| 1. |
- Emilsson, Gustav, 1989, et al.
(författare)
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Identifying bacteria using DNA binding maps
- 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. - 9781632666246 ; 1, s. 473-475
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Konferensbidrag (refereegranskat)abstract
- We have developed an assay, based on nanofluidic channels and fluorescence microscopy, for optical mapping of DNA based on competitive binding between two molecules - one fluorescent and one sequence selective. From the experimental data we can extract binding constants for the two competing DNA binders, which may be subsequently used to calculate a theoretical reference map of any DNA with known sequence. The goal is to create a method for fast identification of bacteria from single DNA molecules without the need for additional cultivation or amplification. We here demonstrate a proof-of-principle experiment on phage DNA and furthermore show that the method can be used to distinguish between two strains of E. coli DNA and to map pieces of DNA onto the full genome.
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| 2. |
- Ohlsson, Gabriel, 1982, et al.
(författare)
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Solute transport on the sub 100 ms scale across the lipid bilayer membrane of individual proteoliposomes
- 2012
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Ingår i: Lab on a Chip. - : Royal Society of Chemistry (RSC). - 1473-0197 .- 1473-0189. ; 12:22, s. 4635-4643
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Tidskriftsartikel (refereegranskat)abstract
- Screening assays designed to probe ligand and drug-candidate regulation of membrane proteins responsible for ion-translocation across the cell membrane are wide spread, while efficient means to screen membrane-protein facilitated transport of uncharged solutes are sparse. We report on a microfluidic-based system to monitor transport of uncharged solutes across the membrane of multiple (>100) individually resolved surface-immobilized liposomes. This was accomplished by rapidly switching (<10 ms) the solution above dye-containing liposomes immobilized on the floor of a microfluidic channel. With liposomes encapsulating the pH-sensitive dye carboxyfluorescein (CF), internal changes in pH induced by transport of a weak acid (acetic acid) could be measured at time scales down to 25 ms. The applicability of the set up to study biological transport reactions was demonstrated by examining the osmotic water permeability of human aquaporin (AQP5) reconstituted in proteoliposomes. In this case, the rate of osmotic-induced volume changes of individual proteoliposomes was time resolved by imaging the self quenching of encapsulated calcein in response to an osmotic gradient. Single-liposome analysis of both pure and AQP5-containing liposomes revealed a relatively large heterogeneity in osmotic permeability. Still, in the case of AQP5-containing liposomes, the single liposome data suggest that the membrane-protein incorporation efficiency depends on liposome size, with higher incorporation efficiency for larger liposomes. The benefit of low sample consumption and automated liquid handling is discussed in terms of pharmaceutical screening applications.
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| 3. |
- Beech, Jason P., et al.
(författare)
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Electrokinetic wall effect mechanisms and applications
- 2020
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Ingår i: MicroTAS 2020 - 24th International Conference on Miniaturized Systems for Chemistry and Life Sciences. - 9781733419017 ; , s. 42-43
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Konferensbidrag (refereegranskat)abstract
- Under the application of longitudinal electric fields in microchannels, microparticles experience lift forces that push them away from the channel walls and affect their trajectories. At high frequencies (>100KHz) the dielectrophoretic forces dominate and are well understood but at lower frequencies there is little agreement as to the exact nature of the forces, how they are generated and how they vary due to the many different experimental conditions that are used in microfluidics devices. Here we present an experimental study of these mechanisms.
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| 4. |
- Beech, Jason P., et al.
(författare)
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Tunable separation and DNA manipulation in metal coated pillar arrays
- 2018
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Ingår i: 22nd International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2018. - 9781510897571 ; 4, s. 2090-2093
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Konferensbidrag (refereegranskat)abstract
- Implementing electrically connected metal-coated posts in a Deterministic Lateral Displacement (DLD) device and applying electric fields, we use electrokinetics to achieve tunable particle separations and to trap and manipulate DNA. The strength of DLD stems from its typically binary behavior. Particles move in one out of two trajectories based on their effective size. For particles that are close to the threshold size, a minute external force is sufficient to nudge the particles from one trajectory to another. Dielectrophoresis (DEP) provides such a force and also gives specificity based on the dielectric properties of the particles.
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| 5. |
- Bogas, Diana, et al.
(författare)
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Applications of optical DNA mapping in microbiology
- 2017
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Ingår i: BioTechniques. - : Future Science Ltd. - 0736-6205 .- 1940-9818. ; 62:6, s. 255-267
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Forskningsöversikt (refereegranskat)abstract
- Optical mapping (OM) has been used in microbiology for the past 20 years, initially as a technique to facilitate DNA sequence-based studies; however, with decreases in DNA sequencing costs and increases in sequence output from automated sequencing platforms, OM has grown into an important auxiliary tool for genome assembly and comparison. Currently, there are a number of new and exciting applications for OM in the field of microbiology, including investigation of disease outbreaks, identification of specific genes of clinical and/or epidemiological relevance, and the possibility of single-cell analysis when combined with cell-sorting approaches. In addition, designing lab-on-a-chip systems based on OM is now feasible and will allow the integrated and automated microbiological analysis of biological fluids. Here, we review the basic technology of OM, detail the current state of the art of the field, and look ahead to possible future developments in OM technology for microbiological applications.
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| 6. |
- Ghasemi, Masoomeh, et al.
(författare)
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Separation of deformable hydrogel microparticles in deterministic lateral displacement devices
- 2012
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Ingår i: Proceedings of the 16th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2012. - 9780979806452 ; , s. 1672-1674
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Konferensbidrag (refereegranskat)abstract
- To better understand how deformable and non-spherical particles behave in sorting devices based on deterministic lateral displacement we generate models of biological particles with tunable size, shape and mechanical properties using stop-flow lithography and we explore how these parameters play a role in our separation devices. Hollow and solid cylinders are compared with respect to their deformability and their overall behavior in the device. Future work will expand the approach to a range of particle shapes and to particles with varied hydrogel composition to independently control the mechanical properties of the material.
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| 7. |
- Kim, Rebekah, et al.
(författare)
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DNA sample cleanup using deterministic lateral displacement
- 2016
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Ingår i: 20th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2016. - 9780979806490 ; , s. 1527-1528
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Konferensbidrag (refereegranskat)abstract
- Optical mapping relies on the preparation of fluorescent DNA. DNA must be imaged with good signal to noise and therefore the background of unwanted DNA fragments, fluorescent dyes and other reagents need to be removed. We use deterministic lateral displacement to separate 48.5 kbp DNA from < 10 kbp DNA. We also show the removal of 48.5 kbp DNA fragments from a background of fluorescent ATTO647N molecules and the recovery of >50 kbp molecules from a background of shorter digested fragments. In both cases improving signal to noise during imaging.
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| 8. |
- Krog, Jens, et al.
(författare)
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Stochastic unfolding of nanoconfined DNA: Experiments, model and Bayesian analysis
- 2018
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 149:21
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Tidskriftsartikel (refereegranskat)abstract
- Nanochannels provide a means for detailed experiments on the effect of confinement on biomacro-molecules, such as DNA. Here we introduce a model for the complete unfolding of DNA from the circular to linear configuration. Two main ingredients are the entropic unfolding force and the friction coefficient for the unfolding process, and we describe the associated dynamics by a non-linear Langevin equation. By analyzing experimental data where DNA molecules are photo-cut and unfolded inside a nanochannel, our model allows us to extract values for the unfolding force as well as the friction coefficient for the first time. In order to extract numerical values for these physical quantities, we employ a recently introduced Bayesian inference framework. We find that the determined unfolding force is in agreement with estimates from a simple Flory-type argument. The estimated friction coefficient is in agreement with theoretical estimates for motion of a cylinder in a channel. We further validate the estimated friction constant by extracting this parameter from DNA's center-of -mass motion before and after unfolding, yielding decent agreement. We provide publically available software for performing the required image and Bayesian analysis. Published by AIP Publishing.
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| 9. |
- Sköld, Niklas, et al.
(författare)
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Nanofluidics in hollow nanowires
- 2010
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Ingår i: NANOTECHNOLOGY. - : IOP Publishing. - 0957-4484 .- 1361-6528. ; 21:15
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Tidskriftsartikel (refereegranskat)abstract
- We present a novel scheme for producing nanotube membranes using free-standing hollow nanowires, with easily controllable dimensions. GaAs–AlInP core–shell nanowires were grown by metal–organic vapor phase epitaxy and were partially embedded in a polymer film. The GaAs core and substrate were etched selectively, leaving tubes with open access to both sides of the membrane. Electrophoretic transport of T4-phage DNA through the hollow nanowires was demonstrated using epifluorescence microscopy.
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| 10. |
- Ström, Oskar E., et al.
(författare)
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KÁRMÁN VORTEX CITY OF DNA STRANDS
- 2021
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Ingår i: MicroTAS 2021 - 25th International Conference on Miniaturized Systems for Chemistry and Life Sciences. - 9781733419031 ; , s. 13-14
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Konferensbidrag (refereegranskat)abstract
- Kármán vortex streets are repeating patterns of swirling vortices, appearing when a fluid passes an obstacle at Re>50. We present an array of interacting vortices, a Kármán vortex city, that arises when a DNA solution flows through an array of micro posts at Re <0.5. Above thresholds in concentration and flow rate, the vortices formed behind posts interact, leading to concentration fluctuation waves. We explore the effect of lattice structure, polymer length and salt and relate the wave formation to the overlap concentration. Our work will allow us to optimize high-concentration DNA manipulation and sorting of DNA in microfluidic arrays.
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