119 research outputs found
Inhomogeneous DNA: conducting exons and insulating introns
Parts of DNA sequences known as exons and introns play very different role in
coding and storage of genetic information. Here we show that their conducting
properties are also very different. Taking into account long-range correlations
among four basic nucleotides that form double-stranded DNA sequence, we
calculate electron localization length for exon and intron regions. Analyzing
different DNA molecules, we obtain that the exons have narrow bands of extended
states, unlike the introns where all the states are well localized. The band of
extended states is due to a specific form of the binary correlation function of
the sequence of basic DNA nucleotides.Comment: 14 pages, 6 figure
Generation of correlated binary sequences from white noise
This article discusses a method for generation of correlated binary sequences from white noise
Signum Function Method for Generation of Correlated Dichotomic Chains
We analyze the signum-generation method for creating random dichotomic
sequences with prescribed correlation properties. The method is based on a
binary mapping of the convolution of continuous random numbers with some
function originated from the Fourier transform of a binary correlator. The goal
of our study is to reveal conditions under which one can construct binary
sequences with a given pair correlator. Our results can be used in the
construction of superlattices and waveguides with selective transport
properties.Comment: 14 pages, 7 figure
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Controlled terahertz frequency response and transparency of Josephson chains and superconducting multilayers
This article discusses controlled terahertz frequency response and transparency of Josephson chains and superconducting multilayers
Analysis of congenital disorder of glycosylation-Id in a yeast model system shows diverse site-specific under-glycosylation of glycoproteins
Asparagine-linked glycosylation is a common post translational modification of proteins in eukaryotes. Mutations in the human ALG3 gene cause changed levels and altered glycan structures on mature glycoproteins and are the cause of a severe congenital disorder of glycosylation (CDG-Id). Diverse glycoproteins are also under-glycosylated in Saccharomyces cerevisae alg3 mutants. Here we analyzed site-specific glycosylation occupancy in this yeast model system using peptide-N-glycosidase F to label glycosylation sites with an asparagine-aspartate conversion that creates a new endoproteinase AspN cleavage site, followed by proteolytic digestion, and detection of peptides and glycopeptides by LC-ESI-MS/MS. We used this analytical method to identify and measure site specific glycosylation occupancy in alg3 mutant and wild type yeast strains. We found decreased site specific N-glycosylation occupancy in the alg3 knockout strain preferentially at Asn-Xaa-Ser sequences located in secondary structural elements, features previously associated with poor glycosylation efficiency. Furthermore, we identified 26 previously experimentally unverified glycosylation sites. Our results provide insights into the underlying mechanisms of disease in CDG-Id, and our methodology will be useful in site specific glycosylation analysis in many model systems and clinical applications
Advances in structure elucidation of small molecules using mass spectrometry
The structural elucidation of small molecules using mass spectrometry plays an important role in modern life sciences and bioanalytical approaches. This review covers different soft and hard ionization techniques and figures of merit for modern mass spectrometers, such as mass resolving power, mass accuracy, isotopic abundance accuracy, accurate mass multiple-stage MS(n) capability, as well as hybrid mass spectrometric and orthogonal chromatographic approaches. The latter part discusses mass spectral data handling strategies, which includes background and noise subtraction, adduct formation and detection, charge state determination, accurate mass measurements, elemental composition determinations, and complex data-dependent setups with ion maps and ion trees. The importance of mass spectral library search algorithms for tandem mass spectra and multiple-stage MS(n) mass spectra as well as mass spectral tree libraries that combine multiple-stage mass spectra are outlined. The successive chapter discusses mass spectral fragmentation pathways, biotransformation reactions and drug metabolism studies, the mass spectral simulation and generation of in silico mass spectra, expert systems for mass spectral interpretation, and the use of computational chemistry to explain gas-phase phenomena. A single chapter discusses data handling for hyphenated approaches including mass spectral deconvolution for clean mass spectra, cheminformatics approaches and structure retention relationships, and retention index predictions for gas and liquid chromatography. The last section reviews the current state of electronic data sharing of mass spectra and discusses the importance of software development for the advancement of structure elucidation of small molecules
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