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  • 1
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    Comparative Expression Dynamics of Intergenic Long Noncoding RNAs in the Genus Drosophila (2016)
    Oxford University Press
    Details
    Publication Date: 2016-06-30
    Description: Thousands of long noncoding RNAs (lncRNAs) have been annotated in eukaryotic genomes, but comparative transcriptomic approaches are necessary to understand their biological impact and evolution. To facilitate such comparative studies in Drosophila , we identified and characterized lncRNAs in a second Drosophilid —the evolutionary model Drosophila pseudoobscura . Using RNA-Seq and computational filtering of protein-coding potential, we identified 1,589 intergenic lncRNA loci in D. pseudoobscura . We surveyed multiple sex-specific developmental stages and found, like in Drosophila melanogaster , increasingly prolific lncRNA expression through male development and an overrepresentation of lncRNAs in the testes. Other trends seen in D. melanogaster , like reduced pupal expression, were not observed. Nonrandom distributions of female-biased and non-testis-specific male-biased lncRNAs between the X chromosome and autosomes are consistent with selection-based models of gene trafficking to optimize genomic location of sex-biased genes. The numerous testis-specific lncRNAs, however, are randomly distributed between the X and autosomes, and we cannot reject the hypothesis that many of these are likely to be spurious transcripts. Finally, using annotated lncRNAs in both species, we identified 134 putative lncRNA homologs between D. pseudoobscura and D. melanogaster and find that many have conserved developmental expression dynamics, making them ideal candidates for future functional analyses.
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
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  • 2
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    Bacteriophage strain typing by rapid single molecule analysis (2015)
    Oxford University Press
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    Publication Date: 2015-10-15
    Description: Rapid characterization of unknown biological samples is under the focus of many current studies. Here we report a method for screening of biological samples by optical mapping of their DNA. We use a novel, one-step chemo-enzymatic reaction to covalently bind fluorophores to DNA at the four-base recognition sites of a DNA methyltransferase. Due to the diffraction limit of light, the dense distribution of labels results in a continuous fluorescent signal along the DNA. The amplitude modulations (AM) of the fluorescence intensity along the stretched DNA molecules exhibit a unique molecular fingerprint that can be used for identification. We show that this labelling scheme is highly informative, allowing accurate genotyping. We demonstrate the method by labelling the genomes of and T7 bacteriophages, resulting in a consistent, unique AM profile for each genome. These profiles are also successfully used for identification of the phages from a background phage library. Our method may provide a facile route for screening and typing of various organisms and has potential applications in metagenomics studies of various ecosystems.
    Keywords: Phsyical and Biochemical Characterisation of DNA
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 3
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    Extension of nanoconfined DNA: Quantitative comparison between experiment and theory (2015)
    American Physical Society (APS)
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    Publication Date: 2015-12-04
    Description: Author(s): V. Iarko, E. Werner, L. K. Nyberg, V. Müller, J. Fritzsche, T. Ambjörnsson, J. P. Beech, J. O. Tegenfeldt, K. Mehlig, F. Westerlund, and B. Mehlig The extension of DNA confined to nanochannels has been studied intensively and in detail. However, quantitative comparisons between experiments and model calculations are difficult because most theoretical predictions involve undetermined prefactors, and because the model parameters (contour length,… [Phys. Rev. E 92, 062701] Published Wed Dec 02, 2015
    Keywords: Biological Physics
    Print ISSN: 1539-3755
    Electronic ISSN: 1550-2376
    Topics: Physics
    Published by American Physical Society (APS)
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  • 4
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    N=50 core excited states studied in the _{46}^{96}Pd_{50} nucleus (2012)
    American Physical Society (APS)
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    Publication Date: 2012-07-18
    Description: Author(s): M. Palacz, J. Nyberg, H. Grawe, K. Sieja, G. de Angelis, P. Bednarczyk, A. Blazhev, D. Curien, Z. Dombradi, O. Dorvaux, J. Ekman, J. Gałkowski, M. Górska, J. Iwanicki, G. Jaworski, J. Kownacki, J. Ljungvall, M. Moszyński, F. Nowacki, D. Rudolph, D. Sohler, D. Wolski, and M. Ziębliński The four-proton hole 96 Pd neighbor of the doubly-magic 100 Sn nucleus was studied in-beam, using a fusion-evaporation reaction of a 58 Ni beam on a 45 Sc target. States of 96 Pd were established up to an excitation energy of 9707 keV. A core-excited odd-parity isomer with T 1/2 =37.7(1.1) ns was identifie... [Phys. Rev. C 86, 014318] Published Tue Jul 17, 2012
    Keywords: Nuclear Structure
    Print ISSN: 0556-2813
    Electronic ISSN: 1089-490X
    Topics: Physics
    Published by American Physical Society (APS)
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  • 5
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    Similar DNA methylation pattern in lung tumours from smokers and never-smokers with second-hand tobacco smoke exposure (2012)
    Oxford University Press
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    Publication Date: 2012-06-26
    Description: Tobacco smoke causes lung cancer in smokers and in never-smokers exposed to second-hand tobacco smoke (SHS). Nonetheless, molecular mechanisms of lung cancer in SHS-exposed never-smokers are still elusive. We studied lung cancers from current smokers ( n = 109), former smokers ( n = 56) and never-smokers ( n = 47) for promoter hypermethylation of five tumour suppressor genes— p16 , RARB , RASSF1 , MGMT and DAPK1 —using methylation-specific polymerase chain reaction. Lung tumours from ever-smokers suggested an increased risk of p16 hypermethylation as compared to never-smokers ( P = 0.073), with former smokers having the highest frequency of p16 hypermethylation ( P = 0.044 versus current smokers and P = 0.009 versus never-smokers). In the never-smoking group, p16 hypermethylation was seen in lung tumours from SHS-exposed individuals (4/33; 12%) but in none of the non-exposed individuals (0/9). The overall occurrence of hypermethylation (measured both as methylation index and as number of genes affected) was similar in those ever exposed to tobacco smoke (smokers, SHS-exposed never-smokers) and differed from non-exposed never-smokers. In multivariate analysis, p16 hypermethylation was more prevalent in lung tumours from male than female patients ( P = 0.018) and in squamous cell carcinomas than in adenocarcinomas ( P = 0.025). Occurrence of TP53 mutation in the tumour was associated with hypermethylation of at least one gene ( P = 0.027). In all, our data suggest that promoter hypermethylation pattern in SHS-exposed never-smokers resembles that observed in smokers. Association between TP53 mutation, a hallmark of smokers’ lung cancer, and methylation of one or more of the lung cancer-related genes studied, provides further evidence for common tobacco smoke-related origin for both types of molecular alterations.
    Print ISSN: 0267-8357
    Electronic ISSN: 1464-3804
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 6
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    Competitive binding-based optical DNA mapping for fast identification of bacteria - multi-ligand transfer matrix theory and experimental applications on Escherichia coli (2014)
    Oxford University Press
    Details
    Publication Date: 2014-09-02
    Description: We demonstrate a single DNA molecule optical mapping assay able to resolve a specific Escherichia coli strain from other strains. The assay is based on competitive binding of the fluorescent dye YOYO-1 and the AT-specific antibiotic netropsin. The optical map is visualized by stretching the DNA molecules in nanofluidic channels. We optimize the experimental conditions to obtain reproducible barcodes containing as much information as possible. We implement a multi-ligand transfer matrix method for calculating theoretical barcodes from known DNA sequences. Our method extends previous theoretical approaches for competitive binding of two types of ligands to many types of ligands and introduces a recursive approach that allows long barcodes to be calculated with standard computer floating point formats. The identification of a specific E . coli strain (CCUG 10979) is based on mapping of 50–160 kilobasepair experimental DNA fragments onto the theoretical genome using the developed theory. Our identification protocol introduces two theoretical constructs: a P -value for a best experiment-theory match and an information score threshold. The developed methods provide a novel optical mapping toolbox for identification of bacterial species and strains. The protocol does not require cultivation of bacteria or DNA amplification, which allows for ultra-fast identification of bacterial pathogens.
    Keywords: Protein-nucleic acid interaction
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 7
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    Heterogeneous staining: a tool for studies of how fluorescent dyes affect the physical properties of DNA (2013)
    Oxford University Press
    Details
    Publication Date: 2013-10-19
    Description: The commonly used fluorescent dye YOYO-1 (YOYO) has, using bulk techniques, been demonstrated to stain DNA heterogeneously at substoichiometric concentrations. We here, using nanofluidic channels and fluorescence microscopy, investigate the heterogeneous staining on the single DNA molecule level and demonstrate that the dye distribution is continuous. The equilibration of YOYO on DNA is extremely slow but can be accelerated by increasing the ionic strength and/or the temperature. Furthermore, we demonstrate how to use the heterogeneous staining as a tool for detailed and time-efficient studies of how fluorescent dyes affect the physical properties of DNA. We show that the relative increase in extension of DNA with increasing amount of YOYO bound is higher at low ionic strengths and also extrapolate the extension of native DNA. Our study reveals important information on how YOYO affects the physical properties of DNA, but it also has broader applications. First, it reveals how cationic intercalators, such as potential DNA drugs, affect DNA under strong confinement. Second, the strategy of using heterogeneous staining is of general use for single molecule studies of DNA interacting with proteins or ligands.
    Keywords: Nucleic acid structure, Phsyical and Biochemical Characterisation of DNA
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 8
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    Electronic energy-loss mechanisms for H, He, and Ne in TiN (2017)
    American Physical Society (APS)
    Details
    Publication Date: 2017-09-07
    Description: Author(s): M. A. Sortica, V. Paneta, B. Bruckner, S. Lohmann, M. Hans, T. Nyberg, P. Bauer, and D. Primetzhofer The specific energy loss of medium-energy hydrogen, helium, and neon ions in titanium nitride is studied. Electronic stopping cross sections of ions in the energy range of 3–140 keV/amu were measured in backscattering geometry using time-of-flight medium-energy ion scattering, from the energy loss e... [Phys. Rev. A 96, 032703] Published Wed Sep 06, 2017
    Keywords: Atomic and molecular collisions and interactions
    Print ISSN: 1050-2947
    Electronic ISSN: 1094-1622
    Topics: Physics
    Published by American Physical Society (APS)
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  • 9
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    Persistence of non-Markovian Gaussian stationary processes in discrete time (2018)
    American Physical Society (APS)
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    Publication Date: 2018-04-13
    Description: Author(s): Markus Nyberg and Ludvig Lizana The persistence of a stochastic variable is the probability that it does not cross a given level during a fixed time interval. Although persistence is a simple concept to understand, it is in general hard to calculate. Here we consider zero mean Gaussian stationary processes in discrete time n . Few ... [Phys. Rev. E 97, 040101(R)] Published Thu Apr 12, 2018
    Keywords: Statistical Physics
    Print ISSN: 1539-3755
    Electronic ISSN: 1550-2376
    Topics: Physics
    Published by American Physical Society (APS)
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  • 10
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    Zero-crossing statistics for non-Markovian time series (2018)
    American Physical Society (APS)
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    Publication Date: 2018-03-15
    Description: Author(s): Markus Nyberg, Ludvig Lizana, and Tobias Ambjörnsson In applications spanning from image analysis and speech recognition to energy dissipation in turbulence and time-to failure of fatigued materials, researchers and engineers want to calculate how often a stochastic observable crosses a specific level, such as zero. At first glance this problem looks ... [Phys. Rev. E 97, 032114] Published Wed Mar 14, 2018
    Keywords: Statistical Physics
    Print ISSN: 1539-3755
    Electronic ISSN: 1550-2376
    Topics: Physics
    Published by American Physical Society (APS)
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