| 1. |
- Elf, Johan, et al.
(författare)
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Mesoscopic kinetics and its applications in protein synthesis
- 2005
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Ingår i: Systems Biology. - Heidelberg : Springer-Verlag GmbH. - 354022968X ; , s. 95-118
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- Molecular biology emerged through unification of genetics and nucleic acid chemistry that took place with the discovery of the double helix (Watson and Crick 1953). Accordingly, molecular biology could be defined as the sum of all techniques used to perform genetic experiments by manipulating DNA. One consequence of the development of these techniques is large-scale sequencing of genomes from an ever increasing number of organisms. However, it became clear from this development that genetic information per se is not enough to grasp the most interesting functional and evolutionary aspects of cells and multi-cellular organisms. In fact, understanding how genotype leads to phenotype depends on concepts and techniques from areas that so far have been largely alien to molecular biological research, like physics, mathematics, and engineering. From the bits and pieces from these and other scientific fields new tools must be generated to make possible an understanding of the dynamic, adapting, and developing living systems that somehow take shape from the instructions given by their genomes. The growing total of these tools and their integration in experimental and theoretical approaches to understand complex biological processes in ways previously out of reach could be a way to define systems biology, in analogy with the above definition of molecular biology.
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| 2. |
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| 3. |
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| 4. |
- Paulsson, Johan, et al.
(författare)
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Stochastic Modeling of Intracellular Kinetics
- 2006
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Ingår i: System Modeling in Cellular Biology. - : The MIT Press, Cambridge. - 0262195488 ; , s. 480-
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Bokkapitel (populärvet., debatt m.m.)
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| 5. |
- Wassélius, Johan, et al.
(författare)
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Treatment of mesenteric vein thrombosis with transjugular mechanical thrombectomy and subsequent simultaneous arterial and venous thrombolysis
- 2014
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Ingår i: Journal of Vascular Surgery: Venous and Lymphatic Disorders. - : Elsevier BV. - 2213-333X. ; 2:3, s. 3-320
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Tidskriftsartikel (refereegranskat)abstract
- Mesenteric vein thrombosis may induce intestinal ischemia and gangrene. In severe cases, it is necessary to restore venous outflow from the small intestine rapidly. We describe a severe case of mesenteric vein thrombosis that was resolved successfully by mechanical thrombectomy from a transjugular approach followed by selective simultaneous venous and arterial thrombolysis via the superior mesenteric vein and artery. In conclusion, the transjugular intrahepatic portosystemic approach was a feasible and safe access for mechanical thrombectomy and thrombolysis of the mesenteric vein in our patient.
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| 6. |
- Ahmad, Abrar, et al.
(författare)
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Evaluation of Expression Level of Apolipoprotein M as a Diagnostic Marker for Primary Venous Thromboembolism
- 2018
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Ingår i: Clinical and Applied Thrombosis/Hemostasis. - : SAGE Publications. - 1938-2723 .- 1076-0296. ; 24:3, s. 416-422
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Tidskriftsartikel (refereegranskat)abstract
- Recently, decreased levels of apolipoprotein M (ApoM) were shown to be associated with higher risk of recurrent venous thromboembolism (VTE) in male patients. However, the role of ApoM in primary VTE is unknown. We aimed in our study to analyze the plasma levels of ApoM in patients with VTE in order to evaluate the diagnostic importance of ApoM in primary VTE. A total of 357 patients with suspected first episode of VTE were recruited prospectively in the SCORE study. Plasma samples from 307 patients were available for quantifying the plasma levels of ApoM in patients with VTE using sandwich enzyme-linked immunosorbent assay method. Among the whole population, plasma levels (mean [standard deviation]) of ApoM were not significantly different between patients with VTE (0.72 [0.20]) and non-VTE patients (0.72 [0.16]), P = .99. Similarly, in regression analyses, no significant association of ApoM plasma levels with the risk of VTE was found on univariate (odds ratio [OR] =1.0, 95% confidence interval [CI] 0.21-4.84, P = .99) and multivariate analysis (OR = 1.25, 95% CI = 0.19-8.34, P = .819) after adjusting for age, body mass index, and smoking. Moreover, results did not differ significantly after stratification of data according to sex ( P > .05). In this study, our results do not suggest a diagnostic role for ApoM plasma levels in patients with primary VTE. Moreover, the current study suggests that role of ApoM as a risk factor may differ for primary VTE and recurrent VTE in male patients.
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| 7. |
- Amselem, Elias, et al.
(författare)
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Real-time single-molecule 3D tracking in E. coli based on cross-entropy minimization
- 2023
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Ingår i: Nature Communications. - : NATURE PORTFOLIO. - 2041-1723. ; 14:1
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Tidskriftsartikel (refereegranskat)abstract
- Reaching sub-millisecond 3D tracking of individual molecules in living cells would enable direct measurements of diffusion-limited macromolecular interactions under physiological conditions. Here, we present a 3D tracking principle that approaches the relevant regime. The method is based on the true excitation point spread function and cross-entropy minimization for position localization of moving fluorescent reporters. Tests on beads moving on a stage reaches 67 nm lateral and 109 nm axial precision with a time resolution of 0.84 ms at a photon count rate of 60 kHz; the measurements agree with the theoretical and simulated predictions. Our implementation also features a method for microsecond 3D PSF positioning and an estimator for diffusion analysis of tracking data. Finally, we successfully apply these methods to track the Trigger Factor protein in living bacterial cells. Overall, our results show that while it is possible to reach sub-millisecond live-cell single-molecule tracking, it is still hard to resolve state transitions based on diffusivity at this time scale.
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| 8. |
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| 9. |
- Baltekin, Özden, et al.
(författare)
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Antibiotic susceptibility testing in less than 30 min using direct single-cell imaging
- 2017
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 114:34, s. 9170-9175
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Tidskriftsartikel (refereegranskat)abstract
- The emergence and spread of antibiotic-resistant bacteria are aggravated by incorrect prescription and use of antibiotics. A core problem is that there is no sufficiently fast diagnostic test to guide correct antibiotic prescription at the point of care. Here, we investigate if it is possible to develop a point-of-care susceptibility test for urinary tract infection, a disease that 100 million women suffer from annually and that exhibits widespread antibiotic resistance. We capture bacterial cells directly from samples with low bacterial counts (10(4) cfu/mL) using a custom-designed microfluidic chip and monitor their individual growth rates using microscopy. By averaging the growth rate response to an antibiotic over many individual cells, we can push the detection time to the biological response time of the bacteria. We find that it is possible to detect changes in growth rate in response to each of nine antibiotics that are used to treat urinary tract infections in minutes. In a test of 49 clinical uropathogenic Escherichia coli (UPEC) isolates, all were correctly classified as susceptible or resistant to ciprofloxacin in less than 10 min. The total time for antibiotic susceptibility testing, from loading of sample to diagnostic readout, is less than 30 min, which allows the development of a point-of-care test that can guide correct treatment of urinary tract infection.
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| 10. |
- Balzarotti, Francisco, et al.
(författare)
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Nanometer resolution imaging and tracking of fluorescent molecules with minimal photon fluxes
- 2017
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 355:6325, s. 606-612
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Tidskriftsartikel (refereegranskat)abstract
- We introduce MINFLUX, a concept for localizing photon emitters in space. By probing the emitter with a local intensity minimum of excitation light, MINFLUX minimizes the fluorescence photons needed for high localization precision. In our experiments, 22 times fewer fluorescence photons are required as compared to popular centroid localization. In superresolutionmicroscopy, MINFLUXattained similar to 1-nanometer precision, resolving molecules only 6 nanometers apart. MINFLUX tracking of single fluorescent proteins increased the temporal resolution and the number of localizations per trace by a factor of 100, as demonstrated with diffusing 30S ribosomal subunits in living Escherichia coli. As conceptual limits have not been reached, we expect this localization modality to break new ground for observing the dynamics, distribution, and structure of macromolecules in living cells and beyond.
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| 11. |
- Bashardanesh, Zahedeh, et al.
(författare)
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Rotational and Translational Diffusion of Proteins as a Function of Concentration
- 2019
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Ingår i: ACS Omega. - : American Chemical Society (ACS). - 2470-1343. ; 4:24, s. 20654-20664
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Tidskriftsartikel (refereegranskat)abstract
- Atomistic simulations of three different proteins at different concentrations are performed to obtain insight into protein mobility as a function of protein concentration. We report on simulations of proteins from diluted to the physiological water concentration (about 70% of the mass). First, the viscosity was computed and found to increase by a factor of 7-9 going from pure water to the highest protein concentration, in excellent agreement with in vivo nuclear magnetic resonance results. At a physiological concentration of proteins, the translational diffusion is found to be slowed down to about 30% of the in vitro values. The slow-down of diffusion found here using atomistic models is slightly more than that of a hard sphere model that neglects the electrostatic interactions. Interestingly, rotational diffusion of proteins is slowed down somewhat more (by about 80-95% compared to in vitro values) than translational diffusion, in line with experimental findings and consistent with the increased viscosity. The finding that rotation is retarded more than translation is attributed to solvent-separated clustering. No direct interactions between the proteins are found, and the clustering can likely be attributed to dispersion interactions that are stronger between proteins than between protein and water. Based on these simulations, we can also conclude that the internal dynamics of the proteins in our study are affected only marginally under crowding conditions, and the proteins become somewhat more stable at higher concentrations. Simulations were performed using a force field that was tuned for dealing with crowding conditions by strengthening the protein-water interactions. This force field seems to lead to a reproducible partial unfolding of an alpha-helix in one of the proteins, an effect that was not observed in the unmodified force field.
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| 12. |
- Berg, Otto G., et al.
(författare)
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The helical structure of DNA facilitates binding
- 2016
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Ingår i: Journal of Physics A. - : IOP Publishing. - 1751-8113 .- 1751-8121. ; 9:36
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- The helical structure of DNA imposes constraints on the rate of diffusion-limited protein binding. Here we solve the reaction-diffusion equations for DNA-like geometries and extend with simulations when necessary. We find that the helical structure can make binding to the DNA more than twice as fast compared to a case where DNA would be reactive only along one side. We also find that this rate advantage remains when the contributions from steric constraints and rotational diffusion of the DNA-binding protein are included. Furthermore, we find that the association rate is insensitive to changes in the steric constraints on the DNA in the helix geometry, while it is much more dependent on the steric constraints on the DNA-binding protein. We conclude that the helical structure of DNA facilitates the nonspecific binding of transcription factors and structural DNA-binding proteins in general.
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| 13. |
- Brandis, Gerrit, 1985-, et al.
(författare)
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Antibiotic perseverance increases the risk of resistance development
- 2023
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences (PNAS). - 0027-8424 .- 1091-6490. ; 120:2
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Tidskriftsartikel (refereegranskat)abstract
- The rise of antibiotic-resistant bacterial infections poses a global threat. Antibiotic resistance development is generally studied in batch cultures which conceals the heterogeneity in cellular responses. Using single-cell imaging, we studied the growth response of Escherichia coli to sub-inhibitory and inhibitory concentrations of nine antibiotics. We found that the heterogeneity in growth increases more than what is expected from growth rate reduction for three out of the nine antibiotics tested. For two antibiotics (rifampicin and nitrofurantoin), we found that sub-populations were able to maintain growth at lethal antibiotic concentrations for up to 10 generations. This perseverance of growth increased the population size and led to an up to 40-fold increase in the frequency of antibiotic resistance mutations in gram-negative and gram-positive species. We conclude that antibiotic perseverance is a common phenomenon that has the potential to impact antibiotic resistance development across pathogenic bacteria.
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| 14. |
- Brink, Annie, et al.
(författare)
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Sex-Specific Risk Factors for Deep Venous Thrombosis and Pulmonary Embolism in a Population-Based Historical Cohort Study of Middle-Aged and Older Individuals
- 2023
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Ingår i: Journal of the American Heart Association. - 2047-9980. ; 12:5, s. 1-13
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Whether sex-specific differences exist for risk factors for pulmonary embolism (PE) and deep venous thrombosis (DVT), with the exception of pregnancy and estrogen therapy, has been sparsely studied. We aimed to study whether sex-specific differences of risk factors exist for noncancer-related DVT and PE in middle-aged and older individuals without cardiovascular history or previous diagnosis in a population-based historical (retrospective) cohort. METHODS AND RESULTS: Potential venous thromboembolism (VTE) risk factors were registered at baseline in 15 807 women and 9996 men aged 44 to 74 years, who participated in the Malmö Diet and Cancer study (1991–1996). We excluded subjects with a previous history of VTE, cancer, a diagnosis of cardiovascular disease, or a diagnosis of cancer-associated VTE during follow-up. Patients were followed up from baseline until the first event of PE or DVT, death, or December 31, 2018. During the follow-up period, 365 (2.3%) women and 168 (1.7%) men were affected by first DVT, and 309 (2.0%) women and 154 (1.5%) men were affected by first PE. In the multivariable Cox regression models, the anthropometric obesity markers of weight, body mass index, waist and hip circumference, fat percentage, and muscle weight were in a dose-dependent way associated with DVT and PE among women but not men. In an analysis that included patients with cardiovascular disease and cancer-related VTE, the results were similar for women. For men, several obesity measures became significantly associated with PE or DVT but were weaker than in women, especially for DVT. CONCLUSIONS: Anthropometric obesity measures are more important risk factors for both DVT and PE among women than men, especially for individuals without cardiovascular history or previous diagnosis or cancer-related VTE.
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| 15. |
- Calling, Susanna, et al.
(författare)
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Lung function, respiratory symptoms and incident venous thromboembolism during a 44-year follow-up
- 2023
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Ingår i: Thrombosis Update. - Oxford : Elsevier. - 2666-5727. ; 12
-
Tidskriftsartikel (refereegranskat)abstract
- Background: Chronic obstructive pulmonary disease (COPD) and infections are risk factors for venous thromboembolism (VTE), but the reasons behind the associations are not fully known. Few studies have investigated whether lung function and respiratory symptoms in individuals without COPD are associated with VTE. Objectives: To study the incidence of VTE in individuals without COPD and other major VTE risk factors, in relation to baseline lung function and respiratory symptoms, through a 44-year follow-up prospective cohort study. Methods: As part of a health screening program, a total of 20,253 men and 7361 women underwent a baseline examination from 1974 to 1992, including a spirometry test and a self-administered questionnaire about respiratory symptoms, e.g., chronic bronchitis, cough, phlegm, and dyspnoea. Lung function was assessed through quartiles of forced expiratory volume in 1 s/forced vital capacity (FEV1/FVC). Through linkage with national registers, all individuals were followed for incidence of VTE. Results: Respiratory symptoms (cough and dyspnoea) at baseline were associated with an increased risk of incident VTE in women after adjustments for age, height, BMI, smoking status, varicose veins, and FEV1/FVC. The adjusted hazard ratio in relation to chronic bronchitis was 1.57 (95% confidence interval 1.17–2.11). Poor lung function was not associated with an increased risk of VTE after adjustments for potential confounders. Conclusion: Women with respiratory symptoms of cough and dyspnoea without COPD have an increased risk of VTE, independent of lung function and major VTE risk factors. Further studies are needed to confirm the association and to study the clinical applicability of the results. © 2023 The Authors
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| 16. |
- Camsund, Daniel, 1980-, et al.
(författare)
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Time-resolved imaging-based CRISPRi screening
- 2020
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Ingår i: Nature Methods. - : NATURE PUBLISHING GROUP. - 1548-7091 .- 1548-7105. ; 17:1, s. 86-92
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Tidskriftsartikel (refereegranskat)abstract
- DuMPLING (dynamic mu-fluidic microscopy phenotyping of a library before in situ genotyping) enables screening of dynamic phenotypes in strain libraries and was used here to study genes that coordinate replication and cell division in Escherichia coli. Our ability to connect genotypic variation to biologically important phenotypes has been seriously limited by the gap between live-cell microscopy and library-scale genomic engineering. Here, we show how in situ genotyping of a library of strains after time-lapse imaging in a microfluidic device overcomes this problem. We determine how 235 different CRISPR interference knockdowns impact the coordination of the replication and division cycles of Escherichia coli by monitoring the location of replication forks throughout on average >500 cell cycles per knockdown. Subsequent in situ genotyping allows us to map each phenotype distribution to a specific genetic perturbation to determine which genes are important for cell cycle control. The single-cell time-resolved assay allows us to determine the distribution of single-cell growth rates, cell division sizes and replication initiation volumes. The technology presented in this study enables genome-scale screens of most live-cell microscopy assays.
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| 17. |
- Deindl, Sebastian, et al.
(författare)
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More Than Just Letters and Chemistry : Genomics Goes Mechanics
- 2021
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Ingår i: TIBS -Trends in Biochemical Sciences. Regular ed.. - : Elsevier. - 0968-0004 .- 1362-4326. ; 46:6, s. 431-432
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Although ubiquitously thought of as a simple string of letters, DNA exhibits complex physicochemical properties. As a result, DNA can store information beyond the extensively studied explicit genetic message. The mechanical code of DNA has not been studied systematically in a genome-wide context until recent groundbreaking work by Basu et al.
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| 18. |
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| 19. |
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| 20. |
- Ehrenberg, Måns, et al.
(författare)
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Systems Biology is Taking
- 2003
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Ingår i: Genome Research. ; 13, s. 2377-2380
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Tidskriftsartikel (refereegranskat)
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| 21. |
- Ehrenberg, Måns, et al.
(författare)
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Systems Biology: Nobel Symposium 146.
- 2009
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Ingår i: FEBS letters. - : Wiley. - 1873-3468 .- 0014-5793. ; 583:24
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 22. |
- Elf, Anna, et al.
(författare)
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Sveriges friluftskommun 2020
- 2020
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Kommunerna har en nyckelroll i att utveckla friluftslivet och många kommuner arbetar aktivt med friluftslivet till nytta och nöje för befolkningens välbefinnande och naturkontakt. Detta arbete vill vi stimulera. Därför genomför vi undersökningen av kommunernas friluftslivsarbete och delar ut priset till Sveriges friluftskommun.Priset delas ut av Naturvårdsverket i samarbete med Svenskt Friluftsliv och Sveriges Kultur- och Fritidschefers förening. Undersökningen är genomförd de senaste tio åren och vi har jämfört resultaten mellan åren för att kunna se utvecklingen i arbetet. Det är många kommuner som visar stora förbättringar i år och många hamnar högt upp i poänglistan och det är väldigt glädjande. Vår förhoppning är att arbetet med Sveriges friluftskommun ska stimulera än fler att arbeta aktivt och planerat med friluftsliv.
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| 23. |
- Elf, Johan, et al.
(författare)
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Bistable bacterial growth rate in response to antibiotics with low membrane permeability
- 2006
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Ingår i: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 97:25, s. 258104-
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Tidskriftsartikel (refereegranskat)abstract
- We demonstrate that growth rate bistability for bacterial cells growing exponentially at a fixed external antibiotic concentration can emerge when the cell wall permeability for the drug is low and the growth rate sensitivity to the intracellular drug concentration is high. Under such conditions, an initially high growth rate can remain high, due to dilution of the intracellular drug concentration by rapid cell volume increase, while an initially low growth rate can remain low, due to slow cell volume increase and insignificant drug dilution. Our findings have implications for the testing of novel antibiotics on growing bacterial strains.
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| 24. |
- Elf, Johan
(författare)
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Clinical probability assessment and biochemical markers in the diagnosis of deep vein thrombosis
- 2010
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The combination of pre-test clinical probability assessment and D-dimer test is now widely applied in the diagnostic process of DVT. The general objective of the present investigation was to validate these results in a Swedish routine emergency setting were the prevalence of the disease is high and were the clinical probability assessment was handled by many junior physicians. Furthermore, our aims were to evaluate our D-dimer method and to make comparisons with other D-dimer methods as with a new marker of coagulation, the APC-PCI complex. In addition, a cost effectiveness analysis was made of this diagnostic strategy. Material and methods: 357 outpatients with clinical suspicion of DVT were included in the clinical management study. The diagnostic workup included estimation of pre-test probability, D-dimer determination, objective imaging as well as 3 month clinical follow up of negative patients (Paper I). 350 plasma samples from the management study was used for comparison between two well established D-dimer methods and the APC-PCI complex (Paper II) and 311 plasma samples for the evaluation of two new D-dimer methods (Paper III). Direct and indirect costs were calculated for the tested diagnostic strategy and for two hypothetical strategies. A decision analysis was performed (Paper IV). Results and conclusions: One out of 110 patients categorized as having a low clinical probability in combination with a negative D-dimer test was diagnosed with DVT during follow up. About 30% of the patients do not need further investigation for DVT. The APC-PCI complex perform inferior to the D-dimer methods for the exclusion of DVT but slightly superior when indicating its presence. The AxSYM® and Innovance™ D-dimer assays perform well and in good agreement with the two well established assays with NPV´s of > 98% in the low clinical probability estimate (CP). Objective imaging in all patients was the least cost effective (€581) strategy, D-dimer screening of all patients before CP (€421) and CP in combination with D-Dimer testing only in patients with low CP (€406). Conclusion: the investigated diagnostic strategy is safe, result in more convenient and cost-effective care for patients.
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| 25. |
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| 26. |
- Elf, Johan
(författare)
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Direct Measurements of Transcription Factor Binding and Dissociation at Individual Chromosomal Operators
- 2014
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Ingår i: Biophysical Journal. - : Elsevier BV. - 0006-3495 .- 1542-0086. ; 106:2, s. 444A-444A
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- I will discuss some of our recent progress in studying transcription factor kinetics at the level of individual molecules in E. coli. I will in particular describe an assay for measuring the rate of dissociation for a LacI repressor from an individual chromosomal operator site. When combined with the corresponding association rate measurement, the assay allows us to test the commonly used assumption that TF kinetics can be considered to be at equilibrium and that the gene expression is proportional to the time the operator is free .
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| 27. |
- Elf, Johan, et al.
(författare)
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Home treatment of patients with small to medium sized acute pulmonary embolism.
- 2015
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Ingår i: Journal of Thrombosis and Thrombolysis. - : Springer Science and Business Media LLC. - 1573-742X .- 0929-5305. ; 39:2, s. 166-172
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Tidskriftsartikel (refereegranskat)abstract
- Most patients with acute pulmonary embolism (PE) are still treated as inpatients. This is a retrospective cohort study of patients with acute PE, diagnosed using V/P SPECT between 2007 and 2011. Patients were treated at home if they were hemodynamically stable, did not require oxygen or parenteral analgetics, had no contraindications to anticoagulant treatment and V/P SPECT showed an extension of the PE of less than 40 %. The aim of the study was to evaluate the efficacy and safety of home treatment with our algorithm. During the study period 416 outpatients were diagnosed with acute symptomatic PE of whom in total 260 (62.5 %) were discharged home from the emergency unit and another 47 (11 %) within 24 h from admission. During 3 months follow-up one (0.3 %) patient had a recurrent thrombotic event. Eleven (3.6 %) patients had a major or clinically relevant bleed and the overall mortality was 2 % (n = 6). There were no PE-related mortality. Home treatment should be considered and is safe in the majority of hemodynamically stable outpatients with small to medium size PE, quantified using V/P SPECT.
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| 28. |
- Elf, Johan
(författare)
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Hypothesis : Homologous Recombination Depends on Parallel Search
- 2016
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Ingår i: CELL SYSTEMS. - : CELL PRESS. - 2405-4712. ; 3:4, s. 325-327
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Tidskriftsartikel (refereegranskat)abstract
- It is not known how a cell manages to find a specific DNA sequence sufficiently fast to repair a broken chromosome through homologous recombination. I propose a solution based on freely diffusing molecules that are programmed with sequences corresponding to those flanking the break site. In such a process, the target search would be parallelized.
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| 29. |
- Elf, Johan, 1975-
(författare)
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Intracellular Flows and Fluctuations
- 2004
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Mathematical models are now gaining in importance for descriptions of biological processes. In this thesis, such models have been used to identify and analyze principles that govern bacterial protein synthesis under amino acid limitation. New techniques, that are generally applicable for analysis of intrinsic fluctuations in systems of chemical reactions, are also presented. It is shown how multi-substrate reactions, such as protein synthesis, may display zero order kinetics below saturation, because an increase in one substrate pool is compensated by a decrease in another, so that the overall flow is unchanged. Under those conditions, metabolite pools display hyper sensitivity and large fluctuations, unless metabolite synthesis is carefully regulated. It is demonstrated that flow coupling in protein synthesis has consequences for transcriptional control of amino acid biosynthetic operons, accuracy of mRNA translation and the stringent response. Flow coupling also determines the choices of synonymous codons in a number of cases. The reason is that tRNA isoacceptors, cognate to the same amino acid, often read different codons and become deacylated to very different degrees when their amino acid is limiting for protein synthesis. This was demonstrated theoretically and used to successfully predict the choices of control codons in ribosome mediated transcriptional attenuation and codon bias in stress response genes. New tools for the analysis of internal fluctuations have been forged, most importantly, an efficient Monte Carlo algorithm for simulation of the Markov-process corresponding to the reaction-diffusion master equation. The algorithm makes it feasible to analyze stochastic kinetics in spatially extended systems. It was used to demonstrate that bi-stable chemical systems can display spontaneous domain separation also in three spatial dimensions. This analysis reveals geometrical constraints on biochemical memory circuits built from bistable systems. Further, biochemical applications of the Fokker-Planck equation and the Linear Noise Approximation have been explored.
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| 30. |
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| 31. |
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| 32. |
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| 33. |
- Elf, Johan, et al.
(författare)
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Performance of two relatively new quantitative D-dimer assays (Innovance D-dimer and AxSYM D-dimer) for the exclusion of deep vein thrombosis.
- 2009
-
Ingår i: Thrombosis Research. - : Elsevier BV. - 1879-2472 .- 0049-3848. ; 124, s. 701-705
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Tidskriftsartikel (refereegranskat)abstract
- INTRODUCTION: D-dimer assays are now widely used as the first-line test in the diagnostic algorithm of suspected deep vein thrombosis (DVT). The aim of this study was to evaluate the performance of two relatively new quantitative D-Dimer assays (Innovance and AxSYM(R)) by comparison with a clinical gold standard. PATIENTS AND METHODS: 311 samples from outpatients with clinical suspicion of DVT, included in a prospective management study, was analysed (prevalence of DVT 23%). The diagnostic workup included estimation of pre-test probability, D-dimer determination, objective imaging as well as 3 month clinical follow up of negative patients. RESULTS: No significant differences were seen in sensitivity and negative predictive values between Innovance, AxSYM and the reference assays. The area under the ROC curve was slightly lower for the AxSYM assay and the correlation to the reference assays was only moderate (r<0.8) whereas the agreement with the Vidas assay was near excellent (kappa=0.8). The Innovance assay reached the highest AUC, showed a strong correlation with the reference assays (r>/=0.9) and a good agreement with the Vidas assay (kappa=0.76). In combination with a low pre-test probability score the Innovance assay reached a NPV of 100% (95% CI, 92-100) and the AxSYM assay 98% (95% CI, 87-100). CONCLUSION: The Innovance and AxSYM assays show an overall good and comparable performance for the exclusion of DVT when compared to the established assays. Our results for the AxSYM assay indicate that the optimal cut-off value needs to be further evaluated.
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| 34. |
- Elf, Johan, et al.
(författare)
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Probing transcription factor dynamics at the single-molecule level in a living cell.
- 2007
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 316:5828, s. 1191-1194
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Transcription factors regulate gene expression through their binding to DNA. In a living Escherichia coli cell, we directly observed specific binding of a lac repressor, labeled with a fluorescent protein, to a chromosomal lac operator. Using single-molecule detection techniques, we measured the kinetics of binding and dissociation of the repressor in response to metabolic signals. Furthermore, we characterized the nonspecific binding to DNA, one-dimensional (1D) diffusion along DNA segments, and 3D translocation among segments through cytoplasm at the single-molecule level. In searching for the operator, a lac repressor spends ~90% of time nonspecifically bound to and diffusing along DNA with a residence time of <5 milliseconds. The methods and findings can be generalized to other nucleic acid binding proteins.
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| 35. |
- Elf, Johan, et al.
(författare)
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Problems of high dimension in molecular biology
- 2003
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Ingår i: Proc. 19th GAMM Seminar Leipzig on High-dimensional problems. - Leipzig, Germany : Max Planck Institute for Mathematics in the Sciences. ; , s. 21-30
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Konferensbidrag (refereegranskat)
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| 36. |
- Elf, Johan, et al.
(författare)
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Problems of High Dimension in Molecular Biology
- 2004
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- The deterministic reaction rate equations are not an accurate description of many systems in molecular biology where the number of molecules of each species often is small. The master equation of chemical reactions is a more accurate stochastic description suitable for small molecular numbers. A computational difficulty is the high dimensionality of the equation. We describe how it can be solved by first approximating it by the Fokker-Planck equation. Then this equation is discretized in space and time by a finite difference method. The method is compared to a Monte Carlo method by Gillespie. The method is applied to a four-dimensional problem of interest in the regulation of cell processes.
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| 37. |
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| 38. |
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| 39. |
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| 40. |
- Elf, Johan, et al.
(författare)
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Single-Molecule Kinetics in Living Cells
- 2019
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Ingår i: Annual Review of Biochemistry. - : ANNUAL REVIEWS. - 0066-4154 .- 1545-4509. - 9780824308889 ; 88, s. 635-659
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Forskningsöversikt (refereegranskat)abstract
- In the past decades, advances in microscopy have made it possible to study the dynamics of individual biomolecules in vitro and resolve intramolecular kinetics that would otherwise be hidden in ensemble averages. More recently, single-molecule methods have been used to image, localize, and track individually labeled macromolecules in the cytoplasm of living cells, allowing investigations of intermolecular kinetics under physiologically relevant conditions. In this review, we illuminate the particular advantages of single-molecule techniques when studying kinetics in living cells and discuss solutions to specific challenges associated with these methods.
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| 41. |
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| 42. |
- Elf, Johan
(författare)
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Staying Clear of the Dragons
- 2016
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Ingår i: CELL SYSTEMS. - : Elsevier BV. - 2405-4712. ; 2:4, s. 219-220
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Tidskriftsartikel (refereegranskat)
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| 43. |
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| 44. |
- Elf, Johan, et al.
(författare)
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The diagnostic performance of APC-PCI complex determination compared to d-dimer in the diagnosis of deep vein thrombosis
- 2010
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Ingår i: Journal of Thrombosis and Thrombolysis. - : Springer Science and Business Media LLC. - 1573-742X .- 0929-5305. ; 29:4, s. 465-470
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Tidskriftsartikel (refereegranskat)abstract
- d-dimer testing is widely used as part of the diagnostic algorithm for the exclusion of deep vein thrombosis (DVT) but is considered of limited in value for ruling DVT in. Since d-dimers are poorly defined, there is no standardization of the assays and this makes reliable comparisons between clinical studies difficult. We report on a performance evaluation of a new marker of activated coagulation (Activated Protein-C in complex with Protein-C inhibitor, APC-PCI complex) compared to two quantitative d-dimer assays (Vidas(A (R)) d-dimer Exclusion (TM) and Autodimer(A (R))). The post-hoc comparison was made on 350 frozen plasma samples from consecutive outpatients suspected of DVT in a multicenter management study including clinical probability score, d-dimer testing, venous ultrasound and contrast venography as part of the diagnostic algorithm. Results: The APC-PCI complex performed inferior to the d-dimer assays in terms of sensitivity: 74 vs. > 93%, negative predictive value: 91 vs. > 96% and area under the curve: 0.82 vs. 0.9, but showed a significantly higher specificity: 80 vs. 40-60%. Specificity for the APC-PCI complex did not decrease with higher clinical probability score and the positive predictive value was significantly higher than that of the d-dimer assays in the intermediate/high probability cohort (66 vs. < 52%). In this probability cohort, high levels of the APC-PCI complex and to a lesser extent, d-dimers, can give positive predictive values of > 90% in up to 20% of the patients which indicates important clinical implications. However, for the exclusion of DVT at the pre-specified cut-off level, the APC-PCI complex perform inferior to the d-dimer assays in this study.
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| 45. |
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| 46. |
- Elf, Marie, 1962-, et al.
(författare)
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The Swedish version of the Normalization Process Theory Measure S-NoMAD : translation, adaptation, and pilot testing
- 2018
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Ingår i: Implementation Science. - : Springer. - 1748-5908. ; 13:1
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundThe original British instrument the Normalization Process Theory Measure (NoMAD) is based on the four core constructs of the Normalization Process Theory: Coherence, Cognitive Participation, Collective Action, and Reflexive Monitoring. They represent ways of thinking about implementation and are focused on how interventions can become part of everyday practice.AimTo translate and adapt the original NoMAD into the Swedish version S-NoMAD and to evaluate its psychometric properties based on a pilot test in a health care context including in-hospital, primary, and community care contexts.MethodsA systematic approach with a four-step process was utilized, including forward and backward translation and expert reviews for the test and improvement of content validity of the S-NoMAD in different stages of development. The final S-NoMAD version was then used for process evaluation in a pilot study aimed at the implementation of a new working method for individualized care planning. The pilot was executed in two hospitals, four health care centres, and two municipalities in a region in northern Sweden. The S-NoMAD pilot results were analysed for validity using confirmatory factor analysis, i.e. a one-factor model fitted for each of the four constructs of the S-NoMAD. Cronbach’s alpha was used to ascertain the internal consistency reliability.ResultsIn the pilot, S-NoMAD data were collected from 144 individuals who were different health care professionals or managers. The initial factor analysis model showed good fit for two of the constructs (Coherence and Cognitive Participation) and unsatisfactory fit for the remaining two (Collective Action and Reflexive Monitoring) based on three items. Deleting those items from the model yielded a good fit and good internal consistency (alphas between 0.78 and 0.83). However, the estimation of correlations between the factors showed that the factor Reflexive Monitoring was highly correlated (around 0.9) with the factors Coherence and Collective Action.ConclusionsThe results show initial satisfactory psychometric properties for the translation and first validation of the S-NoMAD. However, development of a highly valid and reliable instrument is an iterative process, requiring more extensive validation in various settings and populations. Thus, in order to establish the validity and reliability of the S-NoMAD, additional psychometric testing is needed.
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| 47. |
- Elf, Mikael, 1959, et al.
(författare)
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Young carers as co-designers of a web-based support system - the views of two publics.
- 2011
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Ingår i: Advances in Health Care Sciences Conference, Oct 18-19 2011, Karolinska Institutet, Stockholm.
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Konferensbidrag (refereegranskat)abstract
- Aims: The aims of the study was to reveal young carers views of design of a web-base support system directed to them and to reveal differences between their views and the views of project representatives, in a participatory design process. Methods: Eight young people, 17-24, close to and supporting someone with mental illness were involved in either a work or a test group. The work group participated in video recorded design meetings with representatives of the project. Content analysis and Dewey's concept of public were applied on the data. The test group worked from their homes and data were collected via test forms. Data from the test group coherent to the content of the design meetings were added as supplement. Results: Four resulting themes were revealed, constituting key-parts in the design of the WBSS: Communicating the message, ideational working principles, considerations on user interaction, and user interface. Furthermore decisive differences between the views of participants and project representatives were found. Participants view of the user was a person that had a usefulness perspective and the object for support was primarily the person with mental illness. The project representatives' view of the user was a person that had a short- and long-term self-care perspective and the object of support was primarily him-/herself. Conclusion: The design of a WBSS for young carers should consider four key-parts, but early user involvement and critical reflection in the PD process itself may be crucial to discern differences between designers and user, not the least when their different publics overlap.
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| 48. |
- Elf, Mikael, 1959, et al.
(författare)
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Young carers as co-designers of a web-based support system - the views of two publics
- 2012
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Ingår i: Informatics for Health and Social Care. - : Informa UK Limited. - 1753-8157 .- 1753-8165. ; 37:4, s. 203-216
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Tidskriftsartikel (refereegranskat)abstract
- Aim: The aim of the study was to reveal young carers’ views of design of a web-based support system (WBSS) directed to them and the differences between their views and the views of project representatives (PRs), in a participatory design process. Methods: Eight young people, 17–24 years, were involved in either a work or a test group. The work group participated in video-recorded design meetings with representatives of the project. Content analysis and Dewey’s concept of public were applied on the data. The test group worked from their homes and data were collected via test forms and used as supplemental data. Results: Four themes were revealed, constituting key parts in the design of the WBSS: Communicating the message, Ideational working principles, User interaction and User interface. Furthermore, decisive differences between the views of participants and PRs were found. Conclusion: The four key parts should be considered in a WBSS directed to young carers. The study also suggests that early user involvement and critical reflection in the design process itself may be crucial to discern differences in perspective between designers and users.
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| 49. |
- English, Brian P., et al.
(författare)
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Single-molecule investigations of the stringent response machinery in living bacterial cells
- 2011
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 108:31, s. E365-E373
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Tidskriftsartikel (refereegranskat)abstract
- The RelA-mediated stringent response is at the heart of bacterial adaptation to starvation and stress, playing a major role in the bacterial cell cycle and virulence. RelA integrates several environmental cues and synthesizes the alarmone ppGpp, which globally reprograms transcription, translation, and replication. We have developed and implemented novel single-molecule tracking methodology to characterize the intracellular catalytic cycle of RelA. Our single-molecule experiments show that RelA is on the ribosome under nonstarved conditions and that the individual enzyme molecule stays off the ribosome for an extended period of time after activation. This suggests that the catalytically active part of the RelA cycle is performed off, rather than on, the ribosome, and that rebinding to the ribosome is not necessary to trigger each ppGpp synthesis event. Furthermore, we find fast activation of RelA in response to heat stress followed by RelA rapidly being reset to its inactive state, which makes the system sensitive to new environmental cues and hints at an underlying excitable response mechanism.
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| 50. |
- Fange, David, et al.
(författare)
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MesoRD 1.0 : Stochastic reaction-diffusion simulations in the microscopic limit
- 2012
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Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811 .- 1460-2059. ; 28:23, s. 3155-3157
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Tidskriftsartikel (refereegranskat)abstract
- MesoRD is a tool for simulating stochastic reaction-diffusion systems as modeled by the reaction diffusion master equation. The simulated systems are defined in the Systems Biology Markup Language with additions to define compartment geometries. MesoRD 1.0 supports scale-dependent reaction rate constants and reactions between reactants in neighbouring subvolumes. These new features make it possible to construct physically consistent models of diffusion-controlled reactions also at fine spatial discretization.
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