SwePub - search: WFRF:(Tegenfeldt Fredrik)

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1.	Alizadehheidari, Mohammadreza, 1987, et al. (author) Nanoconfined Circular and Linear DNA: Equilibrium Conformations and Unfolding Kinetics 2015 In: Macromolecules. - : American Chemical Society (ACS). - 0024-9297 .- 1520-5835. ; 48:3, s. 871-878 Journal article (peer-reviewed)abstract Studies of circular DNA confined to nanofluidic channels are relevant both from a fundamental polymer-physics perspective and due to the importance of circular DNA molecules in vivo. We here observe the unfolding of confined DNA from the circular to linear configuration as a light-induced double-strand break occurs, characterize the dynamics, and compare the equilibrium conformational statistics of linear and circular configurations. This is important because it allows us to determine to what extent existing statistical theories describe the extension of confined circular DNA. We find that the ratio of the extensions of confined linear and circular DNA configurations increases as the buffer concentration decreases. The experimental results fall between theoretical predictions for the extended de Gennes regime at weaker confinement and the Odijk regime at stronger confinement. We show that it is possible to directly distinguish between circular and linear DNA molecules by measuring the emission intensity from the DNA. Finally, we determine the rate of unfolding and show that this rate is larger for more confined DNA, possibly reflecting the corresponding larger difference in entropy between the circular and linear configurations.
2.	Alizadehheidari, Mohammadreza, et al. (author) Nanoconfined Circular DNA 2014 In: Biophysical Journal. - : Elsevier BV. - 0006-3495 .- 1542-0086. ; 106:2, s. 274A-274A Journal article (other academic/artistic)abstract Nanofluidic channels have become a versatile tool to manipulate single DNA molecules. They allow investigation of confined single DNA molecules from a fundamental polymer physics perspective as well as for example in DNA barcoding techniques.
3.	Alizadehheidari, Mohammadreza, 1987, et al. (author) Unfolding of nanoconfined circular DNA 2015 In: BIOPHYSICAL JOURNAL. - : Elsevier BV. - 0006-3495 .- 1542-0086. ; 108:2 Supplement 1 Journal article (other academic/artistic)
4.	Fritzsche, Joachim, 1977, et al. (author) A lipid-based passivation scheme for nanofluidics 2012 In: 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 Conference paper (peer-reviewed)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.
5.	Kesarimangalam, Sriram, 1983, et al. (author) Fluorescence Microscopy of Nanochannel-Confined DNA 2024 In: Methods in Molecular Biology. - 1940-6029 .- 1064-3745. - 9781071633779 - 9781071633762 ; 2694, s. 175-202 Book chapter (other academic/artistic)abstract Stretching of DNA in nanoscale confinement allows for several important studies. The genetic contents of the DNA can be visualized on the single DNA molecule level, and the polymer physics of confined DNA and also DNA/protein and other DNA/DNA-binding molecule interactions can be explored. This chapter describes the basic steps to fabricate the nanostructures, perform the experiments, and analyze the data.
6.	Nyberg, Lena, 1979, et al. (author) A single-step competitive binding assay for mapping of single DNA molecules 2012 In: Biochemical and Biophysical Research Communications - BBRC. - : Elsevier BV. - 0006-291X .- 1090-2104. ; 417:1, s. 404-408 Journal article (peer-reviewed)abstract Optical mapping of genomic DNA is of relevance for a plethora of applications such as scaffolding for sequencing and detection of structural variations as well as identification cif pathogens like bacteria and viruses. For future clinical applications it is desirable to have a fast and robust mapping method based on as few steps as possible. We here demonstrate a single-step method to obtain a DNA barcode that is directly visualized using nanofluidic devices and fluorescence microscopy. Using a mixture of YOYO-1, a bright DNA dye, and netropsin, a natural antibiotic with very high AT specificity, we obtain a DNA map with a fluorescence intensity profile along the DNA that reflects the underlying sequence. The netropsin binds to AT-tetrads and blocks these binding sites from YOYO-1 binding which results in lower fluorescence intensity from AT-rich regions of the DNA. We thus obtain a DNA barcode that is dark in AT-rich regions and bright in GC-rich regions with kilobasepair resolution. We demonstrate the versatility of the method by obtaining a barcode on DNA from the phage T4 that captures its circular permutation and agrees well with its known sequence.
7.	Persson, Fredrik, et al. (author) Fluorescence microscopy of nanochannel-confined DNA 2011 In: Single Molecule Analysis : Methods and Protocols - Methods and Protocols. - Totowa, NJ : Humana Press. - 1064-3745. - 9781617792816 ; 783, s. 159-179 Book chapter (peer-reviewed)abstract Stretching of DNA in nanoscale confinement allows for direct visualization of the genetic contents of the DNA on the single DNA molecule level. DNA stretched in nanoscale confinement also allows for studies of DNA-protein interactions and DNA polymer physics in confined environments. This chapter describes the basic steps to fabricate the nanostructures, to perform the experiments, and to analyze the data.
8.	Persson, Fredrik, 1979, et al. (author) Lipid-Based Passivation in Nanofluidics 2012 In: Nano Letters. - : American Chemical Society (ACS). - 1530-6992 .- 1530-6984. ; 12:5, s. 2260-2265 Journal article (peer-reviewed)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.
9.	Persson, Fredrik, 1979, et al. (author) Local conformation of confined DNA studied using emission polarization anisotropy 2010 In: Biophysical Society 54th Annual Meeting. Conference paper (other academic/artistic)abstract When confined in nanochannels with dimensions smaller than the DNA radius of gyration, DNA will extend along the channel. We investigate long DNA confined in nanochannels, using fluorescence microscopy and intercalated dyes. Studies of the dynamics and statics of DNA in such nanoscale confinements as a function of e.g. degree of confinement and ionic strength have yielded new insights into the physical properties of DNA with relevance for applications in genomics as well as fundamental understanding of DNA packaging in vivo. Our work extends the field by not only studying the location of the emitting dyes along a confined DNA molecule but also monitoring the polarization of the emitted light. By measuring the emission polarized parallel and perpendicular to the extension axis of the stretched DNA, information on the local spatial distribution of the DNA backbone can be obtained. Comparing polarizations in two directions for DNA confined in channels of effective diameters of 85 nm and 170 nm reveals a striking difference. Whereas the DNA in the larger channels shows an isotropic polarization of the emitted light, the light is to a large extent polarized perpendicular to the elongation of the DNA in the smaller channels. We expect this technique to have a large impact on the studies of changes in DNA conformation induced by protein binding or during DNA compactation as well as in fundamental polymer physics studies of DNA in confined environments, for example in bacterial spores and viruses.
10.	Persson, Fredrik, 1979, et al. (author) Local conformation of confined DNA studied using emission polarization anisotropy 2010 In: NanoBioTech-Montreux 2009. Conference paper (other academic/artistic)abstract In nanochannels with dimensions smaller than the DNA radius of gyration, DNA will extend along the channel. We investigate long DNA confined in nanochannels using fluorescence microscopy and intercalated dyes. Studies of the dynamics and statics of the DNA extension or position in such nanoscale confinements as a function of e.g. DNA contour length, degree and shape of confinement as well as ionic strength have yielded new insights in the physical properties of DNA with relevance for applications in genomics as well as fundamental understanding of DNA packaging in vivo. Our work extends the field by not only studying the location of the emitting dyes along a confined DNA molecule but also monitoring the polarization of the emitted light. We use intercalating dyes (YOYO-1) whose emission is polarized perpendicular to the DNA extension axis, and by measuring the emission polarized parallel and perpendicular to the extension axis of the stretched DNA, information on the local spatial distribution of the DNA backbone can be obtained. The results obtained are analogous to linear dichroism (LD) but on a single-molecule level, and obtained in a highly parallel fashion. We will discuss results in shallow (60 nm) and deep (180 nm) channels and describe an example of how the technique can be used to investigate non-uniform stretching of DNA on the single molecule level. Comparing polarizations in two directions for DNA confined in channels of effective diameters of 85 nm and 170 nm reveals a striking difference. Whereas the DNA in the larger channels shows an isotropic polarization of the emitted light, the light is to a large extent polarized perpendicular to the elongation of the DNA in the smaller channels. The ratio of the polarization parallel and perpendicular to the elongation direction, I\|\| / I⊥, is a measure of the relative local orientation of the DNA backbone. We believe that this technique will have a large impact on the studies of changes in DNA conformation induced by protein binding or during DNA compactation as well as in fundamental polymer physics studies of DNA in confined environments, for example in bacterial spores and viruses.
11.	Persson, Fredrik, et al. (author) Local Conformation of Confined DNA Studied Using Emission Polarization Anisotropy 2009 In: Small. - : Wiley. - 1613-6829 .- 1613-6810. ; 5:2, s. 190-193 Journal article (peer-reviewed)
12.	Persson, Fredrik, et al. (author) Polarization anisotropy of DNA in nanochannels 2008 In: ; , s. 668-670 Conference paper (peer-reviewed)abstract The local alignment of DNA stretched in nanofluidic channels is measured using polarization sensitive detection. With increased degree of stretching the polarization anisotropy increases both in the deGennes and the Odijk regime. The technique is expected to find use in studies of, for example, local conformational changes in polymer physics in confined spaces, studies of protein-DNA interactions and compactation of DNA.
13.	Werner, Erik, et al. (author) Orientational correlations in confined DNA 2012 In: Physical Review E. - 1539-3755 .- 2470-0045 .- 2470-0053. ; 86:4 Journal article (peer-reviewed)abstract We study how the orientational correlations of DNA confined to nanochannels depend on the channel diameter D by means of Monte Carlo simulations and a mean-field theory. This theory describes DNA conformations in the experimentally relevant regime where Flory-de Gennes theory does not apply. We show how local correlations determine the dependence of the end-to-end distance of the DNA molecule upon D. Tapered nanochannels provide the necessary resolution in D to study experimentally how the extension of confined DNA molecules depends upon D. Our experimental and theoretical results are in qualitative agreement.
14.	Westerlund, Fredrik, 1978, et al. (author) Fluorescence Enhancement From Single DNA Molecules Confined In Si/SiO2 Nanochannels 2010 In: Biophysical Society, 54th Annual Meeting. Conference paper (other academic/artistic)abstract A large challenge in biophysics when studying single molecules using fluorescence microscopy is to obtain a signal that is clearly detectable above the background noise. Ways to improve or optimize the fluorescence signal is therefore of great interest. We here study DNA extended in 320 nm deep funnel-shaped SiO2 nanochannels with a width ranging from 40nm to 600nm. The DNA is stained with a fluorescent dye (YOYO-1) and we show that the total emission from the DNA varies significantly with the dimensions of the channels (Figure) and has a peak intensity at half the wavelength of the emitted light. Measurements at varying salt concentrations, where the same confinement leads to different extension of the DNA, confirm that it is solely the geometry of the channel that governs the enhancement effect, ruling out alternative explanations, such as self-quenching. By using polarizers on the emission side we can investigate the light polarized parallel and perpendicular to the channel separately and we see that they show vastly different behavior with the peak in emission only detected in the light polarized parallel to the channels. We will discuss how our data may be explained by cavity-resonance effects when the lateral dimensions of the channels coincide with half the wavelength of the emitted light. Our results suggest that it is possible to fine-tune the size and shape of the nanochannels to maximize the number of photons collected from the molecule under study, for example when studying DNA interacting with single DNA-binding proteins where maximizing the photon budget is paramount.
15.	Westerlund, Fredrik, 1978, et al. (author) Fluorescence enhancement from single DNA molecules confined in SiO 2 nanochannels 2010 In: 14th International Conference on Miniaturized Systems for Chemistry and Life Sciences 2010, MicroTAS 2010; Groningen; Netherlands; 3 October 2010 through 7 October 2010. - 9781618390622 Conference paper (peer-reviewed)abstract We demonstrate that the detected emission intensity from YOYO-labeled DNA molecules confined in 180 nm deep Si/SiO2 nanofunnels changes significantly and not monotonically with the width of the funnel, an emission enhancement that is only detected for emitted light polarized parallel to the channel. We explain the enhancement effect as being due to optical phenomena in the channels. The enhancement effect may be of importance for quantitative fluorescence microscopy and for experiments with a tight photon budget.
16.	Westerlund, Fredrik, 1978, et al. (author) Fluorescence Enhancement of Single DNA Molecules Confined in Si/SiO2 Nanochannels 2010 In: Lab on a Chip. - : Royal Society of Chemistry (RSC). - 1473-0197 .- 1473-0189. ; 10:16, s. 2049-2051 Journal article (peer-reviewed)abstract We demonstrate that the detected emission intensity from YOYO- labeled DNA molecules confined in 180 nm deep Si/SiO2 nano- funnels changes significantly and not monotonically with the width of the funnel. This effect may be of importance for quantitative fluorescence microscopy and for experiments with a tight photon budget.
17.	Westerlund, Fredrik, 1978, et al. (author) Fluorescence microscopy of nanochannel-confined DNA 2018 In: Methods in Molecular Biology. - New York, NY : Springer New York. - 1064-3745 .- 1940-6029. ; 1665, s. 173-198 Book chapter (peer-reviewed)abstract Stretching of DNA in nanoscale confinement allows for several important studies. The genetic contents of the DNA can be visualized on the single DNA molecule level and both the polymer physics of confined DNA and also DNA/protein and other DNA/DNA-binding molecule interactions can be explored. This chapter describes the basic steps to fabricate the nanostructures, perform the experiments and analyze the data.
18.	Abdallah, J., et al. (author) A measurement of the tau hadronic branching ratios 2006 In: European Physical Journal C. - : Springer Science and Business Media LLC. - 1434-6044 .- 1434-6052. ; 46:1, s. 1-26 Journal article (peer-reviewed)abstract The exclusive and semi-exclusive branching ratios of the tau lepton hadronic decay modes (h(-)upsilon(tau), h(-)pi(0)upsilon(tau), h(-)pi(0)pi(0)upsilon(tau), h(-) >= 2 pi(0)nu(tau), 2h(-)h(+)upsilon(tau), 2h(-)h(+)>= 2 pi(0)upsilon(tau), 3h(-)2h(+)upsilon(tau) and 3h(-)2h(+) >= 1 pi(0)upsilon(tau)) were measured with data from the DELPHI detector at LEP.
19.	Abdallah, J., et al. (author) A study of the b-quark fragmentation function with the DELPHI detector at LEP I and an averaged distribution obtained at the Z Pole 2011 In: European Physical Journal C. - : Springer Science and Business Media LLC. - 1434-6044 .- 1434-6052. ; 71:2, s. 1557- Journal article (peer-reviewed)abstract The nature of b-quark jet hadronisation has been investigated using data taken at the Z peak by the DELPHI detector at LEP. Two complementary methods are used to reconstruct the energy of weakly decaying b-hadrons, E-B(weak). The average value of x(B)(weak) = E-B(weak)/E-beam is measured to be 0.699 +/- 0.011. The resulting x(B)(weak) distribution is then analysed in the framework of two choices for the perturbative contribution (parton shower and Next to Leading Log QCD calculation) in order to extract measurements of the non-perturbative contribution to be used in studies of b-hadron production in other experimental environments than LEP. In the parton shower framework, data favour the Lund model ansatz and corresponding values of its parameters have been determined within PYTHIA 6.156 from DELPHI data: a = 1.84(-0.21)(+0.23) and b = 0.642(-0.063)(+0.073) GeV-2, with a correlation factor rho = 92.2%. Combining the data on the b-quark fragmentation distributions with those obtained at the Z peak by ALEPH, OPAL and SLD, the average value of x(B)(weak) is found to be 0.7092 +/- 0.0025 and the non-perturbative fragmentation component is extracted. Using the combined distribution, a better determination of the Lund parameters is also obtained: a = 1.48(-0.10)(+0.11) and b = 0.509(-0.023)(+0.024) GeV-2, with a correlation factor rho = 92.6%.
20.	Abdallah, J., et al. (author) Investigation of colour reconnection in WW events with the DELPHI detector at LEP-2 2007 In: European Physical Journal C. - : Springer Science and Business Media LLC. - 1434-6044 .- 1434-6052. ; 51:2, s. 249-269 Journal article (peer-reviewed)abstract In the reaction e(+)e(-) -> WW -> (q(1) (q) over bar (2))(q(3)(q) over bar (4)) the usual hadronization models treat the colour singlets q(1)(q) over bar (2) and q(3)(q) over bar (4) coming from two W bosons independently. However, since the. nal state partons may coexist in space and time, cross-talk between the two evolving hadronic systems may be possible during fragmentation through soft gluon exchange. This e. ect is known as colour reconnection. In this article the results of the investigation of colour reconnection e. ects in fully hadronic decays of W pairs in DELPHI at LEP are presented. Two complementary analyses were performed, studying the particle. ow between jets and W mass estimators, with negligible correlation between them, and the results were combined and compared to models. In the framework of the SK-I model, the value for its. parameter most compatible with the data was found to be: (SK)-S-kappa-I = 2.2(-1.3) (+2.5) corresponding to the probability of reconnection P-reco to be in the range 0.31 < P-reco < 0.68 at 68% confidence level with its best value at 0.52.
21.	Abdallah, J., et al. (author) Masses, lifetimes and production rates of Xi(-) and Xi(+) at LEP 1 2006 In: Physics Letters B. - : Elsevier BV. - 0370-2693 .- 1873-2445. ; 639:3-4, s. 179-191 Journal article (peer-reviewed)abstract Measurements of the Xi(-) and (Xi) over bar (+) masses, mass differences, lifetimes and lifetime differences are presented. The (Xi) over bar (+) sample used is much larger than those used previously for such measurements. In addition, the S production rates in Z -> b (b) over bar and Z -> q (q) over bar events are compared and the position xi* of the maximum of the distribution in Z -> q (q) over bar events is measured.
22.	Abdallah, J., et al. (author) Measurement of the electron structure function F-2(e) at LEP energies 2014 In: Physics Letters B. - : Elsevier BV. - 0370-2693 .- 1873-2445. ; 737, s. 39-47 Journal article (peer-reviewed)abstract The hadronic part of the electron structure function F-2(e) has been measured for the first time, using e(+)e(-) data collected by the DELPHI experiment at LEP, at centre-of-mass energies of root s = 91.2-209.5 GeV. The data analysis is simpler than that of the measurement of the photon structure function. The electron structure function F-2(e) data are compared to predictions of phenomenological models based on the photon structure function. It is shown that the contribution of large target photon virtualities is significant. The data presented can serve as a cross-check of the photon structure function F-2(gamma) analyses and help in refining existing parameterisations.
23.	Abdallah, J., et al. (author) Search for a fourth generation b '-quark at LEP-II at root s=196-209GeV 2007 In: European Physical Journal C. - : Springer Science and Business Media LLC. - 1434-6044 .- 1434-6052. ; 50:3, s. 507-518 Journal article (peer-reviewed)abstract A search for the pair production of fourth generation b'-quarks was performed using data taken by the DELPHI detector at LEP-II. The analysed data were collected at centre-of-mass energies ranging from 196 to 209 GeV, corresponding to an integrated luminosity of 420 pb(-1). No evidence for a signal was found. Upper limits on BR(b'-> bZ) and BR(b'-> bZ) were obtained for b' masses ranging from 96 to 103 GeV/c(2) stop. These limits, together with the theoretical branching ratios predicted by a sequential four generations model, were used to constrain the value of R-CKM=vertical bar V-cb(') /V-tb'V-tb vertical bar there V-cb', V-tb' and V-tb are elements of the extended CKM matrix.
24.	Abdallah, J, et al. (author) Search for charged Higgs bosons at LEP in general two Higgs doublet models 2004 In: European Physical Journal C. Particles and Fields. - : Springer Science and Business Media LLC. - 1434-6044. ; 34:4, s. 399-418 Journal article (peer-reviewed)
25.	Abdallah, J., et al. (author) Search for excited leptons in e(+)e(-) collisions at root s=189-209 GeV 2006 In: European Physical Journal C. - : Springer Science and Business Media LLC. - 1434-6044 .- 1434-6052. ; 46:2, s. 277-293 Journal article (peer-reviewed)abstract A search for excited lepton production in e(+)e(-) collisions was performed using the data collected by the DELPHI detector at LEP at centre-of-mass energies ranging from 189 GeV to 209 GeV, corresponding to an integrated luminosity of approximately 600 pb(-1). No evidence for excited lepton production was found. In searches for pair-produced excited leptons, lower mass limits were established in the range 94-103 GeV/c(2), depending on the channel and model assumptions. In searches for singly-produced excited leptons, upper limits on the parameter f/Lambda were established as a function of the mass.
26.	Abdallah, J., et al. (author) Search for pentaquarks in the hadronic decays of the Z boson with the DELPHI detector at LEP 2007 In: Physics Letters B. - : Elsevier BV. - 0370-2693 .- 1873-2445. ; 653:2-4, s. 151-160 Journal article (peer-reviewed)abstract The quark model does not exclude states composed of more than three quarks, like pentaquark systems. Controversial evidence for such states has been published in the last years, in particular: for a strange pentaquark Theta(1540)(+); for a double-strange state, the Xi(1862)(--), subsequently called Phi(1860)--; and for a charmed state, the Theta(c)(3100)(0). If confirmed, a full pentaquark family might exist; such pentaquark states could be produced in e(+)e(-) annihilations near the Z energy. In this Letter a search for pentaquarks is described using the DELPHI detector at LEP, characterized by powerful particle identification sub-systems crucial in the separation of the signal from the background for these states. At 95% CL, upper limits are set on the production rates N of such particles and their charge-conjugate state per Z decay: N-Theta+ x Br(Theta(+) -> pK(S)(0)) < 5.1 x 10(-4), N Theta++ < 1.6 x 10(-3), N Phi(1860)-- x Br((P(1860)-- -> Xi(-)pi(-)) < 2.9 x 10(-4), N-Theta c(3100)0 x Br(Theta(c)(3100)(0) -> D*(+)p) < 8.8 x 10(-4).
27.	Abdallah, J., et al. (author) Search for single top quark production via contact interactions at LEP2 2011 In: European Physical Journal C. - : Springer Science and Business Media LLC. - 1434-6044 .- 1434-6052. ; 71:2, s. 1555- Journal article (peer-reviewed)abstract Single top quark production via four-fermion contact interactions associated to flavour-changing neutral currents was searched for in data taken by the DELPHI detector at LEP2. The data were accumulated at centre-of-mass energies ranging from 189 to 209 GeV, with an integrated luminosity of 598.1 pb(-1). No evidence for a signal was found. Limits on the energy scale Lambda, were set for scalar-, vector- and tensor-like coupling scenarios.
28.	Abdallah, J., et al. (author) Study of leading hadrons in gluon and quark fragmentation 2006 In: Physics Letters B. - : Elsevier BV. - 0370-2693 .- 1873-2445. ; 643:3-4, s. 147-157 Journal article (peer-reviewed)abstract The study of quark jets in e(+)e(-) reactions at LEP has demonstrated that the hadronisation process is reproduced well by the Lund string model. However. our understanding of gluon fragmentation is less complete. In this study enriched quark and gluon jet samples of different purities are selected in three-jet events from hadronic decays of the Z collected by the DELPHI experiment in the LEP runs during 1994 and 1995. The leading systems of the two kinds of jets are defined by requiring a rapidity gap and their sum of charges is studied. An excess of leading systems with total charge zero is found for gluon jets in all cases, when compared to Monte Carlo simulations with JETSET (with and without Bose-Einstein correlations included) and ARIADNE. The corresponding leading systems of quark jets do not exhibit such an excess. The influence of the gap size and of the gluon purity on the effect is studied and a concentration of the excess of neutral leading systems at low invariant masses (less than or similar to 2 GeV/c(2)) is observed, indicating that gluon jets might have an additional hitherto undetected fragmentation mode via a two-gluon system. This could be an indication of a possible production of gluonic states as predicted by QCD.
29.	Abdallah, J., et al. (author) Study of triple-gauge-boson couplings ZZZ, ZZ gamma and Z gamma gamma at LEP 2007 In: European Physical Journal C. - : Springer Science and Business Media LLC. - 1434-6044 .- 1434-6052. ; 51:3, s. 525-542 Journal article (peer-reviewed)abstract Neutral triple-gauge-boson couplings ZZZ, ZZγ and Zγγ have been studied with the DELPHI detector using data at energies between 183 and 208 GeV. Limits are derived on these couplings from an analysis of the reactions e+e-→Zγ, using data from the final states γff̄, with f=q or ν, from e+e-→ZZ, using data from the four-fermion final states qq̄qq̄, qq̄μ+μ-, qq̄e+e-, qq̄νν̄, μ+μ-νν̄ and e+e-νν̄, and from e+e-→Zγ*, in which the final state γ is off mass-shell, using data from the four-fermion final states qq̄e+e- and qq̄μ+μ-. No evidence for the presence of such couplings is observed, in agreement with the predictions of the Standard Model.
30.	Alizadehheidari, Mohammadreza, 1987, et al. (author) Nanoconfined circular DNA 2014 In: 18th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2014. - 9780979806476 ; , s. 1353-1355 Conference paper (peer-reviewed)abstract Studies of nanoconfined circular DNA are of interest both from a biological as well as a fundamental polymer physics perspective. We here present the use of nanofluidic channels as a tool for comparing statics and dynamics of the linear and circular configuration of the same DNA molecule.
31.	Alizadehheidari, Mohammadreza, 1987, et al. (author) Nanoconfined Circular DNA 2014 Conference paper (other academic/artistic)
32.	Beech, J. P., et al. (author) What do photons do to fluorescently stained DNA in confinement? 2013 In: 17th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2013; Freiburg; Germany; 27 October 2013 through 31 October 2013. ; 1, s. 5-7 Conference paper (peer-reviewed)abstract We have studied a selection of factors influencing the damage of DNA in nanochannels during fluorescence imaging. For cutting and nicking of DNA we show that the DNA is shortened during imaging. To avoid photodamage over the course of several hours of a typical experiment, we demonstrate the importance of an oxygen free gas to propel the buffer solution through the device. Finally, by varying the size of the channels, we show indications that higher DNA concentrations lead to higher rates of photodamage necessitating a balance between needs for highly stretched DNA and needs for long measurement times.
33.	Bogas, Diana, et al. (author) Applications of optical DNA mapping in microbiology 2017 In: BioTechniques. - : Future Science Ltd. - 0736-6205 .- 1940-9818. ; 62:6, s. 255-267 Research review (peer-reviewed)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.
34.	Botner, Olga, et al. (author) Rapidity-Alignment and p_T Compensation of Particle Pairs in Hadronic Z^0 Decays 2002 In: Phys. Lett.. - : Elsevier Science B.V.. - 0370-2693. ; B:533, s. 243-252 Journal article (peer-reviewed)abstract Observation is made of rapidity-alignment of K+K- and ppbar pairs which results from their asymmetric orientation in rapidity, with respect to the direction from primary quark to antiquark. The K+K- and ppbar data are consistent with predictions from the
35.	Botner, Olga, et al. (author) Search for Charged Higgs Bosons in e+e- Collisions at sqrt(s) =189-202 GeV 2002 In: Phys. Lett.. - : Elsevier Science B.V.. - 0370-2693. ; B:525, s. 17-28 Journal article (peer-reviewed)abstract A search for pair-produced charged Higgs bosons was performed in the high energy data collected by the DELPHI detector at LEP II at centre-of-mass energies from 189 GeV to 202 GeV. The three different final states taunutaunu, cscs and cstaunu were conside
36.	Botner, Olga, et al. (author) Search for neutral MSSM Higgs bosons at LEP 2006 In: Eur. Phys. J.. - : Springer Science and Business Media LLC. - 1434-6044 .- 1434-6052. ; 47, s. 547- Journal article (peer-reviewed)
37.	Botner, Olga, et al. (author) Searches for neutral Higgs bosons in e^+ e^- collisions from sqrt(s) = 191.6 to 201.7 GeV 2002 In: Eur. Phys. J.. - : Springer-Verlag. - 1434-6044 .- 1434-6052. ; C:23, s. 409-435 Journal article (peer-reviewed)abstract Neutral Higgs bosons of the Standard Model (SM) and the Minimal Supersymmetric Standard Model (MSSM) were searched for in the data collected in 1999 by the DELPHI experiment at centre-of-mass energies between 191.6 and 201.7 GeV with a total integrated lu
38.	Conrad, Jan, et al. (author) Applying rule ensembles to the search for super-symmetry at the Large Hadron Collider 2006 In: Journal of High Energy Physics (JHEP). - : Springer Science and Business Media LLC. - 1126-6708 .- 1029-8479. ; :7, s. 040- Journal article (peer-reviewed)abstract In this note we give an example application of a recently presented predictive learning method called Rule Ensembles. The application we present is the search for super-symmetric particles at the Large Hadron Collider. In particular, we consider the problem of separating the background coming from top quark production from the signal of super-symmetric particles. The method is based on an expansion of base learners, each learner being a rule, i.e. a combination of cuts in the variable space describing signal and background. These rules are generated from an ensemble of decision trees. One of the results of the method is a set of rules (cuts) ordered according to their importance, which gives useful tools for diagnosis of the model. We also compare the method to a number of other multivariate methods, in particular Artificial Neural Networks, the likelihood method and the recently presented boosted decision tree method. We find better performance of Rule Ensembles in all cases. For example for a given significance the amount of data needed to claim SUSY discovery could be reduced by 15% using Rule Ensembles as compared to using a likelihood method.
39.	Dahlin, Andreas, et al. (author) A nano-optical sensor for studies of lipid-membranes 2006 In: Book of abstracts: 2nd Intl Symp on Semicond Nanowires, Lund, Sweden (2006). Conference paper (peer-reviewed)
40.	Dahlin, Andreas, et al. (author) Improving the instrumental resolution of sensors based on localized surface plasmon resonance 2006 In: Analytical Chemistry. - : American Chemical Society (ACS). - 1520-6882 .- 0003-2700. ; 78:13, s. 4416-4423 Journal article (peer-reviewed)abstract The colorimetric variations induced upon changes in interfacial refractive index of nanoscale noble metal structures exhibiting localized surface plasmon resonance (LSPR) provides a convenient means of label-free, affinity-based detection of biomolecular recognition reactions. However, despite being similar in nature to conventional SPR, LSPR has so far suffered from significantly lower data quality in terms of its signal-to-noise ratio (S/N) in typical biomolecular recognition analysis. In this work, generic data analysis algorithms and a simple experimental setup that provide a S/N upon protein binding that is comparable to that of state-of-the art SPR systems are presented. Specifically, it is demonstrated how temporal variations ( rate similar to 0.5 Hz) in parameters proportional to the resonance peak position can be recorded simultaneously, yielding a peak position precision of < 5 x 10(-4) nm and an extinction noise level of < 5 x 10(-6) absorbance units (Abs). This, in turn, is shown to provide a S/N of similar to 2000 ( equivalent to a detection limit of < 0.1 ng/cm(2)) for typical protein binding reactions. Furthermore, the importance of utilizing changes in both peak position and magnitude is highlighted by comparing different LSPR active noble metal architectures that respond differently to bulk and interfacial refractive index changes.
41.	Emilsson, Gustav, 1989, et al. (author) Identifying bacteria using DNA binding maps 2013 In: 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 Conference paper (peer-reviewed)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.
42.	Freitag, C., et al. (author) Visualizing the entire DNA from a chromosome in a single frame 2015 In: Biomicrofluidics. - : AIP Publishing. - 1932-1058. ; 9:4 Journal article (peer-reviewed)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.
43.	Fritzsche, Michael, et al. (author) A Highly UV-transparent Fused Silica Biochip for Sensitive Hepatotoxicity Testing by Autofluorescence 2014 In: Biochip Journal. - : Springer Science and Business Media LLC. - 2092-7843 .- 1976-0280. ; 8:2, s. 115-121 Journal article (peer-reviewed)abstract Fabrication and application of a non-fluorescent and UV-transparent microfluidic biochip in fused silica that allows sensitive autofluorescence detection are described. The biochip is particularly useful in cell-based assays where the most informative autofluorescence signals from the cells reside in the ultraviolet spectral range and where plastic labware materials commonly used in cell culture work severely disturb such measurements. In this study the fused silica biochip was used for measuring intrinsic autofluorescence from liver cells in order to assess hepatotoxic effects of drugs. The assessment assay was carried out with the human liver cell line HepG2 under perfusion conditions in the microfluidics of the biochip. The autofluorescence from the.liver cells exposed to quinidine was readily recorded without background disturbance and correlated well with reference toxicity data.
44.	Frykholm, Karolin, 1977, et al. (author) Probing concentration-dependent behavior of DNA-binding proteins on a single-molecule level illustrated by Rad51 2013 In: Analytical Biochemistry. - : Elsevier BV. - 0003-2697 .- 1096-0309. ; 443:2, s. 261-268 Journal article (peer-reviewed)abstract Low throughput is an inherent problem associated with most single-molecule biophysical techniques. We have developed a versatile tool for high-throughput analysis of DNA and DNA-binding molecules by combining microfluidic and dense DNA arrays. We use an easy-to-process microfluidic flow channel system in which dense DNA arrays are prepared for simultaneous imaging of large amounts of DNA molecules with single-molecule resolution. The Y-shaped microfluidic design, where the two inlet channels can be controlled separately and precisely, enables the creation of a concentration gradient across the microfluidic channel as well as rapid and repeated addition and removal of substances from the measurement region. A DNA array stained with the fluorescent DNA-binding dye YOYO-1 in a gradient manner illustrates the method and serves as a proof of concept. We have applied the method to studies of the repair protein Rad51 and could directly probe the concentration-dependent DNA-binding behavior of human Rad51 (HsRad51). In the low-concentration regime used (100 nM HsRad51 and below), we detected binding to double-stranded DNA (dsDNA) without positive cooperativity. (C) 2013 Elsevier Inc. All rights reserved.
45.	Gunnarsson, Anders, et al. (author) Real-time single molecule detection on random arrays for biosensing applications 2006 In: Book of abstracts: 2nd Intl Symp on Semicond Nanowires, Lund, Sweden (2006). Conference paper (peer-reviewed)
46.	Gunnarsson, Anders, et al. (author) Single-molecule Detection and Mismatch Discrimination of Unlabeled DNA Targets 2008 In: Nano Letters. - : American Chemical Society (ACS). - 1530-6992 .- 1530-6984. ; 8:1, s. 183-188 Journal article (peer-reviewed)abstract We report on a single-molecule readout scheme on total internal reflection fluorescence microscopy (TIRFM) demonstrating a detection limit in the low fM regime for short (30-mer) unlabeled DNA strands. Detection of unlabeled DNA targets is accomplished by letting them mediate the binding of suspended fluorescently labeled DNA-modified small unilamellar vesicles (Ø approximately 100 nm) to a DNA-modified substrate. On top of rapid and sensitive detection, the technique is also shown capable of extracting kinetics data from statistics of the residence time of the binding reaction in equilibrium, that is, without following neither the rate of binding upon injection nor release upon rinsing. The potential of this feature is demonstrated by discriminating a single mismatch from a fully complementary sequence. The success of the method is critically dependent on a surface modification that provides sufficiently low background. This was achieved through self-assembly of a biotinylated copolymer, Poly(L-lysine)-g-poly(ethylene glycol) (PLL-g-PEG) on a silicon dioxide surface, followed by subsequent addition of streptavidin and biotinylated DNA. The proposed detection scheme is particularly appealing due to the simplicity of the sensor, which relies on self-assembly principles and conventional TIRFM. Therefore, we foresee a great potential of the concept to serve as an important component in future multiplexed sensing schemes. This holds in particular true in cases when information about binding kinetics is valuable, such as in single nucleotide polymorphism diagnostics.
47.	Iarko, V., et al. (author) Extension of nanoconfined DNA: Quantitative comparison between experiment and theory 2015 In: Physical Review E (Statistical, Nonlinear, and Soft Matter Physics). - 1539-3755 .- 1550-2376. ; 92:6, s. Art. Nr. 062701- Journal article (peer-reviewed)abstract The extension of DNA confined to nanochannels has been studied intensively and in detail. However, quantitative comparisons between experiments and model calculations are difficult because most theoretical predictions involve undetermined prefactors, and because the model parameters (contour length, Kuhn length, effective width) are difficult to compute reliably, leading to substantial uncertainties. Here we use a recent asymptotically exact theory for the DNA extension in the "extended de Gennes regime" that allows us to compare experimental results with theory. For this purpose, we performed experiments measuring the mean DNA extension and its standard deviation while varying the channel geometry, dye intercalation ratio, and ionic strength of the buffer. The experimental results agree very well with theory at high ionic strengths, indicating that the model parameters are reliable. At low ionic strengths, the agreement is less good. We discuss possible reasons. In principle, our approach allows us to measure the Kuhn length and the effective width of a single DNA molecule and more generally of semiflexible polymers in solution.
48.	Jönsson, Peter, et al. (author) A Method Improving the Accuracy of Fluorescence Recovery after Photobleaching Analysis 2008 In: Biophysical Journal. - : Biophysical Society. - 0006-3495 .- 1542-0086. ; 95:11, s. 5334-5348 Journal article (peer-reviewed)abstract Fluorescence recovery after photobleaching has been an established technique of quantifying the mobility of molecular species in cells and cell membranes for more than 30 years. However, under nonideal experimental conditions, the current methods of analysis still suffer from occasional problems; for example, when the signal/noise ratio is low, when there are temporal fluctuations in the illumination, or when there is bleaching during the recovery process. We here present a method of analysis that overcomes these problems, yielding accurate results even under nonideal experimental conditions. The method is based on circular averaging of each image, followed by spatial frequency analysis of the averaged radial data, and requires no prior knowledge of the shape of the bleached area. The method was validated using both simulated and experimental fluorescence recovery after photobleaching data, illustrating that the diffusion coefficient of a single diffusing component can be determined to within similar to 1%, even for small signal levels (100 photon counts), and that at typical signal levels (5000 photon counts) a system with two diffusion coefficients can be analyzed with less than 10% error.
49.	Jönsson, Peter, 1981, et al. (author) Mechanical Behavior of a Supported Lipid Bilayer under External Shear Forces 2009 In: Langmuir. - : American Chemical Society (ACS). - 1520-5827 .- 0743-7463. ; 25:11, s. 6279-6286 Journal article (peer-reviewed)abstract Shear forces from a pressure-driven bulk flow in a microfluidic channel can be used to induce and control the motion of a supported lipid bilayer (SLB) formed on the walls of the channel. We here present a theoretical model that relates the experimentally observed drift velocities of an egg yolk phosphatidylcholine (egg PC) SLB to the hydrodynamic drag force from the bulk flow, the intermonolayer friction coefficient, b, of the bilayer, and the friction coefficient, b(ls) between the lower leaflet of the bilayer and the supporting substrate. The drift velocity and diffusivity of the lipids in the SLB were obtained by photobleaching a delimited area of fluorescently labeled lipids and subsequently monitoring the recovery and convective motion of the bleached spot. A striking observation was that the drift velocity of the lipids was observed to be nearly 6 orders of magnitude smaller than the bulk velocity at the center of the channel. This predicts a value for b(ls) that is at least 25 times as high as predicted by the traditional model with the SLB and the support spaced by a homogeneous 1 nm thick film of water. In addition, the intermonolayer friction coefficient was estimated to 2 x 10(7) Pa s/m, a value that increased after addition of glycerol to the bulk solution. This increase was accompanied by an equal decrease in the lipid diffusivity, with both observations indicating an increased viscous drag within the bilayer when glycerol was added to the bulk solution.
50.	Jönsson, Peter, 1981, et al. (author) Shear-Driven Motion of Supported Lipid Bilayers in Microfluidic Channels 2009 In: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 1520-5126 .- 0002-7863. ; 131:14, s. 5294-5297 Journal article (peer-reviewed)abstract In this work, we demonstrate how a lateral motion of a supported lipid bilayer (SLB) and its constituents can be created without relying on self-spreading forces. The force driving the SLB is instead a viscous shear force arising from a pressure-driven bulk flow acting on the SLB that is formed on a glass wall inside a microfluidic channel. In contrast to self-spreading bilayers, this method allows for accurate control of the bilayer motion by altering the bulk flow in the channel. Experiments showed that an egg yolk phosphatidylcholine SLB formed on a glass support moved in a rolling motion under these shear forces, with the lipids in the upper leaflet of the bilayer moving at twice the velocity of the bilayer front. The drift velocity of different lipid probes in the SLB was observed to be sensitive to the interactions between the lipid probe and the surrounding molecules, resulting in drift velocities that varied by up to I order of magnitude for the different lipid probes in our experiments. Since the method provides a so far unattainable control of the motion of all molecules in an SLB, we foresee great potential for this technique, alone or in combination with other methods, for studies of lipid bilayers and different membrane-associated molecules.

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