| 1. |
- Aquila, Andrew, et al.
(författare)
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Time-resolved protein nanocrystallography using an X-ray free-electron laser
- 2012
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Ingår i: Optics Express. - 1094-4087. ; 20:3, s. 2706-2716
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Tidskriftsartikel (refereegranskat)abstract
- We demonstrate the use of an X-ray free electron laser synchronized with an optical pump laser to obtain X-ray diffraction snapshots from the photoactivated states of large membrane protein complexes in the form of nanocrystals flowing in a liquid jet. Light-induced changes of Photosystem I-Ferredoxin co-crystals were observed at time delays of 5 to 10 µs after excitation. The result correlates with the microsecond kinetics of electron transfer from Photosystem I to ferredoxin. The undocking process that follows the electron transfer leads to large rearrangements in the crystals that will terminally lead to the disintegration of the crystals. We describe the experimental setup and obtain the first time-resolved femtosecond serial X-ray crystallography results from an irreversible photo-chemical reaction at the Linac Coherent Light Source. This technique opens the door to time-resolved structural studies of reaction dynamics in biological systems.
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| 2. |
- Johansson, Linda C, 1983, et al.
(författare)
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Lipidic phase membrane protein serial femtosecond crystallography.
- 2012
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Ingår i: Nature methods. - : Springer Science and Business Media LLC. - 1548-7105 .- 1548-7091. ; 9:3, s. 263-265
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Tidskriftsartikel (refereegranskat)abstract
- X-ray free electron laser (X-FEL)-based serial femtosecond crystallography is an emerging method with potential to rapidly advance the challenging field of membrane protein structural biology. Here we recorded interpretable diffraction data from micrometer-sized lipidic sponge phase crystals of the Blastochloris viridis photosynthetic reaction center delivered into an X-FEL beam using a sponge phase micro-jet.
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| 3. |
- Johansson, Linda C, 1983, et al.
(författare)
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Structure of a photosynthetic reaction centre determined by serial femtosecond crystallography.
- 2013
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Ingår i: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 4
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Tidskriftsartikel (refereegranskat)abstract
- Serial femtosecond crystallography is an X-ray free-electron-laser-based method with considerable potential to have an impact on challenging problems in structural biology. Here we present X-ray diffraction data recorded from microcrystals of the Blastochloris viridis photosynthetic reaction centre to 2.8Å resolution and determine its serial femtosecond crystallography structure to 3.5Å resolution. Although every microcrystal is exposed to a dose of 33MGy, no signs of X-ray-induced radiation damage are visible in this integral membrane protein structure.
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| 4. |
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| 5. |
- Andersson, Magnus, et al.
(författare)
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A proposed time-resolved X-ray scattering approach to track local and global conformational changes in membrane transport proteins
- 2008
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Ingår i: Structure. - : Elsevier BV. - 0969-2126 .- 1878-4186. ; 16:1, s. 21-28
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Tidskriftsartikel (refereegranskat)abstract
- Time-resolved X-ray scattering has emerged as a powerful technique for studying the rapid structural dynamics of small molecules in solution. Membrane-protein-catalyzed transport processes frequently couple large-scale conformational changes of the transporter with local structural changes perturbing the uptake and release of the transported substrate. Using light-driven halide ion transport catalyzed by halorhodopsin as a model system, we combine molecular dynamics simulations with X-ray scattering calculations to demonstrate how small-molecule time-resolved X-ray scattering can be extended to the study of membrane transport processes. In particular, by introducing strongly scattering atoms to label specific positions within the protein and substrate, the technique of time-resolved wide-angle X-ray scattering can reveal both local and global conformational changes. This approach simultaneously enables the direct visualization of global rearrangements and substrate movement, crucial concepts that underpin the alternating access paradigm for membrane transport proteins.
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| 6. |
- Andersson, Magnus, et al.
(författare)
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Structural Dynamics of Light-Driven Proton Pumps
- 2009
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Ingår i: Structure. - : Elsevier BV. - 0969-2126 .- 1878-4186. ; 17:9, s. 1265-1275
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Tidskriftsartikel (refereegranskat)abstract
- Bacteriorhodopsin and proteorhodopsin are simple heptahelical proton pumps containing a retinal chromophore covalently bound to helix G via a protonated Schiff base. Following the absorption of a photon, all-trans retinal is isomerized to a 13-cis conformation, initiating a sequence of conformational changes driving vectorial proton transport. In this study we apply time-resolved wide-angle X-ray scattering to visualize in real time the helical motions associated with proton pumping by bacteriorhodopsin and proteorhodopsin. Our results establish that three conformational states are required to describe their photocycles. Significant motions of the cytoplasmic half of helix F and the extracellular half of helix C are observed prior to the primary proton transfer event, which increase in amplitude following proton transfer. These results both simplify the structural description to emerge from intermediate trapping studies of bacteriorhodopsin and reveal shared dynamical principles for proton pumping.
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| 7. |
- Arnlund, David, et al.
(författare)
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Visualizing a protein quake with time-resolved X-ray scattering at a free-electron laser
- 2014
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Ingår i: Nature Methods. - : Springer Science and Business Media LLC. - 1548-7091 .- 1548-7105. ; 11:9, s. 923-926
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Tidskriftsartikel (refereegranskat)abstract
- We describe a method to measure ultrafast protein structural changes using time-resolved wide-angle X-ray scattering at an X-ray free-electron laser. We demonstrated this approach using multiphoton excitation of the Blastochloris viridis photosynthetic reaction center, observing an ultrafast global conformational change that arises within picoseconds and precedes the propagation of heat through the protein. This provides direct structural evidence for a 'protein quake': the hypothesis that proteins rapidly dissipate energy through quake-like structural motions.
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| 8. |
- Barty, A., et al.
(författare)
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Self-terminating diffraction gates femtosecond X-ray nanocrystallography measurements
- 2012
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Ingår i: Nature Photonics. - 1749-4885 .- 1749-4893. ; 6:1, s. 35-40
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Tidskriftsartikel (refereegranskat)abstract
- X-ray free-electron lasers have enabled new approaches to the structural determination of protein crystals that are too small or radiation-sensitive for conventional analysis1. For sufficiently short pulses, diffraction is collected before significant changes occur to the sample, and it has been predicted that pulses as short as 10 fs may be required to acquire atomic-resolution structural information1, 2, 3, 4. Here, we describe a mechanism unique to ultrafast, ultra-intense X-ray experiments that allows structural information to be collected from crystalline samples using high radiation doses without the requirement for the pulse to terminate before the onset of sample damage. Instead, the diffracted X-rays are gated by a rapid loss of crystalline periodicity, producing apparent pulse lengths significantly shorter than the duration of the incident pulse. The shortest apparent pulse lengths occur at the highest resolution, and our measurements indicate that current X-ray free-electron laser technology5 should enable structural determination from submicrometre protein crystals with atomic resolution.
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| 9. |
- Bertini, Ivano, et al.
(författare)
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Search for satellites near (21) Lutetia using OSIRIS/Rosetta images
- 2012
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Ingår i: Planetary and Space Science. - : Elsevier BV. - 0032-0633 .- 1873-5088. ; 66:1, s. 64-70
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Tidskriftsartikel (refereegranskat)abstract
- On 2010 July 10 the ESA Rosetta mission flew by the large asteroid (21) Lutetia. One of the scientific goals of the onboard OSIRIS instrument was the search for satellites of the asteroid, with more than 20 images specifically dedicated to this topic. An observational campaign was devised with a selection of filters and exposure times tailored to maximize the possibility of detecting small companions and determining their bound orbits. Data were analyzed with suitable methods to remove cosmic ray hits and known background objects, in order to search for persistent detections of potential interesting flux sources. We found no unambiguous detections of a satellite larger than similar to 160 m inside the entire sphere of gravitational influence. Our search confirmed the absence of bound companions larger than similar to 30 m inside 20 primary radii. These limits are a factor of similar to 30 smaller than the values reported so far from large ground-based telescopes using adaptive optics and from the Hubble Space Telescope.
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| 10. |
- Björgvinsson, Erling, et al.
(författare)
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Prototyping Futures
- 2012
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Prototyping Futures gives you a glimpse of what collaborating with academia might look like. Medea and its co-partners share their stories about activities happening at the research centre – projects, methods, tools, and approaches – what challenges lie ahead, and how these can be tackled. Examples of highlighted topics include: What is a living lab and how does it work? What are the visions behind the Connectivity Lab at Medea? And, how can prototyping-methods be used when sketching scenarios for sustainable futures? Other topics are: What is the role of the body when designing technology? What is collaborative media and how can this concept help us understand contemporary media practices? Prototyping Futures also discusses the open-hardware platform Arduino, and the concepts of open data and the Internet of Things, raising questions on how digital media and connected devices can contribute to more sustainable lifestyles, and a better world.
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| 11. |
- Davidsson, Josef, et al.
(författare)
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Relapsed childhood high hyperdiploid acute lymphoblastic leukemia : presence of preleukemic ancestral clones and the secondary nature of microdeletions and RTK-RAS mutations.
- 2010
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Ingår i: Leukemia. - : Springer Science and Business Media LLC. - 0887-6924 .- 1476-5551. ; 24:5, s. 924-31
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Tidskriftsartikel (refereegranskat)abstract
- Although childhood high hyperdiploid acute lymphoblastic leukemia is associated with a favorable outcome, 20% of patients still relapse. It is important to identify these patients already at diagnosis to ensure proper risk stratification. We have investigated 11 paired diagnostic and relapse samples with single nucleotide polymorphism array and mutation analyses of FLT3, KRAS, NRAS and PTPN11 in order to identify changes associated with relapse and to ascertain the genetic evolution patterns. Structural changes, mainly cryptic hemizygous deletions, were significantly more common at relapse (P<0.05). No single aberration was linked to relapse, but four deletions, involving IKZF1, PAX5, CDKN2A/B or AK3, were recurrent. On the basis of the genetic relationship between the paired samples, three groups were delineated: (1) identical genetic changes at diagnosis and relapse (2 of 11 cases), (2) clonal evolution with all changes at diagnosis being present at relapse (2 of 11) and (3) clonal evolution with some changes conserved, lost or gained (7 of 11), suggesting the presence of a preleukemic clone. This ancestral clone was characterized by numerical changes only, with structural changes and RTK-RAS mutations being secondary to the high hyperdiploid pattern.
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| 12. |
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| 13. |
- Davidsson, Jan, et al.
(författare)
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Structural determination of a transient isomer of CH2I2 by picosecond x-ray diffraction
- 2005
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Ingår i: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 94:24
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Tidskriftsartikel (refereegranskat)abstract
- Ultrafast time-resolved spectroscopic studies of complex chemical reactions in solution are frequently hindered by difficulties in recovering accurate structural models for transient photochemical species. Time-resolved x-ray and electron diffraction have recently emerged as techniques for probing the structural dynamics of short lived photointermediates. Here we determine the structure of a transient isomer of photoexcited CH2I2 in solution and observe the downstream reactions of the initial photoproducts. Our results illustrate how geminate recombination proceeds via the formation of a transient covalent bond onto the iodine atom remaining with the parent molecule. Further intramolecular rearrangements are thus required for the CH2I-I isomer to return to CH2I2. The generation of I-3(-) from those iodine radicals escaping the solvent cage is also followed with time.
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| 14. |
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| 15. |
- Davidsson, Pia, et al.
(författare)
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Vascular endothelial growth factor-D plasma levels and VEGFD genetic variants are independently associated with outcomes in patients with cardiovascular disease
- 2023
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Ingår i: Cardiovascular Research. - : Oxford University Press. - 0008-6363 .- 1755-3245. ; 119:7, s. 1596-1605
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Tidskriftsartikel (refereegranskat)abstract
- Aims The vascular endothelial growth factor (VEGF) family is involved in pathophysiological mechanisms underlying cardiovascular (CV) diseases. The aim of this study was to investigate the associations between circulating VEGF ligands and/or soluble receptors and CV outcome in patients with acute coronary syndrome (ACS) and chronic coronary syndrome (CCS).Methods and results Levels of VEGF biomarkers, including bFGF, Flt-1, KDR (VEGFR2), PlGF, Tie-2, VEGF-A, VEGF-C, and VEGF-D, were measured in the PLATO ACS cohort (n = 2091, discovery cohort). Subsequently, VEGF-D was also measured in the STABILITY CCS cohort (n = 4015, confirmation cohort) to verify associations with CV outcomes. Associations between plasma VEGF-D and outcomes were analysed by multiple Cox regression models with hazard ratios (HR [95% CI]) comparing the upper vs. the lower quartile of VEGF-D. Genome-wide association study (GWAS) of VEGF-D in PLATO identified SNPs that were used as genetic instruments in Mendelian randomization (MR) meta-analyses vs. clinical endpoints. GWAS and MR were performed in patients with ACS from PLATO (n = 10 013) and FRISC-II (n = 2952), and with CCS from the STABILITY trial (n = 10 786). VEGF-D, KDR, Flt-1, and PlGF showed significant association with CV outcomes. VEGF-D was most strongly associated with CV death (P = 3.73e-05, HR 1.892 [1.419, 2.522]). Genome-wide significant associations with VEGF-D levels were identified at the VEGFD locus on chromosome Xp22. MR analyses of the combined top ranked SNPs (GWAS P-values; rs192812042, P = 5.82e-20; rs234500, P = 1.97e-14) demonstrated a significant effect on CV mortality [P = 0.0257, HR 1.81 (1.07, 3.04) per increase of one unit in log VEGF-D].Conclusion This is the first large-scale cohort study to demonstrate that both VEGF-D plasma levels and VEGFD genetic variants are independently associated with CV outcomes in patients with ACS and CCS. Measurements of VEGF-D levels and/or VEGFD genetic variants may provide incremental prognostic information in patients with ACS and CCS.
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| 16. |
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| 17. |
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| 18. |
- Davidsson, Richard
(författare)
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Microfluidic biosensing systems based on enzymes, antibodies and cells
- 2004
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The rapid developments within the life science and biotechnology areas put up ever-new demands on more sophisticated techniques and methods for chemical and biological analysis to reach deeper insight into the events at molecular level. Miniaturisation of assays and systems on microchips is one way to increase throughput and advance through parallel analysis lines, multiplexing and integration. This thesis shows some aspects on the use of silicon microchips as a platform for immobilisation of enzymes, antibodies and cells for chemiluminometric biosensing assays. For antibody- and enzyme-based systems, special attention was paid to the immobilisation chemistry due to its influence on stability and activity of the attached biomolecules. In general it was found that surface coatings with a layer of polymer, e.g., polyethylenimine or dextran, increased both stability and signal intensity of the systems, compared to ordinary silanisation-based attachment chemistry. Furthermore, two cell-based monitoring systems, using either yeast cells or a reporter gene modified human (HeLa) cell line, were developed. These systems demonstrated the usefulness and advantages of microfluidics, e.g. in continuous monitoring of cellular events in real time, which stands in great contrast to the common end-point microtiter plate assays. The demands on yeast compared to human cells are however quite different, where the latter has highly specialised requirements on the physical and chemical environment. Special attention was thus paid on investigating different factors that can lead to unspecific and stress-related expression of the reporter gene, hence affecting the quality of the data and overall performance of the system. In conclusion, the main focus of this thesis has been to develop and apply analytical techniques and methods on microchips on flow-format. During the period the which this research was conducted, many interesting and elegant microfluidic analytical systems have been reported in the literature, however, the attention is often drawn mainly to the hardware set-up and construction. The systems developed in this thesis (paper I to V) are technically simple but show real applications in which biological elements, such as living cells, enzymes and antibodies, are handled on silicon microchips.
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| 19. |
- Davidsson, Richard, et al.
(författare)
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Microfluidic biosensing systems - Part I. Development and optimisation of enzymatic chemiluminescent mu-biosensors based on silicon microchips
- 2004
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Ingår i: Lab on a Chip. - : Royal Society of Chemistry (RSC). - 1473-0189. ; 4:5, s. 481-487
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Tidskriftsartikel (refereegranskat)abstract
- Chemiluminescent (CL) enzyme-based flow-through microchip biosensors (mu-biosensors) for detection of glucose and ethanol were developed for the purpose of monitoring real-time production and release of glucose and ethanol from microchip immobilised yeast cells. Part I of this study focuses on the development and optimisation of the mu-biosensors in a microfluidic sequential injection analysis (muSIA) system. Glucose oxidase (GOX) or alcohol oxidase (AOX) was co-immobilised with horseradish peroxidase (HRP) on porous silicon flow through microchips. The hydrogen peroxide ;produced from oxidation of the corresponding analyte (glucose or ethanol) took part in the chemiluminescent (CL) oxidation of luminol catalysed by HRP enhanced by addition of p-iodophenol ( PIP). All steps in the mSIA system, including control of syringe pump, multiposition valve (MPV) and data readout, were computer controlled. The influence of flow rate and luminol- and PIP concentration were investigated using a 2(3)-factor experiment using the GOX-HRP sensor. It was found that all estimated single factors and the highest order of interaction were significant. The optimum was found at 250 muM luminol and 150 muM PIP at a flow rate of 18 mul min(-1), the latter as a compromise between signal intensity and analysis time. Using the optimised system settings one sample was processed within 5 min. Two different immobilisation chemistries were investigated for both m-biosensors based on 3-aminopropyltriethoxsilane (APTS)- or polyethylenimine (PEI) functionalisation followed by glutaraldehyde (GA) activation. GOX-HRP mu-biosensors responded linear in a log-log format within the range 10-1000 mM glucose. Both had an operational stability of at least 8 days, but the PEI-GOX-HRP sensor was more sensitive. The AOX-HRP mu-biosensors responded linear (log-log) in the range between 1 and 10 mM ethanol, but the PEI-AOX-HRP sensor was in general more sensitive. Both sensors had an operational stability of at least 8 h, but with a half-life of 2-3 days.
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| 20. |
- Davidsson, Richard, et al.
(författare)
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Microfluidic biosensing systems - Part II. Monitoring the dynamic production of glucose and ethanol from microchip-immobilised yeast cells using enzymatic chemiluminescent mu-biosensors
- 2004
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Ingår i: Lab on a Chip. - : Royal Society of Chemistry (RSC). - 1473-0189. ; 4:5, s. 488-494
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Tidskriftsartikel (refereegranskat)abstract
- A microfluidic flow injection (muFIA) system was employed for handling and monitoring of cell-released products from living cells immobilised on silicon microchips. The dynamic release of glucose and ethanol produced from sucrose by immobilised Saccharomyces cerevisiae cells was determined using microchip biosensors (mu-biosensors) with either co-immobilised glucose oxidase-horseradish peroxidase (GOX-HRP), or alcohol oxidase-horseradish peroxidase (AOX-HRP), catalysing a series of reactions ending up with chemiluminescence (CL) generated from HRP-catalysed oxidation of luminol in presence of p-iodophenol (PIP). The yeast cells were attached by first treating them with polyethylenimine (PEI) followed by adsorption to the microchip surface. The cell loss during assaying was evaluated qualitatively using scanning electron microscopy (SEM), showing that no cells were lost after 35 min liquid handling of the cell chip at 10 mul min(-1). The enzymes were immobilised on microchips via PEI-treatment followed by glutaraldehyde (GA) activation. The GOX-HRP mu-biosensors could be used during five days without any noticeable decrease in response, while the AOX-HRP mu-biosensors showed continuously decreasing activity, but could still be used employing calibration correction. The glucose and ethanol released from the immobilised yeast chips were quantitatively monitored, by varying the incubation time with sucrose, showing the possibilities and advantages of using a microfluidic system set-up for cell-based assays.
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| 21. |
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| 22. |
- Dods, Robert, 1989, et al.
(författare)
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From Macrocrystals to Microcrystals: A Strategy for Membrane Protein Serial Crystallography.
- 2017
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Ingår i: Structure. - : Elsevier BV. - 1878-4186 .- 0969-2126. ; 25:9, s. 1461-1468
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Tidskriftsartikel (refereegranskat)abstract
- Serial protein crystallography was developed at X-ray free-electron lasers (XFELs) and is now also being applied at storage ring facilities. Robust strategies for the growth and optimization of microcrystals are needed to advance the field. Here we illustrate a generic strategy for recovering high-density homogeneous samples of microcrystals starting from conditions known to yield large (macro) crystals of the photosynthetic reaction center of Blastochloris viridis (RCvir). We first crushed these crystals prior to multiple rounds of microseeding. Each cycle of microseeding facilitated improvements in the RCvir serial femtosecond crystallography (SFX) structure from 3.3-Å to 2.4-Å resolution. This approach may allow known crystallization conditions for other proteins to be adapted to exploit novel scientific opportunities created by serial crystallography.
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| 23. |
- Dods, Robert, 1989, et al.
(författare)
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Ultrafast structural changes within a photosynthetic reaction centre.
- 2021
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 589:7841, s. 310-314
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Tidskriftsartikel (refereegranskat)abstract
- Photosynthetic reaction centres harvest the energy content of sunlight by transporting electrons across an energy-transducing biological membrane. Here we use time-resolved serial femtosecond crystallography1 using an X-ray free-electron laser2 to observe light-induced structural changes in the photosynthetic reaction centre of Blastochloris viridis on a timescale of picoseconds. Structural perturbations first occur at the special pair of chlorophyll molecules of the photosynthetic reaction centre that are photo-oxidized by light. Electron transfer to the menaquinone acceptor on the opposite side of the membrane induces a movement of this cofactor together with lower amplitude protein rearrangements. These observations reveal how proteins use conformational dynamics to stabilize the charge-separation steps of electron-transfer reactions.
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| 24. |
- Georgiou, P., et al.
(författare)
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Picosecond calorimetry: Time-resolved x-ray diffraction studies of liquid CH2Cl2
- 2006
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 124:23, s. 234507-
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Tidskriftsartikel (refereegranskat)abstract
- Liquid phase time-resolved x-ray diffraction with 100 ps resolution has recently emerged as a powerful technique for probing the structural dynamics of transient photochemical species in solution. It is intrinsic to the method, however, that a structural signal is observed not only from the photochemical of interest but also from the embedding solvent matrix. To experimentally characterize the x-ray diffraction signal deriving from the solvent alone we performed time-resolved diffraction studies of a pure liquid sample over a time domain from -250 ps to 2.5 mu s. Multiphoton excitation was used to rapidly heat liquid CH2Cl2 using UV pulses of 100 fs duration. A significant x-ray diffraction signal is visible prior to the onset of thermal expansion, which characterizes a highly compressed superheated liquid. Liquid CH2Cl2 then expands as a shock wave propagates through the sample and the temporal dependence of this phenomenon is in good agreement with theory. An unexpectedly slow initial release of energy into the liquid as heat is observed from multiphoton excited CH2Cl2, revealing the presence of a metastable state of multiphoton excited CH2Cl2.
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| 25. |
- Hautmann, Richard E., et al.
(författare)
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ICUD-EAU International Consultation on Bladder Cancer 2012: Urinary Diversion
- 2013
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Ingår i: European Urology. - : Elsevier BV. - 1873-7560 .- 0302-2838. ; 63:1, s. 67-80
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Forskningsöversikt (refereegranskat)abstract
- Context: A summary of the 2nd International Consultation on Bladder Cancer recommendations on the reconstructive options after radical cystectomy (RC), their outcomes, and their complications. Objective: To review the literature regarding indications, surgical details, postoperative care, complications, functional outcomes, as well as quality-of-life measures of patients with different forms of urinary diversion (UD). Evidence acquisition: An English-language literature review of data published between 1970 and 2012 on patients with UD following RC for bladder cancer was undertaken. No randomized controlled studies comparing conduit diversion with neobladder or continent cutaneous diversion have been performed. Consequently, almost all studies used in this report are of level 3 evidence. Therefore, the recommendations given here are grade C only, meaning expert opinion delivered without a formal analysis. Evidence synthesis: Indications and patient selection criteria have significantly changed over the past 2 decades. Renal function impairment is primarily caused by obstruction. Complications such as stone formation, urine outflow, and obstruction at any level must be recognized early and treated. In patients with orthotopic bladder substitution, daytime and nocturnal continence is achieved in 85-90% and 60-80%, respectively. Continence is inferior in elderly patients with orthotopic reconstruction. Urinary retention remains significant in female patients, ranging from 7% to 50%. Conclusions: RC and subsequent UD have been assessed as the most difficult surgical procedure in urology. Significant disparity on how the surgical complications were reported makes it impossible to compare postoperative morbidity results. Complications rates overall following RC and UD are significant, and when strict reporting criteria are incorporated, they are much higher than previously published. Fortunately, most complications are minor (Clavien grade 1 or 2). Complications can occur up to 20 yr after surgery, emphasizing the need for lifelong monitoring. Evidence suggests an association between surgical volume and outcome in RC; the challenge of optimum care for elderly patients with comorbidities is best mastered at high-volume hospitals by high-volume surgeons. Preoperative patient information, patient selection, surgical techniques, and careful postoperative follow-up are the cornerstones to achieve good long-term results. (C) 2012 European Association of Urology. Published by Elsevier B. V. All rights reserved.
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| 26. |
- Jain, Seema Rani, et al.
(författare)
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A chemiluminescence flow immunosensor based on a porous monolithic metacrylate and polyethylene composite disc modified with Protein G
- 2004
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Ingår i: Biosensors & Bioelectronics. - : Elsevier BV. - 1873-4235 .- 0956-5663. ; 19:8, s. 795-803
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Tidskriftsartikel (refereegranskat)abstract
- A generic, fast, sensitive and new type of flow immunosensor has been developed. The basis is a monolithic porous poly(glycidyl methacrylate-co-trimethylolpropane trimethacrylate) polymer disc modified with protein G, placed in a fountain type flow cell compartment, in close proximity to a photomultiplier tube (PMT). Analyte and HRP labelled analyte derivative (tracer) compete for anti-analyte antibody binding sites. The mixture is then injected into the flow immunosensor system where the formed analyte- and tracer-antibody complexes are trapped by the monolithic protein G disc. The amount of bound tracer, inversely related to the concentration of analyte in the sample, is determined in a second step by injection of luminol, p-iodophenol and H2O2, generating enhanced chemiluminescence (CL) with horseradish peroxidase (HRP). A third and final step is need for regeneration of the protein G disc so that a new analysis cycle can take place. The performance of the disc immunosensor system was compared with a one step continuous flow injection immunoassay (FIIA) system, using the same reagents and a protein G column, in terms of assay sensitivity and influence of matrix effects from various water samples (millipore-, tap- and surface water). The detection limit for the analyte atrazine in PBS and surface water (SW) was 0.208±0.004 g l−1 (PBS) and 0.59±0.120 g l−1 (SW) for the FIIA and 0.033±0.003 g l−1 (PBS) and 0.038±0.003 g l−1 (SW) for the disc immunosensor. Statistical comparison of the two systems shows that the disc immunosensor results were significantly less influenced by the sample matrix, which is explained by the fact that the sample in the FIIA arrives simultaneously with the matrix to the detector, whereas these are separated in time in the disc immunosensor system.
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| 27. |
- Koopmann, Rudolf, et al.
(författare)
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In vivo protein crystallization opens new routes in structural biology
- 2012
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Ingår i: Nature Methods. - : Springer Science and Business Media LLC. - 1548-7091 .- 1548-7105. ; 9:3, s. 259-262
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Tidskriftsartikel (refereegranskat)abstract
- Protein crystallization in cells has been observed several times in nature. However, owing to their small size these crystals have not yet been used for X-ray crystallographic analysis. We prepared nano-sized in vivo–grown crystals of Trypanosoma brucei enzymes and applied the emerging method of free-electron laser-based serial femtosecond crystallography to record interpretable diffraction data. This combined approach will open new opportunities in structural systems biology.
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| 28. |
- Kubo, M., et al.
(författare)
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Nanosecond pump-probe device for time-resolved serial femtosecond crystallography developed at SACLA
- 2017
-
Ingår i: Journal of Synchrotron Radiation. - : International Union of Crystallography (IUCr). - 1600-5775. ; 24, s. 1086-1091
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Tidskriftsartikel (refereegranskat)abstract
- X-ray free-electron lasers (XFELs) have opened new opportunities for timeresolved X-ray crystallography. Here a nanosecond optical-pump XFEL-probe device developed for time-resolved serial femtosecond crystallography (TRSFX) studies of photo-induced reactions in proteins at the SPring-8 Angstrom Compact free-electron LAser (SACLA) is reported. The optical-fiber-based system is a good choice for a quick setup in a limited beam time and allows pump illumination from two directions to achieve high excitation efficiency of protein microcrystals. Two types of injectors are used: one for extruding highly viscous samples such as lipidic cubic phase (LCP) and the other for pulsed liquid droplets. Under standard sample flow conditions from the viscous-sample injector, delay times from nanoseconds to tens of milliseconds are accessible, typical time scales required to study large protein conformational changes. A first demonstration of a TR-SFX experiment on bacteriorhodopsin in bicelle using a setup with a droplet-type injector is also presented.
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| 29. |
- Kubo, Minoru, et al.
(författare)
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Nanosecond pump-probe device for time-resolved serial femtosecond crystallography developed at SACLA
- 2017
-
Ingår i: Journal of Synchrotron Radiation. - : INT UNION CRYSTALLOGRAPHY. - 0909-0495 .- 1600-5775. ; 24, s. 1086-1091
-
Tidskriftsartikel (refereegranskat)abstract
- X-ray free-electron lasers (XFELs) have opened new opportunities for timeresolved X-ray crystallography. Here a nanosecond optical-pump XFEL-probe device developed for time-resolved serial femtosecond crystallography (TRSFX) studies of photo-induced reactions in proteins at the SPring-8 Angstrom Compact free-electron LAser (SACLA) is reported. The optical-fiber-based system is a good choice for a quick setup in a limited beam time and allows pump illumination from two directions to achieve high excitation efficiency of protein microcrystals. Two types of injectors are used: one for extruding highly viscous samples such as lipidic cubic phase (LCP) and the other for pulsed liquid droplets. Under standard sample flow conditions from the viscous-sample injector, delay times from nanoseconds to tens of milliseconds are accessible, typical time scales required to study large protein conformational changes. A first demonstration of a TR-SFX experiment on bacteriorhodopsin in bicelle using a setup with a droplet-type injector is also presented.
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| 30. |
- Malmerberg, Erik, 1980, et al.
(författare)
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Time-Resolved WAXS Reveals Accelerated Conformational Changes in Iodoretinal-Substituted Proteorhodopsin.
- 2011
-
Ingår i: Biophysical journal. - : Elsevier BV. - 1542-0086 .- 0006-3495. ; 101:6, s. 1345-53
-
Tidskriftsartikel (refereegranskat)abstract
- Time-resolved wide-angle x-ray scattering (TR-WAXS) is an emerging biophysical method which probes protein conformational changes with time. Here we present a comparative TR-WAXS study of native green-absorbing proteorhodopsin (pR) from SAR86 and a halogenated derivative for which the retinal chromophore has been replaced with 13-desmethyl-13-iodoretinal (13-I-pR). Transient absorption spectroscopy differences show that the 13-I-pR photocycle is both accelerated and displays more complex kinetics than native pR. TR-WAXS difference data also reveal that protein structural changes rise and decay an order-of-magnitude more rapidly for 13-I-pR than native pR. Despite these differences, the amplitude andnature of the observed helical motions are not significantly affected by the substitution of the retinal's C-20 methyl group with an iodine atom. Molecular dynamics simulations indicate that a significant increase in free energy is associated with the 13-cis conformation of 13-I-pR, consistent with our observation that the transient 13-I-pR conformational state is reached more rapidly. We conclude that although the conformational trajectory is accelerated, the major transient conformation of pR is unaffected by the substitution of an iodinated retinal chromophore.
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| 31. |
- Marcellini, Moreno, et al.
(författare)
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Transient isomers in the photodissociation of bromoiodomethane
- 2018
-
Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 148:13
-
Tidskriftsartikel (refereegranskat)abstract
- The photochemistry of halomethanes is fascinating for the complex cascade reactions toward either the parent or newly synthesized molecules. Here, we address the structural rearrangement of photodissociated CH2IBr in methanol and cyclohexane, probed by time-resolved X-ray scattering in liquid solution. Upon selective laser cleavage of the C-I bond, we follow the reaction cascade of the two geminate geometrical isomers, CH2I-Br and CH2Br-I. Both meta-stable isomers decay on different time scales, mediated by solvent interaction, toward the original parent molecule. We observe the internal rearrangement of CH2Br-I to CH2I-Br in cyclohexane by extending the time window up to 3 mu s. We track the photoproduct kinetics of CH2Br-I in methanol solution where only one isomer is observed. The effect of the polarity of solvent on the geminate recombination pathways is discussed. Published by AIP Publishing.
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| 32. |
- Nango, E., et al.
(författare)
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A three-dimensional movie of structural changes in bacteriorhodopsin
- 2016
-
Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 354:6319, s. 1552-1557
-
Tidskriftsartikel (refereegranskat)abstract
- Bacteriorhodopsin (bR) is a light-driven proton pump and a model membrane transport protein. We used time-resolved serial femtosecond crystallography at an x-ray free electron laser to visualize conformational changes in bR from nanoseconds to milliseconds following photoactivation. An initially twisted retinal chromophore displaces a conserved tryptophan residue of transmembrane helix F on the cytoplasmic side of the protein while dislodging a key water molecule on the extracellular side. The resulting cascade of structural changes throughout the protein shows how motions are choreographed as bR transports protons uphill against a transmembrane concentration gradient.
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| 33. |
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| 34. |
- Nistor, Catalin, et al.
(författare)
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Detection of Escherichia coli in water by culture-based amperometric and luminometric methods.
- 2002
-
Ingår i: Water Science and Technology. - 0273-1223. ; 45:4-5, s. 191-199
-
Tidskriftsartikel (refereegranskat)abstract
- The application of amperometric biosensor- and chemiluminiscence based methods for rapid detection of viable E. coli in water has been investigated. An amplification of the amperometric signal by a factor of 4 was obtained when the cellobiose dehydrogenase (CDH) biosensor was used instead of a plain graphite electrode for detection of b-galactosidase (b-GAL) activity at 22.5 degrees C. A linear correlation was demonstrated for detection time (DT) vs. initial concentrations (logarithmic units) of E. coli IT1 and E. coli in environmental samples, respectively, by use of the CDH biosensor or a chemiluminometric technique. The study has shown that an E. coli concentration > or = 10(4) cfu/100 mL in environmental samples was determined by the CDH biosensor within one working day. However, further reduction of the DT can be obtained, e.g. by increasing the signal amplification factor using other biosensors.
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| 35. |
- Pajola, Maurizio, et al.
(författare)
-
Size-frequency distribution of boulders >= 7 m on comet 67P/Churyumov-Gerasimenko
- 2015
-
Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 583
-
Tidskriftsartikel (refereegranskat)abstract
- Aims. We derive for the first time the size-frequency distribution of boulders on a comet, 67P/Churyumov-Gerasimenko (67P), computed from the images taken by the Rosetta/OSIRIS imaging system. We highlight the possible physical processes that lead to these boulder size distributions. Methods. We used images acquired by the OSIRIS Narrow Angle Camera, NAC. on 5 and 6 August 2014. The scale of these images (2.44-2.03 m/px) is such that boulders >= 7 m can be identified and manually extracted from the datasets with the software ArcGIS. We derived both global and localized size-frequency distributions. The three-pixel sampling detection, coupled with the favorable shadowine of the surface (observation phase angle ranging from 48 to 53), enables unequivocally detecting boulders scattered all over the illuminated side of 67P. Results. We identify 3546 boulders larger than 7 m on the imaged surface (36.4 km(2)), with a global number density of nearly 100/km(2) and a cumulative size-frequency distribution represented by a power-law with index of -3.6 +0.2/-0.3. The two lobes of 67P appear to have slightly different distributions, with an index of -3.5 +0.2/-0.3 for the main lobe (body) and -4.0 +0.31-0.2 for the small lobe (head). The steeper distribution of the small lobe might be due to a more pervasive fracturing. The difference of the distribution for the connecting region (neck) is much more significant, with an index value of -2.2 +0.2/-0.2. We propose that the boulder field located in the neck area is the result of blocks falling from the contiguous Hathor cliff. The lower slope of the size-frequency distribution we see today in the neck area might be due to the concurrent processes acting on the smallest boulders, such as i) disintegration or fragmentation and vanishing through sublimation; ii) uplifting by gas drag and consequent redistribution; and iii) burial beneath a debris blanket. We also derived the cumulative size-frequency distribution per km(2) of localized areas on 67P. By comparing the cumulative size-frequency distributions of similar geomorphological settings, we derived similar power-law index values. This suggests that despite the selected locations on different and often opposite sides of the comet, similar sublimation or activity processes, pit formation or collapses, as well as thermal stresses or fracturing events occurred on multiple areas of the comet, shaping its surface into the appearance we see today.
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| 36. |
- Sierks, Holger, et al.
(författare)
-
On the nucleus structure and activity of comet 67P/Churyumov-Gerasimenko
- 2015
-
Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 347:6220
-
Tidskriftsartikel (refereegranskat)abstract
- Images from the OSIRIS scientific imaging system onboard Rosetta show that the nucleus of 67P/Churyumov-Gerasimenko consists of two lobes connected by a short neck. The nucleus has a bulk density less than half that of water. Activity at a distance from the Sun of >3 astronomical units is predominantly from the neck, where jets have been seen consistently. The nucleus rotates about the principal axis of momentum. The surface morphology suggests that the removal of larger volumes of material, possibly via explosive release of subsurface pressure or via creation of overhangs by sublimation, may be a major mass loss process. The shape raises the question of whether the two lobes represent a contact binary formed 4.5 billion years ago, or a single body where a gap has evolved via mass loss.
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| 37. |
- Sparr Eskilsson, Cecilia, et al.
(författare)
-
Harmful azo colorants in leather. Determination based on their cleavage and extraction of corresponding carcinogenic aromatic amines using modern extraction techniques.
- 2002
-
Ingår i: Journal of Chromatography A. - 0021-9673. ; 955:2, s. 215-227
-
Tidskriftsartikel (refereegranskat)abstract
- This study concerns the possibilities of using microwave-assisted extraction (MAE) or supercritical fluid extraction (SFE) for detection of harmful azo colorants in leather. After degreasing of the leather sample with SFE there follows a reductive cleavage of the azo colorants to their corresponding aromatic amines in the MAE or SFE equipment. The aromatic amines are subsequently extracted using either MAE or SFE and then finally determined by liquid chromatography with diode-array detection. The results have been compared with recoveries obtained using the German DIN method 53316. This standard method, based on conventional solvent extraction, is used in several European countries. Overall much better recoveries were obtained using MAE or SFE. With both MAE and SFE the amine recoveries of spiked leather samples were generally above 50%. The average recoveries were 62% for MAE and 60% for SFE (solvent collection) compared to 24% with the DIN method. For genuine leather samples the recoveries decreased, especially for benzidine. In this case the average values for MAE, SFE and DIN were 54, 38 and 19%, respectively. The quantification limits in leather samples using MAE or SFE were below 1 mg/kg for all amines investigated. The within-laboratory precision was generally better than 10%, varying somewhat with the analyte considered. With the proposed methodology, the amount of hazardous organic solvents used could be decreased and the sample throughput increased with at least a factor of two with less manual handling compared to the DIN method.
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| 38. |
- Thomas, Nicolas, et al.
(författare)
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The morphological diversity of comet 67P/Churyumov-Gerasimenko
- 2015
-
Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 347:6220
-
Tidskriftsartikel (refereegranskat)abstract
- Images of comet 67P/Churyumov-Gerasimenko acquired by the OSIRIS (Optical, Spectroscopic and Infrared Remote Imaging System) imaging system onboard the European Space Agency's Rosetta spacecraft at scales of better than 0.8 meter per pixel show a wide variety of different structures and textures. The data show the importance of airfall, surface dust transport, mass wasting, and insolation weathering for cometary surface evolution, and they offer some support for subsurface fluidization models and mass loss through the ejection of large chunks of material.
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| 39. |
- Thompson, Deborah J, et al.
(författare)
-
Genetic predisposition to mosaic Y chromosome loss in blood
- 2019
-
Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 575, s. 652-657
-
Tidskriftsartikel (refereegranskat)abstract
- Mosaic loss of chromosome Y (LOY) in circulating white blood cells is the most common form of clonal mosaicism1-5, yet our knowledge of the causes and consequences of this is limited. Here, using a computational approach, we estimate that 20% of the male population represented in the UK Biobank study (n = 205,011) has detectable LOY. We identify 156 autosomal genetic determinants of LOY, which we replicate in 757,114 men of European and Japanese ancestry. These loci highlight genes that are involved in cell-cycle regulation and cancer susceptibility, as well as somatic drivers of tumour growth and targets of cancer therapy. We demonstrate that genetic susceptibility to LOY is associated with non-haematological effects on health in both men and women, which supports the hypothesis that clonal haematopoiesis is a biomarker of genomic instability in other tissues. Single-cell RNA sequencing identifies dysregulated expression of autosomal genes in leukocytes with LOY and provides insights into why clonal expansion of these cells may occur. Collectively, these data highlight the value of studying clonal mosaicism to uncover fundamental mechanisms that underlie cancer and other ageing-related diseases.
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| 40. |
- Vincent, Jean-Baptiste, et al.
(författare)
-
Large heterogeneities in comet 67P as revealed by active pits from sinkhole collapse
- 2015
-
Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 523:7558, s. 63-66
-
Tidskriftsartikel (refereegranskat)abstract
- Pits have been observed on many cometary nuclei mapped by spacecraft(1-4). It has been argued that cometary pits are a signature of endogenic activity, rather than impact craters such as those on planetary and asteroid surfaces. Impact experiments(5,6) andmodels(7,8) cannot reproduce the shapes of most of the observed cometary pits, and the predicted collision rates imply that few of the pits are related to impacts(8,9). Alternative mechanisms like explosive activity(10) have been suggested, but the driving process remains unknown. Here we report that pits on comet 67P/Churyumov-Gerasimenko are active, and probably created by a sinkhole process, possibly accompanied by outbursts. We argue that after formation, pits expand slowly in diameter, owing to sublimation-driven retreat of the walls. Therefore, pits characterize how eroded the surface is: a fresh cometary surface will have a ragged structure with many pits, while an evolved surface will look smoother. The size and spatial distribution of pits imply that large heterogeneities exist in the physical, structural or compositional properties of the first few hundred metres below the current nucleus surface.
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| 41. |
- Vincent, Jonathan, et al.
(författare)
-
Solvent dependent structural perturbations of chemical reaction intermediates visualized by time-resolved x-ray diffraction
- 2009
-
Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 130:15, s. 154502-
-
Tidskriftsartikel (refereegranskat)abstract
- Ultrafast time-resolved wide angle x-ray scattering from chemical reactions in solution has recently emerged as a powerful technique for determining the structural dynamics of transient photochemical species. Here we examine the structural evolution of photoexcited CH2I2 in the nonpolar solvent cyclohexane and draw comparisons with a similar study in the polar solvent methanol. As with earlier spectroscopic studies, our data confirm a common initial reaction pathway in both solvents. After photoexcitation, CH2I2 dissociates to form CH2I center dot+I center dot. Iodine radicals remaining within the solvent cage recombine with a nascent CH2I center dot radical to form the transient isomer CH2I-I, whereas those which escape the solvent cage ultimately combine to form I-2 in cyclohexane. Moreover, the transient isomer has a lifetime approximately 30 times longer in the nonpolar solvent. Of greater chemical significance is the property of time-resolved wide angle x-ray diffraction to accurately determine the structure of the of CH2I-I reaction intermediate. Thus we observe that the transient iodine-iodine bond is 0.07 A +/- 0.04 A shorter in cyclohexane than in methanol. A longer iodine-iodine bond length for the intermediate arises in methanol due to favorable H-bond interaction with the polar solvent. These findings establish that time-resolved x-ray diffraction has sufficient sensitivity to enable solvent dependent structural perturbations of transient chemical species to be accurately resolved.
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| 42. |
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| 43. |
- Wallenhammar, Amélie, 1986-, et al.
(författare)
-
Revealing new tick-borne encephalitis foci by screening antibodies in sheep milk
- 2019
-
Ingår i: 16th Smögen Symposium on Virology, August 22-24, 2019.
-
Konferensbidrag (refereegranskat)abstract
- Climate changes have increased the tick-distribution in Sweden, and the prevalence of ticks has been predicted to increase towards the northern parts of the country, increasing the risk of tick-borne zoonosis in new regions. Tick-borne encephalitis (TBE) is the most important viral tick-borne zoonosis in Sweden as well as in Europe. TBE virus (TBEV) infection often leads to severe CNS disease, including encephalitis and severe myelitis, which may lead to paralysis and respiratory failure in humans. TBEV and antibodies against TBEV are excreted in milk of goats, sheep and cattle and the virus can be ingested orally by consumption of non-pasteurized dairy products. Since the prevalence of TBEV in the tick population is low there is a need for new and robust surveillance techniques identifying new risk areas of TBEV at early stages.In this study we have developed a novel strategy for identifying new TBEV foci. We have collected raw milk and colostrum samples from sheep and goats in Örebro County, Sweden. The milk samples were analyzed for the presence of TBEV antibodies by ELISA, and validated by an in-house Western Blot assay where milk samples were used as primary antibody to detect purified TBEV E-protein. By monitoring TBEV antibodies in milk we have found three novel foci in the Örebro County which also overlap with the plausible place of infection of registered human TBE cases reported during 2009-2018. Furthermore, the stability of TBEV in milk and raw milk was studied at different temperatures. Our data indicates that keeping unpasteurized milk at 4 ˚C will preserve the infectivity of TBEV for several days. Ticks have also been collected from areas with TBEV positive milk. We aim to extract total RNA from the sampled ticks, followed by TBEV detection by nested-PCR and next-generation sequencing.Here we present a novel technique to reveal risk areas of TBE in Sweden, which is robust, reliable, and non-invasive and can accordingly be used to map TBEV “hotspots”. In the TBE foci, more than 50 % of the tested animals were antibody positive, and TBEV infectivity in refrigerated milk was preserved, stressing the importance of pasteurization before consumption.
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| 44. |
- Wallenhammar, Amélie, 1986-, et al.
(författare)
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Revealing new tick-borne encephalitis virus foci by screening antibodies in sheep milk
- 2020
-
Ingår i: Parasites & Vectors. - : BioMed Central. - 1756-3305. ; 13:1
-
Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Tick distribution in Sweden has increased in recent years, with the prevalence of ticks predicted to spread towards the northern parts of the country, thus increasing the risk of tick-borne zoonoses in new regions. Tick-borne encephalitis (TBE) is the most significant viral tick-borne zoonotic disease in Europe. The disease is caused by TBE virus (TBEV) infection which often leads to severe encephalitis and myelitis in humans. TBEV is usually transmitted to humans via tick bites; however, the virus can also be excreted in the milk of goats, sheep and cattle and infection may then occur via consumption of unpasteurised dairy products. Virus prevalence in questing ticks is an unreliable indicator of TBE infection risk as viral RNA is rarely detected even in large sample sizes collected at TBE-endemic areas. Hence, there is a need for robust surveillance techniques to identify emerging TBEV risk areas at early stages.METHODS: Milk and colostrum samples were collected from sheep and goats in Örebro County, Sweden. The milk samples were analysed for the presence of TBEV antibodies by ELISA and validated by western blot in which milk samples were used to detect over-expressed TBEV E-protein in crude cell extracts. Neutralising titers were determined by focus reduction neutralisation test (FRNT). The stability of TBEV in milk and colostrum was studied at different temperatures.RESULTS: In this study we have developed a novel strategy to identify new TBEV foci. By monitoring TBEV antibodies in milk, we have identified three previously unknown foci in Örebro County which also overlap with areas of TBE infection reported during 2009-2018. In addition, our data indicates that keeping unpasteurised milk at 4 °C will preserve the infectivity of TBEV for several days.CONCLUSIONS: Altogether, we report a non-invasive surveillance technique for revealing risk areas for TBE in Sweden, by detecting TBEV antibodies in sheep milk. This approach is robust and reliable and can accordingly be used to map TBEV "hotspots". TBEV infectivity in refrigerated milk was preserved, emphasising the importance of pasteurisation (i.e. 72 °C for 15 s) prior to consumption.
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| 45. |
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| 46. |
- Westenhoff, Sebastian, 1978, et al.
(författare)
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Time-resolved structural studies of protein reaction dynamics : a smorgasbord of X-ray approaches
- 2010
-
Ingår i: Acta Crystallographica Section A. - 0108-7673 .- 1600-5724. ; 66:2, s. 207-219
-
Forskningsöversikt (refereegranskat)abstract
- Proteins undergo conformational changes during their biological function. As such, a high-resolution structure of a protein's resting conformation provides a starting point for elucidating its reaction mechanism, but provides no direct information concerning the protein's conformational dynamics. Several X-ray methods have been developed to elucidate those conformational changes that occur during a protein's reaction, including time-resolved Laue diffraction and intermediate trapping studies on three-dimensional protein crystals, and time-resolved wide-angle X-ray scattering and X-ray absorption studies on proteins in the solution phase. This review emphasizes the scope and limitations of these complementary experimental approaches when seeking to understand protein conformational dynamics. These methods are illustrated using a limited set of examples including myoglobin and haemoglobin in complex with carbon monoxide, the simple light-driven proton pump bacteriorhodopsin, and the superoxide scavenger superoxide reductase. In conclusion, likely future developments of these methods at synchrotron X-ray sources and the potential impact of emerging X-ray free-electron laser facilities are speculated upon.
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| 47. |
- Wöhri, Annemarie, 1976, et al.
(författare)
-
Light-Induced Structural Changes in a Photosynthetic Reaction Center Caught by Laue Diffraction
- 2010
-
Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 328:5978, s. 630-633
-
Tidskriftsartikel (refereegranskat)abstract
- Photosynthetic reaction centers convert the energy content of light into a transmembrane potential difference and so provide the major pathway for energy input into the biosphere. We applied time-resolved Laue diffraction to study light-induced conformational changes in the photosynthetic reaction center complex of Blastochloris viridis. The side chain of TyrL162, which lies adjacent to the special pair of bacteriochlorophyll molecules that are photooxidized in the primary light conversion event of photosynthesis, was observed to move 1.3 angstroms closer to the special pair after photoactivation. Free energy calculations suggest that this movement results from the deprotonation of this conserved tyrosine residue and provides a mechanism for stabilizing the primary charge separation reactions of photosynthesis.
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| 48. |
- Yakovleva, J, et al.
(författare)
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Microfluidic enzyme immunoassay using silicon microchip with immobilized antibodies and chemiluminescence detection
- 2002
-
Ingår i: Analytical Chemistry. - : American Chemical Society (ACS). - 1520-6882 .- 0003-2700. ; 74:13, s. 2994-3004
-
Tidskriftsartikel (refereegranskat)abstract
- Silicon microchips with immobilized antibodies were used to develop microfluidic enzyme immunoassays using chemiluminescence detection and horseradish peroxidase (HRP) as the enzyme label. Polyclonal anti-atrazine antibodies were coupled to the silicon microchip surface with an overall dimension of 13.1 x 3.2 mm, comprising 42 porous flow channels of 235-mum depth and 25-mum width. Different immobilization protocols based on covalent or noncovalent modification of the silica surface with 3-aminopropyltriethoxysilane (APTES) or 3-glycidoxypropyltrimethoxysilane (GOPS), linear polyethylenimine (LPEI, MW 750 000), or branched polyethylenimine (BPEI, MW 25 000), followed by adsorption or covalent attachment of the antibody, were evaluated to reach the best reusability, stability, and sensitivity of the microfluidic enzyme immunoassay (muFEIA). Adsorption of antibodies on a LPEI-modified silica surface and covalent attachment to physically adsorbed BPEI lead to unstable antibody coatings. Covalent coupling of antibodies via glutaraldehyde (GA) to three different functionalized silica surfaces (APTES-GA, LPEI-GA, and GOPS-BPEI-GA) resulted in antibody coatings that could be completely regenerated using 0.4 M glycine/HCl, pH 2.2. The buffer composition was shown to have a dramatic effect on the assay stability, where the commonly used phosphate buffer saline was proved to be the least suitable choice. The best long-term stability was obtained for the LPEI-GA surface with no loss of antibody activity during one month. The detection limits in the muFEIA for the three different immuno surfaces were 45, 3.8, and 0.80 ng/L (209, 17.7, and 3.7 pM) for APTES-GA, LPEI-GA, and GOPS-BPEI-GA, respectively.
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| 49. |
- Yakovleva, J, et al.
(författare)
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Microfluidic enzyme immunosensors with immobilised protein A and G using chemiluminescence detection
- 2003
-
Ingår i: Biosensors & Bioelectronics. - 1873-4235. ; 19:1, s. 21-34
-
Tidskriftsartikel (refereegranskat)abstract
- Affinity proteins were covalently immobilised on silicon microchips with overall dimensions of 13.1 x 3.2 mm, comprising 42 porous flow channels of 235 mum depth and 25 pm width, and used to develop microfluidic immunosensors based on horseradish peroxidase (HRP), catalysing the chemiluminescent oxidation of luminol/p-iodophenol (PIP). Different hydrophilic polymers with long flexible chains (polyethylenimine (PEI), dextran (DEX), polyvinyl alcohol, aminodextran) and 3-aminopropyltriethoxysilane (APTS) were employed for modification of the silica surfaces followed by attachment of protein A or G. The resulting immunosensors were compared in an affinity capture assay format, where the competition between the labelled antigen and the analyte for antibody-binding sites took place in the bulk of the solution. The formed immunocomplexes were then trapped by the microchip affinity capture support and the amount of bound tracer was monitored by injection of luminol, PIP and H2O2. All immunosensors were capable of detecting atrazine at the sub-mug 1(-1) level. The most sensitive assays were obtained with PEI and DEX polymer modified supports and immobilised protein G, with limits of detection of 0.006 and 0.010 mug 1-1, and IC50 values of 0.096 and 0.130 mug 1(-1), respectively. The protein G based immunosensors were regenerated with 0.4 M glycine-HCI buffer pH 2.2, with no loss of activity observed for a storage and operating period of over 8 months. To estimate the applicability of the immunosensors to the analysis of real samples, PEI and DEX based protein G microchips were used to detect atrazine in surface water and fruit juice, spiked with known amounts of the atrazine, giving recovery values of 87-102 and 88-124%, at atrazine fortification levels of 0.5-3 and 80-240 mug 1(-1), respectively. (C) 2003 Elsevier Science B.V. All rights reserved.
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