| 1. |
- Cossarizza, A., et al.
(författare)
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Guidelines for the use of flow cytometry and cell sorting in immunological studies (second edition)
- 2019
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Ingår i: European Journal of Immunology. - : Wiley. - 0014-2980 .- 1521-4141. ; 49:10, s. 1457-1973
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Tidskriftsartikel (refereegranskat)abstract
- These guidelines are a consensus work of a considerable number of members of the immunology and flow cytometry community. They provide the theory and key practical aspects of flow cytometry enabling immunologists to avoid the common errors that often undermine immunological data. Notably, there are comprehensive sections of all major immune cell types with helpful Tables detailing phenotypes in murine and human cells. The latest flow cytometry techniques and applications are also described, featuring examples of the data that can be generated and, importantly, how the data can be analysed. Furthermore, there are sections detailing tips, tricks and pitfalls to avoid, all written and peer-reviewed by leading experts in the field, making this an essential research companion.
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| 2. |
- Abila, R., et al.
(författare)
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Oil extraction imperils Africa’s Great Lakes
- 2016
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 354:6312, s. 561-562
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- As the world's demands for hydrocarbons increase (1), remote areas previously made inaccessible by technological limitations are now being prospected for oil and gas deposits. Virtually unnoticed by the public, such activities are ongoing in the East African Great Lakes region, threatening these ecosystems famed for their hyper-diverse biota, including the unique adaptive radiations of cichlid fishes (2). Countries in the region see exploitation of hydrocarbon reserves as a vital economic opportunity. In the Lake Albert region of Uganda, for example, the government foresees a $3.6 billion oil profit per year starting in 2018—a sum almost as high as the country's current annual budget (3). However, oil extraction in the East African Great Lakes region poses grave risks to the environment and local communities.
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| 3. |
- Lestinsky, M., et al.
(författare)
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Physics book: CRYRING@ESR
- 2016
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Ingår i: European Physical Journal: Special Topics. - : Springer Science and Business Media LLC. - 1951-6401 .- 1951-6355. ; 225:5, s. 797-882
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Forskningsöversikt (refereegranskat)abstract
- The exploration of the unique properties of stored and cooled beams of highly-charged ions as provided by heavy-ion storage rings has opened novel and fascinating research opportunities in the realm of atomic and nuclear physics research. Since the late 1980s, pioneering work has been performed at the CRYRING at Stockholm (Abrahamsson et al. 1993) and at the Test Storage Ring (TSR) at Heidelberg (Baumann et al. 1988). For the heaviest ions in the highest charge-states, a real quantum jump was achieved in the early 1990s by the commissioning of the Experimental Storage Ring (ESR) at GSI Helmholtzzentrum für Schwerionenforschung (GSI) in Darmstadt (Franzke 1987) where challenging experiments on the electron dynamics in the strong field regime as well as nuclear physics studies on exotic nuclei and at the borderline to atomic physics were performed. Meanwhile also at Lanzhou a heavy-ion storage ring has been taken in operation, exploiting the unique research opportunities in particular for medium-heavy ions and exotic nuclei (Xia et al. 2002).
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| 4. |
- Mondal, S., et al.
(författare)
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Photoelectron angular distributions for the two-photon sequential double ionization of xenon by ultrashort extreme ultraviolet free electron laser pulses
- 2013
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Ingår i: Journal of Physics B: Atomic, Molecular and Optical Physics. - : IOP Publishing. - 0953-4075 .- 1361-6455. ; 46:16
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Tidskriftsartikel (refereegranskat)abstract
- Xenon atoms are double-ionized by sequential two-photon absorption by ultrashort extreme ultraviolet free-electron laser pulses with a photon energy of 23.0 and 24.3 eV, produced by the SPring-8 Compact SASE Source test accelerator. The angular distributions of photoelectrons generated by two-photon double ionization are obtained using velocity map imaging. The results are reproduced reasonably well by the present theoretical calculations within the multi-configurational Dirac-Fock approach.
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| 5. |
- Barbieri, L, et al.
(författare)
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Two-dimensional TIRF-SIM-traction force microscopy (2D TIRF-SIM-TFM)
- 2021
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Ingår i: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 12:1, s. 2169-
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Tidskriftsartikel (refereegranskat)abstract
- Quantifying small, rapidly evolving forces generated by cells is a major challenge for the understanding of biomechanics and mechanobiology in health and disease. Traction force microscopy remains one of the most broadly applied force probing technologies but typically restricts itself to slow events over seconds and micron-scale displacements. Here, we improve >2-fold spatially and >10-fold temporally the resolution of planar cellular force probing compared to its related conventional modalities by combining fast two-dimensional total internal reflection fluorescence super-resolution structured illumination microscopy and traction force microscopy. This live-cell 2D TIRF-SIM-TFM methodology offers a combination of spatio-temporal resolution enhancement relevant to forces on the nano- and sub-second scales, opening up new aspects of mechanobiology to analysis.
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| 6. |
- Cocolios, T. E., et al.
(författare)
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Early onset of deformation in the neutron-deficient polonium isotopes
- 2012
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Ingår i: Journal of Physics, Conference Series. - : IOP Publishing. - 1742-6588 .- 1742-6596. ; 381:1, s. 012072-
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Tidskriftsartikel (refereegranskat)abstract
- In-source laser spectroscopy has been performed at CERN-ISOLDE with the RILIS laser ion source on 191-204,206,208-211,216,218Po. New information on the β decay of 199Po were extracted in the process, challenging previous results. Large-scale atomic calculations were performed to extract the changes in the mean-square charge radius δr 2 from the isotope shifts. The δ«r» 2 for the even-A isotopes reveal a large deviation from the spherical droplet model for N < 116.
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| 7. |
- Cocolios, T. E., et al.
(författare)
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Early Onset of Ground State Deformation in Neutron Deficient Polonium Isotopes
- 2011
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Ingår i: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 106:5, s. 052503-
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Tidskriftsartikel (refereegranskat)abstract
- In-source resonant ionization laser spectroscopy of the even-A polonium isotopes Po-192-210,Po-216,Po-218 has been performed using the 6p(3)7s S-5(2) to (6)p(3)7p P-5(2) (lambda = 843.38 nm) transition in the polonium atom (Po-I) at the CERN ISOLDE facility. The comparison of the measured isotope shifts in Po200-210 with a previous data set allows us to test for the first time recent large-scale atomic calculations that are essential to extract the changes in the mean-square charge radius of the atomic nucleus. When going to lighter masses, a surprisingly large and early departure from sphericity is observed, which is only partly reproduced by beyond mean field calculations.
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| 8. |
- Felce, JH, et al.
(författare)
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Single-Molecule, Super-Resolution, and Functional Analysis of G Protein-Coupled Receptor Behavior Within the T Cell Immunological Synapse
- 2021
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Ingår i: Frontiers in cell and developmental biology. - : Frontiers Media SA. - 2296-634X. ; 8, s. 608484-
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Tidskriftsartikel (refereegranskat)abstract
- A central process in immunity is the activation of T cells through interaction of T cell receptors (TCRs) with agonistic peptide-major histocompatibility complexes (pMHC) on the surface of antigen presenting cells (APCs). TCR-pMHC binding triggers the formation of an extensive contact between the two cells termed the immunological synapse, which acts as a platform for integration of multiple signals determining cellular outcomes, including those from multiple co-stimulatory/inhibitory receptors. Contributors to this include a number of chemokine receptors, notably CXC-chemokine receptor 4 (CXCR4), and other members of the G protein-coupled receptor (GPCR) family. Although best characterized as mediators of ligand-dependent chemotaxis, some chemokine receptors are also recruited to the synapse and contribute to signaling in the absence of ligation. How these and other GPCRs integrate within the dynamic structure of the synapse is unknown, as is how their normally migratory Gαi-coupled signaling is terminated upon recruitment. Here, we report the spatiotemporal organization of several GPCRs, focusing on CXCR4, and the G protein Gαi2 within the synapse of primary human CD4+ T cells on supported lipid bilayers, using standard- and super-resolution fluorescence microscopy. We find that CXCR4 undergoes orchestrated phases of reorganization, culminating in recruitment to the TCR-enriched center. This appears to be dependent on CXCR4 ubiquitination, and does not involve stable interactions with TCR microclusters, as viewed at the nanoscale. Disruption of this process by mutation impairs CXCR4 contributions to cellular activation. Gαi2 undergoes active exclusion from the synapse, partitioning from centrally-accumulated CXCR4. Using a CRISPR-Cas9 knockout screen, we identify several diverse GPCRs with contributions to T cell activation, most significantly the sphingosine-1-phosphate receptor S1PR1, and the oxysterol receptor GPR183. These, and other GPCRs, undergo organization similar to CXCR4; including initial exclusion, centripetal transport, and lack of receptor-TCR interactions. These constitute the first observations of GPCR dynamics within the synapse, and give insights into how these receptors may contribute to T cell activation. The observation of broad GPCR contributions to T cell activation also opens the possibility that modulating GPCR expression in response to cell status or environment may directly regulate responsiveness to pMHC.
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| 9. |
- Freitag, C., et al.
(författare)
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Visualizing the entire DNA from a chromosome in a single frame
- 2015
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Ingår i: Biomicrofluidics. - : AIP Publishing. - 1932-1058. ; 9:4
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Tidskriftsartikel (refereegranskat)abstract
- The contiguity and phase of sequence information are intrinsic to obtain complete understanding of the genome and its relationship to phenotype. We report the fabrication and application of a novel nanochannel design that folds megabase lengths of genomic DNA into a systematic back-and-forth meandering path. Such meandering nanochannels enabled us to visualize the complete 5.7 Mbp (1mm) stained DNA length of a Schizosaccharomyces pombe chromosome in a single frame of a CCD. We were able to hold the DNA in situ while implementing partial denaturation to obtain a barcode pattern that we could match to a reference map using the Poland-Scheraga model for DNA melting. The facility to compose such long linear lengths of genomic DNA in one field of view enabled us to directly visualize a repeat motif, count the repeat unit number, and chart its location in the genome by reference to unique barcode motifs found at measurable distances from the repeat. Meandering nanochannel dimensions can easily be tailored to human chromosome scales, which would enable the whole genome to be visualized in seconds. (C) 2015 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution 3.0 Unported License.
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| 10. |
- Fritzsche, Joachim, 1977, et al.
(författare)
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A lipid-based passivation scheme for nanofluidics
- 2012
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Ingår i: 16th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2012; Okinawa; Japan; 28 October 2012 through 1 November 2012. - 9780979806452 ; , s. 1876-1878
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Konferensbidrag (refereegranskat)abstract
- Stretching DNA in nanochannels allows for direct, visual studies of genomic DNA at the single molecule level. In order to facilitate the study of the interaction of linear DNA with proteins in nanochannels, we have implemented a highly effective passivation scheme based on lipid bilayers. We show long-term passivation of nanochannel surfaces to several relevant reagents and demonstrate that the performance of the lipid bilayer is significantly better compared to standard bovine serum albumin-based passivation. Moreover, we demonstrate how the passivated devices allow us to monitor single DNA cleavage events during enzymatic degradation.
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| 11. |
- Fritzsche, S., et al.
(författare)
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Photoelectron satellite structure from the 3d and 4d inner-shell ionization of rubidium and cesium: Role of atomic relaxation
- 2008
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Ingår i: Physical Review A (Atomic, Molecular and Optical Physics). - 1050-2947. ; 78:3
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Tidskriftsartikel (refereegranskat)abstract
- The photoelectron satellite structure of rubidium and cesium has been investigated following the photoionization of an nd (n= 3,4) inner-shell electron. The intensity ratios of the nd(-1) ms monopole and nd(-1) m'p conjugated satellite lines have been measured at MAX-lab by using high-resolution electron spectroscopy. For rubidium, moreover, the energy dependence of the 3d(j)6s/3d(j)5s and 3d(j)5p/3d(j)5s intensity ratios with j=3/2 and 5/2 is measured and compared with multiconfiguration Dirac-Fock calculations. A good or at least reasonable agreement is found for both the monopole and conjugated shake-up probabilities if the relaxation of the bound-state electron density is taken into account in the computation of the photoionization cross sections. It is shown that, for the inner-shell ionization of medium and heavy atoms, the orbital relaxation accounts for a significant part of the satellite structure in the photoelectron spectra.
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| 12. |
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| 13. |
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| 14. |
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| 15. |
- Jankala, K., et al.
(författare)
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Inner-shell 2p photoionization and Auger decay of atomic silicon
- 2008
-
Ingår i: Physical Review A (Atomic, Molecular and Optical Physics). - 1050-2947. ; 77:6
-
Tidskriftsartikel (refereegranskat)abstract
- A detailed experiment on 2p photoionization and subsequent Auger decay of atomic silicon is presented. Fine-structure-resolved photoelectron and Auger electron spectra are interpreted with the aid of large-scale multiconfiguration calculations. Energy separation and the relative cross sections of the 2p ionized fine-structure states of Si+ are given. The complete 2p Auger electron spectrum of Si is interpreted, and the intensity distribution to individual doubly ionized final states is studied.
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| 16. |
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| 17. |
- Kosugi, S., et al.
(författare)
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Strong configuration interaction in the 3p photoelectron spectrum of Kr
- 2020
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Ingår i: Physical Review A: covering atomic, molecular, and optical physics and quantum information. - 2469-9926 .- 2469-9934. ; 101:4
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Tidskriftsartikel (refereegranskat)abstract
- We measured the Kr photoelectron spectrum in the region close to the 3p ionization threshold. Our high-resolution measurements allowed a clear observation of spectral structures due to electron correlation effects. Analysis based on relativistic multiconfiguration calculations could explain these observed peaks as due to strong configuration interactions between the 3p(-1) state and 3d(-2) nl states. Calculated and experimental data for peak assignments and intensity distributions are in good agreement. In addition, we measured the anisotropy parameter beta, which also agreed well with theory. These findings provide a detailed view of strong configuration interactions between the 3(-1) and 3d(-2)nl inner-shell hole states.
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| 18. |
- Kozhevnikov, V., et al.
(författare)
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Nonlocal effect and dimensions of Cooper pairs measured by low-energy muons and polarized neutrons in type-I superconductors
- 2013
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Ingår i: Physical Review B Condensed Matter. - : American Physical Society. - 0163-1829 .- 1095-3795. ; 87:10, s. 104508-
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Tidskriftsartikel (refereegranskat)abstract
- The Pippard coherence length xi(0) (the size of a Cooper pair) in two extreme type-I superconductors (In and Sn) was determined directly through high-resolution measurement of the nonlocal electrodynamic effect combining low-energy muon spin rotation spectroscopy and polarized neutron reflectometry. The renormalization factor Z = m*(cp)/2m (m*(cp) and m are the mass of the Cooper pair and the electron, respectively) resulting from the electron-phonon interaction, and the temperature-dependent London penetration depth lambda(L)(T) were determined as well. An expression linking xi(0), Z, and lambda(L)(0) is introduced and experimentally verified. This expression allows one to determine experimentally the Pippard coherence length in any superconductor, independent of whether the superconductor is local or nonlocal, conventional or unconventional.
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| 19. |
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| 20. |
- Niskanen, Johannes, et al.
(författare)
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Photoelectron angular distribution and linear magnetic dichroism in the 4p photoemission from Rb atoms
- 2010
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Ingår i: Physical Review A. Atomic, Molecular, and Optical Physics. - 1050-2947 .- 1094-1622. ; 81:1, s. 013406-
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Tidskriftsartikel (refereegranskat)abstract
- The angular distribution of photoelectrons and linear magnetic dichroism in the angular distribution for the 4p photoemission from Rb atoms in the ground state, oriented by laser pumping, were measured in the photon energy range from 50 to 100 eV. The experimental results are compared with the multiconfiguration Dirac-Fock (MCDF) calculations. We show that the zero-crossing of the dichroism as a function of energy is connected with the Cooper minimum in the cross section. This fact can be used for an accurate determination of the position of the Cooper minimum.
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| 21. |
- Partanen, L., et al.
(författare)
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2s photoionization and subsequent Auger cascade in atomic Si
- 2010
-
Ingår i: Physical Review A (Atomic, Molecular and Optical Physics). - 1050-2947. ; 81:6
-
Tidskriftsartikel (refereegranskat)abstract
- The 2s photoionization and subsequent Auger transition cascade in atomic Si were studied by means of synchrotron-radiation-induced electron spectroscopy. After the 2s photoionization, the core hole states decay predominantly by a two-step Auger transition cascade into the triply ionized [Ne]nl states. The ionization channels of the 2s core-ionized Si+ atoms to Si3+ ions were observed by measuring the conventional Auger electron spectra of the L-1-L2,3M Coster-Kronig transitions and the L2,3M-MMM Auger transitions. The observed L-1-L2,3M and L2,3M-MMM Auger spectra were analyzed by means of extensive multiconfiguration Dirac-Fock computations. We found that the electron correlation plays a prominent role in the Auger cascade, especially for the final-step Auger L2,3M-MMM spectrum. Additionally, it was seen that the L2,3M-MMM Auger spectrum of Si includes more Auger groups than the isoelectronic L-2,L-3-MMAuger spectrum of Al. Thus, more information on the intermediate ionic states is obtained if they are produced by Auger cascade rather than by direct photoionization.
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| 22. |
- Persson, Fredrik, 1979, et al.
(författare)
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Lipid-Based Passivation in Nanofluidics
- 2012
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Ingår i: Nano Letters. - : American Chemical Society (ACS). - 1530-6992 .- 1530-6984. ; 12:5, s. 2260-2265
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Tidskriftsartikel (refereegranskat)abstract
- Stretching DNA in nanochannels is a useful tool for direct, visual studies of genomic DNA at the single molecule level. To facilitate the study of the interaction of linear DNA with proteins in nanochannels, we have implemented a highly effective passivation scheme based on lipid bilayers. We demonstrate virtually complete long-term passivation of nanochannel surfaces to a range of relevant reagents, including streptavidin-coated quantum dots, RecA proteins, and RecA-DNA complexes. We show that the performance of the lipid bilayer is significantly better than that of standard bovine serum albumin-based passivation. Finally, we show how the passivated devices allow us to monitor single DNA cleavage events during enzymatic degradation by DNase I. We expect that our approach will open up for detailed, systematic studies of a wide range of protein-DNA interactions with high spatial and temporal resolution.
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| 23. |
- Seliverstov, M. D., et al.
(författare)
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Charge radii of odd-A Po191-211 isotopes
- 2013
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Ingår i: Physics Letters B. - : Elsevier BV. - 0370-2693 .- 1873-2445. ; 719:4-5, s. 362-366
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Tidskriftsartikel (refereegranskat)abstract
- Isotope shifts have been measured for the odd-A polonium isotopes Po191-211 and changes in the nuclear mean square charge radii delta < r(2 >) have been deduced. The measurements were performed at CERN-ISOLDE using the in-source resonance-ionization spectroscopy technique. The combined analysis of these data and our recent results for even-A polonium isotopes indicates an onset of deformation already at Po-197,Po-198, when going away from stability. This is significantly earlier than was suggested by previous theoretical and experimental studies of the polonium isotopes. Moreover and in contrast to the mercury isotopes, where a strong odd-even staggering of the charge radii of the ground states was observed by approaching the neutron mid-shell at N = 104, no such effect is present in polonium down to Po-191. Consequently the charge radii of both isomeric and ground states of the odd-A polonium isotopes follow the same trend as the even-A isotopes.
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| 24. |
- Spackova, Barbora, 1979, et al.
(författare)
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Label-free nanofluidic scattering microscopy of size and mass of single diffusing molecules and nanoparticles
- 2022
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Ingår i: Nature Methods. - : Springer Science and Business Media LLC. - 1548-7091 .- 1548-7105. ; 19, s. 751-758
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Tidskriftsartikel (refereegranskat)abstract
- Nanofluidic scattering microscopy enables label-free, quantitative measurements of the molecular weight and hydrodynamic radius of biological molecules and nanoparticles freely diffusing inside a nanofluidic channel. Label-free characterization of single biomolecules aims to complement fluorescence microscopy in situations where labeling compromises data interpretation, is technically challenging or even impossible. However, existing methods require the investigated species to bind to a surface to be visible, thereby leaving a large fraction of analytes undetected. Here, we present nanofluidic scattering microscopy (NSM), which overcomes these limitations by enabling label-free, real-time imaging of single biomolecules diffusing inside a nanofluidic channel. NSM facilitates accurate determination of molecular weight from the measured optical contrast and of the hydrodynamic radius from the measured diffusivity, from which information about the conformational state can be inferred. Furthermore, we demonstrate its applicability to the analysis of a complex biofluid, using conditioned cell culture medium containing extracellular vesicles as an example. We foresee the application of NSM to monitor conformational changes, aggregation and interactions of single biomolecules, and to analyze single-cell secretomes.
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| 25. |
- Werner, Erik, et al.
(författare)
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Hairpins in the conformations of a confined polymer
- 2018
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Ingår i: Biomicrofluidics. - : AIP Publishing. - 1932-1058. ; 12:2
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Tidskriftsartikel (refereegranskat)abstract
- If a semiflexible polymer confined to a narrow channel bends around by 180°, the polymer is said to exhibit a hairpin. The equilibrium extension statistics of the confined polymer are well understood when hairpins are vanishingly rare or when they are plentiful. Here, we analyze the extension statistics in the intermediate situation via experiments with DNA coated by the protein RecA, which enhances the stiffness of the DNA molecule by approximately one order of magnitude. We find that the extension distribution is highly non-Gaussian, in good agreement with Monte-Carlo simulations of confined discrete wormlike chains. We develop a simple model that qualitatively explains the form of the extension distribution. The model shows that the tail of the distribution at short extensions is determined by conformations with one hairpin. © 2018 Author(s).
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| 26. |
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| 27. |
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