| 1. |
- Alizadehheidari, Mohammadreza, 1987, et al.
(författare)
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Nanoconfined Circular and Linear DNA: Equilibrium Conformations and Unfolding Kinetics
- 2015
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Ingår i: Macromolecules. - : American Chemical Society (ACS). - 0024-9297 .- 1520-5835. ; 48:3, s. 871-878
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Tidskriftsartikel (refereegranskat)abstract
- Studies of circular DNA confined to nanofluidic channels are relevant both from a fundamental polymer-physics perspective and due to the importance of circular DNA molecules in vivo. We here observe the unfolding of confined DNA from the circular to linear configuration as a light-induced double-strand break occurs, characterize the dynamics, and compare the equilibrium conformational statistics of linear and circular configurations. This is important because it allows us to determine to what extent existing statistical theories describe the extension of confined circular DNA. We find that the ratio of the extensions of confined linear and circular DNA configurations increases as the buffer concentration decreases. The experimental results fall between theoretical predictions for the extended de Gennes regime at weaker confinement and the Odijk regime at stronger confinement. We show that it is possible to directly distinguish between circular and linear DNA molecules by measuring the emission intensity from the DNA. Finally, we determine the rate of unfolding and show that this rate is larger for more confined DNA, possibly reflecting the corresponding larger difference in entropy between the circular and linear configurations.
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| 2. |
- Alizadehheidari, Mohammadreza, et al.
(författare)
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Nanoconfined Circular DNA
- 2014
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Ingår i: Biophysical Journal. - : Elsevier BV. - 0006-3495 .- 1542-0086. ; 106:2, s. 274A-274A
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Nanofluidic channels have become a versatile tool to manipulate single DNA molecules. They allow investigation of confined single DNA molecules from a fundamental polymer physics perspective as well as for example in DNA barcoding techniques.
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| 3. |
- Alizadehheidari, Mohammadreza, 1987, et al.
(författare)
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Unfolding of nanoconfined circular DNA
- 2015
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Ingår i: BIOPHYSICAL JOURNAL. - : Elsevier BV. - 0006-3495 .- 1542-0086. ; 108:2 Supplement 1
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 4. |
- Edlund, Karolina, et al.
(författare)
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CD99 is a novel prognostic stromal marker in non-small cell lung cancer
- 2012
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Ingår i: International Journal of Cancer. - : Wiley. - 0020-7136 .- 1097-0215. ; 131:10, s. 2264-2273
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Tidskriftsartikel (refereegranskat)abstract
- The complex interaction between cancer cells and the microenvironment plays an essential role in all stages of tumourigenesis. Despite the significance of this interplay, alterations in protein composition underlying tumourstroma interactions are largely unknown. The aim of this study was to identify stromal proteins with clinical relevance in non-small cell lung cancer (NSCLC). A list encompassing 203 stromal candidate genes was compiled based on gene expression array data and available literature. The protein expression of these genes in human NSCLC was screened using the Human Protein Atlas. Twelve proteins were selected that showed a differential stromal staining pattern (BGN, CD99, DCN, EMILIN1, FBN1, PDGFRB, PDLIM5, POSTN, SPARC, TAGLN, TNC and VCAN). The corresponding antibodies were applied on tissue microarrays, including 190 NSCLC samples, and stromal staining was correlated with clinical parameters. Higher stromal expression of CD99 was associated with better prognosis in the univariate (p = 0.037) and multivariate (p = 0.039) analysis. The association was independent from the proportion of tumour stroma, the fraction of inflammatory cells and clinical and pathological parameters like stage, performance status and tumour histology. The prognostic impact of stromal CD99 protein expression was confirmed in an independent cohort of 240 NSCLC patients (p = 0.008). Furthermore, double-staining confocal fluorescence microscopy showed that CD99 was expressed in stromal lymphocytes as well as in cancer-associated fibroblasts. Based on a comprehensive screening strategy the membrane protein CD99 was identified as a novel stromal factor with clinical relevance. The results support the concept that stromal properties have an important impact on tumour progression.
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| 5. |
- Nyberg, Harald, et al.
(författare)
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Extreme friction reductions during inital running-in of W-S-C-Ti low-friction coatings
- 2013
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Ingår i: Wear. - : Elsevier. - 0043-1648 .- 1873-2577. ; 302:1-2 SI, s. 987-997
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Tidskriftsartikel (refereegranskat)abstract
- The disulphides of tungsten and molybdenum are known for their low friction properties when used as solid lubricants. Due to their low hardness, their load bearing capacity when used as thin films is poor. When carbon is added to a WS2 coating, both of these shortcomings are improved, and a structure consisting of nanocrystals of WS2, and possibly tungsten carbide, in a matrix of amorphous carbon is formed. In this study, an attempt is made for further increasing the hardness of such coatings, by addition of Ti, a strong carbide former. A number of W–S–C(–Ti) coatings were deposited using magnetron co-sputtering, and characterised with regard to chemical composition, structure and tribological properties. It was seen that addition of Ti significantly increased the hardness of the coatings, while maintaining their excellent low friction properties in dry atmosphere. However, the coatings with Ti showed extremely high initial friction, a feature not seen for the coatings without Ti. The mechanisms behind this running-in behaviour were investigated by studying surfaces at early stages of wear. It was observed that tribofilms formed during sliding for the coatings containing Ti consisted mainly of TiO2, with platelets of WS2 appearing in the contact only after prolonged sliding. For the pure W–S–C coatings, WS2 was observed in the sliding interface almost instantly at the onset of sliding.
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| 6. |
- Nyberg, Lena, 1979, et al.
(författare)
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A single-step competitive binding assay for mapping of single DNA molecules
- 2012
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Ingår i: Biochemical and Biophysical Research Communications - BBRC. - : Elsevier BV. - 0006-291X .- 1090-2104. ; 417:1, s. 404-408
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Tidskriftsartikel (refereegranskat)abstract
- Optical mapping of genomic DNA is of relevance for a plethora of applications such as scaffolding for sequencing and detection of structural variations as well as identification cif pathogens like bacteria and viruses. For future clinical applications it is desirable to have a fast and robust mapping method based on as few steps as possible. We here demonstrate a single-step method to obtain a DNA barcode that is directly visualized using nanofluidic devices and fluorescence microscopy. Using a mixture of YOYO-1, a bright DNA dye, and netropsin, a natural antibiotic with very high AT specificity, we obtain a DNA map with a fluorescence intensity profile along the DNA that reflects the underlying sequence. The netropsin binds to AT-tetrads and blocks these binding sites from YOYO-1 binding which results in lower fluorescence intensity from AT-rich regions of the DNA. We thus obtain a DNA barcode that is dark in AT-rich regions and bright in GC-rich regions with kilobasepair resolution. We demonstrate the versatility of the method by obtaining a barcode on DNA from the phage T4 that captures its circular permutation and agrees well with its known sequence.
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| 7. |
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| 8. |
- Nyberg, Lena, 1979, et al.
(författare)
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Heterogeneous staining: a tool for studies of how fluorescent dyes affect the physical properties of DNA
- 2013
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Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 41:19, s. articlenr e184-
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Tidskriftsartikel (refereegranskat)abstract
- The commonly used fluorescent dye YOYO-1 (YOYO) has, using bulk techniques, been demonstrated to stain DNA heterogeneously at substoichiometric concentrations. We here, using nanofluidic channels and fluorescence microscopy, investigate the heterogeneous staining on the single DNA molecule level and demonstrate that the dye distribution is continuous. The equilibration of YOYO on DNA is extremely slow but can be accelerated by increasing the ionic strength and/or the temperature. Furthermore, we demonstrate how to use the heterogeneous staining as a tool for detailed and time-efficient studies of how fluorescent dyes affect the physical properties of DNA. We show that the relative increase in extension of DNA with increasing amount of YOYO bound is higher at low ionic strengths and also extrapolate the extension of native DNA. Our study reveals important information on how YOYO affects the physical properties of DNA, but it also has broader applications. First, it reveals how cationic intercalators, such as potential DNA drugs, affect DNA under strong confinement. Second, the strategy of using heterogeneous staining is of general use for single molecule studies of DNA interacting with proteins or ligands.
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| 9. |
- Sundberg, Jill, et al.
(författare)
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Influence of Ti addition on the structure and properties of low-friction W–S–C coatings
- 2013
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Ingår i: Surface & Coatings Technology. - : Elsevier. - 0257-8972 .- 1879-3347. ; 232, s. 340-348
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Tidskriftsartikel (refereegranskat)abstract
- Transition metal dichalcogenides, such as WS2 and MoS2, are known for their layered structure and lubricating properties. When deposited as thin coatings, however, their use as solid lubricants is limited by their low hardness and load-bearing capacity. The addition of another element, such as carbon, can improve the mechanical properties, although the hardness of for example W-S-C coatings is still rather low. In this work, Ti has been added to W-S-C coatings in order to further increase the hardness by carbide formation. W-S-C and W-S-C-Ti coatings were deposited by non-reactive magnetron sputtering, and characterized with regard to composition, structure and mechanical and tribological properties. It was found that the addition of Ti leads to the formation of a new carbide phase, and a significant increase in hardness for coatings with moderate carbon contents. The friction properties of W-S-C-Ti coatings were found to be comparable to that of W-S-C coatings, with friction coefficients down to mu approximate to 0.02 and similar wear rates against steel in a dry atmosphere. Formation of WS2 in the wear track of W-S-C-Ti was confirmed by transmission electron microscopy. It has thus been shown that the addition of Ti to W-S-C coatings can increase the hardness, while still maintaining WS2 lubrication.
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| 10. |
- Ahlberg, Patrik, et al.
(författare)
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Defect formation in graphene during low-energy ion bombardment
- 2016
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Ingår i: APL Materials. - : AIP Publishing. - 2166-532X. ; 4:4
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Tidskriftsartikel (refereegranskat)abstract
- This letter reports on a systematic investigation of sputter induced damage in graphene caused by low energy Ar+ ion bombardment. The integral numbers of ions per area (dose) as well as their energies are varied in the range of a few eV's up to 200 eV. The defects in the graphene are correlated to the dose/energy and different mechanisms for the defect formation are presented. The energetic bombardment associated with the conventional sputter deposition process is typically in the investigated energy range. However, during sputter deposition on graphene, the energetic particle bombardment potentially disrupts the crystallinity and consequently deteriorates its properties. One purpose with the present study is therefore to demonstrate the limits and possibilities with sputter deposition of thin films on graphene and to identify energy levels necessary to obtain defect free graphene during the sputter deposition process. Another purpose is to disclose the fundamental mechanisms responsible for defect formation in graphene for the studied energy range.
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