| 31. |
- Deng, Mingtang, et al.
(author)
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Parity independence of the zero-bias conductance peak in a nanowire based topological superconductor-quantum dot hybrid device.
- 2014
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In: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 4
-
Journal article (peer-reviewed)abstract
- We explore the signatures of Majorana fermions in a nanowire based topological superconductor-quantum dot-topological superconductor hybrid device by charge transport measurements. At zero magnetic field, well-defined Coulomb diamonds and the Kondo effect are observed. Under the application of a finite, sufficiently strong magnetic field, a zero-bias conductance peak structure is observed. It is found that the zero-bias conductance peak is present in many consecutive Coulomb diamonds, irrespective of the even-odd parity of the quasi-particle occupation number in the quantum dot. In addition, we find that the zero-bias conductance peak is in most cases accompanied by two differential conductance peaks, forming a triple-peak structure, and the separation between the two side peaks in bias voltage shows oscillations closely correlated to the background Coulomb conductance oscillations of the device. The observed zero-bias conductance peak and the associated triple-peak structure are in line with Majorana fermion physics in such a hybrid topological system.
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| 32. |
- Dogan, Jakob, et al.
(author)
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The transition state structure for coupled binding and folding of disordered protein domains
- 2013
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In: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 3, s. 2076-
-
Journal article (peer-reviewed)abstract
- Intrinsically disordered proteins are abundant in the eukaryotic proteome, and they are implicated in a range of different diseases. However, there is a paucity of experimental data on molecular details of the coupled binding and folding of such proteins. Two interacting and relatively well studied disordered protein domains are the activation domain from the p160 transcriptional co-activator ACTR and the nuclear co-activator binding domain (NCBD) of CREB binding protein. We have analyzed the transition state for their coupled binding and folding by protein engineering and kinetic experiments (Phi-value analysis) and found that it involves weak native interactions between the N-terminal helices of ACTR and NCBD, but is otherwise "disordered-like". Most native hydrophobic interactions in the interface between the two domains form later, after the rate-limiting barrier for association. Linear free energy relationships suggest a cooperative formation of native interactions, reminiscent of the nucleation-condensation mechanism in protein folding.
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| 33. |
- Domkin, Vladimir, et al.
(author)
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Phosphines are ribonucleotide reductase reductants that act via C-terminal cysteines similar to thioredoxins and glutaredoxins
- 2014
-
In: Scientific Reports. - : Macmillan Publishers Ltd.. - 2045-2322. ; 4, s. 5539-
-
Journal article (peer-reviewed)abstract
- Ribonucleotide reductases (RNRs) catalyze the formation of 2'-deoxyribonucleotides. Each polypeptide of the large subunit of eukaryotic RNRs contains two redox-active cysteine pairs, one in the active site and the other at the C-terminus. In each catalytic cycle, the active-site disulfide is reduced by the C-terminal cysteine pair, which in turn is reduced by thioredoxins or glutaredoxins. Dithiols such as DTT are used in RNR studies instead of the thioredoxin or glutaredoxin systems. DTT can directly reduce the disulfide in the active site and does not require the C-terminal cysteines for RNR activity. Here we demonstrate that the phosphines tris(2-carboxyethyl)phosphine (TCEP) and tris(3-hydroxypropyl)phosphine (THP) are efficient non-thiol RNR reductants, but in contrast to the dithiols DTT, bis(2-mercaptoethyl)sulfone (BMS), and (S)-(1,4-dithiobutyl)-2-amine (DTBA) they act specifically via the C-terminal disulfide in a manner similar to thioredoxin and glutaredoxin. The simultaneous use of phosphines and dithiols results in ~3-fold higher activity compared to what is achieved when either type of reductant is used alone. This surprising effect can be explained by the concerted action of dithiols on the active-site cysteines and phosphines on the C-terminal cysteines. As non-thiol and non-protein reductants, phosphines can be used to differentiate between the redox-active cysteine pairs in RNRs.
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| 34. |
- Edman Jönsson, Gustav, 1983, et al.
(author)
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Nanoplasmon-enabled macroscopic thermal management
- 2014
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In: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322 .- 2045-2322. ; 4, s. 5111-
-
Journal article (peer-reviewed)abstract
- In numerous applications of energy harvesting via transformation of light into heat the focus recently shifted towards highly absorptive nanoplasmonic materials. It is currently established that noble metals-based absorptive plasmonic platforms deliver significant light-capturing capability and can be viewed as super-absorbers of optical radiation. Naturally, approaches to the direct experimental probing of macroscopic temperature increase resulting from these absorbers are welcomed. Here we derive a general quantitative method of characterizing heat-generating properties of optically absorptive layers via macroscopic thermal imaging. We further monitor macroscopic areas that are homogeneously heated by several degrees with nanostructures that occupy a mere 8% of the surface, leaving it essentially transparent and evidencing significant heat generation capability of nanoplasmon-enabled light capture. This has a direct bearing to a large number of applications where thermal management is crucial.
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| 35. |
- Etcheverry, Sebastian, et al.
(author)
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Quantum key distribution session with 16-dimensional photonic states
- 2013
-
In: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; :3, s. 2316-
-
Journal article (peer-reviewed)abstract
- The secure transfer of information is an important problem in modern telecommunications. Quantum key distribution (QKD) provides a solution to this problem by using individual quantum systems to generate correlated bits between remote parties, that can be used to extract a secret key. QKD with D-dimensional quantum channels provides security advantages that grow with increasing D. However, the vast majority of QKD implementations has been restricted to two dimensions. Here we demonstrate the feasibility of using higher dimensions for real-world quantum cryptography by performing, for the first time, a fully automated QKD session based on the BB84 protocol with 16-dimensional quantum states. Information is encoded in the single-photon transverse momentum and the required states are dynamically generated with programmable spatial light modulators. Our setup paves the way for future developments in the field of experimental high-dimensional QKD.
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| 36. |
- Feizi, Amir, 1980, et al.
(author)
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Metabolic and protein interaction sub-networks controlling the proliferation rate of cancer cells and their impact on patient survival
- 2013
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In: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322 .- 2045-2322. ; 3
-
Journal article (peer-reviewed)abstract
- Cancer cells can have a broad scope of proliferation rates. Here we aim to identify the molecular mechanisms that allow some cancer cell lines to grow up to 4 times faster than other cell lines. The correlation of gene expression profiles with the growth rate in 60 different cell lines has been analyzed using several genome- scale biological networks and new algorithms. New possible regulatory feedback loops have been suggested and the known roles of several cell cycle related transcription factors have been confirmed. Over 100 growth- correlated metabolic sub-networks have been identified, suggesting a key role of simultaneous lipid synthesis and degradation in the energy supply of the cancer cells growth. Many metabolic sub-networks involved in cell line proliferation appeared also to correlate negatively with the survival expectancy of colon cancer patients.
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| 37. |
- Fitzer, Susan C., et al.
(author)
-
Ocean acidification impacts mussel control on biomineralisation
- 2014
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In: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 4
-
Journal article (peer-reviewed)abstract
- Ocean acidification is altering the oceanic carbonate saturation state and threatening the survival of marine calcifying organisms. Production of their calcium carbonate exoskeletons is dependent not only on the environmental seawater carbonate chemistry but also the ability to produce biominerals through proteins. We present shell growth and structural responses by the economically important marine calcifier Mytilus edulis to ocean acidification scenarios (380, 550, 750, 1000 mu atm pCO(2)). After six months of incubation at 750 matm pCO(2), reduced carbonic anhydrase protein activity and shell growth occurs in M. edulis. Beyond that, at 1000 matm pCO(2), biomineralisation continued but with compensated metabolism of proteins and increased calcite growth. Mussel growth occurs at a cost to the structural integrity of the shell due to structural disorientation of calcite crystals. This loss of structural integrity could impact mussel shell strength and reduce protection from predators and changing environments.
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| 38. |
- Fleetwood, Filippa, et al.
(author)
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Simultaneous targeting of two ligand-binding sites on VEGFR2 using biparatopic Affibody molecules results in dramatically improved affinity
- 2014
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In: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 4, s. 7518-
-
Journal article (peer-reviewed)abstract
- Angiogenesis plays an important role in cancer and ophthalmic disorders such as age-related macular degeneration and diabetic retinopathy. The vascular endothelial growth factor (VEGF) family and corresponding receptors are regulators of angiogenesis and have been much investigated as therapeutic targets. The aim of this work was to generate antagonistic VEGFR2-specific affinity proteins having adjustable pharmacokinetic properties allowing for either therapy or molecular imaging. Two antagonistic Affibody molecules that were cross-reactive for human and murine VEGFR2 were selected by phage and bacterial display. Surprisingly, although both binders independently blocked VEGF-A binding, competition assays revealed interaction with non-overlapping epitopes on the receptor. Biparatopic molecules, comprising the two Affibody domains, were hence engineered to potentially increase affinity even further through avidity. Moreover, an albumin-binding domain was included for half-life extension in future in vivo experiments. The best-performing of the biparatopic constructs demonstrated up to 180-fold slower dissociation than the monomers. The new Affibody constructs were also able to specifically target VEGFR2 on human cells, while simultaneously binding to albumin, as well as inhibit VEGF-induced signaling. In summary, we have generated small antagonistic biparatopic Affibody molecules with high affinity for VEGFR2, which have potential for both future therapeutic and diagnostic purposes in angiogenesis-related diseases.
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| 39. |
- Fors, Yvonne, 1975, et al.
(author)
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Sulfur and iron accumulation in three marine-archaeological shipwrecks in the Baltic Sea. The Ghost, the Crown and the Sword.
- 2014
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In: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 4
-
Journal article (peer-reviewed)abstract
- Sulfur and iron concentrations in wood from three 17th century shipwrecks in the Baltic Sea, the Ghost wreck, the Crown and the Sword, were obtained by X-ray fluorescence (XRF) scanning. In near anaerobic environments symbiotic microorganisms degrade waterlogged wood, reduce sulfate and promote accumulation of low-valent sulfur compounds, as previously found for the famous wrecks of the Vasa and Mary Rose. Sulfur K-edge X-ray absorption near-edge structure (XANES) analyses of Ghost wreck wood show that organic thiols and disulfides dominate, together with elemental sulfur probably generated by sulfur-oxidizing Beggiatoa bacteria. Iron sulfides were not detected, consistent with the relatively low iron concentration in the wood. In a museum climate with high atmospheric humidity oxidation processes, especially of iron sulfides formed in the presence of corroding iron, may induce post-conservation wood degradation. Subject to more general confirmation by further analyses no severe conservation concerns are expected for the Ghost wreck wood.
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| 40. |
- Freedman, Kevin J., et al.
(author)
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Single molecule unfolding and stretching of protein domains inside a solid-state nanopore by electric field
- 2013
-
In: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 3, s. 1638-
-
Journal article (peer-reviewed)abstract
- Single molecule methods have provided a significantly new look at the behavior of biomolecules in both equilibrium and non-equilibrium conditions. Most notable are the stretching experiments performed by atomic force microscopes and laser tweezers. Here we present an alternative single molecule method that can unfold a protein domain, observed at electric fields greater than 106 V/m, and is fully controllable by the application of increasing voltages across the membrane of the pore. Furthermore this unfolding mechanism is characterized by measuring both the residence time of the protein within the nanopore and the current blockade. The unfolding data supports a gradual unfolding mechanism rather than the cooperative transition observed by classical urea denaturation experiments. Lastly it is shown that the voltage-mediated unfolding is a function of the stability of the protein by comparing two mutationally destabilized variants of the protein.
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