| 1. |
- Ameur, Adam, et al.
(author)
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Comprehensive profiling of the vaginal microbiome in HIV positive women using massive parallel semiconductor sequencing
- 2014
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In: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 4, s. 4398-
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Journal article (peer-reviewed)abstract
- Infections by HIV increase the risk of acquiring secondary viral and bacterial infections and methods are needed to determine the spectrum of co-infections for proper treatment. We used rolling circle amplification (RCA) and Ion Proton sequencing to investigate the vaginal microbiome of 20 HIV positive women from South Africa. A total of 46 different human papillomavirus (HPV) types were found, many of which are not detected by existing genotyping assays. Moreover, the complete genomes of two novel HPV types were determined. Abundance of HPV infections was highly correlated with real-time PCR estimates, indicating that the RCA-Proton method can be used for quantification of individual pathogens. We also identified a large number of other viral, bacterial and parasitic co-infections and the spectrum of these co-infections varied widely between individuals. Our method provides rapid detection of a broad range of pathogens and the ability to reconstruct complete genomes of novel infectious agents.
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| 2. |
- Andersson, Richard L., et al.
(author)
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Micromechanics of ultra-toughened electrospun PMMA/PEO fibres as revealed by in-situ tensile testing in an electron microscope
- 2014
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In: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 4, s. 6335-
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Journal article (peer-reviewed)abstract
- A missing cornerstone in the development of tough micro/nano fibre systems is an understanding of the fibre failure mechanisms, which stems from the limitation in observing the fracture of objects with dimensions one hundredth of the width of a hair strand. Tensile testing in the electron microscope is herein adopted to reveal the fracture behaviour of a novel type of toughened electrospun poly(methyl methacrylate)/poly(ethylene oxide) fibre mats for biomedical applications. These fibres showed a toughness more than two orders of magnitude greater than that of pristine PMMA fibres. The in-situ microscopy revealed that the toughness were not only dependent on the initial molecular alignment after spinning, but also on the polymer formulation that could promote further molecular orientation during the formation of micro/nano-necking. The true fibre strength was greater than 150 MPa, which was considerably higher than that of the unmodified PMMA (17 MPa). This necking phenomenon was prohibited by high aspect ratio cellulose nanocrystal fillers in the ultra-tough fibres, leading to a decrease in toughness by more than one order of magnitude. The reported necking mechanism may have broad implications also within more traditional melt-spinning research.
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| 3. |
- Araujo, Carlos Moyses, et al.
(author)
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Disorder-induced Room Temperature Ferromagnetism in Glassy Chromites
- 2014
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In: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 4, s. 4686-
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Journal article (peer-reviewed)abstract
- We report an unusual robust ferromagnetic order above room temperature upon amorphization of perovskite [YCrO3] in pulsed laser deposited thin films. This is contrary to the usual expected formation of a spin glass magnetic state in the resulting disordered structure. To understand the underlying physics of this phenomenon, we combine advanced spectroscopic techniques and first-principles calculations. We find that the observed order-disorder transformation is accompanied by an insulator-metal transition arising from a wide distribution of Cr-O-Cr bond angles and the consequent metallization through free carriers. Similar results also found in YbCrO3-films suggest that the observed phenomenon is more general and should, in principle, apply to a wider range of oxide systems. The ability to tailor ferromagnetic order above room temperature in oxide materials opens up many possibilities for novel technological applications of this counter intuitive effect.
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| 4. |
- Babazadeh, Roja, et al.
(author)
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Rewiring yeast osmostress signalling through the MAPK network reveals essential and non-essential roles of Hog1 in osmoadaptation
- 2014
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In: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 4
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Journal article (peer-reviewed)abstract
- Mitogen-activated protein kinases (MAPKs) have a number of targets which they regulate at transcriptional and post-translational levels to mediate specific responses. The yeast Hog1 MAPK is essential for cell survival under hyperosmotic conditions and it plays multiple roles in gene expression, metabolic regulation, signal fidelity and cell cycle regulation. Here we describe essential and non-essential roles of Hog1 using engineered yeast cells in which osmoadaptation was reconstituted in a Hog1-independent manner. We rewired Hog1-dependent osmotic stress-induced gene expression under the control of Fus3/Kss1 MAPKs, which are activated upon osmostress via crosstalk in hog1Δ cells. This approach revealed that osmotic up-regulation of only two Hog1-dependent glycerol biosynthesis genes, GPD1 and GPP2, is sufficient for successful osmoadaptation. Moreover, some of the previously described Hog1-dependent mechanisms appeared to be dispensable for osmoadaptation in the engineered cells. These results suggest that the number of essential MAPK functions may be significantly smaller than anticipated and that knockout approaches may lead to over-interpretation of phenotypic data.
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| 5. |
- Björkman, Camilla
(author)
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Cryptosporidium parvum IId family: clonal population and dispersal from Western Asia to other geographical regions
- 2014
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In: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 4
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Journal article (peer-reviewed)abstract
- In this study, 111 Cryptosporidium parvum IId isolates from several species of animals in China, Sweden, and Egypt were subtyped by multilocus sequence typing (MLST). One to eleven subtypes were detected at each of the 12 microsatellite, minisatellite, and single nucleotide polymorphism (SNP) loci, forming 25 MLST subtypes. Host-adaptation and significant geographical segregation were both observed in the MLST subtypes. A clonal population structure was seen in C. parvum IId isolates from China and Sweden. Three ancestral lineages and the same RPGR sequence were shared by these isolates examined. Therefore, the present genetic observations including the higher nucleotide diversity of C. parvum IId GP60 sequences in Western Asia, as well as the unique distribution of IId subtypes (almost exclusively found in Asia, Europe, and Egypt) and in combination with the domestication history of cattle, sheep, and goats, indicated that C. parvum IId subtypes were probably dispersed from Western Asia to other geographical regions. More population genetic structure studies involving various C. parvum subtype families using high-resolution tools are needed to better elucidate the origin and dissemination of C. parvum in the world.
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| 6. |
- Boratynski, Zbyszek, et al.
(author)
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Increased radiation from Chernobyl decreases the expression of red colouration in natural populations of bank voles (Myodes glareolus)
- 2014
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In: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 4, s. 7141-
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Journal article (peer-reviewed)abstract
- Pheomelanin is a pink to red version of melanin pigment deposited in skin and hair. Due to its bright colour, pheomelanin plays a crucial function in signalling, in particular sexual signalling. However, production of pheomelanin, as opposed to its dark alternative, eumelanin, bears costs in terms of consumption of antioxidants important for protection of DNA against naturally produced reactive oxidative species. Therefore, decreased expression of pheomelanin is expected in organisms exposed to severe oxidative stress such as that caused by exposure to chronic ionizing radiation. We tested if variable exposure to radiation among natural populations of bank voles Myodes glareolus in Chernobyl affected expression of red colouration in their dorsal fur. The relative redness of dorsal fur was positively correlated with weight, but also negatively correlated with the level of background radiation. These results suggest that the development of the natural red colouration in adult bank voles is affected by ionizing background radiation, and potentially causing elevated levels of oxidative stress. Reduced production of pheomelanin allows more antioxidants to mitigate the oxidative stress caused by radiation. However, changing natural animal colouration for physiological reasons can have ecological costs, if e.g. it causes mismatch with habitat colouration and conspicuousness for predators.
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| 7. |
- Bzhalava, Davit, et al.
(author)
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Deep sequencing extends the diversity of human papillomaviruses in human skin.
- 2014
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In: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 4:Jul 24
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Journal article (peer-reviewed)abstract
- Most viruses in human skin are known to be human papillomaviruses (HPVs). Previous sequencing of skin samples has identified 273 different cutaneous HPV types, including 47 previously unknown types. In the present study, we wished to extend prior studies using deeper sequencing. This deeper sequencing without prior PCR of a pool of 142 whole genome amplified skin lesions identified 23 known HPV types, 3 novel putative HPV types and 4 non-HPV viruses. The complete sequence was obtained for one of the known putative types and almost the complete sequence was obtained for one of the novel putative types. In addition, sequencing of amplimers from HPV consensus PCR of 326 skin lesions detected 385 different HPV types, including 226 previously unknown putative types. In conclusion, metagenomic deep sequencing of human skin samples identified no less than 396 different HPV types in human skin, out of which 229 putative HPV types were previously unknown.
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| 8. |
- Claes, Julien M, et al.
(author)
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Iso-luminance counterillumination drove bioluminescent shark radiation.
- 2014
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In: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 4
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Journal article (peer-reviewed)abstract
- Counterilluminating animals use ventral photogenic organs (photophores) to mimic the residual downwelling light and cloak their silhouette from upward-looking predators. To cope with variable conditions of pelagic light environments they typically adjust their luminescence intensity. Here, we found evidence that bioluminescent sharks instead emit a constant light output and move up and down in the water column to remain cryptic at iso-luminance depth. We observed, across 21 globally distributed shark species, a correlation between capture depth and the proportion of a ventral area occupied by photophores. This information further allowed us, using visual modelling, to provide an adaptive explanation for shark photophore pattern diversity: in species facing moderate predation risk from below, counterilluminating photophores were partially co-opted for bioluminescent signalling, leading to complex patterns. In addition to increase our understanding of pelagic ecosystems our study emphasizes the importance of bioluminescence as a speciation driver.
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| 9. |
- Cui, L., et al.
(author)
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Plasmon-driven dimerization via S-S chemical bond in an aqueous environment
- 2014
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In: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322 .- 2045-2322. ; 4
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Journal article (peer-reviewed)abstract
- The surface-enhanced Raman scattering (SERS) spectra of thioanisole are experimentally investigated in an electrochemical environment in this study. Two Raman peaks, which depend strongly not only on electric potential but also on the local surface plasmon resonances (LSPR), have been observed. Theoretical calculations reveal that thioanisole is first dissociated from thiophenol via the S-CH3 bond; plasmons then drive the dimerisation of thiophenol via the S-S bond, which is strongly potential dependent. One Raman peak corresponds to the S-S vibrational mode of the thiophenol dimer, and the other corresponds to the asymmetric C-C stretching modes of the benzenyl of the thiophenol dimer. The potential-dependent two Raman modes is the potential-dependent dimerisation dynamics of thiophenol via the S-S bond. Our experimental findings provide insight into the structural elucidation of adsorbed molecules and molecular surface reaction dynamics.
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| 10. |
- 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
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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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