| 1. |
- Park, S. W., et al.
(författare)
-
Cyclophilin 20-3 relays a 12-oxo-phytodienoic acid signal during stress responsive regulation of cellular redox homeostasis
- 2013
-
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
-
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.
|
|
| 2. |
- Xing, K. Z., et al.
(författare)
-
The electronic and geometric structures of neutral and potassium-doped poly[3-(4-octylphenyl)thiophene] studied by photoelectron spectroscopy
- 1996
-
Ingår i: Synthetic metals. - : Elsevier. - 0379-6779 .- 1879-3290. ; 76:1-3, s. 263-267
-
Tidskriftsartikel (refereegranskat)abstract
- The electronic and geometric structures of poly [3-(4-octylphenyl)thiophene] have been studied by X-ray and ultraviolet photoelectron spectroscopy (XPS and UPS, respectively). Thermochromic effects, and new charge induced states generated by potassium doping, have been observed by direct UPS measurements. The experimental results are in very good agreement with the results of theoretical quantum chemical calculations performed with the Austin Model 1 semi-empirical model and the valence-effective Hamiltonian pseudo-potential model.
|
|
| 3. |
- Xing, K. Z., et al.
(författare)
-
The electronic structure of neutral and alkali metal-doped poly[3-(4-octylphenyl)thiophene] studied by photoelectron spectroscopy
- 1996
-
Ingår i: Synthetic metals. - : Elsevier. - 0379-6779 .- 1879-3290. ; 80:1, s. 59-66
-
Tidskriftsartikel (refereegranskat)abstract
- The electronic structure of poly [3-(4-octylphenyl)thiophene] (POPT) has been studied by ultraviolet photoelectron spectroscopy (UPS) and X-ray photoelectron spectroscopy (XPS), as well as by quantum chemical calculations. Both temperature-dependent effects on the electronic structure of the neutral system, as well as the generation of new electronic states induced by doping with alkaline metals, have been observed. The experimental results are in good agreement with the results of the quantum chemical calculations.
|
|
| 4. |
- Andersson, Claes R., et al.
(författare)
-
Revealing cell cycle control by combining model-based detection of periodic expression with novel cis-regulatory descriptors
- 2007
-
Ingår i: BMC Systems Biology. - : Springer Science and Business Media LLC. - 1752-0509. ; 1, s. 45-
-
Tidskriftsartikel (refereegranskat)abstract
- Background: We address the issue of explaining the presence or absence of phase-specific transcription in budding yeast cultures under different conditions. To this end we use a model-based detector of gene expression periodicity to divide genes into classes depending on their behavior in experiments using different synchronization methods. While computational inference of gene regulatory circuits typically relies on expression similarity (clustering) in order to find classes of potentially co-regulated genes, this method instead takes advantage of known time profile signatures related to the studied process. Results: We explain the regulatory mechanisms of the inferred periodic classes with cis-regulatory descriptors that combine upstream sequence motifs with experimentally determined binding of transcription factors. By systematic statistical analysis we show that periodic classes are best explained by combinations of descriptors rather than single descriptors, and that different combinations correspond to periodic expression in different classes. We also find evidence for additive regulation in that the combinations of cis-regulatory descriptors associated with genes periodically expressed in fewer conditions are frequently subsets of combinations associated with genes periodically expression in more conditions. Finally, we demonstrate that our approach retrieves combinations that are more specific towards known cell-cycle related regulators than the frequently used clustering approach. Conclusion: The results illustrate how a model-based approach to expression analysis may be particularly well suited to detect biologically relevant mechanisms. Our new approach makes it possible to provide more refined hypotheses about regulatory mechanisms of the cell cycle and it can easily be adjusted to reveal regulation of other, non-periodic, cellular processes.
|
|
| 5. |
- Bergemalm, Daniel, 1977-, et al.
(författare)
-
Systemic Inflammation in Preclinical Ulcerative Colitis
- 2021
-
Ingår i: Gastroenterology. - : AGA Institute. - 0016-5085 .- 1528-0012. ; 161:5, s. 1526-1539.e9
-
Tidskriftsartikel (refereegranskat)abstract
- Background & Aims: Preclinical ulcerative colitis is poorly defined. We aimed to characterize the preclinical systemic inflammation in ulcerative colitis, using a comprehensive set of proteins.Methods: We obtained plasma samples biobanked from individuals who developed ulcerative colitis later in life (n = 72) and matched healthy controls (n = 140) within a population-based screening cohort. We measured 92 proteins related to inflammation using a proximity extension assay. The biologic relevance of these findings was validated in an inception cohort of patients with ulcerative colitis (n = 101) and healthy controls (n = 50). To examine the influence of genetic and environmental factors on these markers, a cohort of healthy twin siblings of patients with ulcerative colitis (n = 41) and matched healthy controls (n = 37) were explored.Results: Six proteins (MMP10, CXCL9, CCL11, SLAMF1, CXCL11 and MCP-1) were up-regulated (P < .05) in preclinical ulcerative colitis compared with controls based on both univariate and multivariable models. Ingenuity Pathway Analyses identified several potential key regulators, including interleukin-1β, tumor necrosis factor, interferon-gamma, oncostatin M, nuclear factor-κB, interleukin-6, and interleukin-4. For validation, we built a multivariable model to predict disease in the inception cohort. The model discriminated treatment-naïve patients with ulcerative colitis from controls with leave-one-out cross-validation (area under the curve = 0.92). Consistently, MMP10, CXCL9, CXCL11, and MCP-1, but not CCL11 and SLAMF1, were significantly up-regulated among the healthy twin siblings, even though their relative abundances seemed higher in incident ulcerative colitis.Conclusions: A set of inflammatory proteins are up-regulated several years before a diagnosis of ulcerative colitis. These proteins were highly predictive of an ulcerative colitis diagnosis, and some seemed to be up-regulated already at exposure to genetic and environmental risk factors.
|
|
| 6. |
- Bundgaard, E., et al.
(författare)
-
Matrix Organization and Merit Factor Evaluation as a Method to Address the Challenge of Finding a Polymer Material for Roll Coated Polymer Solar Cells
- 2015
-
Ingår i: Advanced Energy Materials. - : Wiley. - 1614-6840 .- 1614-6832. ; 5:10, s. Art. no. 1402186-
-
Tidskriftsartikel (refereegranskat)abstract
- The results presented demonstrate how the screening of 104 light-absorbing low band gap polymers for suitability in roll coated polymer solar cells can be accomplished through rational synthesis according to a matrix where 8 donor and 13 acceptor units are organized in rows and columns. Synthesis of all the polymers corresponding to all combinations of donor and acceptor units is followed by characterization of all the materials with respect to molecular weight, electrochemical energy levels, band gaps, photochemical stability, carrier mobility, and photovoltaic parameters. The photovoltaic evaluation is carried out with specific reference to scalable manufacture, which includes large area (1 cm(2)), stable inverted device architecture, an indium-tin-oxide-free fully printed flexible front electrode with ZnO/PEDOT:PSS (poly(3,4-ethylenedioxythiophene):polystyrene sulfonate), and a printed silver comb back electrode structure. The matrix organization enables fast identification of active layer materials according to a weighted merit factor that includes more than simply the power conversion efficiency and is used as a method to identify the lead candidates. Based on several characteristics included in the merit factor, it is found that 13 out of the 104 synthesized polymers outperformed poly(3-hexylthiophene) under the chosen processing conditions and thus can be suitable for further development.
|
|
| 7. |
- Enroth, Stefan, et al.
(författare)
-
A strand specific high resolution normalization method for chip-sequencing data employing multiple experimental control measurements
- 2012
-
Ingår i: Algorithms for Molecular Biology. - : Springer Science and Business Media LLC. - 1748-7188. ; 7, s. 2-
-
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.
|
|
| 8. |
- Gadisa, Abay, et al.
(författare)
-
Transparent polymer cathode for organic photovoltaic devices
- 2006
-
Ingår i: Synthetic metals. - : Elsevier BV. - 0379-6779 .- 1879-3290. ; 156:16-17, s. 1102-1107
-
Tidskriftsartikel (refereegranskat)abstract
- We demonstrate a prototype solar cell with a transparent polymer cathode, and indium-tin-oxide (ITO)/poly (3, 4-ethylene dioxythiophene)-poly (styrene sulphonate) (PEDOT:PSS) anode. As an active layer, thin film of a bulk heterojunction of polyfluorene copolymer poly[2,7-(9,9-dioctyl-fluorene)-alt-5,5-(4′,7′-di-2thienyl-2′,1′3′-benzothiadiazole)] (APFO-3) and an electron acceptor molecule [6] and [6]-phenyl-C61-butyric acid methyl ester (PCBM) (1:4 wt.) was sandwiched between the two transparent polymer electrodes. The cathode is another form of PEDOT formed by vapor phase polymerised PEDOT (VPP PEDOT) of conductivity 102–103 S/cm. The cathode is supported on an elastomeric substrate, and forms a conformal contact to the APFO-3/PCBM blend. Transparent solar cells are useful for building multilayer and tandem solar cells.
|
|
| 9. |
- Loisel, Julie, et al.
(författare)
-
A database and synthesis of northern peatland soil properties and Holocene carbon and nitrogen accumulation
- 2014
-
Ingår i: The Holocene. - : SAGE Publications. - 0959-6836 .- 1477-0911. ; 24:9, s. 1028-1042
-
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.
|
|
| 10. |
- Mihalič, Filip, et al.
(författare)
-
Conservation of Affinity Rather Than Sequence Underlies a Dynamic Evolution of the Motif-Mediated p53/MDM2 Interaction in Ray-Finned Fishes
- 2024
-
Ingår i: Molecular biology and evolution. - : Oxford University Press. - 0737-4038 .- 1537-1719. ; 41:2
-
Tidskriftsartikel (refereegranskat)abstract
- The transcription factor and cell cycle regulator p53 is marked for degradation by the ubiquitin ligase MDM2. The interaction between these 2 proteins is mediated by a conserved binding motif in the disordered p53 transactivation domain (p53TAD) and the folded SWIB domain in MDM2. The conserved motif in p53TAD from zebrafish displays a 20-fold weaker interaction with MDM2, compared to the interaction in human and chicken. To investigate this apparent difference, we tracked the molecular evolution of the p53TAD/MDM2 interaction among ray-finned fishes (Actinopterygii), the largest vertebrate clade. Intriguingly, phylogenetic analyses, ancestral sequence reconstructions, and binding experiments showed that different loss-of-affinity changes in the canonical binding motif within p53TAD have occurred repeatedly and convergently in different fish lineages, resulting in relatively low extant affinities (KD = 0.5 to 5 mu M). However, for 11 different fish p53TAD/MDM2 interactions, nonconserved regions flanking the canonical motif increased the affinity 4- to 73-fold to be on par with the human interaction. Our findings suggest that compensating changes at conserved and nonconserved positions within the motif, as well as in flanking regions of low conservation, underlie a stabilizing selection of "functional affinity" in the p53TAD/MDM2 interaction. Such interplay complicates bioinformatic prediction of binding and calls for experimental validation. Motif-mediated protein-protein interactions involving short binding motifs and folded interaction domains are very common across multicellular life. It is likely that the evolution of affinity in motif-mediated interactions often involves an interplay between specific interactions made by conserved motif residues and nonspecific interactions by nonconserved disordered regions.
|
|
