| 261. |
- Dvirnas, Albertas, et al.
(författare)
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Detection of structural variations in densely-labelled optical DNA barcodes: A hidden Markov model approach
- 2021
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 16:11
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Tidskriftsartikel (refereegranskat)abstract
- Large-scale genomic alterations play an important role in disease, gene expression, and chromosome evolution. Optical DNA mapping (ODM), commonly categorized into sparsely-labelled ODM and densely-labelled ODM, provides sequence-specific continuous intensity profiles (DNA barcodes) along single DNA molecules and is a technique well-suited for detecting such alterations. For sparsely-labelled barcodes, the possibility to detect large genomic alterations has been investigated extensively, while densely-labelled barcodes have not received as much attention. In this work, we introduce HMMSV, a hidden Markov model (HMM) based algorithm for detecting structural variations (SVs) directly in densely-labelled barcodes without access to sequence information. We evaluate our approach using simulated data-sets with 5 different types of SVs, and combinations thereof, and demonstrate that the method reaches a true positive rate greater than 80% for randomly generated barcodes with single variations of size 25 kilobases (kb). Increasing the length of the SV further leads to larger true positive rates. For a real data-set with experimental barcodes on bacterial plasmids, we successfully detect matching barcode pairs and SVs without any particular assumption of the types of SVs present. Instead, our method effectively goes through all possible combinations of SVs. Since ODM works on length scales typically not reachable with other techniques, our methodology is a promising tool for identifying arbitrary combinations of genomic alterations.
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| 262. |
- Dvirnas, Albertas, et al.
(författare)
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Facilitated sequence assembly using densely labeled optical DNA barcodes: A combinatorial auction approach
- 2018
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Ingår i: Plos One. - : Public Library of Science (PLoS). - 1932-6203. ; 13:3
-
Tidskriftsartikel (refereegranskat)abstract
- The output from whole genome sequencing is a set of contigs, i.e. short non-overlapping DNA sequences (sizes 1-100 kilobasepairs). Piecing the contigs together is an especially difficult task for previously unsequenced DNA, and may not be feasible due to factors such as the lack of sufficient coverage or larger repetitive regions which generate gaps in the final sequence. Here we propose a new method for scaffolding such contigs. The proposed method uses densely labeled optical DNA barcodes from competitive binding experiments as scaffolds. On these scaffolds we position theoretical barcodes which are calculated from the contig sequences. This allows us to construct longer DNA sequences from the contig sequences. This proof-of-principle study extends previous studies which use sparsely labeled DNA barcodes for scaffolding purposes. Our method applies a probabilistic approach that allows us to discard "foreign" contigs from mixed samples with contigs from different types of DNA. We satisfy the contig non-overlap constraint by formulating the contig placement challenge as a combinatorial auction problem. Our exact algorithm for solving this problem reduces computational costs compared to previous methods in the combinatorial auction field. We demonstrate the usefulness of the proposed scaffolding method both for synthetic contigs and for contigs obtained using Illumina sequencing for a mixed sample with plasmid and chromosomal DNA.
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| 263. |
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| 264. |
- Dyrssen, Catharina, 1949
(författare)
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Stadens rytmer: Rummet och ljuden
- 2007
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Ingår i: Bebyggelsehistorisk tidskrift. - : Föreningen Bebyggelsehistorisk tidskrift. ; 2007:54, s. 59-72:54, s. 59-72
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Tidskriftsartikel (refereegranskat)
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| 265. |
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| 266. |
- Edhborg, Fredrik, 1990, et al.
(författare)
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Singlet Energy Transfer in Anthracene-Porphyrin Complexes: Mechanism, Geometry, and Implications for Intramolecular Photon Upconversion
- 2019
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 123:46, s. 9934-9943
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Tidskriftsartikel (refereegranskat)abstract
- In this work we show that the mechanism for singlet excitation energy transfer (SET) in coordination complexes changes upon changing a single atom. SET is governed by two different mechanisms; Förster resonance energy transfer (FRET) based on Coulombic, through-space interactions, or Dexter energy transfer relying on exchange, through-bond interactions. On the basis of time-resolved fluorescence and transient absorption measurements, we conduct a mechanistic study of SET from a set of photoexcited anthracene donors to axially coordinated porphyrin acceptors, revealing the effect of coordination geometry and a very profound effect of the porphyrin central metal atom. We found that FRET is the dominating mechanism of SET for complexes with zinc-octaethylporphyrin (ZnOEP) as the acceptor, while Dexter energy transfer is the dominating mechanism of SET in a corresponding ruthenium complex (RuOEP). In addition, by analyzing the coordination geometry of the complexes and its temperature dependence, the binding angle potential energy of axially coordinated porphyrin complexes could be estimated. The results of this study are of fundamental importance and are discussed with respect to the consequences for developing intramolecular triplet-Triplet annihilation photon upconversion in coordination complexes.
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| 267. |
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| 268. |
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| 269. |
- Ek, Gustav, et al.
(författare)
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Hydrogen induced structure and property changes in Eu3Si4
- 2019
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Ingår i: Journal of Solid State Chemistry. - : Elsevier BV. - 0022-4596 .- 1095-726X. ; 277, s. 37-45
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Tidskriftsartikel (refereegranskat)abstract
- Hydrides Eu3Si4H2-X were obtained by exposing the Zintl phase Eu3Si4 to a hydrogen atmosphere at a pressure of 30 bar and temperatures from 25 to 300 degrees C. Structural analysis using powder X-ray diffraction (PXRD) data suggested that hydrogenations in a temperature range 25-200 degrees C afford a uniform hydride phase with an orthorhombic structure (Immm, a approximate to 4.40 angstrom, b approximate to 3.97 angstrom, c approximate to 19.8 angstrom), whereas at 300 degrees C mixtures of two orthorhombic phases with c approximate to 19.86 and approximate to 19.58 angstrom were obtained. The assignment of a composition Eu3Si4H2+x is based on first principles DFT calculations, which indicated a distinct crystallographic site for H in the Eu3Si4 structure. In this position, H atoms are coordinated in a tetrahedral fashion by Eu atoms. The resulting hydride Eu3Si4H2 is stable by -0.46 eV/H atom with respect to Eu3Si4 and gaseous H-2. Deviations between the lattice parameters of the DFT optimized Eu3Si4H2 structure and the ones extracted from PXRD patterns pointed to the presence of additional H in interstitials also involving Si atoms. Subsequent DFT modeling of compositions Eu3Si4H3 and Eu3Si4H4 showed considerably better agreement to the experimental unit cell volumes. It was then concluded that the hydrides of Eu3Si4 have a composition Eu3Si4H2+x (x
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| 270. |
- Ekegren, Titti, et al.
(författare)
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Clinical perspectives of high-resolution mass spectrometry-based proteomics in neuroscience: exemplified in amyotrophic lateral sclerosis biomarker discovery research.
- 2008
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Ingår i: Journal of mass spectrometry : JMS. - : Wiley. - 1076-5174 .- 1096-9888. ; 43:5, s. 559-71
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Forskningsöversikt (refereegranskat)abstract
- Biomarker discovery is a central application in today's proteomic research. There is an urgent need for valid biomarkers to improve diagnostic tools and treatment in many disorders, such as the rapidly progressing neurodegenerative disorder amyotrophic lateral sclerosis (ALS) that has a fatal outcome in about 3 years and yet no curative treatment. Screening for clinically relevant biomarkers puts high demands on high-throughput, rapid and precise proteomic techniques. There is a large variety in the methods of choice involving mainly gel-based approaches as well as chromatographic techniques for multi-dimensional protein and peptide separations followed by mass spectrometry (MS) analysis. This special feature article will discuss some important aspects of MS-based clinical proteomics and biomarker discovery in the field of neurodegenerative diseases and ALS research respectively, with the aim to provide a prospective view on current and future research aspects in the field. Furthermore, examples for application of high-resolution MS-based proteomic strategies for ALS biomarker discovery will be demonstrated with two studies previously reported by our group. These studies include among others, utilization of capillary liquid chromatography-Fourier transform ion cyclotron resonance mass spectrometry (LC-FTICR-MS) for advanced protein pattern classification in cerebrospinal fluid (CSF) samples of ALS patients as well as highly sensitive protein identification in minimal amounts of postmortem spinal cord tissue and laser micro-dissected motor neurons using FT-ICR-MS in conjunction with nanoflow LC coupled to matrix-assisted laser desorption ionization time-of-flight tandem mass spectrometry (LC-MALDI-TOF-TOF-MS).
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