| 1. |
- Eraslan, Basak, et al.
(författare)
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Quantification and discovery of sequence determinants of protein-per-mRNA amount in 29 human tissues
- 2019
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Ingår i: Molecular Systems Biology. - : WILEY. - 1744-4292 .- 1744-4292. ; 15:2
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Tidskriftsartikel (refereegranskat)abstract
- Despite their importance in determining protein abundance, a comprehensive catalogue of sequence features controlling protein-to-mRNA (PTR) ratios and a quantification of their effects are still lacking. Here, we quantified PTR ratios for 11,575 proteins across 29 human tissues using matched transcriptomes and proteomes. We estimated by regression the contribution of known sequence determinants of protein synthesis and degradation in addition to 45 mRNA and 3 protein sequence motifs that we found by association testing. While PTR ratios span more than 2 orders of magnitude, our integrative model predicts PTR ratios at a median precision of 3.2-fold. A reporter assay provided functional support for two novel UTR motifs, and an immobilized mRNA affinity competition-binding assay identified motif-specific bound proteins for one motif. Moreover, our integrative model led to a new metric of codon optimality that captures the effects of codon frequency on protein synthesis and degradation. Altogether, this study shows that a large fraction of PTR ratio variation in human tissues can be predicted from sequence, and it identifies many new candidate post-transcriptional regulatory elements.
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| 2. |
- Reifarth, R., et al.
(författare)
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Nuclear astrophysics with radioactive ions at FAIR
- 2016
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Ingår i: Journal of Physics: Conference Series. - : IOP Publishing. - 1742-6588 .- 1742-6596. ; 665:1
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Konferensbidrag (refereegranskat)abstract
- The nucleosynthesis of elements beyond iron is dominated by neutron captures in the s and r processes. However, 32 stable, proton-rich isotopes cannot be formed during those processes, because they are shielded from the s-process flow and r-process beta-decay chains. These nuclei are attributed to the p and rp process. For all those processes, current research in nuclear astrophysics addresses the need for more precise reaction data involving radioactive isotopes. Depending on the particular reaction, direct or inverse kinematics, forward or time-reversed direction are investigated to determine or at least to constrain the desired reaction cross sections. The Facility for Antiproton and Ion Research (FAIR) will offer unique, unprecedented opportunities to investigate many of the important reactions. The high yield of radioactive isotopes, even far away from the valley of stability, allows the investigation of isotopes involved in processes as exotic as the r or rp processes.
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| 3. |
- Wang, Dongxue, et al.
(författare)
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A deep proteome and transcriptome abundance atlas of 29 healthy human tissues
- 2019
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Ingår i: Molecular Systems Biology. - : WILEY. - 1744-4292 .- 1744-4292. ; 15:2
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Tidskriftsartikel (refereegranskat)abstract
- Genome-, transcriptome- and proteome-wide measurements provide insights into how biological systems are regulated. However, fundamental aspects relating to which human proteins exist, where they are expressed and in which quantities are not fully understood. Therefore, we generated a quantitative proteome and transcriptome abundance atlas of 29 paired healthy human tissues from the Human Protein Atlas project representing human genes by 18,072 transcripts and 13,640 proteins including 37 without prior protein-level evidence. The analysis revealed that hundreds of proteins, particularly in testis, could not be detected even for highly expressed mRNAs, that few proteins show tissue-specific expression, that strong differences between mRNA and protein quantities within and across tissues exist and that protein expression is often more stable across tissues than that of transcripts. Only 238 of 9,848 amino acid variants found by exome sequencing could be confidently detected at the protein level showing that proteogenomics remains challenging, needs better computational methods and requires rigorous validation. Many uses of this resource can be envisaged including the study of gene/protein expression regulation and biomarker specificity evaluation.
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| 4. |
- Lieder, R M, et al.
(författare)
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Gamma-ray tracking arrays
- 2001
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Ingår i: PROGRESS IN PARTICLE AND NUCLEAR PHYSICS, VOL 46. ; , s. 399-407
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Konferensbidrag (refereegranskat)abstract
- The next generation of 4 pi arrays for high-precision gamma -ray spectroscopy will involve "gamma -ray tracking front-end on digital signal processing techniques, which allows to extract energy, timing and spatial information on the interactions of a gamma -ray in the Ge detector by pulse shape analysis of its signals. Utilizing the information on the positions of the interaction points and the energies released at each point the tracks of the gamma -rays in a Ge shell can be reconstructed in three dimensions.
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| 5. |
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| 6. |
- Paulraj, Thomas, et al.
(författare)
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Primary cell wall inspired micro containers as a step towards a synthetic plant cell
- 2020
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Ingår i: Nature Communications. - : Nature Research. - 2041-1723. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- The structural integrity of living plant cells heavily relies on the plant cell wall containing a nanofibrous cellulose skeleton. Hence, if synthetic plant cells consist of such a cell wall, they would allow for manipulation into more complex synthetic plant structures. Herein, we have overcome the fundamental difficulties associated with assembling lipid vesicles with cellulosic nanofibers (CNFs). We prepare plantosomes with an outer shell of CNF and pectin, and beneath this, a thin layer of lipids (oleic acid and phospholipids) that surrounds a water core. By exploiting the phase behavior of the lipids, regulated by pH and Mg2+ ions, we form vesicle-crowded interiors that change the outer dimension of the plantosomes, mimicking the expansion in real plant cells during, e.g., growth. The internal pressure enables growth of lipid tubules through the plantosome cell wall, which paves the way to the development of hierarchical plant structures and advanced synthetic plant cell mimics. © 2020, The Author(s).
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| 7. |
- Raj, Akanksha, et al.
(författare)
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Lubrication synergy : Mixture of hyaluronan and dipalmitoylphosphatidylcholine (DPPC) vesicles
- 2017
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Ingår i: Journal of Colloid and Interface Science. - : Elsevier BV. - 0021-9797 .- 1095-7103. ; 488, s. 225-233
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Tidskriftsartikel (refereegranskat)abstract
- Phospholipids and hyaluronan have been implied to fulfil important roles in synovial joint lubrication. Since both components are present in synovial fluid, self-assembly structures formed by them should also be present. We demonstrate by small angle X-ray scattering that hyaluronan associates with the outer shell of dipalmitoylphophatidylcholine (DPPC) vesicles in bulk solution. Further, we follow adsorption to silica from mixed hyaluronan/DPPC vesicle solution by Quartz Crystal Microbalance with Dissipation measurements. Atomic Force Microscope imaging visualises the adsorbed layer structure consisting of non-homogeneous phospholipid bilayer with hyaluronan/DPPC aggregates on top. The presence of these aggregates generates a long-range repulsive surface force as two such surfaces are brought together. However, the aggregates are easily deformed, partly rearranged into multilayer structures and partly removed from between the surfaces under high loads. These layers offer very low friction coefficient (<0.01), high load bearing capacity (≈23 MPa), and self-healing ability. Surface bound DPPC/hyaluronan aggregates provide a means for accumulation of lubricating DPPC molecules on sliding surfaces.
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| 8. |
- Vogt, Ulrich, et al.
(författare)
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Single-optical-element soft-x-ray interferometry with a laser-plasma x-ray source
- 2005
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Ingår i: Optics Letters. - 0146-9592 .- 1539-4794. ; 30:15, s. 2167-
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Tidskriftsartikel (refereegranskat)abstract
- We report on a compact interferometer for the water-window soft-x-ray range that is suitable for operation with laser-plasma sources. The interferometer consists of a single diffractive optical element that focuses impinging x rays to two focal spots. The light from these two secondary sources forms the interference pattern. The interferometer was operated with a liquid-nitrogen jet laser-plasma source at lambda = 2.88 nm. Scalar wave-field propagation was used to simulate the interference pattern, showing good correspondence between theoretical and experimental results. The diffractive optical element can simultaneously be used as an imaging optic, and we demonstrate soft-x-ray microscopy with interferometric contrast enhancement of a phase object.
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| 9. |
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| 10. |
- Wang, Min, et al.
(författare)
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The effect of temperature on supported dipalmitoylphosphatidylcholine (DPPC) bilayers : Structure and lubrication performance
- 2015
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Ingår i: Journal of Colloid and Interface Science. - : Elsevier BV. - 0021-9797 .- 1095-7103. ; 445, s. 84-92
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Tidskriftsartikel (refereegranskat)abstract
- Phospholipids fulfill an important role in joint lubrication. They, together with hyaluronan and glycoproteins, are the biolubricants that sustain low friction between cartilage surfaces bathed in synovial fluid. In this work we have investigated how the friction force and load bearing capacity of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) bilayers on silica surfaces are affected by temperature, covering the temperature range 25–52 °C. Friction forces have been determined utilizing the AFM colloidal probe technique, which showed that DPPC bilayers are able to provide low friction forces over the whole temperature interval. However, the load bearing capacity is improved at higher temperatures. We interpret this finding as being a consequence of lower rigidity and higher self-healing capacity of the DPPC bilayer in the liquid disordered state compared to the gel state. The corresponding structure of solid supported DPPC bilayers at the silica–liquid interface has been followed using X-ray reflectivity measurements, which suggests that the DPPC bilayer is in the gel phase at 25 °C and 39 °C and in the liquid disordered state at 55 °C. Well-defined bilayer structures were observed for both phases. The deposited DPPC bilayers were also imaged using AFM PeakForce Tapping mode, and these measurements indicated a less homogeneous layer at temperatures below 37 °C.
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