deschout, Hendrik, et al.
(författare)
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Straightforward FRAP for quantitative diffusion measurements with a laser scanning microscope
- 2010
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Ingår i: Optics Express. - 1094-4087. ; 18:22, s. 22886-22905
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Tidskriftsartikel (refereegranskat)abstract
- Confocal or multi-photon laser scanning microscopes are convenient tools to perform FRAP diffusion measurements. Despite its popularity, accurate FRAP remains often challenging since current methods are either limited to relatively large bleach regions or can be complicated for non-specialists. In order to bring reliable quantitative FRAP measurements to the broad community of laser scanning microscopy users, here we have revised FRAP theory and present a new pixel based FRAP method relying on the photo bleaching of rectangular regions of any size and aspect ratio. The method allows for fast and straightforward quantitative diffusion measurements due to a closed–form expression for the recovery process utilizing all available spatial and temporal data. After a detailed validation, its versatility is demonstrated by diffusion studies in heterogeneous biopolymer mixtures.
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| 6. |
- Franck, Niclas, et al.
(författare)
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Identification of adipocyte genes regulated by caloric intake
- 2011
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Ingår i: Journal of Clinical Endocrinology and Metabolism. - : Endocrine society. - 0021-972X .- 1945-7197. ; 96:2, s. E413-E418
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Tidskriftsartikel (refereegranskat)abstract
- CONTEXT: Changes in energy intake have marked and rapid effects on metabolic functions and some of the effects may be due to changes in adipose tissue gene expression that precede alterations in body weight. OBJECTIVE: To identify genes in adipose tissue regulated by changes in caloric intake independent of changes in body weight. RESEARCH DESIGN AND METHODS: Obese subjects were given a very-low calorie diet (VLCD; 450 kcal/day) for 16 weeks. After the diet, ordinary food was gradually reintroduced during 2 weeks while there were minimal changes in body weight. Adipose tissue gene expression was measured by microarray analysis. First, genes regulated during caloric restriction and in the opposite direction during the weight stable re-feeding phase were identified. To verify opposite regulation to that observed during caloric restriction, identified genes were further analyzed using adipocyte expression profiles from healthy subjects before and after overfeeding. Results were confirmed using real time PCR or immunoassay. RESULTS: Using a significance level of p<0.05 for all comparisons, 52 genes were downregulated and 50 were up-regulated by caloric restriction and regulated in the opposite direction by re-feeding and overfeeding. Among these were genes that affect lipogenesis (ACLY, ACACA, FASN, SCD), protein synthesis (4EBP1, 4EBP2), beta-oxidation (CPT1B), liberation of fatty acids (CIDEA) and glyceroneogenesis (PCK2). Interestingly, several of these are under control of the master regulator mTOR. CONCLUSIONS: The observed transcriptional changes indicate that mTOR plays a central role in the control of diet-regulated adipocyte genes involved in lipogenesis and protein synthesis.
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| 7. |
- Jernås, Margareta, 1961, et al.
(författare)
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MS risk genes are transcriptionally regulated in CSF leukocytes at relapse
- 2013
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Ingår i: Multiple sclerosis (Houndmills, Basingstoke, England). - : SAGE Publications. - 1477-0970 .- 1352-4585. ; 19:4, s. 403-410
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Infiltrating T-helper cells, cytotoxic T-cells, B-cells and monocytes are thought to mediate the damage to myelin, oligodendrocytes and axons in multiple sclerosis (MS), which results in progressive disability. OBJECTIVE: The objective of this paper is to explore gene expression profiles of leukocytes in the cerebrospinal fluid (CSF) compartment of MS patients during relapse. METHODS: Global gene expression was analyzed by DNA microarray analysis of cells in CSF from MS patients and controls, and verifications were performed with real-time polymerase chain reaction (PCR) and enzyme-linked immunosorbent assay (ELISA). RESULTS: Fifty percent of the recently described risk genes for MS and 28% of non-risk genes were differently expressed in MS patients compared to controls (χ(2)-test, p=7.7 × 10(-5)). Genes involved in T- and NK-cell processes were up-regulated, and genes involved in processes targeting innate immunity or B-cells were down-regulated in MS. Increased expression of EDN1 and CXCL11 and decreased expression of HMOX1 was verified with real-time PCR and increased expression of CXCL13 was verified with ELISA in CSF. CONCLUSION: DNA microarray analysis is useful in identifying differently expressed genes in CSF leukocytes, which may be important in MS in vivo. Our findings suggest that many of the risk genes for MS are differently expressed in the disease-mediating leukocytes that penetrate the blood-brain barrier.
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| 8. |
- Jonasson, Jenny, 1976, et al.
(författare)
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Pixel-based analysis of FRAP data with a general initial bleaching profile
- 2010
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Ingår i: Journal of Microscopy. - : Wiley. - 0022-2720 .- 1365-2818. ; 239:2, s. 142-153
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Tidskriftsartikel (refereegranskat)abstract
- Jonasson et al. (2008), we presented a new pixel-based maximum likelihood framework for the estimation of diffusion coefficients from data on fluorescence recovery after photobleaching (FRAP) with confocal laser scanning microscopy (CLSM). The main method there, called the Gaussian profile method below, is based on the assumption that the initial intensity profile after photobleaching is approximately Gaussian. In the present paper, we introduce a method, called the Monotone profile method, where the maximum likelihood framework is extended to a general initial bleaching profile only assuming that the profile is a non-decreasing function of the distance to the bleaching centre. The statistical distribution of the image noise is further assumed to be Poisson instead of normal, which should be a more realistic description of the noise in the detector. The new Monotone profile method and the Gaussian profile method are applied to FRAP data on swelling of super absorbent polymers (SAP) in water with a Fluorescein probe. The initial bleaching profile is close to a step function at low degrees of swelling and close to a Gaussian profile at high degrees of swelling. The results obtained from the analysis of the FRAP data are corroborated with NMR diffusometry analysis of SAP with a polyethylene glycol probe having size similar to the Fluorescein. The comparison of the Gaussian and Monotone profile methods is also performed by use of simulated data. It is found that the new Monotone profile method is accurate for all types of initial profiles studied, but it suffers from being computationally slow. The fast Gaussian profile method is sufficiently accurate for most of the profiles studied, but underestimates the diffusion coefficient for profiles close to a step function. We also provide a diagnostic plot, which indicates whether the Gaussian profile method is acceptable or not.
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| 9. |
- Naeye, B, et al.
(författare)
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Hemocompatibility of siRNA loaded dextran nanogels
- 2011
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Ingår i: Biomaterials. - : Elsevier BV. - 0142-9612 .- 1878-5905. ; 32:34, s. 9120-9127
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Tidskriftsartikel (refereegranskat)abstract
- Although the behavior of nanoscopic delivery systems in blood is an important parameter when contemplating their intravenous injection, this aspect is often poorly investigated when advancing from in vitro to in vivo experiments. In this paper, the behavior of siRNA loaded dextran nanogels in human plasma and blood is examined using fluorescence fluctuation spectroscopy, platelet aggregometry, flow cytometry and single particle tracking. Our results show that, in contrast to their negatively charged counterparts, positively charged siRNA loaded dextran nanogels cause platelet aggregation and show increased binding to human blood cells. Although PEGylating the nanogels did not have a significant effect on their interaction with blood cells, single particle tracking revealed that it is necessary to prevent their aggregation in human plasma. We therefore conclude that PEGylated negatively charged dextran nanogels are the most suited for further in vivo studies as they do not aggregate in human plasma and exhibit minimal interactions with blood cells.
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| 10. |
- Nordin, Matias, 1981, et al.
(författare)
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Estimation of mass thickness response of embedded aggregated silica nanospheres from high angle annular dark-field scanning transmission electron micrographs
- 2014
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Ingår i: Journal of Microscopy. - : Wiley. - 0022-2720 .- 1365-2818. ; 253:2, s. 166-170
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Tidskriftsartikel (refereegranskat)abstract
- In this study, we investigate the functional behaviour of the intensity in high-angle annular dark field scanning transmission electron micrograph images. The model material is a silica particle (20 nm) gel at 5 wt%. By assuming that the intensity response is monotonically increasing with increasing mass thickness of silica, an estimate of the functional form is calculated using a maximum likelihood approach. We conclude that a linear functional form of the intensity provides a fair estimate but that a power function is significantly better for estimating the amount of silica in the z-direction. The work adds to the development of quantifying material properties from electron micrographs, especially in the field of tomography methods and three-dimensional quantitative structural characterization from a scanning transmission electron micrograph. It also provides means for direct three-dimensional quantitative structural characterization from a scanning transmission electron micrograph.
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| 11. |
- Röding, Magnus, 1984, et al.
(författare)
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Automatic Particle Detection in Microscopy Using Temporal Correlations
- 2013
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Ingår i: Microscopy Research and Technique. - : Wiley. - 1059-910X. ; 76:10, s. 997-1006
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Tidskriftsartikel (refereegranskat)abstract
- One of the fundamental problems in the analysis of single particle tracking data is the detection of individual particle positions from microscopy images. Distinguishing true particles from noise with a minimum of false positives and false negatives is an important step that will have substantial impact on all further analysis of the data. A common approach is to obtain a plausible set of particles from a larger set of candidate particles by filtering using manually selected threshold values for intensity, size, shape, and other parameters describing a particle. This introduces subjectivity into the analysis and hinders reproducibility. In this paper, we introduce a method for automatic selection of these threshold values based on maximizing temporal correlations in particle count time series. We use Markov Chain Monte Carlo to find the threshold values corresponding to the maximum correlation, and we study several experimental data sets to assess the performance of the method in practice by comparing manually selected threshold values from several independent experts with automatically selected threshold values. We conclude that the method produces useful results, reducing subjectivity and the need for manual intervention, a great benefit being its easy integratability into many already existing particle detection algorithms.
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| 12. |
- Röding, Magnus, 1984, et al.
(författare)
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Identifying directional persistence in intracellular particle motion using Hidden Markov Models
- 2014
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Ingår i: Mathematical Biosciences. - : Elsevier BV. - 0025-5564 .- 1879-3134. ; 248, s. 140-145
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Tidskriftsartikel (refereegranskat)abstract
- Particle tracking is a widely used and promising technique for elucidating complex dynamics of the living cell. The cytoplasm is an active material, in which the kinetics of intracellular structures are highly heterogeneous. Tracer particles typically undergo a combination of random motion and various types of directed motion caused by the activity of molecular motors and other non-equilibrium processes. Random switching between more and less directional persistence of motion generally occurs. We present a method for identifying states of motion with different directional persistence in individual particle trajectories. Our analysis is based on a multi-scale turning angle model to characterize motion locally, together with a Hidden Markov Model with two states representing different directional persistence. We define one of the states by the motion of particles in a reference data set where some active processes have been inhibited. We illustrate the usefulness of the method by studying transport of vesicles along microtubules and transport of nanospheres activated by myosin. We study the results using mean square displacements, durations, and particle speeds within each state. We conclude that the method provides accurate identification of states of motion with different directional persistence, with very good agreement in terms of mean-squared displacement between the reference data set and one of the states in the two-state model.
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| 13. |
- Röding, Magnus, 1984, et al.
(författare)
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Measuring absolute nanoparticle number concentrations from particle count time series
- 2013
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Ingår i: Journal of Microscopy. - : Wiley. - 0022-2720 .- 1365-2818. ; 251:1, s. 19-26
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Tidskriftsartikel (refereegranskat)abstract
- Single-particle microscopy is important for characterization of nanoparticulate matter for which accurate concentration measurements are crucial. We introduce a method for estimating absolute number concentrations in nanoparticle dispersions based on a fluctuating time series of particle counts, known as a Smoluchowski process. Thus, unambiguous tracking of particles is not required and identification of single particles is sufficient. However, the diffusion coefficient of the particles must be estimated separately. The proposed method does not require precalibration of the detection region volume, as this can be estimated directly from the observations. We evaluate the method in a simulation study and on experimental data from a series of dilutions of 0.2- and 0.5-m polymer nanospheres in water, obtaining very good agreement with reference values.
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| 14. |
- Röding, Magnus, 1984, et al.
(författare)
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Measuring absolute number concentrations of nanoparticles using single-particle tracking
- 2011
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Ingår i: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics. - 1539-3755 .- 1550-2376. ; 84:3
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Tidskriftsartikel (refereegranskat)abstract
- Single-particle tracking (SPT) microscopy is increasingly used to characterize nanoparticulate systems. We introduce a concept for estimation of particle number concentration in Brownian particle dispersions using SPT based on a model for the trajectory length distribution of particles to estimate the detection region volume. The resulting method is independent of precalibration reference measurements, and robust with respect to image processing settings. Experimentally estimated concentrations of different dilutions of 0.19- and 0.52-mu m polymer nanospheres are in excellent agreement with estimates computed from the concentrations of the stock solutions.
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| 15. |
- Röding, Magnus, 1984, et al.
(författare)
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Self-calibrated concentration measurements of polydisperse nanoparticles
- 2013
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Ingår i: Journal of Microscopy. - : Wiley. - 0022-2720 .- 1365-2818. ; 252:1, s. 79-88
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Tidskriftsartikel (refereegranskat)abstract
- Summary Quantitative characterization of nanoparticles, e.g. accurate estimation of concentration distributions, is critical to many pharmaceutical and biological applications. We present a method that enables for the first time highly accurate size and absolute concentration measurements of polydisperse nanoparticles in solution, based on fluorescence single particle tracking, that are self-calibrated in the sense that the detection region volume is estimated based on the tracking data. The method is evaluated using simulations and experimental data of polystyrene nanospheres in water/sucrose solution. In addition, the method is used to quantify aggregation and clearance of different types of liposomes after intravenous injection in rats, where additional and more accurate information can be obtained that was previously unavailable, which can help elucidate their usefulness as drug carriers.
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| 16. |
- Röding, Magnus, 1984, et al.
(författare)
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The gamma distribution model for pulsed-field gradient NMR studies of molecular-weight distributions of polymers
- 2012
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Ingår i: Journal of Magnetic Resonance. - : Elsevier BV. - 1090-7807 .- 1096-0856. ; 222, s. 105-111
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Tidskriftsartikel (refereegranskat)abstract
- Self-diffusion in polymer solutions studied with pulsed-field gradient nuclear magnetic resonance (PFG NMR) is typically based either on a single self-diffusion coefficient, or a log-normal distribution of self-diffusion coefficients, or in some cases mixtures of these. Experimental data on polyethylene glycol (PEG) solutions and simulations were used to compare a model based on a gamma distribution of self-diffusion coefficients to more established models such as the single exponential, the stretched exponential, and the log-normal distribution model with regard to performance and consistency. Even though the gamma distribution is very similar to the log-normal distribution, its NMR signal attenuation can be written in a closed form and therefore opens up for increased computational speed. Estimates of the mean self-diffusion coefficient, the spread, and the polydispersity index that were obtained using the gamma model were in excellent agreement with estimates obtained using the log-normal model. Furthermore, we demonstrate that the gamma distribution is by far superior to the log-normal, and comparable to the two other models, in terms of computational speed. This effect is particularly striking for multi-component signal attenuation. Additionally, the gamma distribution as well as the log-normal distribution incorporates explicitly a physically plausible model for polydispersity and spread, in contrast to the single exponential and the stretched exponential. Therefore, the gamma distribution model should be preferred in many experimental situations.
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| 17. |
- Schuster, Erich, et al.
(författare)
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Interactions and diffusion in fine-stranded beta-lactoglobulin gels determined via FRAP and binding
- 2014
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Ingår i: Biophysical Journal. - : Elsevier BV. - 0006-3495 .- 1542-0086. ; 106:1, s. 253-262
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Tidskriftsartikel (refereegranskat)abstract
- The effects of electrostatic interactions and obstruction by the microstructure on probe diffusion were determined in positively charged hydrogels. Probe diffusion in fine-stranded gels and solutions of ?-lactoglobulin at pH 3.5 was determined using fluorescence recovery after photobleaching (FRAP) and binding, which is widely used in biophysics. The microstructures of the ?-lactoglobulin gels were characterized using transmission electron microscopy. The effects of probe size and charge (negatively charged Na2-fluorescein (376Da) and weakly anionic 70kDa FITC-dextran), probe concentration (50 to 200 ppm), and ?-lactoglobulin concentration (9% to 12% w/w) on the diffusion properties and the electrostatic interaction between the negatively charged probes and the positively charged gels or solutions were evaluated. The results show that the diffusion of negatively charged Na2-fluorescein is strongly influenced by electrostatic interactions in the positively charged ?-lactoglobulin systems. A linear relationship between the pseudo-on binding rate constant and the ?-lactoglobulin concentration for three different probe concentrations was found. This validates an important assumption of existing biophysical FRAP and binding models, namely that the pseudo-on binding rate constant equals the product of the molecular binding rate constant and the concentration of the free binding sites. Indicators were established to clarify whether FRAP data should be analyzed using a binding-diffusion model or an obstruction-diffusion model.
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