| 1. |
- Park, S. W., et al.
(författare)
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Cyclophilin 20-3 relays a 12-oxo-phytodienoic acid signal during stress responsive regulation of cellular redox homeostasis
- 2013
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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. ; 110:23, s. 9559-9564
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Tidskriftsartikel (refereegranskat)abstract
- The jasmonate family of phytohormones plays central roles in plant development and stress acclimation. However, the architecture of their signaling circuits remains largely unknown. Here we describe a jasmonate family binding protein, cyclophilin 20-3 (CYP20-3), which regulates stress-responsive cellular redox homeostasis. (+)-12-oxo-phytodienoic acid (OPDA) binding promotes CYP20-3 to form a complex with serine acetyltransferase 1, which triggers the formation of a hetero-oligomeric cysteine synthase complex with O-acetylserine (thiol) lyase B in chloroplasts. The cysteine synthase complex formation then activates sulfur assimilation that leads to increased levels of thiol metabolites and the buildup of cellular reduction potential. The enhanced redox capacity in turn coordinates the expression of a subset of OPDA-responsive genes. Thus, we conclude that CYP20-3 is a key effector protein that links OPDA signaling to amino acid biosynthesis and cellular redox homeostasis in stress responses.
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| 2. |
- Enroth, Stefan, et al.
(författare)
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A strand specific high resolution normalization method for chip-sequencing data employing multiple experimental control measurements
- 2012
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Ingår i: Algorithms for Molecular Biology. - : Springer Science and Business Media LLC. - 1748-7188. ; 7, s. 2-
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Tidskriftsartikel (refereegranskat)abstract
- Background: High-throughput sequencing is becoming the standard tool for investigating protein-DNA interactions or epigenetic modifications. However, the data generated will always contain noise due to e. g. repetitive regions or non-specific antibody interactions. The noise will appear in the form of a background distribution of reads that must be taken into account in the downstream analysis, for example when detecting enriched regions (peak-calling). Several reported peak-callers can take experimental measurements of background tag distribution into account when analysing a data set. Unfortunately, the background is only used to adjust peak calling and not as a preprocessing step that aims at discerning the signal from the background noise. A normalization procedure that extracts the signal of interest would be of universal use when investigating genomic patterns.Results: We formulated such a normalization method based on linear regression and made a proof-of-concept implementation in R and C++. It was tested on simulated as well as on publicly available ChIP-seq data on binding sites for two transcription factors, MAX and FOXA1 and two control samples, Input and IgG. We applied three different peak-callers to (i) raw (un-normalized) data using statistical background models and (ii) raw data with control samples as background and (iii) normalized data without additional control samples as background. The fraction of called regions containing the expected transcription factor binding motif was largest for the normalized data and evaluation with qPCR data for FOXA1 suggested higher sensitivity and specificity using normalized data over raw data with experimental background.Conclusions: The proposed method can handle several control samples allowing for correction of multiple sources of bias simultaneously. Our evaluation on both synthetic and experimental data suggests that the method is successful in removing background noise.
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| 3. |
- Loisel, Julie, et al.
(författare)
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A database and synthesis of northern peatland soil properties and Holocene carbon and nitrogen accumulation
- 2014
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Ingår i: The Holocene. - : SAGE Publications. - 0959-6836 .- 1477-0911. ; 24:9, s. 1028-1042
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Tidskriftsartikel (refereegranskat)abstract
- Here, we present results from the most comprehensive compilation of Holocene peat soil properties with associated carbon and nitrogen accumulation rates for northern peatlands. Our database consists of 268 peat cores from 215 sites located north of 45 degrees N. It encompasses regions within which peat carbon data have only recently become available, such as the West Siberia Lowlands, the Hudson Bay Lowlands, Kamchatka in Far East Russia, and the Tibetan Plateau. For all northern peatlands, carbon content in organic matter was estimated at 42 +/- 3% (standard deviation) for Sphagnum peat, 51 +/- 2% for non-Sphagnum peat, and at 49 +/- 2% overall. Dry bulk density averaged 0.12 +/- 0.07 g/cm(3), organic matter bulk density averaged 0.11 +/- 0.05 g/cm(3), and total carbon content in peat averaged 47 +/- 6%. In general, large differences were found between Sphagnum and non-Sphagnum peat types in terms of peat properties. Time-weighted peat carbon accumulation rates averaged 23 +/- 2 (standard error of mean) g C/m(2)/yr during the Holocene on the basis of 151 peat cores from 127 sites, with the highest rates of carbon accumulation (25-28 g C/m(2)/yr) recorded during the early Holocene when the climate was warmer than the present. Furthermore, we estimate the northern peatland carbon and nitrogen pools at 436 and 10 gigatons, respectively. The database is publicly available at https://peatlands.lehigh.edu.
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| 4. |
- Andersson, Claes R., et al.
(författare)
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Quantitative Chemogenomics : Machine-Learning Models of Protein-Ligand Interaction
- 2011
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Ingår i: Current Topics in Medicinal Chemistry. - : Bentham Science Publishers Ltd.. - 1568-0266 .- 1873-4294. ; 11:15, s. 1978-1993
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Forskningsöversikt (refereegranskat)abstract
- Chemogenomics is an emerging interdisciplinary field that lies in the interface of biology, chemistry, and informatics. Most of the currently used drugs are small molecules that interact with proteins. Understanding protein-ligand interaction is therefore central to drug discovery and design. In the subfield of chemogenomics known as proteochemometrics, protein-ligand-interaction models are induced from data matrices that consist of both protein and ligand information along with some experimentally measured variable. The two general aims of this quantitative multi-structure-property-relationship modeling (QMSPR) approach are to exploit sparse/incomplete information sources and to obtain more general models covering larger parts of the protein-ligand space, than traditional approaches that focuses mainly on specific targets or ligands. The data matrices, usually obtained from multiple sparse/incomplete sources, typically contain series of proteins and ligands together with quantitative information about their interactions. A useful model should ideally be easy to interpret and generalize well to new unseen protein-ligand combinations. Resolving this requires sophisticated machine-learning methods for model induction, combined with adequate validation. This review is intended to provide a guide to methods and data sources suitable for this kind of protein-ligand-interaction modeling. An overview of the modeling process is presented including data collection, protein and ligand descriptor computation, data preprocessing, machine-learning-model induction and validation. Concerns and issues specific for each step in this kind of data-driven modeling will be discussed.
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| 5. |
- Anselmo, Ana Sofia, 1980-, et al.
(författare)
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Characterisation of vertical phase separation in polymer : fullerene blend films for photovoltaics by dSIMS and NEXAFS
- 2011
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Ingår i: E-MRS 2011 Spring Meeting. - Malden, MA : John Wiley & Sons. ; , s. 62-63
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Konferensbidrag (refereegranskat)abstract
- Morphological control and characterization of blend films is key in the development of viable polymer solar cells. Spontaneous formation of vertical compositional gradients during solution processing has been shown for polyfluorene:PCBM blends and rationalized with thermodynamic and kinetic models of nucleation and spinodal decomposition.[1, 2] The extent of vertical stratification is affected by polymer side-chain modification aimed at controlling polymer:fullerene miscibility.[3] Here we present high-resolution film morphology results for several polymer:fullerene systems as obtained from near-edge X-ray fine structure spectroscopy (NEXAFS) in partial and in total electron yield modes. Blend films were found to be polymer- enriched at the surface. Dynamic secondary ion mass spectrometry (dSIMS) and NEXAFS give compositional information at different depths, resulting in a more complete picture of the film morphology.
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| 9. |
- Bergqvist, Jonas, et al.
(författare)
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Sub-glass transition annealing enhances polymer solar cell performance
- 2014
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Ingår i: Journal of Materials Chemistry A. - : Royal Society of Chemistry. - 2050-7488. ; 2:17, s. 6146-6152
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Tidskriftsartikel (refereegranskat)abstract
- Thermal annealing of non-crystalline polymer: fullerene blends typically results in a drastic decrease in solar cell performance. In particular aggressive annealing above the glass transition temperature results in a detrimental coarsening of the blend nanostructure. We demonstrate that mild annealing below the glass transition temperature is a viable avenue to control the nanostructure of a non-crystalline thiophene-quinoxaline copolymer: fullerene blend. Direct imaging methods indicate that coarsening of the blend nanostructure can be avoided. However, a combination of absorption and luminescence spectroscopy reveals that local changes in the polymer conformation as well as limited fullerene aggregation are permitted to occur. As a result, we are able to optimise the solar cell performance evenly across different positions of the coated area, which is a necessary criterion for large-scale, high throughput production.
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| 10. |
- Blaudeck, Thomas, et al.
(författare)
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Simplified Large-Area Manufacturing of Organic Electrochemical Transistors Combining Printing and a Self-Aligning Laser Ablation Step
- 2012
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Ingår i: Advanced Functional Materials. - : Wiley-VCH Verlag Berlin. - 1616-301X .- 1616-3028. ; 22:14, s. 2939-2948
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Tidskriftsartikel (refereegranskat)abstract
- A hybrid manufacturing approach for organic electrochemical transistors (OECTs) on flexible substrates is reported. The technology is based on conventional and digital printing (screen and inkjet printing), laser processing, and post-press technologies. A careful selection of the conductive, dielectric, and semiconductor materials with respect to their optical properties enables a self-aligning pattern formation which results in a significant reduction of the usual registration problems during manufacturing. For the prototype OECTs, based on this technology, on/off ratios up to 600 and switching times of 100 milliseconds at gate voltages in the range of 1 V were obtained.
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