WorldWideScience

Sample records for anonymous dna sequences

  1. Identification of genes in anonymous DNA sequences. Annual performance report, February 1, 1991--January 31, 1992

    Energy Technology Data Exchange (ETDEWEB)

    Fields, C.A.

    1996-06-01

    The objective of this project is the development of practical software to automate the identification of genes in anonymous DNA sequences from the human, and other higher eukaryotic genomes. A software system for automated sequence analysis, gm (gene modeler) has been designed, implemented, tested, and distributed to several dozen laboratories worldwide. A significantly faster, more robust, and more flexible version of this software, gm 2.0 has now been completed, and is being tested by operational use to analyze human cosmid sequence data. A range of efforts to further understand the features of eukaryoyic gene sequences are also underway. This progress report also contains papers coming out of the project including the following: gm: a Tool for Exploratory Analysis of DNA Sequence Data; The Human THE-LTR(O) and MstII Interspersed Repeats are subfamilies of a single widely distruted highly variable repeat family; Information contents and dinucleotide compostions of plant intron sequences vary with evolutionary origin; Splicing signals in Drosophila: intron size, information content, and consensus sequences; Integration of automated sequence analysis into mapping and sequencing projects; Software for the C. elegans genome project.

  2. Isolation of anonymous DNA sequences from within a submicroscopic X chromosomal deletion in a patient with choroideremia, deafness, and mental retardation

    International Nuclear Information System (INIS)

    Choroideremia, an X-chromosome linked retinal dystrophy of unknown pathogenesis, causes progressive nightblindness and eventual central blindness in affected males by the third to fourth decade of life. Choroideremia has been mapped to Xq13-21 by tight linkage to restriction fragment length polymorphism loci. The authors have recently identified two families in which choroideremia is inherited with mental retardation and deafness. In family XL-62, an interstitial deletion Xq21 is visible by cytogenetic analysis and two linked anonymous DNA markers, DXYS1 and DXS72, are deleted. In the second family, XL-45, an interstitial deletion was suspected on phenotypic grounds but could not be confirmed by high-resolution cytogenetic analysis. They used phenol-enhanced reassociation of 48,XXXX DNA in competition with excess XL-45 DNA to generate a library of cloned DNA enriched for sequences that might be deleted in XL-45. Two of the first 83 sequences characterized from the library were found to be deleted in probands from family XL-45 as well as from family XL-62. Isolation of these sequences proves that XL-45 does contain a submicroscopic deletion and provides a starting point for identifying overlapping genomic sequences that span the XL-45 deletion. Each overlapping sequence will be studied to identify exons from the choroideremia locus

  3. Isolation of anonymous DNA sequences from within a submicroscopic X chromosomal deletion in a patient with choroideremia, deafness, and mental retardation

    Energy Technology Data Exchange (ETDEWEB)

    Nussbaum, R.L.; Lesko, J.G.; Lewis, R.A.; Ledbetter, S.A.; Ledbetter, D.H.

    1987-09-01

    Choroideremia, an X-chromosome linked retinal dystrophy of unknown pathogenesis, causes progressive nightblindness and eventual central blindness in affected males by the third to fourth decade of life. Choroideremia has been mapped to Xq13-21 by tight linkage to restriction fragment length polymorphism loci. The authors have recently identified two families in which choroideremia is inherited with mental retardation and deafness. In family XL-62, an interstitial deletion Xq21 is visible by cytogenetic analysis and two linked anonymous DNA markers, DXYS1 and DXS72, are deleted. In the second family, XL-45, an interstitial deletion was suspected on phenotypic grounds but could not be confirmed by high-resolution cytogenetic analysis. They used phenol-enhanced reassociation of 48,XXXX DNA in competition with excess XL-45 DNA to generate a library of cloned DNA enriched for sequences that might be deleted in XL-45. Two of the first 83 sequences characterized from the library were found to be deleted in probands from family XL-45 as well as from family XL-62. Isolation of these sequences proves that XL-45 does contain a submicroscopic deletion and provides a starting point for identifying overlapping genomic sequences that span the XL-45 deletion. Each overlapping sequence will be studied to identify exons from the choroideremia locus.

  4. DNA sequencing conference, 2

    Energy Technology Data Exchange (ETDEWEB)

    Cook-Deegan, R.M. [Georgetown Univ., Kennedy Inst. of Ethics, Washington, DC (United States); Venter, J.C. [National Inst. of Neurological Disorders and Strokes, Bethesda, MD (United States); Gilbert, W. [Harvard Univ., Cambridge, MA (United States); Mulligan, J. [Stanford Univ., CA (United States); Mansfield, B.K. [Oak Ridge National Lab., TN (United States)

    1991-06-19

    This conference focused on DNA sequencing, genetic linkage mapping, physical mapping, informatics and bioethics. Several were used to study this sequencing and mapping. This article also discusses computer hardware and software aiding in the mapping of genes.

  5. DNA sequencing: chemical methods

    International Nuclear Information System (INIS)

    Limited base-specific or base-selective cleavage of a defined DNA fragment yields polynucleotide products, the length of which correlates with the positions of the particular base (or bases) in the original fragment. Sverdlov and co-workers recognized the possibility of using this principle for the determination of DNA sequences. In 1977 a fully elaborated method was introduced based on this principle, which allowed routine analysis of DNA sequences over distances greater than 100 nucleotide unite from a defined, radiolabeled terminus. Six procedures for partial cleavage were described. Simultaneous parallel resolution of an appropriate set of partial cleavage mixtures by polyacrylamide gel electrophoresis, followed by visualization of the radioactive bands by autoradiography, allows the deduction of nucleotide sequence

  6. Evolution of DNA Sequencing

    International Nuclear Information System (INIS)

    Sanger and coworkers introduced DNA sequencing in 1970s for the first time. It principally relied on termination of growing nucleotide chain when a dideoxythymidine triphosphate (ddTTP) was inserted in it. Detection of terminated sequences was done radiographically on Polyacrylamide Gel Electrophoresis (PAGE). Improvements that have evolved over time in original Sanger sequencing include replacement of radiography with fluorescence, use of separate fluorescent markers for each nucleotide, use of capillary electrophoresis instead of polyacrylamide gel electrophoresis and then introduction of capillary array electrophoresis. However, this technique suffered from few inherent limitations like decreased sensitivity for low level mutant alleles, complexities in analyzing highly polymorphic regions like Major Histocompatibility Complex (MHC) and high DNA concentrations required. Several Next Generation Sequencing (NGS) technologies have been introduced by Roche, Illumina and other commercial manufacturers that tend to overcome Sanger sequencing limitations and have been reviewed. Introduction of NGS in clinical research and medical diagnostics is expected to change entire diagnostic approach. These include study of cancer variants, detection of minimal residual disease, exome sequencing, detection of Single Nucleotide Polymorphisms (SNPs) and their disease association, epigenetic regulation of gene expression and sequencing of microorganisms genome. (author)

  7. Information Theory of DNA Sequencing

    CERN Document Server

    Motahari, Abolfazl; Tse, David

    2012-01-01

    DNA sequencing is the basic workhorse of modern day biology and medicine. Shotgun sequencing is the dominant technique used: many randomly located short fragments called reads are extracted from the DNA sequence, and these reads are assembled to reconstruct the original sequence. By drawing an analogy between the DNA sequencing problem and the classic communication problem, we define an information theoretic notion of sequencing capacity. This is the maximum number of DNA base pairs that can be resolved reliably per read, and provides a fundamental limit to the performance that can be achieved by any assembly algorithm. We compute the sequencing capacity explicitly for a simple statistical model of the DNA sequence and the read process. Using this framework, we also study the impact of noise in the read process on the sequencing capacity.

  8. Graphene nanodevices for DNA sequencing

    Science.gov (United States)

    Heerema, Stephanie J.; Dekker, Cees

    2016-02-01

    Fast, cheap, and reliable DNA sequencing could be one of the most disruptive innovations of this decade, as it will pave the way for personalized medicine. In pursuit of such technology, a variety of nanotechnology-based approaches have been explored and established, including sequencing with nanopores. Owing to its unique structure and properties, graphene provides interesting opportunities for the development of a new sequencing technology. In recent years, a wide range of creative ideas for graphene sequencers have been theoretically proposed and the first experimental demonstrations have begun to appear. Here, we review the different approaches to using graphene nanodevices for DNA sequencing, which involve DNA passing through graphene nanopores, nanogaps, and nanoribbons, and the physisorption of DNA on graphene nanostructures. We discuss the advantages and problems of each of these key techniques, and provide a perspective on the use of graphene in future DNA sequencing technology.

  9. Statistical properties of DNA sequences

    Science.gov (United States)

    Peng, C.-K.; Buldyrev, S. V.; Goldberger, A. L.; Havlin, S.; Mantegna, R. N.; Simons, M.; Stanley, H. E.

    1995-02-01

    We review evidence supporting the idea that the DNA sequence in genese containing non-coding regions is correlated, and that the correlation is remarkably long range - indeed, nucleotides thousands of base pairs distant are correlated. We do not find such a long-range correlation in the coding regions of the gene. We resolve the problem of the “non-stationarity” feature of the sequence of base pairs by applying a new algorithm called detrended fluctuation analysis (DFA). We address the claim of Voss that there is no difference in the statistical properties of coding and non-coding regions of DNA by systematically applying the DFA algorithm, as well as standard FFT analysis, to every DNA sequence (33 301 coding and 29 453 non-coding) in the entire GenBank database. Finally, we describe briefly some recent work showing that the non-coding sequences have certain statistical features in common with natural and artificial languages. Specifically, we adapt to DNA the Zipf approach to analyzing linguistic texts. These statistical properties of non-coding sequences support the possibility that non-coding regions of DNA may carry biological information.

  10. Fractals in DNA sequence analysis

    Institute of Scientific and Technical Information of China (English)

    Yu Zu-Guo(喻祖国); Vo Anh; Gong Zhi-Min(龚志民); Long Shun-Chao(龙顺潮)

    2002-01-01

    Fractal methods have been successfully used to study many problems in physics, mathematics, engineering, finance,and even in biology. There has been an increasing interest in unravelling the mysteries of DNA; for example, how can we distinguish coding and noncoding sequences, and the problems of classification and evolution relationship of organisms are key problems in bioinformatics. Although much research has been carried out by taking into consideration the long-range correlations in DNA sequences, and the global fractal dimension has been used in these works by other people, the models and methods are somewhat rough and the results are not satisfactory. In recent years, our group has introduced a time series model (statistical point of view) and a visual representation (geometrical point of view)to DNA sequence analysis. We have also used fractal dimension, correlation dimension, the Hurst exponent and the dimension spectrum (multifractal analysis) to discuss problems in this field. In this paper, we introduce these fractal models and methods and the results of DNA sequence analysis.

  11. Alcoholics Anonymous

    Science.gov (United States)

    ... Banners Site Help What's New Welcome to Alcoholics Anonymous ® NEED HELP WITH A DRINKING PROBLEM? If you ... drinking problem, wish to learn more about Alcoholics Anonymous or want to find A.A. near you, ...

  12. DNA Sequencing Using capillary Electrophoresis

    Energy Technology Data Exchange (ETDEWEB)

    Dr. Barry Karger

    2011-05-09

    The overall goal of this program was to develop capillary electrophoresis as the tool to be used to sequence for the first time the Human Genome. Our program was part of the Human Genome Project. In this work, we were highly successful and the replaceable polymer we developed, linear polyacrylamide, was used by the DOE sequencing lab in California to sequence a significant portion of the human genome using the MegaBase multiple capillary array electrophoresis instrument. In this final report, we summarize our efforts and success. We began our work by separating by capillary electrophoresis double strand oligonucleotides using cross-linked polyacrylamide gels in fused silica capillaries. This work showed the potential of the methodology. However, preparation of such cross-linked gel capillaries was difficult with poor reproducibility, and even more important, the columns were not very stable. We improved stability by using non-cross linked linear polyacrylamide. Here, the entangled linear chains could move when osmotic pressure (e.g. sample injection) was imposed on the polymer matrix. This relaxation of the polymer dissipated the stress in the column. Our next advance was to use significantly lower concentrations of the linear polyacrylamide that the polymer could be automatically blown out after each run and replaced with fresh linear polymer solution. In this way, a new column was available for each analytical run. Finally, while testing many linear polymers, we selected linear polyacrylamide as the best matrix as it was the most hydrophilic polymer available. Under our DOE program, we demonstrated initially the success of the linear polyacrylamide to separate double strand DNA. We note that the method is used even today to assay purity of double stranded DNA fragments. Our focus, of course, was on the separation of single stranded DNA for sequencing purposes. In one paper, we demonstrated the success of our approach in sequencing up to 500 bases. Other

  13. Nanopore DNA sequencing with MspA

    OpenAIRE

    Derrington, Ian M.; Butler, Tom Z.; Collins, Marcus D.; Manrao, Elizabeth; Pavlenok, Mikhail; Niederweis, Michael; Gundlach, Jens H.

    2010-01-01

    Nanopore sequencing has the potential to become a direct, fast, and inexpensive DNA sequencing technology. The simplest form of nanopore DNA sequencing utilizes the hypothesis that individual nucleotides of single-stranded DNA passing through a nanopore will uniquely modulate an ionic current flowing through the pore, allowing the record of the current to yield the DNA sequence. We demonstrate that the ionic current through the engineered Mycobacterium smegmatis porin A, MspA, has the ability...

  14. Nanopore DNA sequencing with MspA.

    Science.gov (United States)

    Derrington, Ian M; Butler, Tom Z; Collins, Marcus D; Manrao, Elizabeth; Pavlenok, Mikhail; Niederweis, Michael; Gundlach, Jens H

    2010-09-14

    Nanopore sequencing has the potential to become a direct, fast, and inexpensive DNA sequencing technology. The simplest form of nanopore DNA sequencing utilizes the hypothesis that individual nucleotides of single-stranded DNA passing through a nanopore will uniquely modulate an ionic current flowing through the pore, allowing the record of the current to yield the DNA sequence. We demonstrate that the ionic current through the engineered Mycobacterium smegmatis porin A, MspA, has the ability to distinguish all four DNA nucleotides and resolve single-nucleotides in single-stranded DNA when double-stranded DNA temporarily holds the nucleotides in the pore constriction. Passing DNA with a series of double-stranded sections through MspA provides proof of principle of a simple DNA sequencing method using a nanopore. These findings highlight the importance of MspA in the future of nanopore sequencing. PMID:20798343

  15. Fluorescence-detected DNA sequencing

    Energy Technology Data Exchange (ETDEWEB)

    Haugland, R.P.

    1990-01-01

    Our research effort funded by this grant primarily focused on development of suitable fluorescent dyes for DNA sequencing studies. Prior to our efforts, the dyes being sued in commercial DNA sequencers were various versions of fluorescein dyes for the shorter wavelengths and of rhodamine dyes for the longer wavelengths. Our initial goal was to synthesize a set of four dyes that could all be excited by the 488 and 514 nm line of the argon laser lines and that have emission spectra that minimize spectral overlap. The specific result sought was higher fluorescent intensity, particularly of the longest wavelength dyes than was available using existing dyes. Another important property of the desired set of dyes was uniform ionic charge in order to have minimum interference on the electrophoretic mobility during the sequencing. During the period of this grant we prepared and characterized four types of dyes: fluorescent bifluorophores, derivatives of rhodamine dyes, derivatives of rhodol dyes and derivatives of boron dipyrromethene difluoride (BODIPY{trademark}) dyes.

  16. Variable copy number DNA sequences in rice.

    Science.gov (United States)

    Kikuchi, S; Takaiwa, F; Oono, K

    1987-12-01

    We have cloned two types of variable copy number DNA sequences from the rice embryo genome. One of these sequences, which was cloned in pRB301, was amplified about 50-fold during callus formation and diminished in copy number to the embryonic level during regeneration. The other clone, named pRB401, showed the reciprocal pattern. The copy numbers of both sequences were changed even in the early developmental stage and eliminated from nuclear DNA along with growth of the plant. Sequencing analysis of the pRB301 insert revealed some open reading frames and direct repeat structures, but corresponding sequences were not identified in the EMBL and LASL DNA databases. Sequencing of the nuclear genomic fragment cloned in pRB401 revealed the presence of the 3'rps12-rps7 region of rice chloroplast DNA. Our observations suggest that during callus formation (dedifferentiation), regeneration and the growth process the copy numbers of some DNA sequences are variable and that nuclear integrated chloroplast DNA acts as a variable copy number sequence in the rice genome. Based on data showing a common sequence in mitochondria and chloroplast DNA of maize (Stern and Lonsdale 1982) and that the rps12 gene of tobacco chloroplast DNA is a divided gene (Torazawa et al. 1986), it is suggested that the sequence on the inverted repeat structure of chloroplast DNA may have the character of a movable genetic element. PMID:3481021

  17. Suicidal nucleotide sequences for DNA polymerization.

    OpenAIRE

    Samadashwily, G M; Dayn, A; Mirkin, S M

    1993-01-01

    Studying the activity of T7 DNA polymerase (Sequenase) on open circular DNAs, we observed virtually complete termination within potential triplex-forming sequences. Mutations destroying the triplex potential of the sequences prevented termination, while compensatory mutations restoring triplex potential restored it. We hypothesize that strand displacement during DNA polymerization of double-helical templates brings three DNA strands (duplex DNA downstream of the polymerase plus a displaced ov...

  18. Fibonacci Sequence and Supramolecular Structure of DNA.

    Science.gov (United States)

    Shabalkin, I P; Grigor'eva, E Yu; Gudkova, M V; Shabalkin, P I

    2016-05-01

    We proposed a new model of supramolecular DNA structure. Similar to the previously developed by us model of primary DNA structure [11-15], 3D structure of DNA molecule is assembled in accordance to a mathematic rule known as Fibonacci sequence. Unlike primary DNA structure, supramolecular 3D structure is assembled from complex moieties including a regular tetrahedron and a regular octahedron consisting of monomers, elements of the primary DNA structure. The moieties of the supramolecular DNA structure forming fragments of regular spatial lattice are bound via linker (joint) sequences of the DNA chain. The lattice perceives and transmits information signals over a considerable distance without acoustic aberrations. Linker sequences expand conformational space between lattice segments allowing their sliding relative to each other under the action of external forces. In this case, sliding is provided by stretching of the stacked linker sequences. PMID:27265133

  19. DNA-catalyzed sequence-specific hydrolysis of DNA

    OpenAIRE

    Chandra, Madhavaiah; Sachdeva, Amit; Silverman, Scott K.

    2009-01-01

    Deoxyribozymes (DNA catalysts) have been reported for cleavage of RNA phosphodiester linkages, but cleaving peptide or DNA phosphodiester linkages is much more challenging. Using in vitro selection, here we identified deoxyribozymes that sequence-specifically hydrolyze DNA with multiple turnover and rate enhancement of 108 (possibly as high as 1014). The new DNA catalysts require both Mn2+ and Zn2+, which is intriguing because many natural DNA nucleases are bimetallic protein enzymes.

  20. Sequence Affects the Cyclization of DNA Minicircles.

    Science.gov (United States)

    Wang, Qian; Pettitt, B Montgomery

    2016-03-17

    Understanding how the sequence of a DNA molecule affects its dynamic properties is a central problem affecting biochemistry and biotechnology. The process of cyclizing short DNA, as a critical step in molecular cloning, lacks a comprehensive picture of the kinetic process containing sequence information. We have elucidated this process by using coarse-grained simulations, enhanced sampling methods, and recent theoretical advances. We are able to identify the types and positions of structural defects during the looping process at a base-pair level. Correlations along a DNA molecule dictate critical sequence positions that can affect the looping rate. Structural defects change the bending elasticity of the DNA molecule from a harmonic to subharmonic potential with respect to bending angles. We explore the subelastic chain as a possible model in loop formation kinetics. A sequence-dependent model is developed to qualitatively predict the relative loop formation time as a function of DNA sequence. PMID:26938490

  1. Nucleotide sequence preservation of human mitochondrial DNA

    International Nuclear Information System (INIS)

    Recombinant DNA techniques have been used to quantitate the amount of nucleotide sequence divergence in the mitochondrial DNA population of individual normal humans. Mitochondrial DNA was isolated from the peripheral blood lymphocytes of five normal humans and cloned in M13 mp11; 49 kilobases of nucleotide sequence information was obtained from 248 independently isolated clones from the five normal donors. Both between- and within-individual differences were identified. Between-individual differences were identified in approximately = to 1/200 nucleotides. In contrast, only one within-individual difference was identified in 49 kilobases of nucleotide sequence information. This high degree of mitochondrial nucleotide sequence homogeneity in human somatic cells is in marked contrast to the rapid evolutionary divergence of human mitochondrial DNA and suggests the existence of mechanisms for the concerted preservation of mammalian mitochondrial DNA sequences in single organisms

  2. Mitochondrial DNA sequence evolution in shorebird populations.

    NARCIS (Netherlands)

    Wenink, P.W.

    1994-01-01

    This thesis describes the global molecular population structure of two shorebird species, in particular of the dunlin, Calidris alpina, by means of comparative sequence analysis of the most variable part of the mitochondrial DNA (mtDNA) genome. There are several reasons why mtDNA is the molecule of

  3. Compressing DNA sequence databases with coil

    OpenAIRE

    Hendy Michael D; White W Timothy J

    2008-01-01

    Abstract Background Publicly available DNA sequence databases such as GenBank are large, and are growing at an exponential rate. The sheer volume of data being dealt with presents serious storage and data communications problems. Currently, sequence data is usually kept in large "flat files," which are then compressed using standard Lempel-Ziv (gzip) compression – an approach which rarely achieves good compression ratios. While much research has been done on compressing individual DNA sequenc...

  4. Anonymous Gossiping

    CERN Document Server

    Datta, Anwitaman

    2010-01-01

    In this paper we introduce a novel gossiping primitive to support privacy preserving data analytics (PPDA). In contrast to existing computational PPDA primitives such as secure multiparty computation and data randomization based approaches, the proposed primitive `anonymous gossiping' is a communication primitive for privacy preserving personalized information aggregation complementing such traditional computational analytics. We realize this novel primitive by composing existing gossiping mechanisms for peer sampling & information aggregation and onion routing technique for establishing anonymous communication. This is more an `ideas' paper, rather than providing concrete and quantified results.

  5. Mitochondrial DNA sequence evolution in shorebird populations.

    OpenAIRE

    Wenink, P W

    1994-01-01

    This thesis describes the global molecular population structure of two shorebird species, in particular of the dunlin, Calidris alpina, by means of comparative sequence analysis of the most variable part of the mitochondrial DNA (mtDNA) genome. There are several reasons why mtDNA is the molecule of choice to probe the recent evolutionary history of a species. Most importantly, mtDNA accumulates substitutions at a high average rate that permits the tracing of genealogies within the time frame ...

  6. DNA display I. Sequence-encoded routing of DNA populations.

    Directory of Open Access Journals (Sweden)

    David R Halpin

    2004-07-01

    Full Text Available Recently reported technologies for DNA-directed organic synthesis and for DNA computing rely on routing DNA populations through complex networks. The reduction of these ideas to practice has been limited by a lack of practical experimental tools. Here we describe a modular design for DNA routing genes, and routing machinery made from oligonucleotides and commercially available chromatography resins. The routing machinery partitions nanomole quantities of DNA into physically distinct subpools based on sequence. Partitioning steps can be iterated indefinitely, with worst-case yields of 85% per step. These techniques facilitate DNA-programmed chemical synthesis, and thus enable a materials biology that could revolutionize drug discovery.

  7. Long range correlations in DNA sequences

    CERN Document Server

    Mohanty, A K

    2002-01-01

    The so called long range correlation properties of DNA sequences are studied using the variance analyses of the density distribution of a single or a group of nucleotides in a model independent way. This new method which was suggested earlier has been applied to extract slope parameters that characterize the correlation properties for several intron containing and intron less DNA sequences. An important aspect of all the DNA sequences is the properties of complimentarity by virtue of which any two complimentary distributions (like GA is complimentary to TC or G is complimentary to ATC) have identical fluctuations at all scales although their distribution functions need not be identical. Due to this complimentarity, the famous DNA walk representation whose statistical interpretation is still unresolved is shown to be a special case of the present formalism with a density distribution corresponding to a purine or a pyrimidine group. Another interesting aspect of most of the DNA sequences is that the factorial m...

  8. Dynamics and Control of DNA Sequence Amplification

    CERN Document Server

    Marimuthu, Karthikeyan

    2014-01-01

    DNA amplification is the process of replication of a specified DNA sequence \\emph{in vitro} through time-dependent manipulation of its external environment. A theoretical framework for determination of the optimal dynamic operating conditions of DNA amplification reactions, for any specified amplification objective, is presented based on first-principles biophysical modeling and control theory. Amplification of DNA is formulated as a problem in control theory with optimal solutions that can differ considerably from strategies typically used in practice. Using the Polymerase Chain Reaction (PCR) as an example, sequence-dependent biophysical models for DNA amplification are cast as control systems, wherein the dynamics of the reaction are controlled by a manipulated input variable. Using these control systems, we demonstrate that there exists an optimal temperature cycling strategy for geometric amplification of any DNA sequence and formulate optimal control problems that can be used to derive the optimal tempe...

  9. Selection of DNA clones with enhancer sequences.

    OpenAIRE

    Asoh, S; Lee-Kwon, W; Mouradian, M M; Nirenberg, M

    1994-01-01

    A method is described for selection of DNA clones that contain enhancer sequences that activate gene expression. An Escherichia coli-rodent cell shuttle vector, pPyE0, was used that contains polyoma viral DNA without the polyoma enhancer region. Replication of pPyE0 DNA in mouse cells is markedly reduced due to deletion of the polyoma enhancer region. Insertion of mouse genomic DNA fragments that contain putative enhancer sequences into pPyE0 adjacent to the polyoma origin of replication rest...

  10. Automated preparation of DNA sequences for publication.

    OpenAIRE

    Shapiro, M B; Senapathy, P

    1986-01-01

    A computer program which draws DNA sequences is described. A simple method is used which enables the user to highlight or annotate specific parts of a sequence. The sizes of the characters in the sequence to be drawn are specified by the user. In addition, vertical spacing between lines and horizontal spacing between characters can be specified. Sequences can be prepared and high quality output produced on a plotter in a short period of time, making the program advantageous to use over typing...

  11. EGNAS: an exhaustive DNA sequence design algorithm

    Directory of Open Access Journals (Sweden)

    Kick Alfred

    2012-06-01

    Full Text Available Abstract Background The molecular recognition based on the complementary base pairing of deoxyribonucleic acid (DNA is the fundamental principle in the fields of genetics, DNA nanotechnology and DNA computing. We present an exhaustive DNA sequence design algorithm that allows to generate sets containing a maximum number of sequences with defined properties. EGNAS (Exhaustive Generation of Nucleic Acid Sequences offers the possibility of controlling both interstrand and intrastrand properties. The guanine-cytosine content can be adjusted. Sequences can be forced to start and end with guanine or cytosine. This option reduces the risk of “fraying” of DNA strands. It is possible to limit cross hybridizations of a defined length, and to adjust the uniqueness of sequences. Self-complementarity and hairpin structures of certain length can be avoided. Sequences and subsequences can optionally be forbidden. Furthermore, sequences can be designed to have minimum interactions with predefined strands and neighboring sequences. Results The algorithm is realized in a C++ program. TAG sequences can be generated and combined with primers for single-base extension reactions, which were described for multiplexed genotyping of single nucleotide polymorphisms. Thereby, possible foldback through intrastrand interaction of TAG-primer pairs can be limited. The design of sequences for specific attachment of molecular constructs to DNA origami is presented. Conclusions We developed a new software tool called EGNAS for the design of unique nucleic acid sequences. The presented exhaustive algorithm allows to generate greater sets of sequences than with previous software and equal constraints. EGNAS is freely available for noncommercial use at http://www.chm.tu-dresden.de/pc6/EGNAS.

  12. Chromatid interchanges at intrachromosomal telomeric DNA sequences

    International Nuclear Information System (INIS)

    Chinese hamster Don cells were exposed to X-rays, mitomycin C and teniposide (VM-26) to induce chromatid exchanges (quadriradials and triradials). After fluorescence in situ hybridization (FISH) of telomere sequences it was found that interstitial telomere-like DNA sequence arrays presented around five times more breakage-rearrangements than the genome overall. This high recombinogenic capacity was independent of the clastogen, suggesting that this susceptibility is not related to the initial mechanisms of DNA damage. (author)

  13. Comparative statistics for DNA and protein sequences: multiple sequence analysis.

    OpenAIRE

    Karlin, S.; Ghandour, G

    1985-01-01

    Concepts and methods [Karlin, S. & Ghandour, G. (1985) Proc. Natl. Acad. Sci. USA 82, 5800-5804] for the analysis of patterns and relationships are extended to multiple DNA and protein sequences. Functionals include multiple sequence common word occurrence distributions, characterizations of high frequency shared words, and ascertainment of long block identities. Various comparisons of sequences using natural alphabets obtained from grouping nucleotides or amino acids by their chemical and fu...

  14. Nucleotide Capacitance Calculation for DNA Sequencing

    OpenAIRE

    Lu, Jun-Qiang; Zhang, X.-G.

    2008-01-01

    Using a first-principles linear response theory, the capacitance of the DNA nucleotides, adenine, cytosine, guanine, and thymine, are calculated. The difference in the capacitance between the nucleotides is studied with respect to conformational distortion. The result suggests that although an alternate current capacitance measurement of a single-stranded DNA chain threaded through a nanogap electrode may not be sufficient to be used as a standalone method for rapid DNA sequencing, the capaci...

  15. Against anonymity.

    Science.gov (United States)

    Baker, Robert

    2014-05-01

    In 'New Threats to Academic Freedom' Francesca Minerva argues that anonymity for the authors of controversial articles is a prerequisite for academic freedom in the Internet age. This argument draws its intellectual and emotional power from the author's account of the reaction to the on-line publication of ' After-birth abortion: why should the baby live?'--an article that provoked cascades of hostile postings and e-mails. Reflecting on these events, Minerva proposes that publishers should offer the authors of controversial articles the option of publishing their articles anonymously. This response reviews the history of anonymous publication and concludes that its reintroduction in the Internet era would recreate problems similar to those that led print journals to abandon the practice: corruption of scholarly discourse by invective and hate speech, masked conflicts of interest, and a diminution of editorial accountability. It also contends that Minerva misreads the intent of the hostile e-mails provoked by 'After-birth abortion,' and that ethicists who publish controversial articles should take responsibility by dialoguing with their critics--even those whose critiques are emotionally charged and hostile. PMID:24724540

  16. Sequencing intractable DNA to close microbial genomes.

    Directory of Open Access Journals (Sweden)

    Richard A Hurt

    Full Text Available Advancement in high throughput DNA sequencing technologies has supported a rapid proliferation of microbial genome sequencing projects, providing the genetic blueprint for in-depth studies. Oftentimes, difficult to sequence regions in microbial genomes are ruled "intractable" resulting in a growing number of genomes with sequence gaps deposited in databases. A procedure was developed to sequence such problematic regions in the "non-contiguous finished" Desulfovibrio desulfuricans ND132 genome (6 intractable gaps and the Desulfovibrio africanus genome (1 intractable gap. The polynucleotides surrounding each gap formed GC rich secondary structures making the regions refractory to amplification and sequencing. Strand-displacing DNA polymerases used in concert with a novel ramped PCR extension cycle supported amplification and closure of all gap regions in both genomes. The developed procedures support accurate gene annotation, and provide a step-wise method that reduces the effort required for genome finishing.

  17. Osmylated DNA, a novel concept for sequencing DNA using nanopores

    International Nuclear Information System (INIS)

    Saenger sequencing has led the advances in molecular biology, while faster and cheaper next generation technologies are urgently needed. A newer approach exploits nanopores, natural or solid-state, set in an electrical field, and obtains base sequence information from current variations due to the passage of a ssDNA molecule through the pore. A hurdle in this approach is the fact that the four bases are chemically comparable to each other which leads to small differences in current obstruction. ‘Base calling’ becomes even more challenging because most nanopores sense a short sequence and not individual bases. Perhaps sequencing DNA via nanopores would be more manageable, if only the bases were two, and chemically very different from each other; a sequence of 1s and 0s comes to mind. Osmylated DNA comes close to such a sequence of 1s and 0s. Osmylation is the addition of osmium tetroxide bipyridine across the C5–C6 double bond of the pyrimidines. Osmylation adds almost 400% mass to the reactive base, creates a sterically and electronically notably different molecule, labeled 1, compared to the unreactive purines, labeled 0. If osmylated DNA were successfully sequenced, the result would be a sequence of osmylated pyrimidines (1), and purines (0), and not of the actual nucleobases. To solve this problem we studied the osmylation reaction with short oligos and with M13mp18, a long ssDNA, developed a UV–vis assay to measure extent of osmylation, and designed two protocols. Protocol A uses mild conditions and yields osmylated thymidines (1), while leaving the other three bases (0) practically intact. Protocol B uses harsher conditions and effectively osmylates both pyrimidines, but not the purines. Applying these two protocols also to the complementary of the target polynucleotide yields a total of four osmylated strands that collectively could define the actual base sequence of the target DNA. (paper)

  18. Physical approaches to DNA sequencing and detection

    CERN Document Server

    Zwolak, Michael

    2007-01-01

    With the continued improvement of sequencing technologies, the prospect of genome-based medicine is now at the forefront of scientific research. To realize this potential, however, we need a revolutionary sequencing method for the cost-effective and rapid interrogation of individual genomes. This capability is likely to be provided by a physical approach to probing DNA at the single nucleotide level. This is in sharp contrast to current techniques and instruments which probe, through chemical elongation, electrophoresis, and optical detection, length differences and terminating bases of strands of DNA. In this Colloquium we review several physical approaches to DNA detection that have the potential to deliver fast and low-cost sequencing. Center-fold to these approaches is the concept of nanochannels or nanopores which allow for the spatial confinement of DNA molecules. In addition to their possible impact in medicine and biology, the methods offer ideal test beds to study open scientific issues and challenge...

  19. Cloned endogenous retroviral sequences from human DNA.

    OpenAIRE

    Bonner, T I; O'Connell, C; Cohen, M.

    1982-01-01

    We have screened a human DNA library using as probe a chimpanzee sequence that contains homology to the polymerase gene of the endogenous baboon virus. One set of overlapping clones spans about 20 kilobases and contains regions of DNA sequence homology to the gag p30, gag p15, and polymerase genes of Moloney murine leukemia virus. Furthermore, the spacings are the same as in Moloney virus between these sequences and a 480-nucleotide region that has the structural characteristics of a 3' copy ...

  20. Dynamics and control of DNA sequence amplification

    International Nuclear Information System (INIS)

    DNA amplification is the process of replication of a specified DNA sequence in vitro through time-dependent manipulation of its external environment. A theoretical framework for determination of the optimal dynamic operating conditions of DNA amplification reactions, for any specified amplification objective, is presented based on first-principles biophysical modeling and control theory. Amplification of DNA is formulated as a problem in control theory with optimal solutions that can differ considerably from strategies typically used in practice. Using the Polymerase Chain Reaction as an example, sequence-dependent biophysical models for DNA amplification are cast as control systems, wherein the dynamics of the reaction are controlled by a manipulated input variable. Using these control systems, we demonstrate that there exists an optimal temperature cycling strategy for geometric amplification of any DNA sequence and formulate optimal control problems that can be used to derive the optimal temperature profile. Strategies for the optimal synthesis of the DNA amplification control trajectory are proposed. Analogous methods can be used to formulate control problems for more advanced amplification objectives corresponding to the design of new types of DNA amplification reactions

  1. Dynamics and control of DNA sequence amplification

    Energy Technology Data Exchange (ETDEWEB)

    Marimuthu, Karthikeyan [Department of Chemical Engineering and Center for Advanced Process Decision-Making, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213 (United States); Chakrabarti, Raj, E-mail: raj@pmc-group.com, E-mail: rajc@andrew.cmu.edu [Department of Chemical Engineering and Center for Advanced Process Decision-Making, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213 (United States); Division of Fundamental Research, PMC Advanced Technology, Mount Laurel, New Jersey 08054 (United States)

    2014-10-28

    DNA amplification is the process of replication of a specified DNA sequence in vitro through time-dependent manipulation of its external environment. A theoretical framework for determination of the optimal dynamic operating conditions of DNA amplification reactions, for any specified amplification objective, is presented based on first-principles biophysical modeling and control theory. Amplification of DNA is formulated as a problem in control theory with optimal solutions that can differ considerably from strategies typically used in practice. Using the Polymerase Chain Reaction as an example, sequence-dependent biophysical models for DNA amplification are cast as control systems, wherein the dynamics of the reaction are controlled by a manipulated input variable. Using these control systems, we demonstrate that there exists an optimal temperature cycling strategy for geometric amplification of any DNA sequence and formulate optimal control problems that can be used to derive the optimal temperature profile. Strategies for the optimal synthesis of the DNA amplification control trajectory are proposed. Analogous methods can be used to formulate control problems for more advanced amplification objectives corresponding to the design of new types of DNA amplification reactions.

  2. Compressing DNA sequence databases with coil

    Directory of Open Access Journals (Sweden)

    Hendy Michael D

    2008-05-01

    Full Text Available Abstract Background Publicly available DNA sequence databases such as GenBank are large, and are growing at an exponential rate. The sheer volume of data being dealt with presents serious storage and data communications problems. Currently, sequence data is usually kept in large "flat files," which are then compressed using standard Lempel-Ziv (gzip compression – an approach which rarely achieves good compression ratios. While much research has been done on compressing individual DNA sequences, surprisingly little has focused on the compression of entire databases of such sequences. In this study we introduce the sequence database compression software coil. Results We have designed and implemented a portable software package, coil, for compressing and decompressing DNA sequence databases based on the idea of edit-tree coding. coil is geared towards achieving high compression ratios at the expense of execution time and memory usage during compression – the compression time represents a "one-off investment" whose cost is quickly amortised if the resulting compressed file is transmitted many times. Decompression requires little memory and is extremely fast. We demonstrate a 5% improvement in compression ratio over state-of-the-art general-purpose compression tools for a large GenBank database file containing Expressed Sequence Tag (EST data. Finally, coil can efficiently encode incremental additions to a sequence database. Conclusion coil presents a compelling alternative to conventional compression of flat files for the storage and distribution of DNA sequence databases having a narrow distribution of sequence lengths, such as EST data. Increasing compression levels for databases having a wide distribution of sequence lengths is a direction for future work.

  3. Group Anonymity

    CERN Document Server

    Chertov, Oleg; 10.1007/978-3-642-14058-7_61

    2010-01-01

    In recent years the amount of digital data in the world has risen immensely. But, the more information exists, the greater is the possibility of its unwanted disclosure. Thus, the data privacy protection has become a pressing problem of the present time. The task of individual privacy-preserving is being thoroughly studied nowadays. At the same time, the problem of statistical disclosure control for collective (or group) data is still open. In this paper we propose an effective and relatively simple (wavelet-based) way to provide group anonymity in collective data. We also provide a real-life example to illustrate the method.

  4. cDNA sequence quality data - Budding yeast cDNA sequencing project | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available Budding yeast cDNA sequencing project cDNA sequence quality data Data detail Data name cDNA sequence quality... data Description of data contents Phred's quality score. PHD format, one file to a single cDNA data, and co...ription Download License Update History of This Database Site Policy | Contact Us cDNA sequence quality data - Budding yeast cDNA sequencing project | LSDB Archive ...

  5. Quantum-Sequencing: Fast electronic single DNA molecule sequencing

    Science.gov (United States)

    Casamada Ribot, Josep; Chatterjee, Anushree; Nagpal, Prashant

    2014-03-01

    A major goal of third-generation sequencing technologies is to develop a fast, reliable, enzyme-free, high-throughput and cost-effective, single-molecule sequencing method. Here, we present the first demonstration of unique ``electronic fingerprint'' of all nucleotides (A, G, T, C), with single-molecule DNA sequencing, using Quantum-tunneling Sequencing (Q-Seq) at room temperature. We show that the electronic state of the nucleobases shift depending on the pH, with most distinct states identified at acidic pH. We also demonstrate identification of single nucleotide modifications (methylation here). Using these unique electronic fingerprints (or tunneling data), we report a partial sequence of beta lactamase (bla) gene, which encodes resistance to beta-lactam antibiotics, with over 95% success rate. These results highlight the potential of Q-Seq as a robust technique for next-generation sequencing.

  6. Simplifying the mosaic description of DNA sequences

    CERN Document Server

    Azad, R K; Li, W; Ramaswamy, R; Azad, Rajeev K.; Li, Wentian; Ramaswamy, Ramakrishna

    2002-01-01

    By using the Jensen-Shannon divergence, genomic DNA can be divided into compositionally distinct domains through a standard recursive segmentation procedure. Each domain, while significantly different from its neighbours, may however share compositional similarity with one or more distant (non--neighbouring) domains. We thus obtain a coarse--grained description of the given DNA string in terms of a smaller set of distinct domain labels. This yields a minimal domain description of a given DNA sequence, significantly reducing its organizational complexity. This procedure gives a new means of evaluating genomic complexity as one examines organisms ranging from bacteria to human. The mosaic organization of DNA sequences could have originated from the insertion of fragments of one genome (the parasite) inside another (the host), and we present numerical experiments that are suggestive of this scenario.

  7. Indexing for Large DNA Database Sequences

    Directory of Open Access Journals (Sweden)

    S. M. Wohoush & M.H. Saheb

    2011-10-01

    Full Text Available Bioinformatics data consists of a huge amount of information due to the large number ofsequences, the very high sequences lengths and the daily new additions. This data need to beefficiently accessed for many needs. What makes one DNA data item distinct from another is itsDNA sequence. DNA sequence consists of a combination of four characters which are A, C, G, Tand have different lengths. Use a suitable representation of DNA sequences, and a suitable indexstructure to hold this representation at main memory will lead to have efficient processing byaccessing the DNA sequences through indexing, and will reduce number of disk I/O accesses.I/O operations needed at the end, to avoid false hits, we reduce the number of candidate DNAsequences that need to be checked by pruning, so no need to search the whole database. Weneed to have a suitable index for searching DNA sequences efficiently, with suitable index sizeand searching time. The suitable selection of relation fields, where index is build upon has a bigeffect on index size and search time. Our experiments use the n-gram wavelet transformationupon one field and multi-fields index structure under the relational DBMS environment. Resultsshow the need to consider index size and search time while using indexing carefully. Increasingwindow size decreases the amount of I/O reference. The use of a single field and multiple fieldsindexing is highly affected by window size value. Increasing window size value lead to bettersearching time with special type index using single filed indexing. While the search time is almostgood and the same with most index types when using multiple field indexing. Storage spaceneeded for RDMS indexing types are almost the same or greater than the actual data.

  8. Detecting seeded motifs in DNA sequences

    OpenAIRE

    Pizzi, Cinzia; Bortoluzzi, Stefania; Bisognin, Andrea; Coppe, Alessandro; Danieli, Gian Antonio

    2005-01-01

    The problem of detecting DNA motifs with functional relevance in real biological sequences is difficult due to a number of biological, statistical and computational issues and also because of the lack of knowledge about the structure of searched patterns. Many algorithms are implemented in fully automated processes, which are often based upon a guess of input parameters from the user at the very first step. In this paper, we present a novel method for the detection of seeded DNA motifs, compo...

  9. Sequence-Specific Ultrasonic Cleavage of DNA

    OpenAIRE

    Grokhovsky, Sergei L.; Il'icheva, Irina A.; Nechipurenko, Dmitry Yu.; Golovkin, Michail V.; Panchenko, Larisa A.; Polozov, Robert V.; Nechipurenko, Yury D.

    2011-01-01

    We investigated the phenomenon of ultrasonic cleavage of DNA by analyzing a large set of cleavage patterns of DNA restriction fragments using polyacrylamide gel electrophoresis. The cleavage intensity of individual phosphodiester bonds was found to depend on the nucleotide sequence and the position of the bond with respect to the ends of the fragment. The relative intensities of cleavage of the central phosphodiester bond in 16 dinucleotides and 256 tetranucleotides were determined by multiva...

  10. Chromosome number9 specific repetitive DNA sequence

    International Nuclear Information System (INIS)

    Human repetitive DNA libraries have been constructed and various recombinant DNA clones isolated that are likely candidates for chromosome specific sequences. The first clone tested (pHuR 98; plasmid human repeat 98) was biotinylated and hybridized to human chromosomes in situ. The hybridized recombinant probe was detected with fluoresceinated avidin, and chromosomes were counter-stained with either propidium iodide or distamycin-DAPI. Specific hybridization to chromosome band 9q1 was obtained. The localization was confirmed by hybridizing radiolabeled pHuR 98 DNA to human chromosomes sorted by flow cytometry. Various methods, including orthogonal field pulsed gel electrophoresis analysis indicate that 75 kilobase blocks of this sequence are interspersed with other repetitive DNA sequences in this chromosome band. This study is the first to report a human repetitive DNA sequence uniquely localized to a specific chromosome. This clone provides an easily detected and highly specific chromosomal marker for molecular cytogenetic analyses in numerous basic research and clinical studies

  11. Statistical and linguistic features of DNA sequences

    Science.gov (United States)

    Havlin, S.; Buldyrev, S. V.; Goldberger, A. L.; Mantegna, R. N.; Peng, C. K.; Simons, M.; Stanley, H. E.

    1995-01-01

    We present evidence supporting the idea that the DNA sequence in genes containing noncoding regions is correlated, and that the correlation is remarkably long range--indeed, base pairs thousands of base pairs distant are correlated. We do not find such a long-range correlation in the coding regions of the gene. We resolve the problem of the "non-stationary" feature of the sequence of base pairs by applying a new algorithm called Detrended Fluctuation Analysis (DFA). We address the claim of Voss that there is no difference in the statistical properties of coding and noncoding regions of DNA by systematically applying the DFA algorithm, as well as standard FFT analysis, to all eukaryotic DNA sequences (33 301 coding and 29 453 noncoding) in the entire GenBank database. We describe a simple model to account for the presence of long-range power-law correlations which is based upon a generalization of the classic Levy walk. Finally, we describe briefly some recent work showing that the noncoding sequences have certain statistical features in common with natural languages. Specifically, we adapt to DNA the Zipf approach to analyzing linguistic texts, and the Shannon approach to quantifying the "redundancy" of a linguistic text in terms of a measurable entropy function. We suggest that noncoding regions in plants and invertebrates may display a smaller entropy and larger redundancy than coding regions, further supporting the possibility that noncoding regions of DNA may carry biological information.

  12. DNA sequencing by synthesis with degenerate primers

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    The degenerate primer-based sequencing Was developed by a synthesis method(DP-SBS)for high-throughput DNA sequencing,in which a set of degenerate primers are hybridized on the arrayed DNA templates and extended by DNA polymerase on microarrays.In this method,adifferent set of degenerate primers containing a give nnumber(n)of degenerate nucleotides at the 3'-ends were annealed to the sequenced templates that were immobilized on the solid surface.The nucleotides(n+1)on the template sequences were determined by detecting the incorporation of fluorescent labeled nucleotides.The fluorescent labeled nucleotide was incorporated into the primer in a base-specific manner after the enzymatic primer extension reactions and nine-base length were read out accurately.The main advanmge of the DP-SBS is that the method only uses very conventional biochemical reagents and avoids the complicated special chemical reagents for removing the labeled nucleotides and reactivating the primer for further extension.From the present study,it is found that the DP-SBS method is reliable,simple,and cost-effective for laboratory-sequencing a large amount of short DNA fragments.

  13. Modified Genetic Algorithm for DNA Sequence Assembly by Shotgun and Hybridization Sequencing Techniques

    OpenAIRE

    Prof.Narayan Kumar Sahu; Prof.Somesh Dewangan; Prof.Akash Wanjari

    2012-01-01

    Since the advent of rapid DNA sequencing methods in 1976, scientists have had the problem of inferring DNA sequences from sequenced fragments. Shotgun sequencing is a well-established biological and computational method used in practice. Many conventional algorithms for shotgun sequencing are based on the notion of pair wise fragment overlap. While shotgun sequencing infers a DNA sequence given the sequences of overlapping fragments, a recent and complementary method, called sequencing by hy...

  14. The DNA sequence of human chromosome 7.

    Science.gov (United States)

    Hillier, Ladeana W; Fulton, Robert S; Fulton, Lucinda A; Graves, Tina A; Pepin, Kymberlie H; Wagner-McPherson, Caryn; Layman, Dan; Maas, Jason; Jaeger, Sara; Walker, Rebecca; Wylie, Kristine; Sekhon, Mandeep; Becker, Michael C; O'Laughlin, Michelle D; Schaller, Mark E; Fewell, Ginger A; Delehaunty, Kimberly D; Miner, Tracie L; Nash, William E; Cordes, Matt; Du, Hui; Sun, Hui; Edwards, Jennifer; Bradshaw-Cordum, Holland; Ali, Johar; Andrews, Stephanie; Isak, Amber; Vanbrunt, Andrew; Nguyen, Christine; Du, Feiyu; Lamar, Betty; Courtney, Laura; Kalicki, Joelle; Ozersky, Philip; Bielicki, Lauren; Scott, Kelsi; Holmes, Andrea; Harkins, Richard; Harris, Anthony; Strong, Cynthia Madsen; Hou, Shunfang; Tomlinson, Chad; Dauphin-Kohlberg, Sara; Kozlowicz-Reilly, Amy; Leonard, Shawn; Rohlfing, Theresa; Rock, Susan M; Tin-Wollam, Aye-Mon; Abbott, Amanda; Minx, Patrick; Maupin, Rachel; Strowmatt, Catrina; Latreille, Phil; Miller, Nancy; Johnson, Doug; Murray, Jennifer; Woessner, Jeffrey P; Wendl, Michael C; Yang, Shiaw-Pyng; Schultz, Brian R; Wallis, John W; Spieth, John; Bieri, Tamberlyn A; Nelson, Joanne O; Berkowicz, Nicolas; Wohldmann, Patricia E; Cook, Lisa L; Hickenbotham, Matthew T; Eldred, James; Williams, Donald; Bedell, Joseph A; Mardis, Elaine R; Clifton, Sandra W; Chissoe, Stephanie L; Marra, Marco A; Raymond, Christopher; Haugen, Eric; Gillett, Will; Zhou, Yang; James, Rose; Phelps, Karen; Iadanoto, Shawn; Bubb, Kerry; Simms, Elizabeth; Levy, Ruth; Clendenning, James; Kaul, Rajinder; Kent, W James; Furey, Terrence S; Baertsch, Robert A; Brent, Michael R; Keibler, Evan; Flicek, Paul; Bork, Peer; Suyama, Mikita; Bailey, Jeffrey A; Portnoy, Matthew E; Torrents, David; Chinwalla, Asif T; Gish, Warren R; Eddy, Sean R; McPherson, John D; Olson, Maynard V; Eichler, Evan E; Green, Eric D; Waterston, Robert H; Wilson, Richard K

    2003-07-10

    Human chromosome 7 has historically received prominent attention in the human genetics community, primarily related to the search for the cystic fibrosis gene and the frequent cytogenetic changes associated with various forms of cancer. Here we present more than 153 million base pairs representing 99.4% of the euchromatic sequence of chromosome 7, the first metacentric chromosome completed so far. The sequence has excellent concordance with previously established physical and genetic maps, and it exhibits an unusual amount of segmentally duplicated sequence (8.2%), with marked differences between the two arms. Our initial analyses have identified 1,150 protein-coding genes, 605 of which have been confirmed by complementary DNA sequences, and an additional 941 pseudogenes. Of genes confirmed by transcript sequences, some are polymorphic for mutations that disrupt the reading frame. PMID:12853948

  15. An Improvised DNA Sequence Compressor Using Pattern Recognition

    Directory of Open Access Journals (Sweden)

    Panneer Arokiaraj S

    2014-01-01

    Full Text Available Genome contains the hereditary information of biological organisms. Currently, there are large number of DNA sequences are stored in DNA databases. This paper presents an improvised version of (PRDNAC Pattern Recognition based DNA Sequence Compression algorithm which compresses the DNA sequences. The development takes place in the area of time complexity factor and compression ratio.

  16. Special Issue: Next Generation DNA Sequencing

    Directory of Open Access Journals (Sweden)

    Paul Richardson

    2010-10-01

    Full Text Available Next Generation Sequencing (NGS refers to technologies that do not rely on traditional dideoxy-nucleotide (Sanger sequencing where labeled DNA fragments are physically resolved by electrophoresis. These new technologies rely on different strategies, but essentially all of them make use of real-time data collection of a base level incorporation event across a massive number of reactions (on the order of millions versus 96 for capillary electrophoresis for instance. The major commercial NGS platforms available to researchers are the 454 Genome Sequencer (Roche, Illumina (formerly Solexa Genome analyzer, the SOLiD system (Applied Biosystems/Life Technologies and the Heliscope (Helicos Corporation. The techniques and different strategies utilized by these platforms are reviewed in a number of the papers in this special issue. These technologies are enabling new applications that take advantage of the massive data produced by this next generation of sequencing instruments. [...

  17. New stopping criteria for segmenting DNA sequences

    CERN Document Server

    Li, W

    2001-01-01

    We propose a solution on the stopping criterion in segmenting inhomogeneous DNA sequences with complex statistical patterns. This new stopping criterion is based on Bayesian Information Criterion (BIC) in the model selection framework. When this stopping criterion is applied to a left telomere sequence of yeast Saccharomyces cerevisiae and the complete genome sequence of bacterium Escherichia coli, borders of biologically meaningful units were identified (e.g. subtelomeric units, replication origin, and replication terminus), and a more reasonable number of domains was obtained. We also introduce a measure called segmentation strength which can be used to control the delineation of large domains. The relationship between the average domain size and the threshold of segmentation strength is determined for several genome sequences.

  18. ASTRAL, a hyperspectral imaging DNA sequencer

    Science.gov (United States)

    O'Brien, Kevin M.; Wren, Jonathan; Davé, Varshal K.; Bai, Diane; Anderson, Richard D.; Rayner, Simon; Evans, Glen A.; Dabiri, Ali E.; Garner, Harold R.

    1998-05-01

    We are developing a prototype automatic DNA sequencer which utilizes polyacrylamide slab gels imaged through a novel optical detection system. The design of this prototype sequencer allows the ability to perform direct optical coupling over the entire read area of the gel and hyperspectrographic separation and detection of the fluorescence emission. The machine has no moving parts. All the major components incorporated in this prototype are all currently available "off the shelf," thus reducing equipment development time and decreasing costs. Software developed for data acquisition, analysis, and conversion to other standard formats facilitates compatibility.

  19. A DNA Structure-Based Bionic Wavelet Transform and Its Application to DNA Sequence Analysis

    OpenAIRE

    Fei Chen; Yuan-Ting Zhang

    2003-01-01

    DNA sequence analysis is of great significance for increasing our understanding of genomic functions. An important task facing us is the exploration of hidden structural information stored in the DNA sequence. This paper introduces a DNA structure-based adaptive wavelet transform (WT) – the bionic wavelet transform (BWT) – for DNA sequence analysis. The symbolic DNA sequence can be separated into four channels of indicator sequences. An adaptive symbol-to-number mapping, determined from the s...

  20. Inferring Coalescence Times from DNA Sequence Data

    OpenAIRE

    Tavare, S; Balding, D. J.; Griffiths, R. C.; Donnelly, P

    1997-01-01

    The paper is concerned with methods for the estimation of the coalescence time (time since the most recent common ancestor) of a sample of intraspecies DNA sequences. The methods take advantage of prior knowledge of population demography, in addition to the molecular data. While some theoretical results are presented, a central focus is on computational methods. These methods are easy to implement, and, since explicit formulae tend to be either unavailable or unilluminating, they are also mor...

  1. Vector sequences - Budding yeast cDNA sequencing project | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available Budding yeast cDNA sequencing project Vector sequences Data detail Data name Vector sequences Description of data contents Vector seq...wnload License Update History of This Database Site Policy | Contact Us Vector sequences - Budding yeast cDNA sequencing project | LSDB Archive ... ...uences used for sequencing. Multi FASTA format. 7 entries. Data file File name: vec

  2. Dog Y chromosomal DNA sequence: identification, sequencing and SNP discovery

    OpenAIRE

    Kirkness Ewen; Lundeberg Joakim; Angleby Helen; Oskarsson Mattias CR; Natanaelsson Christian; Savolainen Peter

    2006-01-01

    Abstract Background Population genetic studies of dogs have so far mainly been based on analysis of mitochondrial DNA, describing only the history of female dogs. To get a picture of the male history, as well as a second independent marker, there is a need for studies of biallelic Y-chromosome polymorphisms. However, there are no biallelic polymorphisms reported, and only 3200 bp of non-repetitive dog Y-chromosome sequence deposited in GenBank, necessitating the identification of dog Y chromo...

  3. Laser mass spectrometry for DNA sequencing, disease diagnosis, and fingerprinting

    Energy Technology Data Exchange (ETDEWEB)

    Winston Chen, C.H.; Taranenko, N.I.; Zhu, Y.F.; Chung, C.N.; Allman, S.L.

    1997-03-01

    Since laser mass spectrometry has the potential for achieving very fast DNA analysis, the authors recently applied it to DNA sequencing, DNA typing for fingerprinting, and DNA screening for disease diagnosis. Two different approaches for sequencing DNA have been successfully demonstrated. One is to sequence DNA with DNA ladders produced from Snager`s enzymatic method. The other is to do direct sequencing without DNA ladders. The need for quick DNA typing for identification purposes is critical for forensic application. The preliminary results indicate laser mass spectrometry can possibly be used for rapid DNA fingerprinting applications at a much lower cost than gel electrophoresis. Population screening for certain genetic disease can be a very efficient step to reducing medical costs through prevention. Since laser mass spectrometry can provide very fast DNA analysis, the authors applied laser mass spectrometry to disease diagnosis. Clinical samples with both base deletion and point mutation have been tested with complete success.

  4. Method for priming and DNA sequencing

    Energy Technology Data Exchange (ETDEWEB)

    Mugasimangalam, R.C.; Ulanovsky, L.E.

    1997-12-01

    A method is presented for improving the priming specificity of an oligonucleotide primer that is non-unique in a nucleic acid template which includes selecting a continuous stretch of several nucleotides in the template DNA where one of the four bases does not occur in the stretch. This also includes bringing the template DNA in contract with a non-unique primer partially or fully complimentary to the sequence immediately upstream of the selected sequence stretch. This results in polymerase-mediated differential extension of the primer in the presence of a subset of deoxyribonucleotide triphosphates that does not contain the base complementary to the base absent in the selected sequence stretch. These reactions occur at a temperature sufficiently low for allowing the extension of the non-unique primer. The method causes polymerase-mediated extension reactions in the presence of all four natural deoxyribonucleotide triphosphates or modifications. At this high temperature discrimination occurs against priming sites of the non-unique primer where the differential extension has not made the primer sufficiently stable to prime. However, the primer extended at the selected stretch is sufficiently stable to prime.

  5. Understanding Long-Range Correlations in DNA sequences

    CERN Document Server

    Li, W; Kaneko, K; Wentian Li; Thomas G Marr; Kunihiko Kaneko

    1994-01-01

    Abstract: In this paper, we review the literature on statistical long-range correlation in DNA sequences. We examine the current evidence for these correlations, and conclude that a mixture of many length scales (including some relatively long ones) in DNA sequences is responsible for the observed 1/f-like spectral component. We note the complexity of the correlation structure in DNA sequences. The observed complexity often makes it hard, or impossible, to decompose the sequence into a few statistically stationary regions. We suggest that, based on the complexity of DNA sequences, a fruitful approach to understand long-range correlation is to model duplication, and other rearrangement processes, in DNA sequences. One model, called ``expansion-modification system", contains only point duplication and point mutation. Though simplistic, this model is able to generate sequences with 1/f spectra. We emphasize the importance of DNA duplication in its contribution to the observed long-range correlation in DNA sequen...

  6. Poincaré recurrences of DNA sequences

    Science.gov (United States)

    Frahm, K. M.; Shepelyansky, D. L.

    2012-01-01

    We analyze the statistical properties of Poincaré recurrences of Homo sapiens, mammalian, and other DNA sequences taken from the Ensembl Genome data base with up to 15 billion base pairs. We show that the probability of Poincaré recurrences decays in an algebraic way with the Poincaré exponent β≈4 even if the oscillatory dependence is well pronounced. The correlations between recurrences decay with an exponent ν≈0.6 that leads to an anomalous superdiffusive walk. However, for Homo sapiens sequences, with the largest available statistics, the diffusion coefficient converges to a finite value on distances larger than one million base pairs. We argue that the approach based on Poncaré recurrences determines new proximity features between different species and sheds a new light on their evolution history.

  7. Recent advances in DNA sequencing techniques

    Science.gov (United States)

    Singh, Rama Shankar

    2013-06-01

    Successful mapping of the draft human genome in 2001 and more recent mapping of the human microbiome genome in 2012 have relied heavily on the parallel processing of the second generation/Next Generation Sequencing (NGS) DNA machines at a cost of several millions dollars and long computer processing times. These have been mainly biochemical approaches. Here a system analysis approach is used to review these techniques by identifying the requirements, specifications, test methods, error estimates, repeatability, reliability and trends in the cost reduction. The first generation, NGS and the Third Generation Single Molecule Real Time (SMART) detection sequencing methods are reviewed. Based on the National Human Genome Research Institute (NHGRI) data, the achieved cost reduction of 1.5 times per yr. from Sep. 2001 to July 2007; 7 times per yr., from Oct. 2007 to Apr. 2010; and 2.5 times per yr. from July 2010 to Jan 2012 are discussed.

  8. Image correlation method for DNA sequence alignment.

    Directory of Open Access Journals (Sweden)

    Millaray Curilem Saldías

    Full Text Available The complexity of searches and the volume of genomic data make sequence alignment one of bioinformatics most active research areas. New alignment approaches have incorporated digital signal processing techniques. Among these, correlation methods are highly sensitive. This paper proposes a novel sequence alignment method based on 2-dimensional images, where each nucleic acid base is represented as a fixed gray intensity pixel. Query and known database sequences are coded to their pixel representation and sequence alignment is handled as object recognition in a scene problem. Query and database become object and scene, respectively. An image correlation process is carried out in order to search for the best match between them. Given that this procedure can be implemented in an optical correlator, the correlation could eventually be accomplished at light speed. This paper shows an initial research stage where results were "digitally" obtained by simulating an optical correlation of DNA sequences represented as images. A total of 303 queries (variable lengths from 50 to 4500 base pairs and 100 scenes represented by 100 x 100 images each (in total, one million base pair database were considered for the image correlation analysis. The results showed that correlations reached very high sensitivity (99.01%, specificity (98.99% and outperformed BLAST when mutation numbers increased. However, digital correlation processes were hundred times slower than BLAST. We are currently starting an initiative to evaluate the correlation speed process of a real experimental optical correlator. By doing this, we expect to fully exploit optical correlation light properties. As the optical correlator works jointly with the computer, digital algorithms should also be optimized. The results presented in this paper are encouraging and support the study of image correlation methods on sequence alignment.

  9. Structure-guided reprogramming of serine recombinase DNA sequence specificity

    OpenAIRE

    Gaj, Thomas; Mercer, Andrew C.; Gersbach, Charles A; Gordley, Russell M.; Barbas III, Carlos F.

    2010-01-01

    Routine manipulation of cellular genomes is contingent upon the development of proteins and enzymes with programmable DNA sequence specificity. Here we describe the structure-guided reprogramming of the DNA sequence specificity of the invertase Gin from bacteriophage Mu and Tn3 resolvase from Escherichia coli. Structure-guided and comparative sequence analyses were used to predict a network of amino acid residues that mediate resolvase and invertase DNA sequence specificity. Using saturation ...

  10. Detecting seeded motifs in DNA sequences.

    Science.gov (United States)

    Pizzi, Cinzia; Bortoluzzi, Stefania; Bisognin, Andrea; Coppe, Alessandro; Danieli, Gian Antonio

    2005-01-01

    The problem of detecting DNA motifs with functional relevance in real biological sequences is difficult due to a number of biological, statistical and computational issues and also because of the lack of knowledge about the structure of searched patterns. Many algorithms are implemented in fully automated processes, which are often based upon a guess of input parameters from the user at the very first step. In this paper, we present a novel method for the detection of seeded DNA motifs, composed by regions with a different extent of variability. The method is based on a multi-step approach, which was implemented in a motif searching web tool (MOST). Overrepresented exact patterns are extracted from input sequences and clustered to produce motifs core regions, which are then extended and scored to generate seeded motifs. The combination of automated pattern discovery algorithms and different display tools for the evaluation and selection of results at several analysis steps can potentially lead to much more meaningful results than complete automation can produce. Experimental results on different yeast and human real datasets proved the methodology to be a promising solution for finding seeded motifs. MOST web tool is freely available at http://telethon.bio.unipd.it/bioinfo/MOST. PMID:16141193

  11. Detecting seeded motifs in DNA sequences

    Science.gov (United States)

    Pizzi, Cinzia; Bortoluzzi, Stefania; Bisognin, Andrea; Coppe, Alessandro; Danieli, Gian Antonio

    2005-01-01

    The problem of detecting DNA motifs with functional relevance in real biological sequences is difficult due to a number of biological, statistical and computational issues and also because of the lack of knowledge about the structure of searched patterns. Many algorithms are implemented in fully automated processes, which are often based upon a guess of input parameters from the user at the very first step. In this paper, we present a novel method for the detection of seeded DNA motifs, composed by regions with a different extent of variability. The method is based on a multi-step approach, which was implemented in a motif searching web tool (MOST). Overrepresented exact patterns are extracted from input sequences and clustered to produce motifs core regions, which are then extended and scored to generate seeded motifs. The combination of automated pattern discovery algorithms and different display tools for the evaluation and selection of results at several analysis steps can potentially lead to much more meaningful results than complete automation can produce. Experimental results on different yeast and human real datasets proved the methodology to be a promising solution for finding seeded motifs. MOST web tool is freely available at . PMID:16141193

  12. DNA Sequence Optimization Based on Continuous Particle Swarm Optimization for Reliable DNA Computing and DNA Nanotechnology

    Directory of Open Access Journals (Sweden)

    N. K. Khalid

    2008-01-01

    Full Text Available Problem statement: In DNA based computation and DNA nanotechnology, the design of good DNA sequences has turned out to be an essential problem and one of the most practical and important research topics. Basically, the DNA sequence design problem is a multi-objective problem and it can be evaluated using four objective functions, namely, Hmeasure, similarity, continuity and hairpin. Approach: There are several ways to solve multi-objective problem, however, in order to evaluate the correctness of PSO algorithm in DNA sequence design, this problem is converted into single objective problem. Particle Swarm Optimization (PSO is proposed to minimize the objective in the problem, subjected to two constraints: melting temperature and GCcontent. A model is developed to present the DNA sequence design based on PSO computation. Results: Based on experiments and researches done, 20 particles are used in the implementation of the optimization process, where the average values and the standard deviation for 100 runs are shown along with comparison to other existing methods. Conclusion: The results achieve verified that PSO can suitably solves the DNA sequence design problem using the proposed method and model, comparatively better than other approaches.

  13. A DNA Structure-Based Bionic Wavelet Transform and Its Application to DNA Sequence Analysis

    Directory of Open Access Journals (Sweden)

    Fei Chen

    2003-01-01

    Full Text Available DNA sequence analysis is of great significance for increasing our understanding of genomic functions. An important task facing us is the exploration of hidden structural information stored in the DNA sequence. This paper introduces a DNA structure-based adaptive wavelet transform (WT – the bionic wavelet transform (BWT – for DNA sequence analysis. The symbolic DNA sequence can be separated into four channels of indicator sequences. An adaptive symbol-to-number mapping, determined from the structural feature of the DNA sequence, was introduced into WT. It can adjust the weight value of each channel to maximise the useful energy distribution of the whole BWT output. The performance of the proposed BWT was examined by analysing synthetic and real DNA sequences. Results show that BWT performs better than traditional WT in presenting greater energy distribution. This new BWT method should be useful for the detection of the latent structural features in future DNA sequence analysis.

  14. Non-random DNA fragmentation in next-generation sequencing

    Science.gov (United States)

    Poptsova, Maria S.; Il'Icheva, Irina A.; Nechipurenko, Dmitry Yu.; Panchenko, Larisa A.; Khodikov, Mingian V.; Oparina, Nina Y.; Polozov, Robert V.; Nechipurenko, Yury D.; Grokhovsky, Sergei L.

    2014-03-01

    Next Generation Sequencing (NGS) technology is based on cutting DNA into small fragments, and their massive parallel sequencing. The multiple overlapping segments termed ``reads'' are assembled into a contiguous sequence. To reduce sequencing errors, every genome region should be sequenced several dozen times. This sequencing approach is based on the assumption that genomic DNA breaks are random and sequence-independent. However, previously we showed that for the sonicated restriction DNA fragments the rates of double-stranded breaks depend on the nucleotide sequence. In this work we analyzed genomic reads from NGS data and discovered that fragmentation methods based on the action of the hydrodynamic forces on DNA, produce similar bias. Consideration of this non-random DNA fragmentation may allow one to unravel what factors and to what extent influence the non-uniform coverage of various genomic regions.

  15. 5'-end sequences of budding yeast full-length cDNA clones - Budding yeast cDNA sequencing project | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available Budding yeast cDNA sequencing project 5'-end sequences of budding yeast full-length cDNA clones Data detail Data name 5'-end sequence...s of budding yeast full-length cDNA clones Description of data contents cDNA sequence...e Update History of This Database Site Policy | Contact Us 5'-end sequences of budding yeast full-length cDNA clones - Budding yeast cDNA sequencing project | LSDB Archive ...

  16. Use of an automated capillary DNA sequencer to investigate the interaction of cisplatin with telomeric DNA sequences.

    Science.gov (United States)

    Paul, Moumita; Murray, Vincent

    2012-03-01

    The determination of the sequence selectivity of DNA-damaging agents is very important in elucidating the mechanism of action of anti-tumour drugs. The development of automated capillary DNA sequencers with fluorescent labelling has enabled a more precise method for DNA sequence specificity analysis. In this work we utilized the ABI 3730 capillary sequencer with laser-induced fluorescence to examine the sequence selectivity of cisplatin with purified DNA sequences. The use of this automated machine enabled a higher degree of precision of both position and intensity of cisplatin-DNA adducts than previously possible with manual and automated slab gel procedures. A problem with artefact bands was overcome by ethanol precipitation. It was found that cisplatin strongly formed adducts with telomeric DNA sequences. PMID:21678458

  17. Species-specific patterns of DNA bending and sequence.

    OpenAIRE

    VanWye, J D; Bronson, E C; Anderson, J N

    1991-01-01

    Nucleotide sequences in the GenEMBL database were analyzed using strategies designed to reveal species-specific patterns of DNA bending and DNA sequence. The results uncovered striking species-dependent patterns of bending with more variations among individual organisms than between prokaryotes and eukaryotes. The frequency of bent sites in sequences from different bacteria was related to genomic A + T content and this relationship was confirmed by electrophoretic analysis of genomic DNA. How...

  18. Next-generation sequencing offers new insights into DNA degradation

    DEFF Research Database (Denmark)

    Overballe-Petersen, Søren; Orlando, Ludovic Antoine Alexandre; Willerslev, Eske

    2012-01-01

    rates that previously were obtained only from extrapolations of results from in vitro kinetic experiments performed over short timescales. For example, recent next-generation sequencing of ancient DNA reveals purine bases as one of the main targets of postmortem hydrolytic damage, through base......The processes underlying DNA degradation are central to various disciplines, including cancer research, forensics and archaeology. The sequencing of ancient DNA molecules on next-generation sequencing platforms provides direct measurements of cytosine deamination, depurination and fragmentation...

  19. Protection of DNA sequences by triplex-bridge formation.

    OpenAIRE

    Kiyama, R; Oishi, M

    1995-01-01

    We have demonstrated that the DNA sequence between two triplex-forming polypurine.polypyrimidine (Pu.Py) tracts was protected from DNA modifying enzymes upon formation of triplex DNA structures with an oligodeoxyribonucleotide in which two triplex-forming Pu or Py tracts were placed at the termini (triplex-bridge formation). In model experiments, when two triplex structures were formed between double-stranded DNA with the sequence (AG)17-(N)18-(T)34, and an oligodeoxyribonucleotide, (T)34-(N)...

  20. Effect of Noise on DNA Sequencing via Transverse Electronic Transport

    OpenAIRE

    Krems, Matt; Zwolak, Michael; Pershin, Yuriy V.; Di Ventra, Massimiliano

    2009-01-01

    Previous theoretical studies have shown that measuring the transverse current across DNA strands while they translocate through a nanopore or channel may provide a statistically distinguishable signature of the DNA bases, and may thus allow for rapid DNA sequencing. However, fluctuations of the environment, such as ionic and DNA motion, introduce important scattering processes that may affect the viability of this approach to sequencing. To understand this issue, we have analyzed a simple mod...

  1. DNA Sequence Representation and Comparison Based on Quaternion Number System

    Directory of Open Access Journals (Sweden)

    Hsuan-T. Chang

    2012-12-01

    Full Text Available Conventional schemes for DNA sequence representation, storage, and processing areusually developed based on the character-based formats.We propose the quaternion number system for numerical representation and further processing on DNA sequences.In the proposed method, the quaternion cross-correlation operation can be used to obtain both the global and local matching/mismatching information between two DNA sequences from the depicted one-dimensional curve and two-dimensional pattern, respectively.Simulation results on various DNA sequences and the comparison result with the wellknown BLAST method are obtained to verify the effectiveness of the proposed method.

  2. Anonymity in Voting Revisited

    Science.gov (United States)

    Jonker, Hugo; Pieters, Wolter

    According to international law, anonymity of the voter is a fundamental precondition for democratic elections. In electronic voting, several aspects of voter anonymity have been identified. In this paper, we re-examine anonymity with respect to voting, and generalise existing notions of anonymity in e-voting. First, we identify and categorise the types of attack that can be a threat to anonymity of the voter, including different types of vote buying and coercion. This analysis leads to a categorisation of anonymity in voting in terms of a) the strength of the anonymity achieved and b) the extent of interaction between voter and attacker. Some of the combinations, including weak and strong receipt-freeness, are formalised in epistemic logic.

  3. SWORDS: A statistical tool for analysing large DNA sequences

    Indian Academy of Sciences (India)

    Probal Chaudhuri; Sandip Das

    2002-02-01

    In this article, we present some simple yet effective statistical techniques for analysing and comparing large DNA sequences. These techniques are based on frequency distributions of DNA words in a large sequence, and have been packaged into a software called SWORDS. Using sequences available in public domain databases housed in the Internet, we demonstrate how SWORDS can be conveniently used by molecular biologists and geneticists to unmask biologically important features hidden in large sequences and assess their statistical significance.

  4. A novel constraint for thermodynamically designing DNA sequences.

    Directory of Open Access Journals (Sweden)

    Qiang Zhang

    Full Text Available Biotechnological and biomolecular advances have introduced novel uses for DNA such as DNA computing, storage, and encryption. For these applications, DNA sequence design requires maximal desired (and minimal undesired hybridizations, which are the product of a single new DNA strand from 2 single DNA strands. Here, we propose a novel constraint to design DNA sequences based on thermodynamic properties. Existing constraints for DNA design are based on the Hamming distance, a constraint that does not address the thermodynamic properties of the DNA sequence. Using a unique, improved genetic algorithm, we designed DNA sequence sets which satisfy different distance constraints and employ a free energy gap based on a minimum free energy (MFE to gauge DNA sequences based on set thermodynamic properties. When compared to the best constraints of the Hamming distance, our method yielded better thermodynamic qualities. We then used our improved genetic algorithm to obtain lower-bound DNA sequence sets. Here, we discuss the effects of novel constraint parameters on the free energy gap.

  5. A novel constraint for thermodynamically designing DNA sequences.

    Science.gov (United States)

    Zhang, Qiang; Wang, Bin; Wei, Xiaopeng; Zhou, Changjun

    2013-01-01

    Biotechnological and biomolecular advances have introduced novel uses for DNA such as DNA computing, storage, and encryption. For these applications, DNA sequence design requires maximal desired (and minimal undesired) hybridizations, which are the product of a single new DNA strand from 2 single DNA strands. Here, we propose a novel constraint to design DNA sequences based on thermodynamic properties. Existing constraints for DNA design are based on the Hamming distance, a constraint that does not address the thermodynamic properties of the DNA sequence. Using a unique, improved genetic algorithm, we designed DNA sequence sets which satisfy different distance constraints and employ a free energy gap based on a minimum free energy (MFE) to gauge DNA sequences based on set thermodynamic properties. When compared to the best constraints of the Hamming distance, our method yielded better thermodynamic qualities. We then used our improved genetic algorithm to obtain lower-bound DNA sequence sets. Here, we discuss the effects of novel constraint parameters on the free energy gap. PMID:24015217

  6. Guanine-rich sequences inhibit proofreading DNA polymerases

    Science.gov (United States)

    Zhu, Xiao-Jing; Sun, Shuhui; Xie, Binghua; Hu, Xuemei; Zhang, Zunyi; Qiu, Mengsheng; Dai, Zhong-Min

    2016-01-01

    DNA polymerases with proofreading activity are important for accurate amplification of target DNA. Despite numerous efforts have been made to improve the proofreading DNA polymerases, they are more susceptible to be failed in PCR than non-proofreading DNA polymerases. Here we showed that proofreading DNA polymerases can be inhibited by certain primers. Further analysis showed that G-rich sequences such as GGGGG and GGGGHGG can cause PCR failure using proofreading DNA polymerases but not Taq DNA polymerase. The inhibitory effect of these G-rich sequences is caused by G-quadruplex and is dose dependent. G-rich inhibitory sequence-containing primers can be used in PCR at a lower concentration to amplify its target DNA fragment. PMID:27349576

  7. DNA display I. Sequence-encoded routing of DNA populations.

    OpenAIRE

    Halpin, David R; Pehr B Harbury

    2004-01-01

    Recently reported technologies for DNA-directed organic synthesis and for DNA computing rely on routing DNA populations through complex networks. The reduction of these ideas to practice has been limited by a lack of practical experimental tools. Here we describe a modular design for DNA routing genes, and routing machinery made from oligonucleotides and commercially available chromatography resins. The routing machinery partitions nanomole quantities of DNA into physically distinct subpools ...

  8. Polymorphic DNA sequences and their application in paternity testing

    International Nuclear Information System (INIS)

    Characteristics of polymorphic sequences of DNA, especially satellite, mini satellite and micro satellite sequences are presented. Own experience from the use of multi and single locus analysis of DNA in paternity testing has been compared with the results of research in other laboratories. Critical points of both types of analysis are discussed. (author). 53 refs, 4 figs, 2 tabs

  9. DNA Polymerases Drive DNA Sequencing-by-Synthesis Technologies: Both Past and Present

    Directory of Open Access Journals (Sweden)

    Cheng-Yao eChen

    2014-06-01

    Full Text Available Next-generation sequencing (NGS technologies have revolutionized modern biological and biomedical research. The engines responsible for this innovation are DNA polymerases; they catalyze the biochemical reaction for deriving template sequence information. In fact, DNA polymerase has been a cornerstone of DNA sequencing from the very beginning. E. coli DNA polymerase I proteolytic (Klenow fragment was originally utilized in Sanger's dideoxy chain terminating DNA sequencing chemistry. From these humble beginnings followed an explosion of organism-specific, genome sequence information accessible via public database. Family A/B DNA polymerases from mesophilic/thermophilic bacteria/archaea were modified and tested in today's standard capillary electrophoresis (CE and NGS sequencing platforms. These enzymes were selected for their efficient incorporation of bulky dye-terminator and reversible dye-terminator nucleotides respectively. Third generation, real-time single molecule sequencing platform requires slightly different enzyme properties. Enterobacterial phage ⱷ29 DNA polymerase copies long stretches of DNA and possesses a unique capability to efficiently incorporate terminal phosphate-labeled nucleoside polyphosphates. Furthermore, ⱷ29 enzyme has also been utilized in emerging DNA sequencing technologies including nanopore-, and protein-transistor-based sequencing. DNA polymerase is, and will continue to be, a crucial component of sequencing technologies.

  10. Food Fish Identification from DNA Extraction through Sequence Analysis

    Science.gov (United States)

    Hallen-Adams, Heather E.

    2015-01-01

    This experiment exposed 3rd and 4th y undergraduates and graduate students taking a course in advanced food analysis to DNA extraction, polymerase chain reaction (PCR), and DNA sequence analysis. Students provided their own fish sample, purchased from local grocery stores, and the class as a whole extracted DNA, which was then subjected to PCR,…

  11. Immunostimulatory DNA sequences influence the course of adjuvant arthritis

    NARCIS (Netherlands)

    Ronaghy, A; Prakken, BJ; Takabayashi, K; Firestein, GS; Boyle, D; Zvailfler, NJ; Roord, STA; Albani, S; Carson, DA; Raz, E

    2002-01-01

    Bacterial DNA is enriched in unmethylated CpG motifs that have been shown to activate the innate immune system. These immunostimulatory DNA sequences (ISS) induce inflammation when injected directly into joints. However, the role of bacterial DNA in systemic arthritis is not known. The purpose of th

  12. Cloning and sequencing of mouse GABA transporter complementary DNA

    Institute of Scientific and Technical Information of China (English)

    TAMANTHONYC.W.; LIHEGUO; 等

    1994-01-01

    A cDNA encoding the mouse GABA transporter has been isolated and sequenced.The results show that the mouse GABA transporter cDNA differs from that of the rat by 60 base pairs at the open reading frame region but the deduced amino acid sequences of the two cDNAs are identical and both composed of 599 amino acids.However,the amino acid sequence is different from the sequence deduced from a recently published mouse GABA transporter cDNA.

  13. Shotgun DNA sequencing using cloned DNase I-generated fragments.

    OpenAIRE

    Anderson, S

    1981-01-01

    A method for DNA sequencing has been developed that utilises libraries of cloned randomly-fragmented DNA. The DNA to be sequenced is first subjected to limit attach by a non-specific endonuclease (DNase I in the presence of Mn++), fractionated by size and cloned in a single-stranded phage vector. Clones are then picked at random and used to provide a template for sequencing by the dideoxynucleotide chain termination method. This technique was used to sequence completely a 4257 bp EcoRI fragme...

  14. Spatially localized generation of nucleotide sequence-specific DNA damage

    OpenAIRE

    Oh, Dennis H.; King, Brett A.; Boxer, Steven G.; Hanawalt, Philip C.

    2001-01-01

    Psoralens linked to triplex-forming oligonucleotides (psoTFOs) have been used in conjunction with laser-induced two-photon excitation (TPE) to damage a specific DNA target sequence. To demonstrate that TPE can initiate photochemistry resulting in psoralen–DNA photoadducts, target DNA sequences were incubated with psoTFOs to form triple-helical complexes and then irradiated in liquid solution with pulsed 765-nm laser light, which is half the quantum energy required for ...

  15. Effects of Sequence on Transmission Properties of DNA Molecules

    Institute of Scientific and Technical Information of China (English)

    DONG Rui-Xin; YAN Xun-Ling; YANG Bing

    2008-01-01

    A double helix model of charge transport in DNA molecule is given and the transmission spectra of four DNA sequences are obtained. The calculated results show that the transmission characteristics of DNA are not only related to the longitudinal transport but also to the transverse transport of molecule. The periodic sequence with the same composition has stronger conduction ability. With the increasing of bases composition, the conductive ability reduces, but the weight of θ direction rises in charge transfer.

  16. Anonymizing Unstructured Data

    CERN Document Server

    Motwani, Rajeev

    2008-01-01

    In this paper we consider the problem of anonymizing datasets in which each individual is associated with a set of items that constitute private information about the individual. Illustrative datasets include market-basket datasets and search engine query logs. We formalize the notion of k-anonymity for set-valued data as a variant of the k-anonymity model for traditional relational datasets. We define an optimization problem that arises from this definition of anonymity and provide a constant factor approximation algorithm for the same. We evaluate our algorithms on the America Online query log dataset.

  17. An Anonymity Revocation Technology for Anonymous Communication

    Science.gov (United States)

    Antoniou, Giannakis; Batten, Lynn; Parampalli, Udaya

    A number of privacy-enhancing technologies (PETs) have been proposed in the last three decades offering unconditional communication anonymity to their users. Unconditional anonymity can, however, be a security threat because it allows users to employ a PET in order to act maliciously while hiding their identity. In the last few years, several technologies which revoke the identity of users who use PETs have been proposed. These are known as anonymity revocation technologies (ARTs). However, the construction of ARTs has been developed in an ad hoc manner without a theoretical basis outlining the goals and underlying principles. In this chapter we present a set of fundamental principles and requirements for construction of an ART, identifying the necessary features. We then propose an abstract scheme for construction of an ART based on these features.

  18. Quantum anonymous voting with anonymity check

    International Nuclear Information System (INIS)

    We propose a new protocol for quantum anonymous voting having serious advantages over the existing protocols: it protects both the voters from a curious tallyman and all the participants from a dishonest voter in unconditional way. The central idea of the protocol is that the ballots are given back to the voters after the voting process, which gives a possibility for two voters to check the anonymity of the vote counting process by preparing a special entangled state of two ballots. Any attempt of cheating from the side of the tallyman results in destroying the entanglement, which can be detected by the voters.

  19. Advances in DNA sequencing technologies for high resolution HLA typing.

    Science.gov (United States)

    Cereb, Nezih; Kim, Hwa Ran; Ryu, Jaejun; Yang, Soo Young

    2015-12-01

    This communication describes our experience in large-scale G group-level high resolution HLA typing using three different DNA sequencing platforms - ABI 3730 xl, Illumina MiSeq and PacBio RS II. Recent advances in DNA sequencing technologies, so-called next generation sequencing (NGS), have brought breakthroughs in deciphering the genetic information in all living species at a large scale and at an affordable level. The NGS DNA indexing system allows sequencing multiple genes for large number of individuals in a single run. Our laboratory has adopted and used these technologies for HLA molecular testing services. We found that each sequencing technology has its own strengths and weaknesses, and their sequencing performances complement each other. HLA genes are highly complex and genotyping them is quite challenging. Using these three sequencing platforms, we were able to meet all requirements for G group-level high resolution and high volume HLA typing. PMID:26423536

  20. Multiplexed Sequence Encoding: A Framework for DNA Communication.

    Science.gov (United States)

    Zakeri, Bijan; Carr, Peter A; Lu, Timothy K

    2016-01-01

    Synthetic DNA has great propensity for efficiently and stably storing non-biological information. With DNA writing and reading technologies rapidly advancing, new applications for synthetic DNA are emerging in data storage and communication. Traditionally, DNA communication has focused on the encoding and transfer of complete sets of information. Here, we explore the use of DNA for the communication of short messages that are fragmented across multiple distinct DNA molecules. We identified three pivotal points in a communication-data encoding, data transfer & data extraction-and developed novel tools to enable communication via molecules of DNA. To address data encoding, we designed DNA-based individualized keyboards (iKeys) to convert plaintext into DNA, while reducing the occurrence of DNA homopolymers to improve synthesis and sequencing processes. To address data transfer, we implemented a secret-sharing system-Multiplexed Sequence Encoding (MuSE)-that conceals messages between multiple distinct DNA molecules, requiring a combination key to reveal messages. To address data extraction, we achieved the first instance of chromatogram patterning through multiplexed sequencing, thereby enabling a new method for data extraction. We envision these approaches will enable more widespread communication of information via DNA. PMID:27050646

  1. A ROBUST DIGITAL IMAGE WATERMARKING ALGORITHM USING DNA SEQUENCES

    Directory of Open Access Journals (Sweden)

    V. Santhi

    2010-11-01

    Full Text Available Digital watermarking technique emerged as a tool for protecting the multimedia data from copyright infringement. In digital watermarking an imperceptible signal is embedded into the host image, which uniquely identifies the ownership. In the proposed algorithms, DNA sequence is used as a digital watermark, as the DNA sequences are unique and difficult to copy. This paper proposes two algorithms namely content based watermark algorithm using DNA sequence (CBDNA and user specified watermark algorithm using DNA sequence (USDNA. In CBDNA the DNA sequence is generated from the cover data itself whereas in USDNA input data is chosen by the user and DNA sequence is generated based on the input data. These DNA sequences serve as a watermark for the cover data. The quality of the cover image and extracted watermark is measured using peak signal to noise ratio (PSNR and normalized correlation (NC respectively. The calculated values are tabulated and it shows that the proposed algorithm is withstanding many attacks, since watermark is available in all the frequency range of cover data.

  2. True Anonymity Without Mixes

    Science.gov (United States)

    Molina-Jimenez, C.; Marshall, L.

    2002-04-01

    Anonymizers based on mix computers interposed between the sender and the receiver of an e-mail message have been used in the Internet for several years by senders of e-mail messages who do not wish to disclose their identity. Unfortunately, the degree of anonymity provided by this paradigm is limited and fragile. First, the messages sent are not truly anonymous but pseudo-anonymous since one of the mixes, at least, always knows the sender's identity. Secondly, the strength of the system to protect the sender's identity depends on the ability and the willingness of the mixes to keep the secret. If the mixes fail, the sender/'s anonymity is reduced to pieces. In this paper, we propose a novel approach for sending truly anonymous messages over the Internet where the anonymous message is sent from a PDA which uses dynamically assigned temporary, non-personal, random IP and MAC addresses. Anonymous E-cash is used to pay for the service.

  3. Economical quantum anonymous transmissions

    International Nuclear Information System (INIS)

    We present a new information-theoretically secure protocol for the anonymous transmission of quantum information. Different from the pioneering works, we use single photons to construct anonymous entanglement instead of multi-partite entangled states in this protocol, and therefore we reduce the complexity of physical implementation in practice.

  4. Anonymity, Deindividuation and Aggression.

    Science.gov (United States)

    Baron, Robert S.

    Several writers suggest that reducing one's sense of individuality reduces social restraints. The author suggests that the effect of uniformity of appearance on aggression is unclear when anonymity is held constant. This poses a problem of interpretation given that a distinction must be made between lack of individuality and anonymity. One must…

  5. Biological nanopore MspA for DNA sequencing

    Science.gov (United States)

    Manrao, Elizabeth A.

    Unlocking the information hidden in the human genome provides insight into the inner workings of complex biological systems and can be used to greatly improve health-care. In order to allow for widespread sequencing, new technologies are required that provide fast and inexpensive readings of DNA. Nanopore sequencing is a third generation DNA sequencing technology that is currently being developed to fulfill this need. In nanopore sequencing, a voltage is applied across a small pore in an electrolyte solution and the resulting ionic current is recorded. When DNA passes through the channel, the ionic current is partially blocked. If the DNA bases uniquely modulate the ionic current flowing through the channel, the time trace of the current can be related to the sequence of DNA passing through the pore. There are two main challenges to realizing nanopore sequencing: identifying a pore with sensitivity to single nucleotides and controlling the translocation of DNA through the pore so that the small single nucleotide current signatures are distinguishable from background noise. In this dissertation, I explore the use of Mycobacterium smegmatis porin A (MspA) for nanopore sequencing. In order to determine MspA's sensitivity to single nucleotides, DNA strands of various compositions are held in the pore as the resulting ionic current is measured. DNA is immobilized in MspA by attaching it to a large molecule which acts as an anchor. This technique confirms the single nucleotide resolution of the pore and additionally shows that MspA is sensitive to epigenetic modifications and single nucleotide polymorphisms. The forces from the electric field within MspA, the effective charge of nucleotides, and elasticity of DNA are estimated using a Freely Jointed Chain model of single stranded DNA. These results offer insight into the interactions of DNA within the pore. With the nucleotide sensitivity of MspA confirmed, a method is introduced to controllably pass DNA through the pore

  6. DNA splice site sequences clustering method for conservativeness analysis

    Institute of Scientific and Technical Information of China (English)

    Quanwei Zhang; Qinke Peng; Tao Xu

    2009-01-01

    DNA sequences that are near to splice sites have remarkable conservativeness,and many researchers have contributed to the prediction of splice site.In order to mine the underlying biological knowledge,we analyze the conservativeness of DNA splice site adjacent sequences by clustering.Firstly,we propose a kind of DNA splice site sequences clustering method which is based on DBSCAN,and use four kinds of dissimilarity calculating methods.Then,we analyze the conservative feature of the clustering results and the experimental data set.

  7. DNA sequence analysis with droplet-based microfluidics

    Science.gov (United States)

    Abate, Adam R.; Hung, Tony; Sperling, Ralph A.; Mary, Pascaline; Rotem, Assaf; Agresti, Jeremy J.; Weiner, Michael A.; Weitz, David A.

    2014-01-01

    Droplet-based microfluidic techniques can form and process micrometer scale droplets at thousands per second. Each droplet can house an individual biochemical reaction, allowing millions of reactions to be performed in minutes with small amounts of total reagent. This versatile approach has been used for engineering enzymes, quantifying concentrations of DNA in solution, and screening protein crystallization conditions. Here, we use it to read the sequences of DNA molecules with a FRET-based assay. Using probes of different sequences, we interrogate a target DNA molecule for polymorphisms. With a larger probe set, additional polymorphisms can be interrogated as well as targets of arbitrary sequence. PMID:24185402

  8. Transcriptional sequencing: A method for DNA sequencing using RNA polymerase

    OpenAIRE

    Sasaki, Nobuya; Izawa, Masaki; Watahiki, Masanori; Ozawa, Kaori; Tanaka, Takumi; Yoneda, Yuko; Matsuura, Shuji; Carninci, Piero; Muramatsu, Masami; Okazaki, Yasushi; Hayashizaki, Yoshihide

    1998-01-01

    We have developed a sequencing method based on the RNA polymerase chain termination reaction with rhodamine dye attached to 3′-deoxynucleoside triphosphate (3′-dNTP). This method enables us to conduct a rapid isothermal sequencing reaction in

  9. Numerical Characterization of DNA Sequence Based on Dinucleotides

    OpenAIRE

    Xingqin Qi; Edgar Fuller; Qin Wu; Cun-Quan Zhang

    2012-01-01

    Sequence comparison is a primary technique for the analysis of DNA sequences. In order to make quantitative comparisons, one devises mathematical descriptors that capture the essence of the base composition and distribution of the sequence. Alignment methods and graphical techniques (where each sequence is represented by a curve in high-dimension Euclidean space) have been used popularly for a long time. In this contribution we will introduce a new nongraphical and nonalignment approach based...

  10. Nucleotide sequence analysis of regions of adenovirus 5 DNA containing the origins of DNA replication

    International Nuclear Information System (INIS)

    The purpose of the investigations described is the determination of nucleotide sequences at the molecular ends of the linear adenovirus type 5 DNA. Knowledge of the primary structure at the termini of this DNA molecule is of particular interest in the study of the mechanism of replication of adenovirus DNA. The initiation- and termination sites of adenovirus DNA replication are located at the ends of the DNA molecule. (Auth.)

  11. Spectroscopic investigation on the telomeric DNA base sequence repeat

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Telomeres are protein-DNA complexes at the terminals of linear chromosomes, which protect chromosomal integrity and maintain cellular replicative capacity.From single-cell organisms to advanced animals and plants,structures and functions of telomeres are both very conservative. In cells of human and vertebral animals, telomeric DNA base sequences all are (TTAGGG)n. In the present work, we have obtained absorption and fluorescence spectra measured from seven synthesized oligonucleotides to simulate the telomeric DNA system and calculated their relative fluorescence quantum yields on which not only telomeric DNA characteristics are predicted but also possibly the shortened telomeric sequences during cell division are imrelative fluorescence quantum yield and remarkable excitation energy innerconversion, which tallies with the telomeric sequence of (TTAGGG)n. This result shows that telomeric DNA has a strong non-radiative or innerconvertible capability.``

  12. What Advances Are Being Made in DNA Sequencing?

    Science.gov (United States)

    ... of DNA sequencing , including that caused by the introduction of new technologies, is provided by the National ... Library of Medicine Lister Hill National Center for Biomedical Communications 8600 Rockville Pike, Bethesda, MD 20894, USA ...

  13. ATRF Houses the Latest DNA Sequencing Technologies | Poster

    Science.gov (United States)

    By Ashley DeVine, Staff Writer By the end of October, the Advanced Technology Research Facility (ATRF) will be one of the few facilities in the world to house all of the latest DNA sequencing technologies.

  14. Pyrimidine-specific chemical reactions useful for DNA sequencing.

    OpenAIRE

    Rubin, C M; Schmid, C. W.

    1980-01-01

    Potassium permanganate reacts selectively with thymidine residues in DNA (1) while hydroxylamine hydrochloride at pH 6 specifically attacks cytosine (2). We have adopted these reactions for use with the chemical sequencing method developed by Maxam and Gilbert (3).

  15. Anonymous nuclear markers data supporting species tree phylogeny and divergence time estimates in a cactus species complex in South America.

    Science.gov (United States)

    Perez, Manolo F; Carstens, Bryan C; Rodrigues, Gustavo L; Moraes, Evandro M

    2016-03-01

    Supportive data related to the article "Anonymous nuclear markers reveal taxonomic incongruence and long-term disjunction in a cactus species complex with continental-island distribution in South America" (Perez et al., 2016) [1]. Here, we present pyrosequencing results, primer sequences, a cpDNA phylogeny, and a species tree phylogeny. PMID:26900589

  16. Statistical methods for detecting periodic fragments in DNA sequence data

    OpenAIRE

    Ying Hua; Epps Julien; Huttley Gavin A

    2011-01-01

    Abstract Background Period 10 dinucleotides are structurally and functionally validated factors that influence the ability of DNA to form nucleosomes, histone core octamers. Robust identification of periodic signals in DNA sequences is therefore required to understand nucleosome organisation in genomes. While various techniques for identifying periodic components in genomic sequences have been proposed or adopted, the requirements for such techniques have not been considered in detail and con...

  17. Sequence dependence of electron-induced DNA strand breakage revealed by DNA nanoarrays

    DEFF Research Database (Denmark)

    Keller, Adrian; Rackwitz, Jenny; Cauët, Emilie; Liévin, Jacques; Körzdörfer, Thomas; Rotaru, Alexandru; Gothelf, Kurt Vesterager; Besenbacher, Flemming; Bald, Ilko

    2014-01-01

    The electronic structure of DNA is determined by its nucleotide sequence, which is for instance exploited in molecular electronics. Here we demonstrate that also the DNA strand breakage induced by low-energy electrons (18 eV) depends on the nucleotide sequence. To determine the absolute cross sec...

  18. Inferring ethnicity from mitochondrial DNA sequence

    OpenAIRE

    Lee, Chih; Măndoiu, Ion I; Nelson, Craig E.

    2011-01-01

    Background The assignment of DNA samples to coarse population groups can be a useful but difficult task. One such example is the inference of coarse ethnic groupings for forensic applications. Ethnicity plays an important role in forensic investigation and can be inferred with the help of genetic markers. Being maternally inherited, of high copy number, and robust persistence in degraded samples, mitochondrial DNA may be useful for inferring coarse ethnicity. In this study, we compare the per...

  19. Anonymity in science.

    Science.gov (United States)

    Neuroskeptic

    2013-05-01

    The history of science is replete with important works that were originally published without the author's legal name being revealed. Most modern scientists will have worked anonymously in their capacity as peer reviewers. But why is anonymity so popular? And is it a valid approach? I argue that pseudonymity and anonymity, although not appropriate for all forms of scientific communication, have a vital role to play in academic discourse. They can facilitate the free expression of interpretations and ideas, and can help to ensure that suggestions and criticisms are evaluated dispassionately, regardless of their source. PMID:23570959

  20. Trust in Anonymity Networks

    Science.gov (United States)

    Sassone, Vladimiro; Hamadou, Sardaouna; Yang, Mu

    Anonymity is a security property of paramount importance, as we move steadily towards a wired, online community. Its import touches upon subjects as different as eGovernance, eBusiness and eLeisure, as well as personal freedom of speech in authoritarian societies. Trust metrics are used in anonymity networks to support and enhance reliability in the absence of verifiable identities, and a variety of security attacks currently focus on degrading a user's trustworthiness in the eyes of the other users. In this paper, we analyse the privacy guarantees of the Crowds anonymity protocol, with and without onion forwarding, for standard and adaptive attacks against the trust level of honest users.

  1. Discovering simple DNA sequences by the algorithmic significance method.

    Science.gov (United States)

    Milosavljević, A; Jurka, J

    1993-08-01

    A new method, 'algorithmic significance', is proposed as a tool for discovery of patterns in DNA sequences. The main idea is that patterns can be discovered by finding ways to encode the observed data concisely. In this sense, the method can be viewed as a formal version of the Occam's Razor principle. In this paper the method is applied to discover significantly simple DNA sequences. We define DNA sequences to be simple if they contain repeated occurrences of certain 'words' and thus can be encoded in a small number of bits. Such definition includes minisatellites and microsatellites. A standard dynamic programming algorithm for data compression is applied to compute the minimal encoding lengths of sequences in linear time. An electronic mail server for identification of simple sequences based on the proposed method has been installed at the Internet address pythia/anl.gov. PMID:8402207

  2. Nuclear and mitochondrial DNA sequences from two Denisovan individuals.

    Science.gov (United States)

    Sawyer, Susanna; Renaud, Gabriel; Viola, Bence; Hublin, Jean-Jacques; Gansauge, Marie-Theres; Shunkov, Michael V; Derevianko, Anatoly P; Prüfer, Kay; Kelso, Janet; Pääbo, Svante

    2015-12-22

    Denisovans, a sister group of Neandertals, have been described on the basis of a nuclear genome sequence from a finger phalanx (Denisova 3) found in Denisova Cave in the Altai Mountains. The only other Denisovan specimen described to date is a molar (Denisova 4) found at the same site. This tooth carries a mtDNA sequence similar to that of Denisova 3. Here we present nuclear DNA sequences from Denisova 4 and a morphological description, as well as mitochondrial and nuclear DNA sequence data, from another molar (Denisova 8) found in Denisova Cave in 2010. This new molar is similar to Denisova 4 in being very large and lacking traits typical of Neandertals and modern humans. Nuclear DNA sequences from the two molars form a clade with Denisova 3. The mtDNA of Denisova 8 is more diverged and has accumulated fewer substitutions than the mtDNAs of the other two specimens, suggesting Denisovans were present in the region over an extended period. The nuclear DNA sequence diversity among the three Denisovans is comparable to that among six Neandertals, but lower than that among present-day humans. PMID:26630009

  3. PREDICTION OF CHROMATIN STATES USING DNA SEQUENCE PROPERTIES

    KAUST Repository

    Bahabri, Rihab R.

    2013-06-01

    Activities of DNA are to a great extent controlled epigenetically through the internal struc- ture of chromatin. This structure is dynamic and is influenced by different modifications of histone proteins. Various combinations of epigenetic modification of histones pinpoint to different functional regions of the DNA determining the so-called chromatin states. How- ever, the characterization of chromatin states by the DNA sequence properties remains largely unknown. In this study we aim to explore whether DNA sequence patterns in the human genome can characterize different chromatin states. Using DNA sequence motifs we built binary classifiers for each chromatic state to eval- uate whether a given genomic sequence is a good candidate for belonging to a particular chromatin state. Of four classification algorithms (C4.5, Naive Bayes, Random Forest, and SVM) used for this purpose, the decision tree based classifiers (C4.5 and Random Forest) yielded best results among those we evaluated. Our results suggest that in general these models lack sufficient predictive power, although for four chromatin states (insulators, het- erochromatin, and two types of copy number variation) we found that presence of certain motifs in DNA sequences does imply an increased probability that such a sequence is one of these chromatin states.

  4. Biased distribution of DNA uptake sequences towards genome maintenance genes

    DEFF Research Database (Denmark)

    Davidsen, T.; Rodland, E.A.; Lagesen, K.; Seeberg, E.; Rognes, Torbjørn; Tonjum, T.

    2004-01-01

    coding regions are the DNA uptake sequences (DUS) required for natural genetic transformation. More importantly, we found a significantly higher density of DUS within genes involved in DNA repair, recombination, restriction-modification and replication than in any other annotated gene group in these...

  5. Mitochondrial DNA sequence variation and risk of pancreatic cancer

    OpenAIRE

    Lam, Ernest T.; Bracci, Paige M.; Holly, Elizabeth A; Chu, Catherine; Poon, Annie; Wan, Eunice; White, Krystal; Kwok, Pui-Yan; Pawlikowska, Ludmila; Tranah, Gregory J

    2011-01-01

    Although the mitochondrial genome exhibits high mutation rates, common mitochondrial DNA (mtDNA) variation has not been consistently associated with pancreatic cancer. Here, we comprehensively examined mitochondrial genomic variation by sequencing the mtDNA of participants (cases=286, controls=283) in a San Francisco Bay Area pancreatic cancer case-control study. Five common variants were associated with pancreatic cancer at nominal statistical significance (p

  6. Reiterated DNA Sequences in Rhizobium and Agrobacterium spp

    OpenAIRE

    Flores, M.; González, V.; Brom, S; Martínez, E.; Piñero, D; Romero, D.; Dávila, G; Palacios, R

    1988-01-01

    Repeated DNA sequences are a general characteristic of eucaryotic genomes. Although several examples of DNA reiteration have been found in procaryotic organisms, only in the case of the archaebacteria Halobacterium halobium and Halobacterium volcanii [C. Sapienza and W. F. Doolittle, Nature (London) 295:384-389, 1982], has DNA reiteration been reported as a common genomic feature. The genomes of two Rhizobium phaseoli strains, one Rhizobium meliloti strain, and one Agrobacterium tumefaciens s...

  7. Biased distribution of DNA uptake sequences towards genome maintenance genes

    DEFF Research Database (Denmark)

    Davidsen, T.; Rodland, E.A.; Lagesen, K.;

    2004-01-01

    Repeated sequence signatures are characteristic features of all genomic DNA. We have made a rigorous search for repeat genomic sequences in the human pathogens Neisseria meningitidis, Neisseria gonorrhoeae and Haemophilus influenzae and found that by far the most frequent 9-10mers residing within...

  8. An integer programming approach to DNA sequence assembly.

    Science.gov (United States)

    Chang, Youngjung; Sahinidis, Nikolaos V

    2011-08-10

    De novo sequence assembly is a ubiquitous combinatorial problem in all DNA sequencing technologies. In the presence of errors in the experimental data, the assembly problem is computationally challenging, and its solution may not lead to a unique reconstruct. The enumeration of all alternative solutions is important in drawing a reliable conclusion on the target sequence, and is often overlooked in the heuristic approaches that are currently available. In this paper, we develop an integer programming formulation and global optimization solution strategy to solve the sequence assembly problem with errors in the data. We also propose an efficient technique to identify all alternative reconstructs. When applied to examples of sequencing-by-hybridization, our approach dramatically increases the length of DNA sequences that can be handled with global optimality certificate to over 10,000, which is more than 10 times longer than previously reported. For some problem instances, alternative solutions exhibited a wide range of different ability in reproducing the target DNA sequence. Therefore, it is important to utilize the methodology proposed in this paper in order to obtain all alternative solutions to reliably infer the true reconstruct. These alternative solutions can be used to refine the obtained results and guide the design of further experiments to correctly reconstruct the target DNA sequence. PMID:21864794

  9. Applications of parallel processing algorithms for DNA sequence analysis.

    OpenAIRE

    Collins, J. F.; Coulson, A F

    1984-01-01

    Programs have been written to apply parallel processing algorithms to the main methods of DNA sequence analysis. These programs allow the largest of currently interesting problems to be handled on a medium-sized computer system. The abundance of information otherwise not readily available has suggested new methods for the detection of homology and order in sequences.

  10. Do short, frequent DNA sequence motifs mould the epigenome?

    Science.gov (United States)

    Quante, Timo; Bird, Adrian

    2016-04-01

    'Epigenome' refers to the panoply of chemical modifications borne by DNA and its associated proteins that locally affect genome function. Epigenomic patterns are thought to be determined by external constraints resulting from development, disease and the environment, but DNA sequence is also a potential influence. We propose that domains of relatively uniform DNA base composition may modulate the epigenome through cell type-specific proteins that recognize short, frequent sequence motifs. Differential recruitment of epigenomic modifiers may adjust gene expression in multigene blocks as an alternative to tuning the activity of each gene separately, thus simplifying gene expression programming. PMID:26837845

  11. Mitochondrial DNA sequence variation in single cells from leukemia patients

    OpenAIRE

    Yao, Yong-Gang; Ogasawara, Yoji; Kajigaya, Sachiko; Molldrem, Jeffrey J.; Falcão, Roberto P; Pintão, Maria-Carolina; McCoy, J. Philip; Rizzatti, Edgar Gil; Young, Neal S

    2007-01-01

    A high frequency of mtDNA somatic mutation has been observed in many tumors as well as in aging tissues. In this study, we analyzed the mtDNA control region sequence variation in 3534 single normal cells and individual blasts from 18 patients with leukemia and 10 healthy donors, to address the mutation process in leukemic cells. We found significant differences in mtDNA sequence, as represented by the number of haplotypes and the mean number of cells with each nonaggregate haplotype in a popu...

  12. Anonymity in the Internet

    OpenAIRE

    Federrath, Hannes

    2006-01-01

    Research in Privacy Enhancing Technology has meanwhile a tradition of at least 20 years. One application (if not the most significant at the present) of Privacy Enhancing Technology is anonymous Web surfing. While weak protection can be achieved by simple proxy solutions, strong anonymity needs more effort: Systems like JAP and TOR are based on the idea of the "mix network" introduced by David Chaum in 1981. The talk presents selected basic privacy enhancing techniques, available practical so...

  13. Fluorescent signatures for variable DNA sequences

    OpenAIRE

    Rice, John E; Arthur H. Reis; Rice, Lisa M.; Carver-Brown, Rachel K.; Wangh, Lawrence J.

    2012-01-01

    Life abounds with genetic variations writ in sequences that are often only a few hundred nucleotides long. Rapid detection of these variations for identification of genetic diseases, pathogens and organisms has become the mainstay of molecular science and medicine. This report describes a new, highly informative closed-tube polymerase chain reaction (PCR) strategy for analysis of both known and unknown sequence variations. It combines efficient quantitative amplification of single-stranded DN...

  14. Sequence specificity of DNA cleavage by Micrococcus luteus γ endonuclease

    International Nuclear Information System (INIS)

    DNA fragments of defined sequence have been used to determine the sites of cleavage by γ-endonuclease activity in extracts prepared from Micrococcus luteus. End-labeled DNA restriction fragments of pBR322 DNA that had been irradiated under nitrogen in the presence of potassium iodide or t-butanol were treated with M. luteus γ endonuclease and analyzed on irradiated DNA preferentially at the positions of cytosines and thymines. DNA cleavage occurred immediately to the 3' side of pyrimidines in irradiated DNA and resulted in fragments that terminate in a 5'-phosphoryl group. These studies indicate that both altered cytosines and thymines may be important DNA lesions requiring repair after exposure to γ radiation

  15. Electronic Transport and Thermopower in Aperiodic DNA Sequences

    Science.gov (United States)

    Roche, Stephan; Maciá, Enrique

    A detailed study of charge transport properties of synthetic and genomic DNA sequences is reported. Genomic sequences of the Chromosome 22, λ-bacteriophage, and D1s80 genes of Human and Pygmy chimpanzee are considered in this work, and compared with both periodic and quasiperiodic (Fibonacci) sequences of nucleotides. Charge transfer efficiency is compared for all these different sequences, and large variations in charge transfer efficiency, stemming from sequence-dependent effects, are reported. In addition, basic characteristics of tunneling currents, including contact effects, are described. Finally, the thermoelectric power of nucleobases connected in between metallic contacts at different temperatures is presented.

  16. Sequencing of chloroplast genome using whole cellular DNA and Solexa sequencing technology

    Directory of Open Access Journals (Sweden)

    Jian eWu

    2012-11-01

    Full Text Available Sequencing of the chloroplast genome using traditional sequencing methods has been difficult because of its size (>120 kb and the complicated procedures required to prepare templates. To explore the feasibility of sequencing the chloroplast genome using DNA extracted from whole cells and Solexa sequencing technology, we sequenced whole cellular DNA isolated from leaves of three Brassica rapa accessions with one lane per accession. In total, 246 Mb, 362Mb, 361 Mb sequence data were generated for the three accessions Chiifu-401-42, Z16 and FT, respectively. Microreads were assembled by reference-guided assembly using the cpDNA sequences of B. rapa, Arabidopsis thaliana, and Nicotiana tabacum. We achieved coverage of more than 99.96% of the cp genome in the three tested accessions using the B. rapa sequence as the reference. When A. thaliana or N. tabacum sequences were used as references, 99.7–99.8% or 95.5–99.7% of the B. rapa chloroplast genome was covered, respectively. These results demonstrated that sequencing of whole cellular DNA isolated from young leaves using the Illumina Genome Analyzer is an efficient method for high-throughput sequencing of chloroplast genome.

  17. Zinc finger recombinases with adaptable DNA sequence specificity.

    Directory of Open Access Journals (Sweden)

    Chris Proudfoot

    Full Text Available Site-specific recombinases have become essential tools in genetics and molecular biology for the precise excision or integration of DNA sequences. However, their utility is currently limited to circumstances where the sites recognized by the recombinase enzyme have been introduced into the DNA being manipulated, or natural 'pseudosites' are already present. Many new applications would become feasible if recombinase activity could be targeted to chosen sequences in natural genomic DNA. Here we demonstrate efficient site-specific recombination at several sequences taken from a 1.9 kilobasepair locus of biotechnological interest (in the bovine β-casein gene, mediated by zinc finger recombinases (ZFRs, chimaeric enzymes with linked zinc finger (DNA recognition and recombinase (catalytic domains. In the "Z-sites" tested here, 22 bp casein gene sequences are flanked by 9 bp motifs recognized by zinc finger domains. Asymmetric Z-sites were recombined by the concomitant action of two ZFRs with different zinc finger DNA-binding specificities, and could be recombined with a heterologous site in the presence of a third recombinase. Our results show that engineered ZFRs may be designed to promote site-specific recombination at many natural DNA sequences.

  18. cDNA cloning and sequencing of ostrich Growth hormone

    Directory of Open Access Journals (Sweden)

    Doosti Abbas

    2012-01-01

    Full Text Available In recent years, industrial breeding of ostrich (Struthio camelus has been widely developed in Iran. Growth hormone (GH is a peptide hormone that stimulates growth and cell reproduction in different animals. The aim of this study was to clone and sequence the ostrich growth hormone gene in E. coli, done for the first time in Iran. The cDNA that encodes ostrich growth hormone was isolated from total mRNA of the pituitary gland and amplified by RT-PCR using GH specific PCR primers. Then GH cDNA was cloned by T/A cloning technique and the construct was transformed into E. coli. Finally, GH cDNA sequence was submitted to the GenBank (Accession number: JN559394. The results of present study showed that GH cDNA was successfully cloned in E. coli. Sequencing confirmed that GH cDNA was cloned and that the length of ostrich GH cDNA was 672 bp; BLAST search showed that the sequence of growth hormone cDNA of the ostrich from Iran has 100% homology with other records existing in GenBank.

  19. Apple II software for M13 shotgun DNA sequencing.

    OpenAIRE

    Larson, R; Messing, J

    1982-01-01

    A set of programs is presented for the reconstruction of a DNA sequence from data generated by the M13 shotgun sequencing technique. Once the sequence has been established and stored other programs are used for its analysis. The programs have been written for the Apple II microcomputer. A minimum investment is required for the hardware and the software is easily interchangeable between the growing number of interested researchers. Copies are available in ready to use form.

  20. Nanopore-based Fourth-generation DNA Sequencing Technology

    Institute of Scientific and Technical Information of China (English)

    Yanxiao Feng; Yuechuan Zhang; Cuifeng Ying; Deqiang Wang; Chunlei Du

    2015-01-01

    Nanopore-based sequencers, as the fourth-generation DNA sequencing technology, have the potential to quickly and reliably sequence the entire human genome for less than $1000, and possibly for even less than$100. The single-molecule techniques used by this technology allow us to further study the interaction between DNA and protein, as well as between protein and protein. Nanopore analysis opens a new door to molecular biology investigation at the single-molecule scale. In this article, we have reviewed academic achievements in nanopore technology from the past as well as the latest advances, including both biological and solid-state nanopores, and discussed their recent and potential applications.

  1. DNA sequence context conceals α-anomeric lesions.

    Science.gov (United States)

    Johnson, Christopher N; Spring, Alexander M; Desai, Sunil; Cunningham, Richard P; Germann, Markus W

    2012-02-24

    DNA sequence context has long been known to modulate detection and repair of DNA damage. Recent studies using experimental and computational approaches have sought to provide a basis for this observation. We have previously shown that an α-anomeric adenosine (αA) flanked by cytosines (5'CαAC-3') resulted in a kinked DNA duplex with an enlarged minor groove. Comparison of different flanking sequences revealed that a DNA duplex containing a 5'CαAG-3' motif exhibits unique substrate properties. However, this substrate was not distinguished by unusual thermodynamic properties. To understand the structural basis of the altered recognition, we have determined the solution structure of a DNA duplex with a 5'CαAG-3' core, using an extensive set of restraints including dipolar couplings and backbone torsion angles. The NMR structure exhibits an excellent agreement with the data (total R(X) twist), resulting in a straighter DNA with narrower minor groove. Overall, these features result in a less perturbed DNA helix and obscure the presence of the lesion compared to the 5'CαAC-3' sequence. The improved stacking of the 5'CαAG-3' core also affects the energetics of the DNA deformation that is required to form a catalytically competent complex. These traits provide a rationale for the modulation of the recognition by endonuclease IV. PMID:22227386

  2. Folding complex DNA nanostructures from limited sets of reusable sequences

    Science.gov (United States)

    Niekamp, Stefan; Blumer, Katy; Nafisi, Parsa M.; Tsui, Kathy; Garbutt, John; Douglas, Shawn M.

    2016-01-01

    Scalable production of DNA nanostructures remains a substantial obstacle to realizing new applications of DNA nanotechnology. Typical DNA nanostructures comprise hundreds of DNA oligonucleotide strands, where each unique strand requires a separate synthesis step. New design methods that reduce the strand count for a given shape while maintaining overall size and complexity would be highly beneficial for efficiently producing DNA nanostructures. Here, we report a method for folding a custom template strand by binding individual staple sequences to multiple locations on the template. We built several nanostructures for well-controlled testing of various design rules, and demonstrate folding of a 6-kb template by as few as 10 unique strand sequences binding to 10 ± 2 locations on the template strand. PMID:27036861

  3. Elongation method for electronic structure calculations of random DNA sequences.

    Science.gov (United States)

    Orimoto, Yuuichi; Liu, Kai; Aoki, Yuriko

    2015-10-30

    We applied ab initio order-N elongation (ELG) method to calculate electronic structures of various deoxyribonucleic acid (DNA) models. We aim to test potential application of the method for building a database of DNA electronic structures. The ELG method mimics polymerization reactions on a computer and meets the requirements for linear scaling computational efficiency and high accuracy, even for huge systems. As a benchmark test, we applied the method for calculations of various types of random sequenced A- and B-type DNA models with and without counterions. In each case, the ELG method maintained high accuracy with small errors in energy on the order of 10(-8) hartree/atom compared with conventional calculations. We demonstrate that the ELG method can provide valuable information such as stabilization energies and local densities of states for each DNA sequence. In addition, we discuss the "restarting" feature of the ELG method for constructing a database that exhaustively covers DNA species. PMID:26337429

  4. DNA sequence of the yeast transketolase gene.

    Science.gov (United States)

    Fletcher, T S; Kwee, I L; Nakada, T; Largman, C; Martin, B M

    1992-02-18

    Transketolase (EC 2.2.1.1) is the enzyme that, together with aldolase, forms a reversible link between the glycolytic and pentose phosphate pathways. We have cloned and sequenced the transketolase gene from yeast (Saccharomyces cerevisiae). This is the first transketolase gene of the pentose phosphate shunt to be sequenced from any source. The molecular mass of the proposed translated protein is 73,976 daltons, in good agreement with the observed molecular mass of about 75,000 daltons. The 5'-nontranslated region of the gene is similar to other yeast genes. There is no evidence of 5'-splice junctions or branch points in the sequence. The 3'-nontranslated region contains the polyadenylation signal (AATAAA), 80 base pairs downstream from the termination codon. A high degree of homology is found between yeast transketolase and dihydroxyacetone synthase (formaldehyde transketolase) from the yeast Hansenula polymorpha. The overall sequence identity between these two proteins is 37%, with four regions of much greater similarity. The regions from amino acid residues 98-131, 157-182, 410-433, and 474-489 have sequence identities of 74%, 66%, 83%, and 82%, respectively. One of these regions (157-182) includes a possible thiamin pyrophosphate (TPP) binding domain, and another (410-433) may contain the catalytic domain. PMID:1737042

  5. Spatial Control of DNA Reaction Networks by DNA Sequence

    OpenAIRE

    Ellington, Andrew D.; Xi Chen; Allen, Peter B.

    2012-01-01

    We have developed a set of DNA circuits that execute during gel electrophoresis to yield immobile, fluorescent features in the gel. The parallel execution of orthogonal circuits led to the simultaneous production of different fluorescent lines at different positions in the gel. The positions of the lines could be rationally manipulated by changing the mobilities of the reactants. The ability to program at the nanoscale so as to produce patterns at the macroscale is a step towards programmable...

  6. Compiling Multicopy Single-Stranded DNA Sequences from Bacterial Genome Sequences

    OpenAIRE

    Yoo, Wonseok; Lim, Dongbin; Kim, Sangsoo

    2016-01-01

    A retron is a bacterial retroelement that encodes an RNA gene and a reverse transcriptase (RT). The former, once transcribed, works as a template primer for reverse transcription by the latter. The resulting DNA is covalently linked to the upstream part of the RNA; this chimera is called multicopy single-stranded DNA (msDNA), which is extrachromosomal DNA found in many bacterial species. Based on the conserved features in the eight known msDNA sequences, we developed a detection method and ap...

  7. cDNA sequence for human erythrocyte ankyrin

    International Nuclear Information System (INIS)

    The cDNA for human erythrocyte ankyrin has been isolated from a series of overlapping clones obtained from a reticulocyte cDNA library. The composite cDNA sequence has a large open reading frame of 5636 base pairs (bp) with the complete coding sequence for a polypeptide of 1879 amino acids with a predicted molecular mass of 206 kDa. The derived amino acid sequence contained 194 residues that were identical to those obtained by direct amino acid sequencing of 11 ankyrin proteolytic peptides. The primary sequence contained 23 highly homologous repeat units of 33 amino acids within the 90-kDa band 3 binding domain. Two cDNA clones showed evidence of apparent mRNA processing, resulting in the deletions of 486 bp and 135 bp, respectively. The 486-bp deletion resulted in the removal of a 16-kDa highly acidic peptide, and the smaller deletion had the effect of altering the COOH terminus of the molecule. Radiolabeled ankyrin cDNAs recognized two erythroid message sizes by RNA blot analysis, one of which was predominantly associated with early erythroid cell types. An ankyrin message was also observed in RNA from the human cerebellum by the same method. The ankyrin gene is assigned to chromosome 8 using genomic DNA from a panel of sorted human chromosomes

  8. How effective is graphene nanopore geometry on DNA sequencing?

    CERN Document Server

    Satarifard, Vahid; Ejtehadi, Mohammad Reza

    2015-01-01

    In this paper we investigate the effects of graphene nanopore geometry on homopolymer ssDNA pulling process through nanopore using steered molecular dynamic (SMD) simulations. Different graphene nanopores are examined including axially symmetric and asymmetric monolayer graphene nanopores as well as five layer graphene polyhedral crystals (GPC). The pulling force profile, moving fashion of ssDNA, work done in irreversible DNA pulling and orientations of DNA bases near the nanopore are assessed. Simulation results demonstrate the strong effect of the pore shape as well as geometrical symmetry on free energy barrier, orientations and dynamic of DNA translocation through graphene nanopore. Our study proposes that the symmetric circular geometry of monolayer graphene nanopore with high pulling velocity can be used for DNA sequencing.

  9. Mitochondrial DNA Sequence Analysis - Validation and Use for Forensic Casework.

    Science.gov (United States)

    Holland, M M; Parsons, T J

    1999-06-01

    With the discovery of the polymerase chain reaction (PCR) in the mid-1980's, the last in a series of critical molecular biology techniques (to include the isolation of DNA from human and non-human biological material, and primary sequence analysis of DNA) had been developed to rapidly analyze minute quantities of mitochondrial DNA (mtDNA). This was especially true for mtDNA isolated from challenged sources, such as ancient or aged skeletal material and hair shafts. One of the beneficiaries of this work has been the forensic community. Over the last decade, a significant amount of research has been conducted to develop PCR-based sequencing assays for the mtDNA control region (CR), which have subsequently been used to further characterize the CR. As a result, the reliability of these assays has been investigated, the limitations of the procedures have been determined, and critical aspects of the analysis process have been identified, so that careful control and monitoring will provide the basis for reliable testing. With the application of these assays to forensic identification casework, mtDNA sequence analysis has been properly validated, and is a reliable procedure for the examination of biological evidence encountered in forensic criminalistic cases. PMID:26255820

  10. MetaGeneAnnotator: Detecting Species-Specific Patterns of Ribosomal Binding Site for Precise Gene Prediction in Anonymous Prokaryotic and Phage Genomes

    OpenAIRE

    Noguchi, Hideki; Taniguchi, Takeaki; Itoh, Takehiko

    2008-01-01

    Recent advances in DNA sequencers are accelerating genome sequencing, especially in microbes, and complete and draft genomes from various species have been sequenced in rapid succession. Here, we present a comprehensive gene prediction tool, the MetaGeneAnnotator (MGA), which precisely predicts all kinds of prokaryotic genes from a single or a set of anonymous genomic sequences having a variety of lengths. The MGA integrates statistical models of prophage genes, in addition to those of bacter...

  11. PIMS sequencing extension: a laboratory information management system for DNA sequencing facilities

    Directory of Open Access Journals (Sweden)

    Baldwin Stephen A

    2011-03-01

    Full Text Available Abstract Background Facilities that provide a service for DNA sequencing typically support large numbers of users and experiment types. The cost of services is often reduced by the use of liquid handling robots but the efficiency of such facilities is hampered because the software for such robots does not usually integrate well with the systems that run the sequencing machines. Accordingly, there is a need for software systems capable of integrating different robotic systems and managing sample information for DNA sequencing services. In this paper, we describe an extension to the Protein Information Management System (PIMS that is designed for DNA sequencing facilities. The new version of PIMS has a user-friendly web interface and integrates all aspects of the sequencing process, including sample submission, handling and tracking, together with capture and management of the data. Results The PIMS sequencing extension has been in production since July 2009 at the University of Leeds DNA Sequencing Facility. It has completely replaced manual data handling and simplified the tasks of data management and user communication. Samples from 45 groups have been processed with an average throughput of 10000 samples per month. The current version of the PIMS sequencing extension works with Applied Biosystems 3130XL 96-well plate sequencer and MWG 4204 or Aviso Theonyx liquid handling robots, but is readily adaptable for use with other combinations of robots. Conclusions PIMS has been extended to provide a user-friendly and integrated data management solution for DNA sequencing facilities that is accessed through a normal web browser and allows simultaneous access by multiple users as well as facility managers. The system integrates sequencing and liquid handling robots, manages the data flow, and provides remote access to the sequencing results. The software is freely available, for academic users, from http://www.pims-lims.org/.

  12. PIMS sequencing extension: a laboratory information management system for DNA sequencing facilities

    Science.gov (United States)

    2011-01-01

    Background Facilities that provide a service for DNA sequencing typically support large numbers of users and experiment types. The cost of services is often reduced by the use of liquid handling robots but the efficiency of such facilities is hampered because the software for such robots does not usually integrate well with the systems that run the sequencing machines. Accordingly, there is a need for software systems capable of integrating different robotic systems and managing sample information for DNA sequencing services. In this paper, we describe an extension to the Protein Information Management System (PIMS) that is designed for DNA sequencing facilities. The new version of PIMS has a user-friendly web interface and integrates all aspects of the sequencing process, including sample submission, handling and tracking, together with capture and management of the data. Results The PIMS sequencing extension has been in production since July 2009 at the University of Leeds DNA Sequencing Facility. It has completely replaced manual data handling and simplified the tasks of data management and user communication. Samples from 45 groups have been processed with an average throughput of 10000 samples per month. The current version of the PIMS sequencing extension works with Applied Biosystems 3130XL 96-well plate sequencer and MWG 4204 or Aviso Theonyx liquid handling robots, but is readily adaptable for use with other combinations of robots. Conclusions PIMS has been extended to provide a user-friendly and integrated data management solution for DNA sequencing facilities that is accessed through a normal web browser and allows simultaneous access by multiple users as well as facility managers. The system integrates sequencing and liquid handling robots, manages the data flow, and provides remote access to the sequencing results. The software is freely available, for academic users, from http://www.pims-lims.org/. PMID:21385349

  13. A novel chaotic image encryption scheme using DNA sequence operations

    Science.gov (United States)

    Wang, Xing-Yuan; Zhang, Ying-Qian; Bao, Xue-Mei

    2015-10-01

    In this paper, we propose a novel image encryption scheme based on DNA (Deoxyribonucleic acid) sequence operations and chaotic system. Firstly, we perform bitwise exclusive OR operation on the pixels of the plain image using the pseudorandom sequences produced by the spatiotemporal chaos system, i.e., CML (coupled map lattice). Secondly, a DNA matrix is obtained by encoding the confused image using a kind of DNA encoding rule. Then we generate the new initial conditions of the CML according to this DNA matrix and the previous initial conditions, which can make the encryption result closely depend on every pixel of the plain image. Thirdly, the rows and columns of the DNA matrix are permuted. Then, the permuted DNA matrix is confused once again. At last, after decoding the confused DNA matrix using a kind of DNA decoding rule, we obtain the ciphered image. Experimental results and theoretical analysis show that the scheme is able to resist various attacks, so it has extraordinarily high security.

  14. Sequence specificity of DNA cleavage by Micrococcus luteus gamma endonuclease

    International Nuclear Information System (INIS)

    Gamma irradiation induces the formation of lesions in DNA that are cleaved by an endonuclease activity in Micrococcus luteus extract. DNA fragments of defined sequence an DNA sequencing techniques were used to determine the sites of cleavage by this activity. /sup 32/P end-labelled DNA restriction fragments were gamma irradiated under N/sub 2/ and in the presence of KI (conditions which maximize the enzyme sensitive site to strand break ratio), treated with M. luteus extract, and analyzed by electrophoresis on denaturing polyacrylamide gels. Irradiated DNA was preferentially cleaved by the extract at sites of cytosine and thymine. Little or no cleavage was observed at purines. Scission of 3' end-labelled DNA at altered pyrimidines resulted in fragments that had electrophoretic mobilities similar to those of DNA fragments that were phosphorylated at the 5' terminus. The presence of a 5' phosphate was confirmed by a change in electrophoretic mobility after phosphatase treatment of the fragments. The sites of endonucleolytic cleavage by M. luteus extract were compared to those of the purified Escherichia coli endonuclease III, which has been shown to be active against x-irradiated DNA. Preliminary results from velocity sedimentation studies indicate that these two enzyme preparations differ in specificity

  15. Network clustering coefficient approach to DNA sequence analysis

    Energy Technology Data Exchange (ETDEWEB)

    Gerhardt, Guenther J.L. [Universidade Federal do Rio Grande do Sul-Hospital de Clinicas de Porto Alegre, Rua Ramiro Barcelos 2350/sala 2040/90035-003 Porto Alegre (Brazil); Departamento de Fisica e Quimica da Universidade de Caxias do Sul, Rua Francisco Getulio Vargas 1130, 95001-970 Caxias do Sul (Brazil); Lemke, Ney [Programa Interdisciplinar em Computacao Aplicada, Unisinos, Av. Unisinos, 950, 93022-000 Sao Leopoldo, RS (Brazil); Corso, Gilberto [Departamento de Biofisica e Farmacologia, Centro de Biociencias, Universidade Federal do Rio Grande do Norte, Campus Universitario, 59072 970 Natal, RN (Brazil)]. E-mail: corso@dfte.ufrn.br

    2006-05-15

    In this work we propose an alternative DNA sequence analysis tool based on graph theoretical concepts. The methodology investigates the path topology of an organism genome through a triplet network. In this network, triplets in DNA sequence are vertices and two vertices are connected if they occur juxtaposed on the genome. We characterize this network topology by measuring the clustering coefficient. We test our methodology against two main bias: the guanine-cytosine (GC) content and 3-bp (base pairs) periodicity of DNA sequence. We perform the test constructing random networks with variable GC content and imposed 3-bp periodicity. A test group of some organisms is constructed and we investigate the methodology in the light of the constructed random networks. We conclude that the clustering coefficient is a valuable tool since it gives information that is not trivially contained in 3-bp periodicity neither in the variable GC content.

  16. Network clustering coefficient approach to DNA sequence analysis

    International Nuclear Information System (INIS)

    In this work we propose an alternative DNA sequence analysis tool based on graph theoretical concepts. The methodology investigates the path topology of an organism genome through a triplet network. In this network, triplets in DNA sequence are vertices and two vertices are connected if they occur juxtaposed on the genome. We characterize this network topology by measuring the clustering coefficient. We test our methodology against two main bias: the guanine-cytosine (GC) content and 3-bp (base pairs) periodicity of DNA sequence. We perform the test constructing random networks with variable GC content and imposed 3-bp periodicity. A test group of some organisms is constructed and we investigate the methodology in the light of the constructed random networks. We conclude that the clustering coefficient is a valuable tool since it gives information that is not trivially contained in 3-bp periodicity neither in the variable GC content

  17. Multiplexed DNA sequence capture of mitochondrial genomes using PCR products.

    Directory of Open Access Journals (Sweden)

    Tomislav Maricic

    Full Text Available BACKGROUND: To utilize the power of high-throughput sequencers, target enrichment methods have been developed. The majority of these require reagents and equipment that are only available from commercial vendors and are not suitable for the targets that are a few kilobases in length. METHODOLOGY/PRINCIPAL FINDINGS: We describe a novel and economical method in which custom made long-range PCR products are used to capture complete human mitochondrial genomes from complex DNA mixtures. We use the method to capture 46 complete mitochondrial genomes in parallel and we sequence them on a single lane of an Illumina GA(II instrument. CONCLUSIONS/SIGNIFICANCE: This method is economical and simple and particularly suitable for targets that can be amplified by PCR and do not contain highly repetitive sequences such as mtDNA. It has applications in population genetics and forensics, as well as studies of ancient DNA.

  18. Multiple Base Substitution Corrections in DNA Sequence Evolution

    Science.gov (United States)

    Kowalczuk, M.; Mackiewicz, P.; Szczepanik, D.; Nowicka, A.; Dudkiewicz, M.; Dudek, M. R.; Cebrat, S.

    We discuss the Jukes and Cantor's one-parameter model and Kimura's two-parameter model unability to describe evolution of asymmetric DNA molecules. The standard distance measure between two DNA sequences, which is the number of substitutions per site, should include the effect of multiple base substitutions separately for each type of the base. Otherwise, the respective tables of substitutions cannot reconstruct the asymmetric DNA molecule with respect to the composition. Basing on Kimura's neutral theory, we have derived a linear law for the correlation of the mean survival time of nucleotides under constant mutation pressure and their fraction in the genome. According to the law, the corrections to Kimura's theory have been discussed to describe evolution of genomes with asymmetric nucleotide composition. We consider the particular case of the strongly asymmetric Borrelia burgdorferi genome and we discuss in detail the corrections, which should be introduced into the distance measure between two DNA sequences to include multiple base substitutions.

  19. Facilitated diffusion on mobile DNA: configurational traps and sequence heterogeneity

    CERN Document Server

    Brackley, C A; Marenduzzo, D; 10.1103/PhysRevLett.109.168103

    2012-01-01

    We present Brownian dynamics simulations of the facilitated diffusion of a protein, modelled as a sphere with a binding site on its surface, along DNA, modelled as a semi-flexible polymer. We consider both the effect of DNA organisation in 3D, and of sequence heterogeneity. We find that in a network of DNA loops, as are thought to be present in bacterial DNA, the search process is very sensitive to the spatial location of the target within such loops. Therefore, specific genes might be repressed or promoted by changing the local topology of the genome. On the other hand, sequence heterogeneity creates traps which normally slow down facilitated diffusion. When suitably positioned, though, these traps can, surprisingly, render the search process much more efficient.

  20. Ancient mtDNA sequences from the First Australians revisited.

    Science.gov (United States)

    Heupink, Tim H; Subramanian, Sankar; Wright, Joanne L; Endicott, Phillip; Westaway, Michael Carrington; Huynen, Leon; Parson, Walther; Millar, Craig D; Willerslev, Eske; Lambert, David M

    2016-06-21

    The publication in 2001 by Adcock et al. [Adcock GJ, et al. (2001) Proc Natl Acad Sci USA 98(2):537-542] in PNAS reported the recovery of short mtDNA sequences from ancient Australians, including the 42,000-y-old Mungo Man [Willandra Lakes Hominid (WLH3)]. This landmark study in human ancient DNA suggested that an early modern human mitochondrial lineage emerged in Asia and that the theory of modern human origins could no longer be considered solely through the lens of the "Out of Africa" model. To evaluate these claims, we used second generation DNA sequencing and capture methods as well as PCR-based and single-primer extension (SPEX) approaches to reexamine the same four Willandra Lakes and Kow Swamp 8 (KS8) remains studied in the work by Adcock et al. Two of the remains sampled contained no identifiable human DNA (WLH15 and WLH55), whereas the Mungo Man (WLH3) sample contained no Aboriginal Australian DNA. KS8 reveals human mitochondrial sequences that differ from the previously inferred sequence. Instead, we recover a total of five modern European contaminants from Mungo Man (WLH3). We show that the remaining sample (WLH4) contains ∼1.4% human DNA, from which we assembled two complete mitochondrial genomes. One of these was a previously unidentified Aboriginal Australian haplotype belonging to haplogroup S2 that we sequenced to a high coverage. The other was a contaminating modern European mitochondrial haplotype. Although none of the sequences that we recovered matched those reported by Adcock et al., except a contaminant, these findings show the feasibility of obtaining important information from ancient Aboriginal Australian remains. PMID:27274055

  1. Perspectives of DNA microarray and next-generation DNA sequencing technologies

    Institute of Scientific and Technical Information of China (English)

    TENG XiaoKun; XIAO HuaSheng

    2009-01-01

    DNA microarray and next-generation DNA sequencing technologies are important tools for high-throughput genome research, in revealing both the structural and functional characteristics of genomes. In the past decade the DNA microarray technologies have been widely applied in the studies of functional genomics, systems biology and pharmacogenomics. The next-generation DNA sequenc-ing method was first introduced by the 454 Company in 2003, immediately followed by the establish-ment of the Solexa and Solid techniques by other biotech companies. Though it has not been long since the first emergence of this technology, with the fast and impressive improvement, the application of this technology has extended to almost all fields of genomics research, as a rival challenging the existing DNA microarray technology. This paper briefly reviews the working principles of these two technologies as well as their application and perspectives in genome research.

  2. Mitochondrial DNA sequence evolution in the Arctoidea.

    OpenAIRE

    Zhang, Y P; Ryder, O. A.

    1993-01-01

    Some taxa in the superfamily Arctoidea, such as the giant panda and the lesser panda, have presented puzzles to taxonomists. In the present study, approximately 397 bases of the cytochrome b gene, 364 bases of the 12S rRNA gene, and 74 bases of the tRNA(Thr) and tRNA(Pro) genes from the giant panda, lesser panda, kinkajou, raccoon, coatimundi, and all species of the Ursidae were sequenced. The high transition/transversion ratios in cytochrome b and RNA genes prior to saturation suggest that t...

  3. Computational optimisation of targeted DNA sequencing for cancer detection.

    OpenAIRE

    Pierre Martinez; Nicholas McGranahan; Nicolai Juul Birkbak; Marco Gerlinger; Charles Swanton

    2013-01-01

    Despite recent progress thanks to next-generation sequencing technologies, personalised cancer medicine is still hampered by intra-tumour heterogeneity and drug resistance. As most patients with advanced metastatic disease face poor survival, there is need to improve early diagnosis. Analysing circulating tumour DNA (ctDNA) might represent a non-invasive method to detect mutations in patients, facilitating early detection. In this article, we define reduced gene panels from publicly available...

  4. DNA sequence analysis with droplet-based microfluidics

    OpenAIRE

    Abate, Adam R.; Hung, Tony; Sperling, Ralph A.; Mary, Pascaline; Rotem, Assaf; Agresti, Jeremy J.; Weiner, Michael A.; Weitz, David A.

    2013-01-01

    Droplet-based microfluidic techniques can form and process micrometer scale droplets at thousands per second. Each droplet can house an individual biochemical reaction, allowing millions of reactions to be performed in minutes with small amounts of total reagent. This versatile approach has been used for engineering enzymes, quantifying concentrations of DNA in solution, and screening protein crystallization conditions. Here, we use it to read the sequences of DNA molecules with a FRET-based ...

  5. Thermodynamics of sequence-specific binding of PNA to DNA

    DEFF Research Database (Denmark)

    Ratilainen, T; Holmén, A; Tuite, E; Nielsen, P E; Nordén, B

    2000-01-01

    For further characterization of the hybridization properties of peptide nucleic acids (PNAs), the thermodynamics of hybridization of mixed sequence PNA-DNA duplexes have been studied. We have characterized the binding of PNA to DNA in terms of binding affinity (perfectly matched duplexes) and...... relative to that of the perfectly matched sequence with a corresponding free energy penalty of about 15 kJ mol(-1) bp(-1). The average cost of a single mismatch is therefore estimated to be on the order of or larger than the gain of two matched base pairs, resulting in an apparent binding constant of only...

  6. Anaplasma phagocytophilum in Danish sheep: confirmation by DNA sequencing

    Directory of Open Access Journals (Sweden)

    Thamsborg Stig M

    2009-12-01

    Full Text Available Abstract Background The presence of Anaplasma phagocytophilum, an Ixodes ricinus transmitted bacterium, was investigated in two flocks of Danish grazing lambs. Direct PCR detection was performed on DNA extracted from blood and serum with subsequent confirmation by DNA sequencing. Methods 31 samples obtained from clinically normal lambs in 2000 from Fussingø, Jutland and 12 samples from ten lambs and two ewes from a clinical outbreak at Feddet, Zealand in 2006 were included in the study. Some of the animals from Feddet had shown clinical signs of polyarthritis and general unthriftiness prior to sampling. DNA extraction was optimized from blood and serum and detection achieved by a 16S rRNA targeted PCR with verification of the product by DNA sequencing. Results Five DNA extracts were found positive by PCR, including two samples from 2000 and three from 2006. For both series of samples the product was verified as A. phagocytophilum by DNA sequencing. Conclusions A. phagocytophilum was detected by molecular methods for the first time in Danish grazing lambs during the two seasons investigated (2000 and 2006.

  7. Anonymous Mobile Payment Solution

    Directory of Open Access Journals (Sweden)

    Alhaj Ali Jalila

    2015-09-01

    Full Text Available The evolution and increasing popularity of mobile handheld devices has led to the development of payment applications. The global acceptance of mobile payments is hindered by security and privacy concerns. One of the main problems evoked is the anonymity related with banking transactions. In this paper I propose a new secured architecture for mobile banking. Anonymity and privacy protection are the measures to be enhanced in order to satisfy people’s current needs. The banking platform must provide the highest level of security for messages exchanged between bank and the customer.

  8. An Uncompressed Image Encryption Algorithm Based on DNA Sequences

    Directory of Open Access Journals (Sweden)

    Shima Ramesh Maniyath

    2011-07-01

    Full Text Available The rapid growth of the Internet and digitized content made image and video distribution simpler. Hence the need for image and video data protection is on the rise. In this paper, we propose a secure and computationally feasible image and video encryption/decryption algorithm based on DNA sequences. The main purpose of this algorithm is to reduce the big image encryption time. This algorithm is implemented by using the natural DNA sequences as main keys. The first part is the process of pixel scrambling. The original image is confused in the light of the scrambling sequence which is generated by the DNA sequence. The second part is the process of pixel replacement. The pixel gray values of the new image and the one of the three encryption templates generated by the other DNA sequence are XORed bit-by-bit in turn. The main scope of this paper is to propose an extension of this algorithm to videos and making it secure using modern Biological technology. A security analysis for the proposed system is performed and presented.

  9. Fast comparison of DNA sequences by oligonucleotide profiling

    Directory of Open Access Journals (Sweden)

    Marín Ignacio

    2008-02-01

    Full Text Available Abstract Background The comparison of DNA sequences is a traditional problem in genomics and bioinformatics. Many new opportunities emerge due to the improvement of personal computers, allowing the implementation of novel strategies of analysis. Findings We describe a new program, called UVWORD, which determines the number of times that each DNA word present in a sequence (target is found in a second sequence (source, a procedure that we have called oligonucleotide profiling. On a standard computer, the user may search for words of a size ranging from k = 1 to k = 14 nucleotides. Average counts for groups of contiguous words may also be established. The rate of analysis on standard computers is from 3.4 (k = 14 to 16 millions of words per second (1 ≤ k ≤ 8. This makes feasible the fast screening of even the longest known DNA molecules. Discussion We show that the combination of the ability of analyzing words of relatively long size, which occur very rarely by chance, and the fast speed of the program allows to perform novel types of screenings, complementary to those provided by standard programs such as BLAST. This method can be used to determine oligonucleotide content, to characterize the distribution of repetitive sequences in chromosomes, to determine the evolutionary conservation of sequences in different species, to establish regions of similar DNA among chromosomes or genomes, etc.

  10. Mitochondrial DNA sequences in the nuclear genome of a locust.

    Science.gov (United States)

    Gellissen, G; Bradfield, J Y; White, B N; Wyatt, G R

    The endosymbiotic theory of the origin of mitochondria is widely accepted, and implies that loss of genes from the mitochondria to the nucleus of eukaryotic cells has occurred over evolutionary time. However, evidence at the DNA sequence level for gene transfer between these organelles has so far been limited to a single example, the demonstration that a mitochondrial ATPase subunit gene of Neurospora crassa has an homologous partner in the nuclear genome. From a gene library of the insect, Locusta migratoria, we have now isolated two clones, representing separate fragments of nuclear DNA, which contain sequences homologous to the mitochondrial genes for ribosomal RNA, as well as regions of homology with highly repeated nuclear sequences. The results suggest the transfer of sequences between mitochondrial and nuclear genomes, followed by evolutionary divergence. PMID:6298629

  11. A Comparison of Computation Techniques for DNA Sequence Comparison

    Directory of Open Access Journals (Sweden)

    Harshita G. Patil

    2012-04-01

    Full Text Available This Project shows a comparison survey done on DNA sequence comparison techniques. The various techniques implemented are sequential comparison, multithreading on a single computer and multithreading using parallel processing. This Project shows the issues involved in implementing a dynamic programming algorithm for biological sequence comparison on a general purpose parallel computing platform Tiling is an important technique for extraction of parallelism. Informally, tiling consists of partitioning the iteration space into several chunks of computation called tiles (blocks such that sequential traversal of the tiles covers the entire iteration space. The idea behind tiling is to increase the granularity of computation and decrease the amount of communication incurred between processors. This makes tiling more suitable for distributed memory architectures where communication startup costs are very high and hence frequent communication is undesirable. Our work to develop sequence- comparison mechanism and software supports the identification of sequences of DNA.

  12. DNA qualification workflow for next generation sequencing of histopathological samples.

    Directory of Open Access Journals (Sweden)

    Michele Simbolo

    Full Text Available Histopathological samples are a treasure-trove of DNA for clinical research. However, the quality of DNA can vary depending on the source or extraction method applied. Thus a standardized and cost-effective workflow for the qualification of DNA preparations is essential to guarantee interlaboratory reproducible results. The qualification process consists of the quantification of double strand DNA (dsDNA and the assessment of its suitability for downstream applications, such as high-throughput next-generation sequencing. We tested the two most frequently used instrumentations to define their role in this process: NanoDrop, based on UV spectroscopy, and Qubit 2.0, which uses fluorochromes specifically binding dsDNA. Quantitative PCR (qPCR was used as the reference technique as it simultaneously assesses DNA concentration and suitability for PCR amplification. We used 17 genomic DNAs from 6 fresh-frozen (FF tissues, 6 formalin-fixed paraffin-embedded (FFPE tissues, 3 cell lines, and 2 commercial preparations. Intra- and inter-operator variability was negligible, and intra-methodology variability was minimal, while consistent inter-methodology divergences were observed. In fact, NanoDrop measured DNA concentrations higher than Qubit and its consistency with dsDNA quantification by qPCR was limited to high molecular weight DNA from FF samples and cell lines, where total DNA and dsDNA quantity virtually coincide. In partially degraded DNA from FFPE samples, only Qubit proved highly reproducible and consistent with qPCR measurements. Multiplex PCR amplifying 191 regions of 46 cancer-related genes was designated the downstream application, using 40 ng dsDNA from FFPE samples calculated by Qubit. All but one sample produced amplicon libraries suitable for next-generation sequencing. NanoDrop UV-spectrum verified contamination of the unsuccessful sample. In conclusion, as qPCR has high costs and is labor intensive, an alternative effective standard

  13. Fast DNA sequencing by electrical means inches closer

    International Nuclear Information System (INIS)

    The sequencing of the human genome offered a glimpse of future medical practices, where information retrieved from the genome could be harnessed to inform treatment decisions. However, making DNA sequencing accessible enough for widespread use poses a number of challenges. This perspective article traces the progress made in the field so far and looks at how close we may be already to real-life applications. (perspective)

  14. Base-sequence-dependent sliding of proteins on DNA

    OpenAIRE

    Barbi, M; Place, C.; Popkov, V.; Salerno, M.

    2004-01-01

    The possibility that the sliding motion of proteins on DNA is influenced by the base sequence through a base pair reading interaction, is considered. Referring to the case of the T7 RNA-polymerase, we show that the protein should follow a noise-influenced sequence-dependent motion which deviate from the standard random walk usually assumed. The general validity and the implications of the results are discussed.

  15. Restriction and sequence alterations affect DNA uptake sequence-dependent transformation in Neisseria meningitidis.

    Science.gov (United States)

    Ambur, Ole Herman; Frye, Stephan A; Nilsen, Mariann; Hovland, Eirik; Tønjum, Tone

    2012-01-01

    Transformation is a complex process that involves several interactions from the binding and uptake of naked DNA to homologous recombination. Some actions affect transformation favourably whereas others act to limit it. Here, meticulous manipulation of a single type of transforming DNA allowed for quantifying the impact of three different mediators of meningococcal transformation: NlaIV restriction, homologous recombination and the DNA Uptake Sequence (DUS). In the wildtype, an inverse relationship between the transformation frequency and the number of NlaIV restriction sites in DNA was observed when the transforming DNA harboured a heterologous region for selection (ermC) but not when the transforming DNA was homologous with only a single nucleotide heterology. The influence of homologous sequence in transforming DNA was further studied using plasmids with a small interruption or larger deletions in the recombinogenic region and these alterations were found to impair transformation frequency. In contrast, a particularly potent positive driver of DNA uptake in Neisseria sp. are short DUS in the transforming DNA. However, the molecular mechanism(s) responsible for DUS specificity remains unknown. Increasing the number of DUS in the transforming DNA was here shown to exert a positive effect on transformation. Furthermore, an influence of variable placement of DUS relative to the homologous region in the donor DNA was documented for the first time. No effect of altering the orientation of DUS was observed. These observations suggest that DUS is important at an early stage in the recognition of DNA, but does not exclude the existence of more than one level of DUS specificity in the sequence of events that constitute transformation. New knowledge on the positive and negative drivers of transformation may in a larger perspective illuminate both the mechanisms and the evolutionary role(s) of one of the most conserved mechanisms in nature: homologous recombination. PMID

  16. Assurances of past donor anonymity are meaningless

    OpenAIRE

    Blyth, Eric

    2005-01-01

    The New Scientist recently recounted the story of an American teenager conceived through ostensibly anonymous donor insemination who had been able to identify his donor through DNA testing and an internet genetic database service (also see BioNews issue 333, at http://www.bionews.org.uk/new.lasso?storyid=2808). In fact, we have known since Barry Stevens' remarkable documentary, Offspring, released in 2001, that with some genetic background information, access to DNA testing and the intern...

  17. A simple method encoding linear single strain DNA sequence with natural numbers

    Institute of Scientific and Technical Information of China (English)

    LI Jiye; XU Yuan; ZHANG Wang

    2008-01-01

    A simple method presenting linear single strain DNA (LssDNA) sequence with natural numbers is introduced in this paper. The method presents LssDNA correspondingly with the numerals 1, 2, 3 and 4. After calculation, the sequence can be coded in natural numbers which can also be decoded into the DNA sequence. Thus, an LssDNA sequence can be expressed in a natural number and a dot at coordinate axes. In the future, a new LssDNA sequences database termed "DotBank" would be realized in which each LssDNA sequence is determined as a dot.

  18. Anonymous Biometric Access Control

    Directory of Open Access Journals (Sweden)

    Shuiming Ye

    2009-01-01

    Full Text Available Access control systems using the latest biometric technologies can offer a higher level of security than conventional password-based systems. Their widespread deployments, however, can severely undermine individuals' rights of privacy. Biometric signals are immutable and can be exploited to associate individuals' identities to sensitive personal records across disparate databases. In this paper, we propose the Anonymous Biometric Access Control (ABAC system to protect user anonymity. The ABAC system uses novel Homomorphic Encryption (HE based protocols to verify membership of a user without knowing his/her true identity. To make HE-based protocols scalable to large biometric databases, we propose the k-Anonymous Quantization (kAQ framework that provides an effective and secure tradeoff of privacy and complexity. kAQ limits server's knowledge of the user to k maximally dissimilar candidates in the database, where k controls the amount of complexity-privacy tradeoff. kAQ is realized by a constant-time table lookup to identity the k candidates followed by a HE-based matching protocol applied only on these candidates. The maximal dissimilarity protects privacy by destroying any similarity patterns among the returned candidates. Experimental results on iris biometrics demonstrate the validity of our framework and illustrate a practical implementation of an anonymous biometric system.

  19. Privacy-Enhanced Methods for Comparing Compressed DNA Sequences

    CERN Document Server

    Eppstein, David; Baldi, Pierre

    2011-01-01

    In this paper, we study methods for improving the efficiency and privacy of compressed DNA sequence comparison computations, under various querying scenarios. For instance, one scenario involves a querier, Bob, who wants to test if his DNA string, $Q$, is close to a DNA string, $Y$, owned by a data owner, Alice, but Bob does not want to reveal $Q$ to Alice and Alice is willing to reveal $Y$ to Bob \\emph{only if} it is close to $Q$. We describe a privacy-enhanced method for comparing two compressed DNA sequences, which can be used to achieve the goals of such a scenario. Our method involves a reduction to set differencing, and we describe a privacy-enhanced protocol for set differencing that achieves absolute privacy for Bob (in the information theoretic sense), and a quantifiable degree of privacy protection for Alice. One of the important features of our protocols, which makes them ideally suited to privacy-enhanced DNA sequence comparison problems, is that the communication complexity of our solutions is pr...

  20. Derivatized versions of ligase enzymes for constructing DNA sequences

    Science.gov (United States)

    Mariella, Jr., Raymond P.; Christian, Allen T.; Tucker, James D.; Dzenitis, John M.; Papavasiliou, Alexandros P.

    2006-08-15

    A method of making very long, double-stranded synthetic poly-nucleotides. A multiplicity of short oligonucleotides is provided. The short oligonucleotides are sequentially hybridized to each other. Enzymatic ligation of the oligonucleotides provides a contiguous piece of PCR-ready DNA of predetermined sequence.

  1. RNA-DNA sequence differences spell genetic code ambiguities

    DEFF Research Database (Denmark)

    Bentin, Thomas; Nielsen, Michael L

    2013-01-01

    A recent paper in Science by Li et al. 2011(1) reports widespread sequence differences in the human transcriptome between RNAs and their encoding genes termed RNA-DNA differences (RDDs). The findings could add a new layer of complexity to gene expression but the study has been criticized. ...

  2. Decoding long nanopore sequencing reads of natural DNA.

    Science.gov (United States)

    Laszlo, Andrew H; Derrington, Ian M; Ross, Brian C; Brinkerhoff, Henry; Adey, Andrew; Nova, Ian C; Craig, Jonathan M; Langford, Kyle W; Samson, Jenny Mae; Daza, Riza; Doering, Kenji; Shendure, Jay; Gundlach, Jens H

    2014-08-01

    Nanopore sequencing of DNA is a single-molecule technique that may achieve long reads, low cost and high speed with minimal sample preparation and instrumentation. Here, we build on recent progress with respect to nanopore resolution and DNA control to interpret the procession of ion current levels observed during the translocation of DNA through the pore MspA. As approximately four nucleotides affect the ion current of each level, we measured the ion current corresponding to all 256 four-nucleotide combinations (quadromers). This quadromer map is highly predictive of ion current levels of previously unmeasured sequences derived from the bacteriophage phi X 174 genome. Furthermore, we show nanopore sequencing reads of phi X 174 up to 4,500 bases in length, which can be unambiguously aligned to the phi X 174 reference genome, and demonstrate proof-of-concept utility with respect to hybrid genome assembly and polymorphism detection. This work provides a foundation for nanopore sequencing of long, natural DNA strands. PMID:24964173

  3. Functionalized nanopore-embedded electrodes for rapid DNA sequencing

    CERN Document Server

    He, Haiying; Pandey, Ravindra; Rocha, Alexandre Reily; Sanvito, Stefano; Grigoriev, Anton; Ahuja, Rajeev; Karna, Shashi P

    2007-01-01

    The determination of a patient's DNA sequence can, in principle, reveal an increased risk to fall ill with particular diseases [1,2] and help to design "personalized medicine" [3]. Moreover, statistical studies and comparison of genomes [4] of a large number of individuals are crucial for the analysis of mutations [5] and hereditary diseases, paving the way to preventive medicine [6]. DNA sequencing is, however, currently still a vastly time-consuming and very expensive task [4], consisting of pre-processing steps, the actual sequencing using the Sanger method, and post-processing in the form of data analysis [7]. Here we propose a new approach that relies on functionalized nanopore-embedded electrodes to achieve an unambiguous distinction of the four nucleic acid bases in the DNA sequencing process. This represents a significant improvement over previously studied designs [8,9] which cannot reliably distinguish all four bases of DNA. The transport properties of the setup investigated by us, employing state-o...

  4. Statistical assignment of DNA sequences using Bayesian phylogenetics

    DEFF Research Database (Denmark)

    Terkelsen, Kasper Munch; Boomsma, Wouter Krogh; Huelsenbeck, John P;

    2008-01-01

    We provide a new automated statistical method for DNA barcoding based on a Bayesian phylogenetic analysis. The method is based on automated database sequence retrieval, alignment, and phylogenetic analysis using a custom-built program for Bayesian phylogenetic analysis. We show on real data that...

  5. A Nano-Biosensor for DNA Sequence Detection Using Absorption Spectra of SWNT-DNA Composite

    Directory of Open Access Journals (Sweden)

    J. Bansal

    2011-01-01

    Full Text Available A biosensor based on Single Walled Carbon Nanotube (SWNT-Poly (GTn ssDNA hybrid has been developed for medical diagnostics. The absorption spectrum of this assay is determined with the help of a Shimadzu UV-VIS-NIR spectrophotometer. Two distinct bands each containing three peaks corresponding to first and second van Hove singularities in the density of states of the nanotubes were observed in the absorption spectrum. When a single-stranded DNA (ssDNA having a sequence complementary to probic DNA is added to the ssDNA-SWNT conjugates, hybridization takes place, which causes the red shift of absorption spectrum of nanotubes. On the other hand, when the DNA is noncomplementary, no shift in the absorption spectrum occurs since hybridization between the DNA and probe does not take place. The red shifting of the spectrum is considered to be due to change in the dielectric environment around nanotubes.

  6. Sequence heterogeneity accelerates protein search for targets on DNA

    International Nuclear Information System (INIS)

    The process of protein search for specific binding sites on DNA is fundamentally important since it marks the beginning of all major biological processes. We present a theoretical investigation that probes the role of DNA sequence symmetry, heterogeneity, and chemical composition in the protein search dynamics. Using a discrete-state stochastic approach with a first-passage events analysis, which takes into account the most relevant physical-chemical processes, a full analytical description of the search dynamics is obtained. It is found that, contrary to existing views, the protein search is generally faster on DNA with more heterogeneous sequences. In addition, the search dynamics might be affected by the chemical composition near the target site. The physical origins of these phenomena are discussed. Our results suggest that biological processes might be effectively regulated by modifying chemical composition, symmetry, and heterogeneity of a genome

  7. Solid-State Nanopore-Based DNA Sequencing Technology

    Directory of Open Access Journals (Sweden)

    Zewen Liu

    2016-01-01

    Full Text Available The solid-state nanopore-based DNA sequencing technology is becoming more and more attractive for its brand new future in gene detection field. The challenges that need to be addressed are diverse: the effective methods to detect base-specific signatures, the control of the nanopore’s size and surface properties, and the modulation of translocation velocity and behavior of the DNA molecules. Among these challenges, the realization of the high-quality nanopores with the help of modern micro/nanofabrication technologies is a crucial one. In this paper, typical technologies applied in the field of solid-state nanopore-based DNA sequencing have been reviewed.

  8. Sequence heterogeneity accelerates protein search for targets on DNA

    Energy Technology Data Exchange (ETDEWEB)

    Shvets, Alexey A.; Kolomeisky, Anatoly B., E-mail: tolya@rice.edu [Department of Chemistry and Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005 (United States)

    2015-12-28

    The process of protein search for specific binding sites on DNA is fundamentally important since it marks the beginning of all major biological processes. We present a theoretical investigation that probes the role of DNA sequence symmetry, heterogeneity, and chemical composition in the protein search dynamics. Using a discrete-state stochastic approach with a first-passage events analysis, which takes into account the most relevant physical-chemical processes, a full analytical description of the search dynamics is obtained. It is found that, contrary to existing views, the protein search is generally faster on DNA with more heterogeneous sequences. In addition, the search dynamics might be affected by the chemical composition near the target site. The physical origins of these phenomena are discussed. Our results suggest that biological processes might be effectively regulated by modifying chemical composition, symmetry, and heterogeneity of a genome.

  9. Sequence analysis of 16S rRNA from mycoplasmas by direct solid-phase DNA sequencing.

    OpenAIRE

    Pettersson, B; Johansson, K. E.; Uhlén, M

    1994-01-01

    Automated solid-phase DNA sequencing was used for determination of partial 16S ribosomal DNA sequences of mycoplasmas. The sequence information was used to establish phylogenetic relationships of 11 different mycoplasmas whose 16S rRNA sequences had not been determined earlier. A biotinylated fragment corresponding to positions 344 to 939 in the Escherichia coli sequence was generated by PCR. The PCR product was immobilized onto streptavidin-coated paramagnetic beads, and direct sequencing wa...

  10. DNA watermarks in non-coding regulatory sequences

    Directory of Open Access Journals (Sweden)

    Pyka Martin

    2009-07-01

    Full Text Available Abstract Background DNA watermarks can be applied to identify the unauthorized use of genetically modified organisms. It has been shown that coding regions can be used to encrypt information into living organisms by using the DNA-Crypt algorithm. Yet, if the sequence of interest presents a non-coding DNA sequence, either the function of a resulting functional RNA molecule or a regulatory sequence, such as a promoter, could be affected. For our studies we used the small cytoplasmic RNA 1 in yeast and the lac promoter region of Escherichia coli. Findings The lac promoter was deactivated by the integrated watermark. In addition, the RNA molecules displayed altered configurations after introducing a watermark, but surprisingly were functionally intact, which has been verified by analyzing the growth characteristics of both wild type and watermarked scR1 transformed yeast cells. In a third approach we introduced a second overlapping watermark into the lac promoter, which did not affect the promoter activity. Conclusion Even though the watermarked RNA and one of the watermarked promoters did not show any significant differences compared to the wild type RNA and wild type promoter region, respectively, it cannot be generalized that other RNA molecules or regulatory sequences behave accordingly. Therefore, we do not recommend integrating watermark sequences into regulatory regions.

  11. POSA: Perl Objects for DNA Sequencing Data Analysis

    Directory of Open Access Journals (Sweden)

    Jungerius Bart J

    2004-08-01

    Full Text Available Abstract Background Capillary DNA sequencing machines allow the generation of vast amounts of data with little hands-on time. With this expansion of data generation, there is a growing need for automated data processing. Most available software solutions, however, still require user intervention or provide modules that need advanced informatics skills to allow implementation in pipelines. Results Here we present POSA, a pair of new perl objects that describe DNA sequence traces and Phrap contig assemblies in detail. Methods included in POSA include basecalling with quality scores (by Phred, contig assembly (by Phrap, generation of primer3 input and automated SNP annotation (by PolyPhred. Although easily implemented by users with only limited programming experience, these objects considerabily reduce hands-on analysis time compared to using the Staden package for extracting sequence information from raw sequencing files and for SNP discovery. Conclusions The POSA objects allow a flexible and easy design, implementation and usage of perl-based pipelines to handle and analyze DNA sequencing data, while requiring only minor programming skills.

  12. The DNA sequence and comparative analysis of human chromosome 10.

    Science.gov (United States)

    Deloukas, P; Earthrowl, M E; Grafham, D V; Rubenfield, M; French, L; Steward, C A; Sims, S K; Jones, M C; Searle, S; Scott, C; Howe, K; Hunt, S E; Andrews, T D; Gilbert, J G R; Swarbreck, D; Ashurst, J L; Taylor, A; Battles, J; Bird, C P; Ainscough, R; Almeida, J P; Ashwell, R I S; Ambrose, K D; Babbage, A K; Bagguley, C L; Bailey, J; Banerjee, R; Bates, K; Beasley, H; Bray-Allen, S; Brown, A J; Brown, J Y; Burford, D C; Burrill, W; Burton, J; Cahill, P; Camire, D; Carter, N P; Chapman, J C; Clark, S Y; Clarke, G; Clee, C M; Clegg, S; Corby, N; Coulson, A; Dhami, P; Dutta, I; Dunn, M; Faulkner, L; Frankish, A; Frankland, J A; Garner, P; Garnett, J; Gribble, S; Griffiths, C; Grocock, R; Gustafson, E; Hammond, S; Harley, J L; Hart, E; Heath, P D; Ho, T P; Hopkins, B; Horne, J; Howden, P J; Huckle, E; Hynds, C; Johnson, C; Johnson, D; Kana, A; Kay, M; Kimberley, A M; Kershaw, J K; Kokkinaki, M; Laird, G K; Lawlor, S; Lee, H M; Leongamornlert, D A; Laird, G; Lloyd, C; Lloyd, D M; Loveland, J; Lovell, J; McLaren, S; McLay, K E; McMurray, A; Mashreghi-Mohammadi, M; Matthews, L; Milne, S; Nickerson, T; Nguyen, M; Overton-Larty, E; Palmer, S A; Pearce, A V; Peck, A I; Pelan, S; Phillimore, B; Porter, K; Rice, C M; Rogosin, A; Ross, M T; Sarafidou, T; Sehra, H K; Shownkeen, R; Skuce, C D; Smith, M; Standring, L; Sycamore, N; Tester, J; Thorpe, A; Torcasso, W; Tracey, A; Tromans, A; Tsolas, J; Wall, M; Walsh, J; Wang, H; Weinstock, K; West, A P; Willey, D L; Whitehead, S L; Wilming, L; Wray, P W; Young, L; Chen, Y; Lovering, R C; Moschonas, N K; Siebert, R; Fechtel, K; Bentley, D; Durbin, R; Hubbard, T; Doucette-Stamm, L; Beck, S; Smith, D R; Rogers, J

    2004-05-27

    The finished sequence of human chromosome 10 comprises a total of 131,666,441 base pairs. It represents 99.4% of the euchromatic DNA and includes one megabase of heterochromatic sequence within the pericentromeric region of the short and long arm of the chromosome. Sequence annotation revealed 1,357 genes, of which 816 are protein coding, and 430 are pseudogenes. We observed widespread occurrence of overlapping coding genes (either strand) and identified 67 antisense transcripts. Our analysis suggests that both inter- and intrachromosomal segmental duplications have impacted on the gene count on chromosome 10. Multispecies comparative analysis indicated that we can readily annotate the protein-coding genes with current resources. We estimate that over 95% of all coding exons were identified in this study. Assessment of single base changes between the human chromosome 10 and chimpanzee sequence revealed nonsense mutations in only 21 coding genes with respect to the human sequence. PMID:15164054

  13. Terminal region sequence variations in variola virus DNA.

    Science.gov (United States)

    Massung, R F; Loparev, V N; Knight, J C; Totmenin, A V; Chizhikov, V E; Parsons, J M; Safronov, P F; Gutorov, V V; Shchelkunov, S N; Esposito, J J

    1996-07-15

    Genome DNA terminal region sequences were determined for a Brazilian alastrim variola minor virus strain Garcia-1966 that was associated with an 0.8% case-fatality rate and African smallpox strains Congo-1970 and Somalia-1977 associated with variola major (9.6%) and minor (0.4%) mortality rates, respectively. A base sequence identity of > or = 98.8% was determined after aligning 30 kb of the left- or right-end region sequences with cognate sequences previously determined for Asian variola major strains India-1967 (31% death rate) and Bangladesh-1975 (18.5% death rate). The deduced amino acid sequences of putative proteins of > or = 65 amino acids also showed relatively high identity, although the Asian and African viruses were clearly more related to each other than to alastrim virus. Alastrim virus contained only 10 of 70 proteins that were 100% identical to homologs in Asian strains, and 7 alastrim-specific proteins were noted. PMID:8661439

  14. Perspectives of DNA microarray and next-generation DNA sequencing technologies

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    DNA microarray and next-generation DNA sequencing technologies are important tools for high-throughput genome research,in revealing both the structural and functional characteristics of genomes.In the past decade the DNA microarray technologies have been widely applied in the studies of functional genomics,systems biology and pharmacogenomics.The next-generation DNA sequencing method was first introduced by the 454 Company in 2003,immediately followed by the establishment of the Solexa and Solid techniques by other biotech companies.Though it has not been long since the first emergence of this technology,with the fast and impressive improvement,the application of this technology has extended to almost all fields of genomics research,as a rival challenging the existing DNA microarray technology.This paper briefly reviews the working principles of these two technologies as well as their application and perspectives in genome research.

  15. Environmental DNA sequencing primers for eutardigrades and bdelloid rotifers

    Directory of Open Access Journals (Sweden)

    Martin Andrew P

    2009-12-01

    Full Text Available Abstract Background The time it takes to isolate individuals from environmental samples and then extract DNA from each individual is one of the problems with generating molecular data from meiofauna such as eutardigrades and bdelloid rotifers. The lack of consistent morphological information and the extreme abundance of these classes makes morphological identification of rare, or even common cryptic taxa a large and unwieldy task. This limits the ability to perform large-scale surveys of the diversity of these organisms. Here we demonstrate a culture-independent molecular survey approach that enables the generation of large amounts of eutardigrade and bdelloid rotifer sequence data directly from soil. Our PCR primers, specific to the 18s small-subunit rRNA gene, were developed for both eutardigrades and bdelloid rotifers. Results The developed primers successfully amplified DNA of their target organism from various soil DNA extracts. This was confirmed by both the BLAST similarity searches and phylogenetic analyses. Tardigrades showed much better phylogenetic resolution than bdelloids. Both groups of organisms exhibited varying levels of endemism. Conclusion The development of clade-specific primers for characterizing eutardigrades and bdelloid rotifers from environmental samples should greatly increase our ability to characterize the composition of these taxa in environmental samples. Environmental sequencing as shown here differs from other molecular survey methods in that there is no need to pre-isolate the organisms of interest from soil in order to amplify their DNA. The DNA sequences obtained from methods that do not require culturing can be identified post-hoc and placed phylogenetically as additional closely related sequences are obtained from morphologically identified conspecifics. Our non-cultured environmental sequence based approach will be able to provide a rapid and large-scale screening of the presence, absence and diversity of

  16. IMAGE HIDING IN DNA SEQUENCE USING ARITHMETIC ENCODING

    Directory of Open Access Journals (Sweden)

    Prof. Samir Kumar Bandyopadhyay

    2011-05-01

    Full Text Available Recently, biological techniques become more and more popular, as they are applied to many kinds of applications, authentication protocols, biochemistry, and cryptography. One of the most interesting biology techniques is deoxyribo nucleic acid and using it in such domains. Hiding secret data in deoxyribo nucleic acid becomes an important and interesting research topic. Some researchers hide the secret data in transcribed deoxyribo nucleic acid, translated ribo nucleic acid regions, or active coding segments where it doesn't mention to modify the original sequence, but others hide data in non-transcribed deoxyribo nucleic acid, non-translated ribo nucleic acid regions, or active coding segments. Unfortunately, these schemes either alter the functionalities or modify the original deoxyribo nucleic acid sequences. DNA has the ability to store large amount of digital data. This paper presents a method to hide an image in DNA sequence using arithmetic encoding.

  17. DNA sequence analysis using hierarchical ART-based classification networks

    Energy Technology Data Exchange (ETDEWEB)

    LeBlanc, C.; Hruska, S.I. [Florida State Univ., Tallahassee, FL (United States); Katholi, C.R.; Unnasch, T.R. [Univ. of Alabama, Birmingham, AL (United States)

    1994-12-31

    Adaptive resonance theory (ART) describes a class of artificial neural network architectures that act as classification tools which self-organize, work in real-time, and require no retraining to classify novel sequences. We have adapted ART networks to provide support to scientists attempting to categorize tandem repeat DNA fragments from Onchocerca volvulus. In this approach, sequences of DNA fragments are presented to multiple ART-based networks which are linked together into two (or more) tiers; the first provides coarse sequence classification while the sub- sequent tiers refine the classifications as needed. The overall rating of the resulting classification of fragments is measured using statistical techniques based on those introduced to validate results from traditional phylogenetic analysis. Tests of the Hierarchical ART-based Classification Network, or HABclass network, indicate its value as a fast, easy-to-use classification tool which adapts to new data without retraining on previously classified data.

  18. VoSeq: a voucher and DNA sequence web application.

    Directory of Open Access Journals (Sweden)

    Carlos Peña

    Full Text Available There is an ever growing number of molecular phylogenetic studies published, due to, in part, the advent of new techniques that allow cheap and quick DNA sequencing. Hence, the demand for relational databases with which to manage and annotate the amassing DNA sequences, genes, voucher specimens and associated biological data is increasing. In addition, a user-friendly interface is necessary for easy integration and management of the data stored in the database back-end. Available databases allow management of a wide variety of biological data. However, most database systems are not specifically constructed with the aim of being an organizational tool for researchers working in phylogenetic inference. We here report a new software facilitating easy management of voucher and sequence data, consisting of a relational database as back-end for a graphic user interface accessed via a web browser. The application, VoSeq, includes tools for creating molecular datasets of DNA or amino acid sequences ready to be used in commonly used phylogenetic software such as RAxML, TNT, MrBayes and PAUP, as well as for creating tables ready for publishing. It also has inbuilt BLAST capabilities against all DNA sequences stored in VoSeq as well as sequences in NCBI GenBank. By using mash-ups and calls to web services, VoSeq allows easy integration with public services such as Yahoo! Maps, Flickr, Encyclopedia of Life (EOL and GBIF (by generating data-dumps that can be processed with GBIF's Integrated Publishing Toolkit.

  19. Patterns of nucleotide misincorporations during enzymatic amplification and direct large-scale sequencing of ancient DNA

    OpenAIRE

    Stiller, M.; Green, R. E.; Ronan, M.; Simons, J F; Du, L; He, W.; Egholm, M; Rothberg, J. M.; Keates, S.G.; Ovodov, N. D.; Antipina, E. E.; Baryshnikov, G. F.; Kuzmin, Y.V.; Vasilevski, A. A.; Wuenschell, G. E.

    2006-01-01

    Whereas evolutionary inferences derived from present-day DNA sequences are by necessity indirect, ancient DNA sequences provide a direct view of past genetic variants. However, base lesions that accumulate in DNA over time may cause nucleotide misincorporations when ancient DNA sequences are replicated. By repeated amplifications of mitochondrial DNA sequences from a large number of ancient wolf remains, we show that C/G-to-T/A transitions are the predominant type of such misincorporations. U...

  20. Complete nucleotide sequence of cDNA and deduced amino acid sequence of rat liver catalase.

    OpenAIRE

    Furuta, S.; Hayashi, H; Hijikata, M; Miyazawa, S.; Osumi, T; Hashimoto, T.

    1986-01-01

    We have isolated five cDNA clones for rat liver catalase (hydrogen peroxide:hydrogen peroxide oxidoreductase, EC 1.11.1.6). These clones overlapped with each other and covered the entire length of the mRNA, which had been estimated to be 2.4 kilobases long by blot hybridization analysis of electrophoretically fractionated RNA. Nucleotide sequencing was carried out on these five clones and the composite nucleotide sequence of catalase cDNA was determined. The 5' noncoding region contained 83 b...

  1. Anonymous Authentication for Smartcards

    Directory of Open Access Journals (Sweden)

    J. Hajny

    2010-06-01

    Full Text Available The paper presents an innovative solution in the field of RFID (Radio-Frequency IDentification smartcard authentication. Currently the smartcards are used for many purposes - e.g. employee identification, library cards, student cards or even identity credentials. Personal identity is revealed to untrustworthy entities every time we use these cards. Such information could later be used without our knowledge and for harmful reasons like shopping pattern scanning or even movement tracking. We present a communication scheme for keeping one’s identity private in this paper. Although our system provides anonymity, it does not allow users to abuse this feature. The system is based on strong cryptographic primitives that provide features never available before. Besides theoretical design of the anonymous authentication scheme and its analysis we also provide implementation results.

  2. Development of a protein microarray using sequence-specific DNA binding domain on DNA chip surface

    International Nuclear Information System (INIS)

    A protein microarray based on DNA microarray platform was developed to identify protein-protein interactions in vitro. The conventional DNA chip surface by 156-bp PCR product was prepared for a substrate of protein microarray. High-affinity sequence-specific DNA binding domain, GAL4 DNA binding domain, was introduced to the protein microarray as fusion partner of a target model protein, enhanced green fluorescent protein. The target protein was oriented immobilized directly on the DNA chip surface. Finally, monoclonal antibody of the target protein was used to identify the immobilized protein on the surface. This study shows that the conventional DNA chip can be used to make a protein microarray directly, and this novel protein microarray can be applicable as a tool for identifying protein-protein interactions

  3. A CLIQUE algorithm using DNA computing techniques based on closed-circle DNA sequences.

    Science.gov (United States)

    Zhang, Hongyan; Liu, Xiyu

    2011-07-01

    DNA computing has been applied in broad fields such as graph theory, finite state problems, and combinatorial problem. DNA computing approaches are more suitable used to solve many combinatorial problems because of the vast parallelism and high-density storage. The CLIQUE algorithm is one of the gird-based clustering techniques for spatial data. It is the combinatorial problem of the density cells. Therefore we utilize DNA computing using the closed-circle DNA sequences to execute the CLIQUE algorithm for the two-dimensional data. In our study, the process of clustering becomes a parallel bio-chemical reaction and the DNA sequences representing the marked cells can be combined to form a closed-circle DNA sequences. This strategy is a new application of DNA computing. Although the strategy is only for the two-dimensional data, it provides a new idea to consider the grids to be vertexes in a graph and transform the search problem into a combinatorial problem. PMID:21511001

  4. The influence of DNA sequence on epigenome-induced pathologies

    Directory of Open Access Journals (Sweden)

    Meagher Richard B

    2012-07-01

    Full Text Available Abstract Clear cause-and-effect relationships are commonly established between genotype and the inherited risk of acquiring human and plant diseases and aberrant phenotypes. By contrast, few such cause-and-effect relationships are established linking a chromatin structure (that is, the epitype with the transgenerational risk of acquiring a disease or abnormal phenotype. It is not entirely clear how epitypes are inherited from parent to offspring as populations evolve, even though epigenetics is proposed to be fundamental to evolution and the likelihood of acquiring many diseases. This article explores the hypothesis that, for transgenerationally inherited chromatin structures, “genotype predisposes epitype”, and that epitype functions as a modifier of gene expression within the classical central dogma of molecular biology. Evidence for the causal contribution of genotype to inherited epitypes and epigenetic risk comes primarily from two different kinds of studies discussed herein. The first and direct method of research proceeds by the examination of the transgenerational inheritance of epitype and the penetrance of phenotype among genetically related individuals. The second approach identifies epitypes that are duplicated (as DNA sequences are duplicated and evolutionarily conserved among repeated patterns in the DNA sequence. The body of this article summarizes particularly robust examples of these studies from humans, mice, Arabidopsis, and other organisms. The bulk of the data from both areas of research support the hypothesis that genotypes predispose the likelihood of displaying various epitypes, but for only a few classes of epitype. This analysis suggests that renewed efforts are needed in identifying polymorphic DNA sequences that determine variable nucleosome positioning and DNA methylation as the primary cause of inherited epigenome-induced pathologies. By contrast, there is very little evidence that DNA sequence directly

  5. Early Lyme disease with spirochetemia - diagnosed by DNA sequencing

    Directory of Open Access Journals (Sweden)

    Jones William

    2010-11-01

    Full Text Available Abstract Background A sensitive and analytically specific nucleic acid amplification test (NAAT is valuable in confirming the diagnosis of early Lyme disease at the stage of spirochetemia. Findings Venous blood drawn from patients with clinical presentations of Lyme disease was tested for the standard 2-tier screen and Western Blot serology assay for Lyme disease, and also by a nested polymerase chain reaction (PCR for B. burgdorferi sensu lato 16S ribosomal DNA. The PCR amplicon was sequenced for B. burgdorferi genomic DNA validation. A total of 130 patients visiting emergency room (ER or Walk-in clinic (WALKIN, and 333 patients referred through the private physicians' offices were studied. While 5.4% of the ER/WALKIN patients showed DNA evidence of spirochetemia, none (0% of the patients referred from private physicians' offices were DNA-positive. In contrast, while 8.4% of the patients referred from private physicians' offices were positive for the 2-tier Lyme serology assay, only 1.5% of the ER/WALKIN patients were positive for this antibody test. The 2-tier serology assay missed 85.7% of the cases of early Lyme disease with spirochetemia. The latter diagnosis was confirmed by DNA sequencing. Conclusion Nested PCR followed by automated DNA sequencing is a valuable supplement to the standard 2-tier antibody assay in the diagnosis of early Lyme disease with spirochetemia. The best time to test for Lyme spirochetemia is when the patients living in the Lyme disease endemic areas develop unexplained symptoms or clinical manifestations that are consistent with Lyme disease early in the course of their illness.

  6. Privacy and Anonymity

    OpenAIRE

    Wacks, R

    2014-01-01

    Since the beginning of the digital area, privacy and anonymity have been impacted drastically (both, positively and negatively), by the different technologies developed for communications purposes. The broad possibilities that the Internet offers since its conception, makes it a mandatory target for those entities that are aiming to know and control the different channels of communication and the information that flows through. In this paper, we address the current threats against privacy and...

  7. Mediated Traceable Anonymous Encryption

    OpenAIRE

    Izabachène, Malika; Pointcheval, David; Vergnaud, Damien

    2010-01-01

    The notion of key privacy for asymmetric encryption schemes was formally defined by Bellare, Boldyreva, Desai and Pointcheval in 2001: it states that an eavesdropper in possession of a ciphertext is not able to tell which specifi key, out of a set of known public keys, is the one under which the ciphertext was created. Since anonymity can be misused by dishonest users, some situations could require a tracing authority capable of revoking key privacy when illegal behavior is detected. Prior wo...

  8. Prediction of fine-tuned promoter activity from DNA sequence

    Science.gov (United States)

    Siwo, Geoffrey; Rider, Andrew; Tan, Asako; Pinapati, Richard; Emrich, Scott; Chawla, Nitesh; Ferdig, Michael

    2016-01-01

    The quantitative prediction of transcriptional activity of genes using promoter sequence is fundamental to the engineering of biological systems for industrial purposes and understanding the natural variation in gene expression. To catalyze the development of new algorithms for this purpose, the Dialogue on Reverse Engineering Assessment and Methods (DREAM) organized a community challenge seeking predictive models of promoter activity given normalized promoter activity data for 90 ribosomal protein promoters driving expression of a fluorescent reporter gene. By developing an unbiased modeling approach that performs an iterative search for predictive DNA sequence features using the frequencies of various k-mers, inferred DNA mechanical properties and spatial positions of promoter sequences, we achieved the best performer status in this challenge. The specific predictive features used in the model included the frequency of the nucleotide G, the length of polymeric tracts of T and TA, the frequencies of 6 distinct trinucleotides and 12 tetranucleotides, and the predicted protein deformability of the DNA sequence. Our method accurately predicted the activity of 20 natural variants of ribosomal protein promoters (Spearman correlation r = 0.73) as compared to 33 laboratory-mutated variants of the promoters (r = 0.57) in a test set that was hidden from participants. Notably, our model differed substantially from the rest in 2 main ways: i) it did not explicitly utilize transcription factor binding information implying that subtle DNA sequence features are highly associated with gene expression, and ii) it was entirely based on features extracted exclusively from the 100 bp region upstream from the translational start site demonstrating that this region encodes much of the overall promoter activity. The findings from this study have important implications for the engineering of predictable gene expression systems and the evolution of gene expression in naturally occurring

  9. An automated annotation tool for genomic DNA sequences using GeneScan and BLAST

    Indian Academy of Sciences (India)

    Andrew M. Lynn; Chakresh Kumar Jain; K. Kosalai; Pranjan Barman; Nupur Thakur; Harish Batra; Alok Bhattacharya

    2001-04-01

    Genomic sequence data are often available well before the annotated sequence is published. We present a method for analysis of genomic DNA to identify coding sequences using the GeneScan algorithm and characterize these resultant sequences by BLAST. The routines are used to develop a system for automated annotation of genome DNA sequences.

  10. The DNA sequence, annotation and analysis of human chromosome 3

    DEFF Research Database (Denmark)

    Muzny, Donna M; Scherer, Steven E; Kaul, Rajinder;

    2006-01-01

    chromosomes. Chromosome 3 comprises just four contigs, one of which currently represents the longest unbroken stretch of finished DNA sequence known so far. The chromosome is remarkable in having the lowest rate of segmental duplication in the genome. It also includes a chemokine receptor gene cluster as well...... as numerous loci involved in multiple human cancers such as the gene encoding FHIT, which contains the most common constitutive fragile site in the genome, FRA3B. Using genomic sequence from chimpanzee and rhesus macaque, we were able to characterize the breakpoints defining a large pericentric...

  11. Effect of dephasing on DNA sequencing via transverse electronic transport

    Energy Technology Data Exchange (ETDEWEB)

    Zwolak, Michael [Los Alamos National Laboratory; Krems, Matt [NON LANL; Pershin, Yuriy V [NON LANL; Di Ventra, Massimiliano [NON LANL

    2009-01-01

    We study theoretically the effects of dephasing on DNA sequencing in a nanopore via transverse electronic transport. To do this, we couple classical molecular dynamics simulations with transport calculations using scattering theory. Previous studies, which did not include dephasing, have shown that by measuring the transverse current of a particular base multiple times, one can get distributions of currents for each base that are distinguishable. We introduce a dephasing parameter into transport calculations to simulate the effects of the ions and other fluctuations. These effects lower the overall magnitude of the current, but have little effect on the current distributions themselves. The results of this work further implicate that distinguishing DNA bases via transverse electronic transport has potential as a sequencing tool.

  12. Recent progress in atomistic simulation of electrical current DNA sequencing.

    Science.gov (United States)

    Kim, Han Seul; Kim, Yong-Hoon

    2015-07-15

    We review recent advances in the DNA sequencing method based on measurements of transverse electrical currents. Device configurations proposed in the literature are classified according to whether the molecular fingerprints appear as the major (Mode I) or perturbing (Mode II) current signals. Scanning tunneling microscope and tunneling electrode gap configurations belong to the former category, while the nanochannels with or without an embedded nanopore belong to the latter. The molecular sensing mechanisms of Modes I and II roughly correspond to the electron tunneling and electrochemical gating, respectively. Special emphasis will be given on the computer simulation studies, which have been playing a critical role in the initiation and development of the field. We also highlight low-dimensional nanomaterials such as carbon nanotubes, graphene, and graphene nanoribbons that allow the novel Mode II approach. Finally, several issues in previous computational studies are discussed, which points to future research directions toward more reliable simulation of electrical current DNA sequencing devices. PMID:25744599

  13. Silicene as a new potential DNA sequencing device

    Science.gov (United States)

    Amorim, Rodrigo G.; Scheicher, Ralph H.

    2015-04-01

    Silicene, a hexagonal buckled 2D allotrope of silicon, shows potential as a platform for numerous new applications, and may allow for easier integration with existing silicon-based microelectronics than graphene. Here, we show that silicene could function as an electrical DNA sequencing device. We investigated the stability of this novel nano-bio system, its electronic properties and the pronounced effects on the transverse electronic transport, i.e., changes in the transmission and the conductance caused by adsorption of each nucleobase, explored by us through the non-equilibrium Green’s function method. Intriguingly, despite the relatively weak interaction between nucleobases and silicene, significant changes in the transmittance at zero bias are predicted by us, in particular for the two nucleobases cytosine and guanine. Our findings suggest that silicene could be utilized as an integrated-circuit biosensor as part of a lab-on-a-chip device for DNA sequencing.

  14. A DNA sequence alignment algorithm using quality information and a fuzzy inference method

    Institute of Scientific and Technical Information of China (English)

    Kwangbaek Kim; Minhwan Kim; Youngwoon Woo

    2008-01-01

    DNA sequence alignment algorithms in computational molecular biology have been improved by diverse methods.In this paper.We propose a DNA sequence alignment that Uses quality information and a fuzzy inference method developed based on the characteristics of DNA fragments and a fuzzy logic system in order to improve conventional DNA sequence alignment methods that uses DNA sequence quality information.In conventional algorithms.DNA sequence alignment scores are calculated by the global sequence alignment algorithm proposed by Needleman-Wunsch,which is established by using quality information of each DNA fragment.However,there may be errors in the process of calculating DNA sequence alignment scores when the quality of DNA fragment tips is low.because only the overall DNA sequence quality information are used.In our proposed method.an exact DNA sequence alignment can be achieved in spite of the low quality of DNA fragment tips by improvement of conventional algorithms using quality information.Mapping score parameters used to calculate DNA sequence alignment scores are dynamically adjusted by the fuzzy logic system utilizing lengths of DNA fragments and frequencies of low quality DNA bases in the fragments.From the experiments by applying real genome data of National Center for Bioteclmology Information,we could see that the proposed method is more efficient than conventional algorithms.

  15. Revised phylogeny of whales suggested by mitochondrial ribosomal DNA sequences

    OpenAIRE

    Milinkovitch, M.C.; Orti, G.; Meyer, A.

    1993-01-01

    Living cetaceans are subdivided into two highly distinct suborders, Odontoceti (the echolocating toothed whales) and Mysticeti (the filter-feeding baleen whales), which are believed to have had a long independent history. Here we report the determination of DNA sequences from two mitochondrial ribosomal gene segments (930 base pairs per species) for 16 species of cetaceans, a perissodactyl and a sloth, and construct the first phylogeny for whales and dolphins based on explicit cladistic metho...

  16. Multiplexed DNA Sequence Capture of Mitochondrial Genomes Using PCR Products

    OpenAIRE

    Tomislav Maricic; Mark Whitten; Svante Pääbo

    2010-01-01

    BACKGROUND: To utilize the power of high-throughput sequencers, target enrichment methods have been developed. The majority of these require reagents and equipment that are only available from commercial vendors and are not suitable for the targets that are a few kilobases in length. METHODOLOGY/PRINCIPAL FINDINGS: We describe a novel and economical method in which custom made long-range PCR products are used to capture complete human mitochondrial genomes from complex DNA mixtures. We use th...

  17. DNA sequencing methods in human genetics and disease research

    OpenAIRE

    Lehrach, Hans

    2013-01-01

    DNA sequencing has revolutionized biological and medical research, and is poised to have a similar impact in medicine. This tool is just one of a number of developments in our capability to identify, quantitate and functionally characterize the components of the biological networks keeping us healthy or making us sick, but in many respects it has played the leading role in this process. The new technologies do, however, also provide a bridge between genotype and phenotype, both in man and mod...

  18. Roche genome sequencer FLX based high-throughput sequencing of ancient DNA

    DEFF Research Database (Denmark)

    Alquezar-Planas, David E; Fordyce, Sarah Louise

    2012-01-01

    Since the development of so-called "next generation" high-throughput sequencing in 2005, this technology has been applied to a variety of fields. Such applications include disease studies, evolutionary investigations, and ancient DNA. Each application requires a specialized protocol to ensure tha...

  19. Application of synthetic DNA probes to the analysis of DNA sequence variants in man

    International Nuclear Information System (INIS)

    Oligonucleotide probes provide a tool to discriminate between any two alleles on the basis of hybridization. Random sampling of the genome with different oligonucleotide probes should reveal polymorphism in a certain percentage of the cases. In the hope of identifying polymorphic regions more efficiently, we chose to take advantage of the proposed hypermutability of repeated DNA sequences and the specificity of oligonucleotide hybridization. Since, under appropriate conditions, oligonucleotide probes require complete base pairing for hybridization to occur, they will only hybridize to a subset of the members of a repeat family when all members of the family are not identical. The results presented here suggest that oligonucleotide hybridization can be used to extend the genomic sequences that can be tested for the presence of RFLPs. This expands the tools available to human genetics. In addition, the results suggest that repeated DNA sequences are indeed more polymorphic than single-copy sequences. 28 references, 2 figures

  20. Computational optimisation of targeted DNA sequencing for cancer detection.

    Science.gov (United States)

    Martinez, Pierre; McGranahan, Nicholas; Birkbak, Nicolai Juul; Gerlinger, Marco; Swanton, Charles

    2013-01-01

    Despite recent progress thanks to next-generation sequencing technologies, personalised cancer medicine is still hampered by intra-tumour heterogeneity and drug resistance. As most patients with advanced metastatic disease face poor survival, there is need to improve early diagnosis. Analysing circulating tumour DNA (ctDNA) might represent a non-invasive method to detect mutations in patients, facilitating early detection. In this article, we define reduced gene panels from publicly available datasets as a first step to assess and optimise the potential of targeted ctDNA scans for early tumour detection. Dividing 4,467 samples into one discovery and two independent validation cohorts, we show that up to 76% of 10 cancer types harbour at least one mutation in a panel of only 25 genes, with high sensitivity across most tumour types. Our analyses demonstrate that targeting "hotspot" regions would introduce biases towards in-frame mutations and would compromise the reproducibility of tumour detection. PMID:24296834

  1. Contrasting DNA sequence organisation patterns in sauropsidian genomes.

    Science.gov (United States)

    Epplen, J T; Diedrich, U; Wagenmann, M; Schmidtke, J; Engel, W

    1979-11-01

    The genomic DNA organisation patterns of four sauropsidian species, namely Python reticularis, Caiman crocodilus, Terrapene carolina triungius and Columba livia domestica were investigated by reassociation of short and long DNA fragments, by hyperchromicity measurements of reannealed fragments and by length estimations of S1-nuclease resistant repetitive duplexes. While the genomic DNA of the three reptilian species shows a short period interspersion pattern, the genome of the avian species is organised in a long period interspersion pattern apparently typical for birds. These findings are discussed in view of the close phylogenetic relationships of birds and reptiles, and also with regard to a possible relationship between the extent of sequence interspersion and genome size. PMID:533670

  2. DNA topology confers sequence specificity to nonspecific architectural proteins.

    Science.gov (United States)

    Wei, Juan; Czapla, Luke; Grosner, Michael A; Swigon, David; Olson, Wilma K

    2014-11-25

    Topological constraints placed on short fragments of DNA change the disorder found in chain molecules randomly decorated by nonspecific, architectural proteins into tightly organized 3D structures. The bacterial heat-unstable (HU) protein builds up, counter to expectations, in greater quantities and at particular sites along simulated DNA minicircles and loops. Moreover, the placement of HU along loops with the "wild-type" spacing found in the Escherichia coli lactose (lac) and galactose (gal) operons precludes access to key recognition elements on DNA. The HU protein introduces a unique spatial pathway in the DNA upon closure. The many ways in which the protein induces nearly the same closed circular configuration point to the statistical advantage of its nonspecificity. The rotational settings imposed on DNA by the repressor proteins, by contrast, introduce sequential specificity in HU placement, with the nonspecific protein accumulating at particular loci on the constrained duplex. Thus, an architectural protein with no discernible DNA sequence-recognizing features becomes site-specific and potentially assumes a functional role upon loop formation. The locations of HU on the closed DNA reflect long-range mechanical correlations. The protein responds to DNA shape and deformability—the stiff, naturally straight double-helical structure—rather than to the unique features of the constituent base pairs. The structures of the simulated loops suggest that HU architecture, like nucleosomal architecture, which modulates the ability of regulatory proteins to recognize their binding sites in the context of chromatin, may influence repressor-operator interactions in the context of the bacterial nucleoid. PMID:25385626

  3. Comparison of DNA Quantification Methods for Next Generation Sequencing.

    Science.gov (United States)

    Robin, Jérôme D; Ludlow, Andrew T; LaRanger, Ryan; Wright, Woodring E; Shay, Jerry W

    2016-01-01

    Next Generation Sequencing (NGS) is a powerful tool that depends on loading a precise amount of DNA onto a flowcell. NGS strategies have expanded our ability to investigate genomic phenomena by referencing mutations in cancer and diseases through large-scale genotyping, developing methods to map rare chromatin interactions (4C; 5C and Hi-C) and identifying chromatin features associated with regulatory elements (ChIP-seq, Bis-Seq, ChiA-PET). While many methods are available for DNA library quantification, there is no unambiguous gold standard. Most techniques use PCR to amplify DNA libraries to obtain sufficient quantities for optical density measurement. However, increased PCR cycles can distort the library's heterogeneity and prevent the detection of rare variants. In this analysis, we compared new digital PCR technologies (droplet digital PCR; ddPCR, ddPCR-Tail) with standard methods for the titration of NGS libraries. DdPCR-Tail is comparable to qPCR and fluorometry (QuBit) and allows sensitive quantification by analysis of barcode repartition after sequencing of multiplexed samples. This study provides a direct comparison between quantification methods throughout a complete sequencing experiment and provides the impetus to use ddPCR-based quantification for improvement of NGS quality. PMID:27048884

  4. DNA Sequencing via Quantum Mechanics and Machine Learning

    CERN Document Server

    Yuen, Henry; Zhang, Kevin J; Nomura, Ken-ichi; Kalia, Rajiv K; Nakano, Aiichiro; Vashishta, Priya

    2010-01-01

    Rapid sequencing of individual human genome is prerequisite to genomic medicine, where diseases will be prevented by preemptive cures. Quantum-mechanical tunneling through single-stranded DNA in a solid-state nanopore has been proposed for rapid DNA sequencing, but unfortunately the tunneling current alone cannot distinguish the four nucleotides due to large fluctuations in molecular conformation and solvent. Here, we propose a machine-learning approach applied to the tunneling current-voltage (I-V) characteristic for efficient discrimination between the four nucleotides. We first combine principal component analysis (PCA) and fuzzy c-means (FCM) clustering to learn the "fingerprints" of the electronic density-of-states (DOS) of the four nucleotides, which can be derived from the I-V data. We then apply the hidden Markov model and the Viterbi algorithm to sequence a time series of DOS data (i.e., to solve the sequencing problem). Numerical experiments show that the PCA-FCM approach can classify unlabeled DOS ...

  5. DNA Sequence Determinants Controlling Affinity, Stability and Shape of DNA Complexes Bound by the Nucleoid Protein Fis.

    Science.gov (United States)

    Hancock, Stephen P; Stella, Stefano; Cascio, Duilio; Johnson, Reid C

    2016-01-01

    The abundant Fis nucleoid protein selectively binds poorly related DNA sequences with high affinities to regulate diverse DNA reactions. Fis binds DNA primarily through DNA backbone contacts and selects target sites by reading conformational properties of DNA sequences, most prominently intrinsic minor groove widths. High-affinity binding requires Fis-stabilized DNA conformational changes that vary depending on DNA sequence. In order to better understand the molecular basis for high affinity site recognition, we analyzed the effects of DNA sequence within and flanking the core Fis binding site on binding affinity and DNA structure. X-ray crystal structures of Fis-DNA complexes containing variable sequences in the noncontacted center of the binding site or variations within the major groove interfaces show that the DNA can adapt to the Fis dimer surface asymmetrically. We show that the presence and position of pyrimidine-purine base steps within the major groove interfaces affect both local DNA bending and minor groove compression to modulate affinities and lifetimes of Fis-DNA complexes. Sequences flanking the core binding site also modulate complex affinities, lifetimes, and the degree of local and global Fis-induced DNA bending. In particular, a G immediately upstream of the 15 bp core sequence inhibits binding and bending, and A-tracts within the flanking base pairs increase both complex lifetimes and global DNA curvatures. Taken together, our observations support a revised DNA motif specifying high-affinity Fis binding and highlight the range of conformations that Fis-bound DNA can adopt. The affinities and DNA conformations of individual Fis-DNA complexes are likely to be tailored to their context-specific biological functions. PMID:26959646

  6. Anonymity in Large Societies

    OpenAIRE

    Andrei Gomberg; Cesar Martinelli; Ricard Torres

    2002-01-01

    In a social choice model with an infinite number of agents, there may occur "equal size" coalitions that a preference aggregation rule should treat in the same manner. We introduce an axiom of equal treatment with respect to a measure of coalition size and explore its interaction with common axioms of social choice. We show that, provided the measure space is sufficiently rich in coalitions of the same measure, the new axiom is the natural extension of the concept of anonymity, and in particu...

  7. Denoising DNA deep sequencing data-high-throughput sequencing errors and their correction.

    Science.gov (United States)

    Laehnemann, David; Borkhardt, Arndt; McHardy, Alice Carolyn

    2016-01-01

    Characterizing the errors generated by common high-throughput sequencing platforms and telling true genetic variation from technical artefacts are two interdependent steps, essential to many analyses such as single nucleotide variant calling, haplotype inference, sequence assembly and evolutionary studies. Both random and systematic errors can show a specific occurrence profile for each of the six prominent sequencing platforms surveyed here: 454 pyrosequencing, Complete Genomics DNA nanoball sequencing, Illumina sequencing by synthesis, Ion Torrent semiconductor sequencing, Pacific Biosciences single-molecule real-time sequencing and Oxford Nanopore sequencing. There is a large variety of programs available for error removal in sequencing read data, which differ in the error models and statistical techniques they use, the features of the data they analyse, the parameters they determine from them and the data structures and algorithms they use. We highlight the assumptions they make and for which data types these hold, providing guidance which tools to consider for benchmarking with regard to the data properties. While no benchmarking results are included here, such specific benchmarks would greatly inform tool choices and future software development. The development of stand-alone error correctors, as well as single nucleotide variant and haplotype callers, could also benefit from using more of the knowledge about error profiles and from (re)combining ideas from the existing approaches presented here. PMID:26026159

  8. The most frequent short sequences in non-coding DNA.

    Science.gov (United States)

    Subirana, Juan A; Messeguer, Xavier

    2010-03-01

    The purpose of this work is to determine the most frequent short sequences in non-coding DNA. They may play a role in maintaining the structure and function of eukaryotic chromosomes. We present a simple method for the detection and analysis of such sequences in several genomes, including Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster and Homo sapiens. We also study two chromosomes of man and mouse with a length similar to the whole genomes of the other species. We provide a list of the most common sequences of 9-14 bases in each genome. As expected, they are present in human Alu sequences. Our programs may also give a graph and a list of their position in the genome. Detection of clusters is also possible. In most cases, these sequences contain few alternating regions. Their intrinsic structure and their influence on nucleosome formation are not known. In particular, we have found new features of short sequences in C. elegans, which are distributed in heterogeneous clusters. They appear as punctuation marks in the chromosomes. Such clusters are not found in either A. thaliana or D. melanogaster. We discuss the possibility that they play a role in centromere function and homolog recognition in meiosis. PMID:19966278

  9. Maternal Plasma DNA and RNA Sequencing for Prenatal Testing.

    Science.gov (United States)

    Tamminga, Saskia; van Maarle, Merel; Henneman, Lidewij; Oudejans, Cees B M; Cornel, Martina C; Sistermans, Erik A

    2016-01-01

    Cell-free DNA (cfDNA) testing has recently become indispensable in diagnostic testing and screening. In the prenatal setting, this type of testing is often called noninvasive prenatal testing (NIPT). With a number of techniques, using either next-generation sequencing or single nucleotide polymorphism-based approaches, fetal cfDNA in maternal plasma can be analyzed to screen for rhesus D genotype, common chromosomal aneuploidies, and increasingly for testing other conditions, including monogenic disorders. With regard to screening for common aneuploidies, challenges arise when implementing NIPT in current prenatal settings. Depending on the method used (targeted or nontargeted), chromosomal anomalies other than trisomy 21, 18, or 13 can be detected, either of fetal or maternal origin, also referred to as unsolicited or incidental findings. For various biological reasons, there is a small chance of having either a false-positive or false-negative NIPT result, or no result, also referred to as a "no-call." Both pre- and posttest counseling for NIPT should include discussing potential discrepancies. Since NIPT remains a screening test, a positive NIPT result should be confirmed by invasive diagnostic testing (either by chorionic villus biopsy or by amniocentesis). As the scope of NIPT is widening, professional guidelines need to discuss the ethics of what to offer and how to offer. In this review, we discuss the current biochemical, clinical, and ethical challenges of cfDNA testing in the prenatal setting and its future perspectives including novel applications that target RNA instead of DNA. PMID:27117661

  10. Electromechanical Signatures for DNA Sequencing through a Mechanosensitive Nanopore.

    Science.gov (United States)

    Farimani, A Barati; Heiranian, M; Aluru, N R

    2015-02-19

    Biological nanopores have been extensively used for DNA base detection since these pores are widely available and tunable through mutations. Distinguishing bases of nucleic acids by passing them through nanopores has so far primarily relied on electrical signals-specifically, ionic currents through the nanopores. However, the low signal-to-noise ratio makes detection of ionic currents difficult. In this study, we show that the initially closed mechanosensitive channel of large conductance (MscL) protein pore opens for single-stranded DNA (ssDNA) translocation under an applied electric field. As each nucleotide translocates through the pore, a unique mechanical signal is observed-specifically, the tension in the membrane containing the MscL pore is different for each nucleotide. In addition to the membrane tension, we found that the ionic current is also different for the four nucleotide types. The initially closed MscL adapts its opening for nucleotide translocation due to the flexibility of the pore. This unique operation of MscL provides single nucleotide resolution in both electrical and mechanical signals. Finally, we also show that the speed of DNA translocation is roughly 1 order of magnitude slower in MscL compared to Mycobacterium smegmatis porin A (MspA), suggesting MscL to be an attractive protein pore for DNA sequencing. PMID:26262481

  11. Next generation sequencing of DNA-launched Chikungunya vaccine virus.

    Science.gov (United States)

    Hidajat, Rachmat; Nickols, Brian; Forrester, Naomi; Tretyakova, Irina; Weaver, Scott; Pushko, Peter

    2016-03-01

    Chikungunya virus (CHIKV) represents a pandemic threat with no approved vaccine available. Recently, we described a novel vaccination strategy based on iDNA® infectious clone designed to launch a live-attenuated CHIKV vaccine from plasmid DNA in vitro or in vivo. As a proof of concept, we prepared iDNA plasmid pCHIKV-7 encoding the full-length cDNA of the 181/25 vaccine. The DNA-launched CHIKV-7 virus was prepared and compared to the 181/25 virus. Illumina HiSeq2000 sequencing revealed that with the exception of the 3' untranslated region, CHIKV-7 viral RNA consistently showed a lower frequency of single-nucleotide polymorphisms than the 181/25 RNA including at the E2-12 and E2-82 residues previously identified as attenuating mutations. In the CHIKV-7, frequencies of reversions at E2-12 and E2-82 were 0.064% and 0.086%, while in the 181/25, frequencies were 0.179% and 0.133%, respectively. We conclude that the DNA-launched virus has a reduced probability of reversion mutations, thereby enhancing vaccine safety. PMID:26855330

  12. Structural properties of replication origins in yeast DNA sequences

    International Nuclear Information System (INIS)

    Sequence-dependent DNA flexibility is an important structural property originating from the DNA 3D structure. In this paper, we investigate the DNA flexibility of the budding yeast (S. Cerevisiae) replication origins on a genome-wide scale using flexibility parameters from two different models, the trinucleotide and the tetranucleotide models. Based on analyzing average flexibility profiles of 270 replication origins, we find that yeast replication origins are significantly rigid compared with their surrounding genomic regions. To further understand the highly distinctive property of replication origins, we compare the flexibility patterns between yeast replication origins and promoters, and find that they both contain significantly rigid DNAs. Our results suggest that DNA flexibility is an important factor that helps proteins recognize and bind the target sites in order to initiate DNA replication. Inspired by the role of the rigid region in promoters, we speculate that the rigid replication origins may facilitate binding of proteins, including the origin recognition complex (ORC), Cdc6, Cdt1 and the MCM2-7 complex

  13. Sequencing of mitochondrial HV1 and HV2 DNA with length heteroplasmy

    DEFF Research Database (Denmark)

    Rasmussen, E. Michael; Eriksen, Birthe; Larsen, Hans Jakob;

    2003-01-01

    This study presents a fast method for sequencing the poly C/G regions in HV1 and HV2 in the mitochondrial DNA (mtDNA)......This study presents a fast method for sequencing the poly C/G regions in HV1 and HV2 in the mitochondrial DNA (mtDNA)...

  14. Characterization of Expressed Sequence Tags From a Gallus gallus Pineal Gland cDNA Library

    OpenAIRE

    Stefanie Hartman; Greg Touchton; Jessica Wynn; Tuoyu Geng; Chong, Nelson W.; Ed Smith

    2005-01-01

    The pineal gland is the circadian oscillator in the chicken, regulating diverse functions ranging from egg laying to feeding. Here, we describe the isolation and characterization of expressed sequence tags (ESTs) isolated from a chicken pineal gland cDNA library. A total of 192 unique sequences were analysed and submitted to GenBank; 6% of the ESTs matched neither GenBank cDNA sequences nor the newly assembled chicken genomic DNA sequence, three ESTs aligned with sequences d...

  15. Using Synthetic Nanopores for Single-Molecule Analyses: Detecting SNPs, Trapping DNA Molecules, and the Prospects for Sequencing DNA

    Science.gov (United States)

    Dimitrov, Valentin V.

    2009-01-01

    This work focuses on studying properties of DNA molecules and DNA-protein interactions using synthetic nanopores, and it examines the prospects of sequencing DNA using synthetic nanopores. We have developed a method for discriminating between alleles that uses a synthetic nanopore to measure the binding of a restriction enzyme to DNA. There exists…

  16. Isolation and analysis of high quality nuclear DNA with reduced organellar DNA for plant genome sequencing and resequencing

    Directory of Open Access Journals (Sweden)

    Zdepski Anna

    2011-05-01

    Full Text Available Abstract Background High throughput sequencing (HTS technologies have revolutionized the field of genomics by drastically reducing the cost of sequencing, making it feasible for individual labs to sequence or resequence plant genomes. Obtaining high quality, high molecular weight DNA from plants poses significant challenges due to the high copy number of chloroplast and mitochondrial DNA, as well as high levels of phenolic compounds and polysaccharides. Multiple methods have been used to isolate DNA from plants; the CTAB method is commonly used to isolate total cellular DNA from plants that contain nuclear DNA, as well as chloroplast and mitochondrial DNA. Alternatively, DNA can be isolated from nuclei to minimize chloroplast and mitochondrial DNA contamination. Results We describe optimized protocols for isolation of nuclear DNA from eight different plant species encompassing both monocot and eudicot species. These protocols use nuclei isolation to minimize chloroplast and mitochondrial DNA contamination. We also developed a protocol to determine the number of chloroplast and mitochondrial DNA copies relative to the nuclear DNA using quantitative real time PCR (qPCR. We compared DNA isolated from nuclei to total cellular DNA isolated with the CTAB method. As expected, DNA isolated from nuclei consistently yielded nuclear DNA with fewer chloroplast and mitochondrial DNA copies, as compared to the total cellular DNA prepared with the CTAB method. This protocol will allow for analysis of the quality and quantity of nuclear DNA before starting a plant whole genome sequencing or resequencing experiment. Conclusions Extracting high quality, high molecular weight nuclear DNA in plants has the potential to be a bottleneck in the era of whole genome sequencing and resequencing. The methods that are described here provide a framework for researchers to extract and quantify nuclear DNA in multiple types of plants.

  17. Anonymous Publish-Subscribe Overlays

    OpenAIRE

    Daubert, Jörg

    2016-01-01

    Freedom of speech is a core value of our society. While it can be exercised anonymously towards undesired observers in the physical world, the Internet is based on unique and nonanonymous identifiers (IDs) for every participant. Anonymity, however, is a crucial requirement to exercise freedom of speech using the Internet without having to face political persecution. To achieve anonymity, messages must be unlinkable to senders an receivers. That means that messages cannot be linked to IDs and ...

  18. Unintended Effects of Anonymous Resumes

    OpenAIRE

    Behaghel, Luc; Crépon, Bruno; Le Barbanchon, Thomas

    2014-01-01

    We evaluate an experimental program in which the French public employment service anonymized resumes for firms that were hiring. Firms were free to participate or not; participating firms were then randomly assigned to receive either anonymous resumes or name-bearing ones. We find that participating firms become less likely to interview and hire minority candidates when receiving anonymous resumes. We show how these unexpected results can be explained by the self-selection of firms into the p...

  19. PCR master mixes harbour murine DNA sequences. Caveat emptor!

    Directory of Open Access Journals (Sweden)

    Philip W Tuke

    Full Text Available BACKGROUND: XMRV is the most recently described retrovirus to be found in Man, firstly in patients with prostate cancer (PC and secondly in 67% of patients with chronic fatigue syndrome (CFS and 3.7% of controls. Both disease associations remain contentious. Indeed, a recent publication has concluded that "XMRV is unlikely to be a human pathogen". Subsequently related but different polytropic MLV (pMLV sequences were also reported from the blood of 86.5% of patients with CFS. and 6.8% of controls. Consequently we decided to investigate blood donors for evidence of XMRV/pMLV. METHODOLOGY/PRINCIPAL FINDINGS: Testing of cDNA prepared from the whole blood of 80 random blood donors, generated gag PCR signals from two samples (7C and 9C. These had previously tested negative for XMRV by two other PCR based techniques. To test whether the PCR mix was the source of these sequences 88 replicates of water were amplified using Invitrogen Platinum Taq (IPT and Applied Biosystems Taq Gold LD (ABTG. Four gag sequences (2D, 3F, 7H, 12C were generated with the IPT, a further sequence (12D by ABTG re-amplification of an IPT first round product. Sequence comparisons revealed remarkable similarities between these sequences, endogeous MLVs and the pMLV sequences reported in patients with CFS. CONCLUSIONS/SIGNIFICANCE: Methodologies for the detection of viruses highly homologous to endogenous murine viruses require special caution as the very reagents used in the detection process can be a source of contamination and at a level where it is not immediately apparent. It is suggested that such contamination is likely to explain the apparent presence of pMLV in CFS.

  20. Sequence analysis of four caprine mitochondria DNA lineages

    Directory of Open Access Journals (Sweden)

    Yue-Hui Ma

    2012-10-01

    Full Text Available The complete mitochondrial DNA (mtDNA (16640bp in length was sequenced from four Chinese goat lineages representing the four major mtDNA haplogroups in goats. A total of 124 single nucleotide polymorphisms (SNPs were found in encoding regions, and the overall ratio of transitions:transversions was 40:1 revealing a heavy transition/transversion rate in domestic goats. Eighteen non-synonymous sites were found for the total number of SNPs; the sites did not affect the predicted functions of protein for these four goat mtDNA lineages. In the region for coding tRNA and rRNA, SNPs occurred in loops, unstructured single strand and stems that were conformed with the principle of G-U pairing. We came to the conclusion that these substitutions could not change secondary structure of RNAs, and there was no positive selection on goat mitochondrial coding region according to the result of dN/dS (0.0399-0.1529 by comparing the goat with other reported mitochondrial genomes.

  1. New scoring schema for finding motifs in DNA Sequences

    Directory of Open Access Journals (Sweden)

    Nowzari-Dalini Abbas

    2009-03-01

    Full Text Available Abstract Background Pattern discovery in DNA sequences is one of the most fundamental problems in molecular biology with important applications in finding regulatory signals and transcription factor binding sites. An important task in this problem is to search (or predict known binding sites in a new DNA sequence. For this reason, all subsequences of the given DNA sequence are scored based on an scoring function and the prediction is done by selecting the best score. By assuming no dependency between binding site base positions, most of the available tools for known binding site prediction are designed. Recently Tomovic and Oakeley investigated the statistical basis for either a claim of dependence or independence, to determine whether such a claim is generally true, and they presented a scoring function for binding site prediction based on the dependency between binding site base positions. Our primary objective is to investigate the scoring functions which can be used in known binding site prediction based on the assumption of dependency or independency in binding site base positions. Results We propose a new scoring function based on the dependency between all positions in biding site base positions. This scoring function uses joint information content and mutual information as a measure of dependency between positions in transcription factor binding site. Our method for modeling dependencies is simply an extension of position independency methods. We evaluate our new scoring function on the real data sets extracted from JASPAR and TRANSFAC data bases, and compare the obtained results with two other well known scoring functions. Conclusion The results demonstrate that the new approach improves known binding site discovery and show that the joint information content and mutual information provide a better and more general criterion to investigate the relationships between positions in the TFBS. Our scoring function is formulated by simple

  2. Protein Coding Sequence Identification by Simultaneously Characterizing the Periodic and Random Features of DNA Sequences

    Directory of Open Access Journals (Sweden)

    Gao Jianbo

    2005-01-01

    Full Text Available Most codon indices used today are based on highly biased nonrandom usage of codons in coding regions. The background of a coding or noncoding DNA sequence, however, is fairly random, and can be characterized as a random fractal. When a gene-finding algorithm incorporates multiple sources of information about coding regions, it becomes more successful. It is thus highly desirable to develop new and efficient codon indices by simultaneously characterizing the fractal and periodic features of a DNA sequence. In this paper, we describe a novel way of achieving this goal. The efficiency of the new codon index is evaluated by studying all of the 16 yeast chromosomes. In particular, we show that the method automatically and correctly identifies which of the three reading frames is the one that contains a gene.

  3. Assessing the fidelity of ancient DNA sequences amplified from nuclear genes

    DEFF Research Database (Denmark)

    Binladen, Jonas; Wiuf, Carsten Henrik; Gilbert, M. Thomas P.;

    2006-01-01

    To date, the field of ancient DNA has relied almost exclusively on mitochondrial DNA (mtDNA) sequences. However, a number of recent studies have reported the successful recovery of ancient nuclear DNA (nuDNA) sequences, thereby allowing the characterization of genetic loci directly involved in...... phenotypic traits of extinct taxa. It is well documented that postmortem damage in ancient mtDNA can lead to the generation of artifactual sequences. However, as yet no one has thoroughly investigated the damage spectrum in ancient nuDNA. By comparing clone sequences from 23 fossil specimens, recovered from...... environments ranging from permafrost to desert, we demonstrate the presence of miscoding lesion damage in both the mtDNA and nuDNA, resulting in insertion of erroneous bases during amplification. Interestingly, no significant differences in the frequency of miscoding lesion damage are recorded between mtDNA...

  4. PDNAsite: Identification of DNA-binding Site from Protein Sequence by Incorporating Spatial and Sequence Context.

    Science.gov (United States)

    Zhou, Jiyun; Xu, Ruifeng; He, Yulan; Lu, Qin; Wang, Hongpeng; Kong, Bing

    2016-01-01

    Protein-DNA interactions are involved in many fundamental biological processes essential for cellular function. Most of the existing computational approaches employed only the sequence context of the target residue for its prediction. In the present study, for each target residue, we applied both the spatial context and the sequence context to construct the feature space. Subsequently, Latent Semantic Analysis (LSA) was applied to remove the redundancies in the feature space. Finally, a predictor (PDNAsite) was developed through the integration of the support vector machines (SVM) classifier and ensemble learning. Results on the PDNA-62 and the PDNA-224 datasets demonstrate that features extracted from spatial context provide more information than those from sequence context and the combination of them gives more performance gain. An analysis of the number of binding sites in the spatial context of the target site indicates that the interactions between binding sites next to each other are important for protein-DNA recognition and their binding ability. The comparison between our proposed PDNAsite method and the existing methods indicate that PDNAsite outperforms most of the existing methods and is a useful tool for DNA-binding site identification. A web-server of our predictor (http://hlt.hitsz.edu.cn:8080/PDNAsite/) is made available for free public accessible to the biological research community. PMID:27282833

  5. Mitochondrial DNA sequence variation in the Anatolian Peninsula (Turkey)

    Indian Academy of Sciences (India)

    Hatice Mergen; Reyhan Öner; Cihan Öner

    2004-04-01

    Throughout human history, the region known today as the Anatolian peninsula (Turkey) has served as a junction connecting the Middle East, Europe and Central Asia, and, thus, has been subject to major population movements. The present study is undertaken to obtain information about the distribution of the existing mitochondrial D-loop sequence variations in the Turkish population of Anatolia. A few studies have previously reported mtDNA sequences in Turks. We attempted to extend these results by analysing a cohort that is not only larger, but also more representative of the Turkish population living in Anatolia. In order to obtain a descriptive picture for the phylogenetic distribution of the mitochondrial genome within Turkey, we analysed mitochondrial D-loop region sequence variations in 75 individuals from different parts of Anatolia by direct sequencing. Analysis of the two hypervariable segments within the noncoding region of the mitochondrial genome revealed the existence of 81 nucleotide mutations at 79 sites. The neighbour-joining tree of Kimura’s distance matrix has revealed the presence of six main clusters, of which H and U are the most common. The data obtained are also compared with several European and Turkic Central Asian populations.

  6. Analyzing large-scale DNA Sequences on Multi-core Architectures

    OpenAIRE

    Memeti, Suejb; Pllana, Sabri

    2015-01-01

    Rapid analysis of DNA sequences is important in preventing the evolution of different viruses and bacteria during an early phase, early diagnosis of genetic predispositions to certain diseases (cancer, cardiovascular diseases), and in DNA forensics. However, real-world DNA sequences may comprise several Gigabytes and the process of DNA analysis demands adequate computational resources to be completed within a reasonable time. In this paper we present a scalable approach for parallel DNA analy...

  7. Mitochondrial DNA sequences in single hairs from a southern African population.

    OpenAIRE

    Vigilant, L.; Pennington, R; Harpending, H; Kocher, T.D.; Wilson, A C

    1989-01-01

    Hypervariable parts of mitochondrial DNA (mtDNA) were amplified enzymatically and sequenced directly by using genomic DNA from single plucked human hairs. This method has been applied to study mtDNA sequence variation among 15 members of the !Kung population. A genealogical tree relating these aboriginal, Khoisan-speaking southern Africans to 68 other humans and to one chimpanzee has the deepest branches occurring amongst the !Kung, a result consistent with an African origin of human mtDNA. F...

  8. Facile, High Quality Sequencing of Bacterial Genomes from Small Amounts of DNA

    OpenAIRE

    Momchilo Vuyisich; Ayesha Arefin; Karen Davenport; Shihai Feng; Cheryl Gleasner; Kim McMurry; Beverly Parson-Quintana; Jennifer Price; Matthew Scholz; Patrick Chain

    2014-01-01

    Sequencing bacterial genomes has traditionally required large amounts of genomic DNA (~1 μg). There have been few studies to determine the effects of the input DNA amount or library preparation method on the quality of sequencing data. Several new commercially available library preparation methods enable shotgun sequencing from as little as 1 ng of input DNA. In this study, we evaluated the NEBNext Ultra library preparation reagents for sequencing bacterial genomes. We have evaluated the util...

  9. Sequence depth, not PCR replication, improves ecological inference from next generation DNA sequencing.

    Directory of Open Access Journals (Sweden)

    Dylan P Smith

    Full Text Available Recent advances in molecular approaches and DNA sequencing have greatly progressed the field of ecology and allowed for the study of complex communities in unprecedented detail. Next generation sequencing (NGS can reveal powerful insights into the diversity, composition, and dynamics of cryptic organisms, but results may be sensitive to a number of technical factors, including molecular practices used to generate amplicons, sequencing technology, and data processing. Despite the popularity of some techniques over others, explicit tests of the relative benefits they convey in molecular ecology studies remain scarce. Here we tested the effects of PCR replication, sequencing depth, and sequencing platform on ecological inference drawn from environmental samples of soil fungi. We sequenced replicates of three soil samples taken from pine biomes in North America represented by pools of either one, two, four, eight, or sixteen PCR replicates with both 454 pyrosequencing and Illumina MiSeq. Increasing the number of pooled PCR replicates had no detectable effect on measures of α- and β-diversity. Pseudo-β-diversity - which we define as dissimilarity between re-sequenced replicates of the same sample - decreased markedly with increasing sampling depth. The total richness recovered with Illumina was significantly higher than with 454, but measures of α- and β-diversity between a larger set of fungal samples sequenced on both platforms were highly correlated. Our results suggest that molecular ecology studies will benefit more from investing in robust sequencing technologies than from replicating PCRs. This study also demonstrates the potential for continuous integration of older datasets with newer technology.

  10. On Backward-Style Anonymity Verification

    Science.gov (United States)

    Kawabe, Yoshinobu; Mano, Ken; Sakurada, Hideki; Tsukada, Yasuyuki

    Many Internet services and protocols should guarantee anonymity; for example, an electronic voting system should guarantee to prevent the disclosure of who voted for which candidate. To prove trace anonymity, which is an extension of the formulation of anonymity by Schneider and Sidiropoulos, this paper presents an inductive method based on backward anonymous simulations. We show that the existence of an image-finite backward anonymous simulation implies trace anonymity. We also demonstrate the anonymity verification of an e-voting protocol (the FOO protocol) with our backward anonymous simulation technique. When proving the trace anonymity, this paper employs a computer-assisted verification tool based on a theorem prover.

  11. Statistical methods for detecting periodic fragments in DNA sequence data

    Directory of Open Access Journals (Sweden)

    Ying Hua

    2011-04-01

    Full Text Available Abstract Background Period 10 dinucleotides are structurally and functionally validated factors that influence the ability of DNA to form nucleosomes, histone core octamers. Robust identification of periodic signals in DNA sequences is therefore required to understand nucleosome organisation in genomes. While various techniques for identifying periodic components in genomic sequences have been proposed or adopted, the requirements for such techniques have not been considered in detail and confirmatory testing for a priori specified periods has not been developed. Results We compared the estimation accuracy and suitability for confirmatory testing of autocorrelation, discrete Fourier transform (DFT, integer period discrete Fourier transform (IPDFT and a previously proposed Hybrid measure. A number of different statistical significance procedures were evaluated but a blockwise bootstrap proved superior. When applied to synthetic data whose period-10 signal had been eroded, or for which the signal was approximately period-10, the Hybrid technique exhibited superior properties during exploratory period estimation. In contrast, confirmatory testing using the blockwise bootstrap procedure identified IPDFT as having the greatest statistical power. These properties were validated on yeast sequences defined from a ChIP-chip study where the Hybrid metric confirmed the expected dominance of period-10 in nucleosome associated DNA but IPDFT identified more significant occurrences of period-10. Application to the whole genomes of yeast and mouse identified ~ 21% and ~ 19% respectively of these genomes as spanned by period-10 nucleosome positioning sequences (NPS. Conclusions For estimating the dominant period, we find the Hybrid period estimation method empirically to be the most effective for both eroded and approximate periodicity. The blockwise bootstrap was found to be effective as a significance measure, performing particularly well in the problem of

  12. Polymorphic DNA sequences and their application in paternity testing; Polimorficzne sekwencje DNA i ich zastosowanie w dochodzeniu spornego ojcostwa

    Energy Technology Data Exchange (ETDEWEB)

    Slomski, R. [Polska Akademia Nauk, Poznan (Poland). Zaklad Genetyki Czlowieka]|[Akademia Rolnicza, Poznan (Poland)]|[Laboratorium Genetyki Molekularnej, Poznan (Poland); Kwiatkowska, J.; Chlebowska, H. [Polska Akademia Nauk, Poznan (Poland). Zaklad Genetyki Czlowieka; Siemieniallo, B. [Akademia Rolnicza, Poznan (Poland); Slomska, M. [Laboratorium Genetyki Molekularnej, Poznan (Poland)

    1994-12-31

    Characteristics of polymorphic sequences of DNA, especially satellite, mini satellite and micro satellite sequences are presented. Own experience from the use of multi and single locus analysis of DNA in paternity testing has been compared with the results of research in other laboratories. Critical points of both types of analysis are discussed. (author). 53 refs, 4 figs, 2 tabs.

  13. Incomplete primer extension during in vitro DNA amplification catalyzed by Taq polymerase; exploitation for DNA sequencing.

    OpenAIRE

    Olsen, D. B.; Eckstein, F.

    1989-01-01

    Polyacrylamide gel electrophoresis of DNA fragments obtained by the polymerase chain reaction using Taq polymerase revealed the presence of multiple fragments shorter than the expected product. These abortive extension products were observed even when analysis by agarose gel electrophoresis showed only a single band. The production of prematurely terminated fragments can be exploited for the sequencing of PCR products if phosphorothioate groups are incorporated base specifically during the re...

  14. Construction of a Sequencing Library from Circulating Cell-Free DNA.

    Science.gov (United States)

    Fang, Nan; Löffert, Dirk; Akinci-Tolun, Rumeysa; Heitz, Katja; Wolf, Alexander

    2016-01-01

    Circulating DNA is cell-free DNA (cfDNA) in serum or plasma that can be used for non-invasive prenatal testing, as well as cancer diagnosis, prognosis, and stratification. High-throughput sequence analysis of the cfDNA with next-generation sequencing technologies has proven to be a highly sensitive and specific method in detecting and characterizing mutations in cancer and other diseases, as well as aneuploidy during pregnancy. This unit describes detailed procedures to extract circulating cfDNA from human serum and plasma and generate sequencing libraries from a wide concentration range of circulating DNA. © 2016 by John Wiley & Sons, Inc. PMID:27038390

  15. Long-range correlations and charge transport properties of DNA sequences

    Science.gov (United States)

    Liu, Xiao-liang; Ren, Yi; Xie, Qiong-tao; Deng, Chao-sheng; Xu, Hui

    2010-04-01

    By using Hurst's analysis and transfer approach, the rescaled range functions and Hurst exponents of human chromosome 22 and enterobacteria phage lambda DNA sequences are investigated and the transmission coefficients, Landauer resistances and Lyapunov coefficients of finite segments based on above genomic DNA sequences are calculated. In a comparison with quasiperiodic and random artificial DNA sequences, we find that λ-DNA exhibits anticorrelation behavior characterized by a Hurst exponent 0.5sequence displays a transition from correlation behavior to anticorrelation behavior. The resonant peaks of the transmission coefficient in genomic sequences can survive in longer sequence length than in random sequences but in shorter sequence length than in quasiperiodic sequences. It is shown that the genomic sequences have long-range correlation properties to some extent but the correlations are not strong enough to maintain the scale invariance properties.

  16. Long-range correlations and charge transport properties of DNA sequences

    Energy Technology Data Exchange (ETDEWEB)

    Liu Xiaoliang, E-mail: xlliucsu@yahoo.com.c [College of Physical Science and Technology and College of Metallurgical Science and Engineering, Central South University, Changsha 410083 (China); Ren, Yi [College of Physical Science and Technology and College of Metallurgical Science and Engineering, Central South University, Changsha 410083 (China); Xie, Qiong-tao [Key Laboratory of Low Dimensional Quantum Structures and Quantum Control of Ministry of Education (Hunan Normal University), Changsha 410081 (China); Deng, Chao-sheng; Xu, Hui [College of Physical Science and Technology and College of Metallurgical Science and Engineering, Central South University, Changsha 410083 (China)

    2010-04-26

    By using Hurst's analysis and transfer approach, the rescaled range functions and Hurst exponents of human chromosome 22 and enterobacteria phage lambda DNA sequences are investigated and the transmission coefficients, Landauer resistances and Lyapunov coefficients of finite segments based on above genomic DNA sequences are calculated. In a comparison with quasiperiodic and random artificial DNA sequences, we find that lambda-DNA exhibits anticorrelation behavior characterized by a Hurst exponent 0.5sequence displays a transition from correlation behavior to anticorrelation behavior. The resonant peaks of the transmission coefficient in genomic sequences can survive in longer sequence length than in random sequences but in shorter sequence length than in quasiperiodic sequences. It is shown that the genomic sequences have long-range correlation properties to some extent but the correlations are not strong enough to maintain the scale invariance properties.

  17. DNA sequence recognition protein associated with a multiprotein form of DNA polymerase alpha

    International Nuclear Information System (INIS)

    The majority of DNA polymerase α activity in HeLa cells has been isolated and purified as a multiprotein Mr 640,000 form. A number of accessory activities cofractionate with this form of polymerase α. Among these are: Cl, C2 primer recognition proteins, primase, a 5' → 3' exonuclease, and a 5',5''',P1,P4-diadenosine tetraphosphate (Ap4A) binding protein. Preliminary results suggest an additional factor(s) or protein(s) is present in the multiprotein form of the HeLa cell DNA polymerase α which has an affinity for DNA sequences rich in A and T residues. Affinity chromatography on poly(dA)-or oligo(dT)-cellulose yields a highly purified protein. This protein has the ability to bind 3H-poly (dA) and 3H-poly(dT) in a nitrocellulose filter binding assay. The further physical properties of this protein and its DNA sequence binding specificity will be discussed

  18. Single-stranded DNA ligation and XLF-stimulated incompatible DNA end ligation by the XRCC4-DNA ligase IV complex: influence of terminal DNA sequence.

    Science.gov (United States)

    Gu, Jiafeng; Lu, Haihui; Tsai, Albert G; Schwarz, Klaus; Lieber, Michael R

    2007-01-01

    The double-strand DNA break repair pathway, non-homologous DNA end joining (NHEJ), is distinctive for the flexibility of its nuclease, polymerase and ligase activities. Here we find that the joining of ends by XRCC4-ligase IV is markedly influenced by the terminal sequence, and a steric hindrance model can account for this. XLF (Cernunnos) stimulates the joining of both incompatible DNA ends and compatible DNA ends at physiologic concentrations of Mg2+, but only of incompatible DNA ends at higher concentrations of Mg2+, suggesting charge neutralization between the two DNA ends within the ligase complex. XRCC4-DNA ligase IV has the distinctive ability to ligate poly-dT single-stranded DNA and long dT overhangs in a Ku- and XLF-independent manner, but not other homopolymeric DNA. The dT preference of the ligase is interesting given the sequence bias of the NHEJ polymerase. These distinctive properties of the XRCC4-DNA ligase IV complex explain important aspects of its in vivo roles. PMID:17717001

  19. DNA sequences, recombinant DNA molecules and processes for producing bovine growth hormone-like polypeptides in high yield

    International Nuclear Information System (INIS)

    This patent describes a process for increasing the yield of a bovine growth hormone-like polypeptide to at least 100 times that of a bovine growth hormone-like polypeptide encoded by a DNA sequence. The process comprises the steps of culturing a host transformed with a recombinant DNA molecule comprising DNA sequence encoding a Met Λ or Λ bovine growth hormone-like polypetide operatively linked to an expression control sequence. The Λ is an amino terminal deletion from the amino acid sequence of mature bovine growth hormone

  20. The evolution processes of DNA sequences, languages and carols

    Science.gov (United States)

    Hauck, Jürgen; Henkel, Dorothea; Mika, Klaus

    2001-04-01

    The sequences of bases A, T, C and G of about 100 enolase, secA and cytochrome DNA were analyzed for attractive or repulsive interactions by the numbers T 1,T 2,T 3; r of nearest, next-nearest and third neighbor bases of the same kind and the concentration r=other bases/analyzed base. The area of possible T1, T2 values is limited by the linear borders T 2=2T 1-2, T 2=0 or T1=0 for clustering, attractive or repulsive interactions and the border T2=-2 T1+2(2- r) for a variation from repulsive to attractive interactions at r⩽2. Clustering is preferred by most bases in sequences of enolases and secA’ s. Major deviations with repulsive interactions of some bases are observed for archaea bacteria in secA and for highly developed animals and the human species in enolase sequences. The borders of the structure map for enthalpy stabilized structures with maximum interactions are approached in few cases. Most letters of the natural languages and some music notes are at the borders of the structure map.

  1. Complete Genome Sequence of Pelosinus sp. Strain UFO1 Assembled Using Single-Molecule Real-Time DNA Sequencing Technology

    OpenAIRE

    Brown, Steven D.; Utturkar, Sagar M.; Magnuson, Timothy S.; Ray, Allison E.; Poole, Farris L.; Lancaster, W Andrew; Thorgersen, Michael P.; Adams, Michael W. W.; Elias, Dwayne A.

    2014-01-01

    Pelosinus species can reduce metals such as Fe(III), U(VI), and Cr(VI) and have been isolated from diverse geographical regions. Five draft genome sequences have been published. We report the complete genome sequence for Pelosinus sp. strain UFO1 using only PacBio DNA sequence data and without manual finishing.

  2. Structural analysis of DNA sequence: evidence for lateral gene transfer in Thermotoga maritima

    DEFF Research Database (Denmark)

    Worning, Peder; Jensen, Lars Juhl; Nelson, K. E.;

    2000-01-01

    The recently published complete DNA sequence of the bacterium Thermotoga maritima provides evidence, based on protein sequence conservation, for lateral gene transfer between Archaea and Bacteria. We introduce a new method of periodicity analysis of DNA sequences, based on structural parameters, ...

  3. Challenges in DNA motion control and sequence readout using nanopore devices

    International Nuclear Information System (INIS)

    Nanopores are being hailed as a potential next-generation DNA sequencer that could provide cheap, high-throughput DNA analysis. In this review we present a detailed summary of the various sensing techniques being investigated for use in DNA sequencing and mapping applications. A crucial impasse to the success of nanopores as a reliable DNA analysis tool is the fast and stochastic nature of DNA translocation. We discuss the incorporation of biological motors to step DNA through a pore base-by-base, as well as the many experimental modifications attempted for the purpose of slowing and controlling DNA transport. (paper)

  4. No-wash ethanol precipitation of dye-labeled reaction products improves DNA sequencing reads.

    Science.gov (United States)

    Fujikura, Kohei

    2015-01-01

    The advent of DNA sequencing has significantly accelerated molecular biology and clinical genetic testing. Despite recent increases in next-generation sequencing throughput, the most popular platform for DNA sequencing is still the multi-capillary DNA sequencer, which is ideally suited for small-scale sequencing projects and is highly accurate. However, the methods remain time-consuming and laborious. Here, I describe a modified ethylenediaminetetraacetic acid (EDTA) method that skips the washing step in ethanol precipitation. My improvements to standard methods save labor, time, and cost per run and increase the sequence reads by 5 to 10%. This modified method will provide immediate benefits to many researchers. PMID:25256164

  5. Efficient Anonymizations with Enhanced Utility

    Directory of Open Access Journals (Sweden)

    Jacob Goldberger

    2010-08-01

    Full Text Available One of the most well studied models of privacy preservation is k-anonymity. Previous studies of k-anonymization used various utility measures that aim at enhancing the correlation between the original public data and the generalized public data. We, bearing in mind that a primary goal in releasing the anonymized database for datamining is to deducemethods of predicting the private data from the public data, propose a new information-theoretic measure that aims at enhancing the correlation between the generalized public data and the private data. Such a measure significantly enhances the utility of the released anonymized database for data mining. We then proceed to describe a new algorithm that is designed to achieve k-anonymity with high utility, independently of the underlying utility measure. That algorithm is based on a modified version of sequential clustering which is the method of choice in clustering. Experimental comparison with four well known algorithms of k-anonymity show that the sequential clustering algorithm is an efficient algorithm that achieves the best utility results. We also describe a modification of the algorithm that outputs k-anonymizations which respect the additional security measure of l-diversity.

  6. Narcotics Anonymous: Anonymity, admiration, and prestige in an egalitarian community

    OpenAIRE

    Snyder, Jeffrey K.; Fessler, Daniel M.T.

    2014-01-01

    Narcotics Anonymous (NA) supports long-term recovery for those addicted to drugs. Paralleling social dynamics in many small-scale societies, NA exhibits tension between egalitarianism and prestige-based hierarchy, a problem exacerbated by the addict’s personality as characterized by NA’s ethnopsychology.  We explore how NA’s central principle of anonymity normatively translates into egalitarianism among group members.  Turning to the lived reality of membership, building on Carr’s (2011) conc...

  7. Unusual conformational effect exerted by Z-DNA upon its neighboring sequences.

    OpenAIRE

    Kohwi-Shigematsu, T; Manes, T; Kohwi, Y

    1987-01-01

    Supercoiled plasmid DNA harboring an insert of (dG-dC)16, a sequence known to form Z-DNA upon negative supercoiling, was reacted with chloroacetaldehyde. Chloroacetaldehyde, like bromoacetaldehyde, was found to be a specific probe for detecting unpaired DNA bases in supercoiled plasmid DNA. Under torsional stress (at bacterial superhelical density), chloroacetaldehyde reacted at multiple discrete regions within the neighboring sequences of the (dG-dC)16 insert. When the plasmid population was...

  8. Complete DNA sequence of the linear mitochondrial genome of the pathogenic yeast Candida parapsilosis

    DEFF Research Database (Denmark)

    Nosek, J.; Novotna, M.; Hlavatovicova, Z.; Ussery, David; Fajkus, J.; Tomaska, L.

    2004-01-01

    The complete sequence of the mitochondrial DNA of the opportunistic yeast pathogen Candida parapsilosis was determined. The mitochondrial genome is represented by linear DNA molecules terminating with tandem repeats of a 738-bp unit. The number of repeats varies, thus generating a population of...... mitochondrial genome of its close relative C. albicans. The complete sequence has implications for both mitochondrial DNA replication and the evolution of linear DNA genomes....

  9. True single-molecule DNA sequencing of a Pleistocene horse bone

    DEFF Research Database (Denmark)

    Orlando, Ludovic Antoine Alexandre; Ginolhac, Aurelien; Raghavan, Maanasa;

    2011-01-01

    -preserved Pleistocene horse bone using the Helicos HeliScope and Illumina GAIIx platforms, respectively. We find that the percentage of endogenous DNA sequences derived from the horse is higher among the Helicos data than Illumina data. This result indicates that the molecular biology tools used to generate sequencing...... standard Helicos DNA template preparation protocol further increase the proportion of horse DNA for this sample by 3-fold. Comparison of Helicos-specific biases and sequence errors in modern DNA with those in ancient DNA also reveals extensive cytosine deamination damage at the 3' ends of ancient templates...

  10. Anonymous Transactions in Computer Networks

    Science.gov (United States)

    Dolev, Shlomi; Kopeetsky, Marina

    We present schemes for providing anonymous transactions while privacy and anonymity are preserved, providing user anonymous authentication in distributed networks such as the Internet. We first present a practical scheme for anonymous transactions while the transaction resolution is assisted by a Trusted Authority. This practical scheme is extended to a theoretical scheme where a Trusted Authority is not involved in the transaction resolution. Given an authority that generates for each player hard to produce evidence EVID (e. g., problem instance with or without a solution) to each player, the identity of a user U is defined by the ability to prove possession of said evidence. We use Zero-Knowledge proof techniques to repeatedly identify U by providing a proof that U has evidence EVID, without revealing EVID, therefore avoiding identity theft.

  11. Anonymity-Proof Voting Rules

    OpenAIRE

    Conitzer, Vincent

    2007-01-01

    A (randomized, anonymous) voting rule maps any multiset of total orders of (aka. votes over) a fixed set of alternatives to a probability distribution over these alternatives. A voting rule f is neutral if it treats all alternatives symmetrically. It satisfies participation if no voter ever benefits from not casting her vote. It is falsename-proof if no voter ever benefits from casting additional (potentially different) votes. It is anonymity-proof if it satisfies participation and it i...

  12. Comparisons of ape and human sequences that regulate mitochondrial DNA transcription and D-loop DNA synthesis.

    OpenAIRE

    Foran, D R; Hixson, J E; Brown, W. M.

    1988-01-01

    The mitochondrial DNA (mtDNA) control regions for common chimpanzee, pygmy chimpanzee and gorilla were sequenced and the lengths and termini of their D-loop DNA's characterized. In these and all other species for which there are data, 5' termini map to sequences that contain the trinucleotide YAY. 3' termini are 25-51 nucleotides downstream from a sequence that is moderately conserved among vertebrates. Substitutions were greater than 1.5 times more frequent in the control region than in regi...

  13. Organization and Evolution of Primate Centromeric DNA from Whole-Genome Shotgun Sequence Data

    OpenAIRE

    Alkan, Can; Eichler, Evan E.; Ventura, Mario; Archidiacono, Nicoletta; Rocchi, Mariano; Sahinalp, S Cenk

    2007-01-01

    Author Summary Centromeric DNA has been described as the last frontier of genomic sequencing; such regions are typically poorly assembled during the whole-genome shotgun sequence assembly process due to their repetitive complexity. This paper develops a computational algorithm to systematically extract data regarding primate centromeric DNA structure and organization from that ∼5% of sequence that is not included as part of standard genome sequence assemblies. Using this computational approac...

  14. Highly conserved repetitive DNA sequence, (TTAGGG)n, present at the telomeres of human chromosomes

    International Nuclear Information System (INIS)

    A highly conserved repetitive DNA sequence, (TTAGGG)n, has been isolated from a human recombinant repetitive DNA library. Quantitative hybridization to chromosomes sorted by flow cytometry indicates that comparable amounts of this sequence are present on each human chromosome. Both fluorescent in situ hybridization and BAL-31 nuclease digestion experiments reveal major clusters of this sequence at the telomeres of all human chromosomes. The evolutionary conservation of this DNA sequence, its terminal chromosomal location in a variety of higher eukaryotes (regardless of chromosome number or chromosome length), and its similarity to functional telomeres isolated from lower eukaryotes suggest that this sequence is a functional human telomere

  15. Sequencing of megabase plus DNA by hybridization: Method development ENT. Final technical progress report

    Energy Technology Data Exchange (ETDEWEB)

    Crkvenjakov, R.; Drmanac, R.

    1991-01-31

    Sequencing by hybridization (SBH) is the only sequencing method based on the experimental determination of the content of oligonucleotide sequences. The data acquisition relies on the natural process of base pairing. It is possible to determine the content of complementary oligosequences in the target DNA by the process of hybridization with oligonucleotide probes of known sequences.

  16. MultiPipMaker and supporting tools: alignments and analysis of multiple genomic DNA sequences

    OpenAIRE

    Schwartz, Scott; Elnitski, Laura; Li, Mei; Weirauch, Matt; Riemer, Cathy; Smit, Arian; Green, Eric D; Hardison, Ross C.; Miller, Webb

    2003-01-01

    Analysis of multiple sequence alignments can generate important, testable hypotheses about the phylogenetic history and cellular function of genomic sequences. We describe the MultiPipMaker server, which aligns multiple, long genomic DNA sequences quickly and with good sensitivity (available at http://bio.cse.psu.edu/ since May 2001). Alignments are computed between a contiguous reference sequence and one or more secondary sequences, which can be finished or draft sequence. The outputs includ...

  17. A Novel Method for Comparative Analysis of DNA Sequences by Ramanujan-Fourier Transform

    OpenAIRE

    Yin, Changchuan; Yin, Xuemeng E.; Wang, Jiasong

    2014-01-01

    Alignment-free sequence analysis approaches provide important alternatives over multiple sequence alignment (MSA) in biological sequence analysis because alignment-free approaches have low computation complexity and are not dependent on high level of sequence identity, however, most of the existing alignment-free methods do not employ true full information content of sequences and thus can not accurately reveal similarities and differences among DNA sequences. We present a novel alignment-fre...

  18. [Sequencing of low-molecular-weight DNA in blood plasma of irradiated rats].

    Science.gov (United States)

    Vasilieva, I N; Bespalov, V G; Zinkin, V N; Podgornaya, O I

    2015-01-01

    Extracellular low-molecular-weight DNA in blood of irradiated rats was sequenced for the first time. The screening of sequences in the DDBJ database displayed homology of various parts of the rodent genome. Sequences of low-molecular-weight DNA in rat's plasma are enriched with G/C pairs and long interspersed elements relative to rat genome. DNA sequences in blood of rats irradiated at the doses of 8 and 100 Gy have marked distinctions. Data of sequencing of extracellular DNA from normal humans and with pathology were analyzed. DNA sequences of irradiated rats differ from the human ones by a wealth of long interspersed elements. This new knowledge lays the foundation for development of minimally invasive technologies of diagnosing the probability of pathology and controlling the adaptive resources of people in extreme environments. PMID:25958466

  19. DUC-Curve, a highly compact 2D graphical representation of DNA sequences and its application in sequence alignment

    Science.gov (United States)

    Li, Yushuang; Liu, Qian; Zheng, Xiaoqi

    2016-08-01

    A highly compact and simple 2D graphical representation of DNA sequences, named DUC-Curve, is constructed through mapping four nucleotides to a unit circle with a cyclic order. DUC-Curve could directly detect nucleotide, di-nucleotide compositions and microsatellite structure from DNA sequences. Moreover, it also could be used for DNA sequence alignment. Taking geometric center vectors of DUC-Curves as sequence descriptor, we perform similarity analysis on the first exons of β-globin genes of 11 species, oncogene TP53 of 27 species and twenty-four Influenza A viruses, respectively. The obtained reasonable results illustrate that the proposed method is very effective in sequence comparison problems, and will at least play a complementary role in classification and clustering problems.

  20. Water Mediates Recognition of DNA Sequence via Ionic Current Blockade in a Biological Nanopore.

    Science.gov (United States)

    Bhattacharya, Swati; Yoo, Jejoong; Aksimentiev, Aleksei

    2016-04-26

    Electric field-driven translocation of DNA strands through biological nanopores has been shown to produce blockades of the nanopore ionic current that depend on the nucleotide composition of the strands. Coupling a biological nanopore MspA to a DNA processing enzyme has made DNA sequencing via measurement of ionic current blockades possible. Nevertheless, the physical mechanism enabling the DNA sequence readout has remained undetermined. Here, we report the results of all-atom molecular dynamics simulations that elucidated the physical mechanism of ionic current blockades in the biological nanopore MspA. We find that the amount of water displaced from the nanopore by the DNA strand determines the nanopore ionic current, whereas the steric and base-stacking properties of the DNA nucleotides determine the amount of water displaced. Unexpectedly, we find the effective force on DNA in MspA to undergo large fluctuations, which may produce insertion errors in the DNA sequence readout. PMID:27054820

  1. Microfluidics for the upstream pipeline of DNA sequencing--a worthy application?

    Science.gov (United States)

    Coupland, Paul

    2010-03-01

    Technological advances and economic investment into DNA sequencing during this decade has provided the industry of genome sequencing with a suite of dedicated sequencing machines capable of rapidly generating vast quantities of sequence data. This next generation of equipment for DNA sequencing is freely available and is utilised more commonly; this has lead to the traditional bottle-neck in the sequencing pipeline transferring from the sequencing process, i.e. reading the bases on the older capillary based machines, to the upstream processes of sample preparation, i.e. creating the DNA libraries that are to be read. Essentially, advancement in sequencing technology is running faster than the equivalent for sample preparation technology and, without a remedy, we will no longer be able to provide samples quick enough to keep the sequencing machines running at full capacity. PMID:20162226

  2. Analysis and location of a rice BAC clone containing telomeric DNA sequences

    Institute of Scientific and Technical Information of China (English)

    翟文学; 陈浩; 颜辉煌; 严长杰; 王国梁; 朱立煌

    1999-01-01

    BAC2, a rice BAC clone containing (TTTAGGG)n homologous sequences, was analyzed by Southern hybridization and DNA sequencing of its subclones. It was disclosed that there were many tandem repeated satellite DNA sequences, called TA352, as well as simple tandem repeats consisting of TTTAGGG or its variant within the BAC2 insert. A 0. 8 kb (TTTAGGG) n-containing fragment in BAC2 was mapped in the telomere regions of at least 5 pairs of rice chromosomes by using fluorescence in situ hybridization (FISH). By RFLP analysis of low copy sequences the BAC2 clone was localized in one terminal region of chromosome 6. All the results strongly suggest that the telomeric DNA sequences of rice are TTTAGGG or its variant, and the linked satellite DNA TA352 sequences belong to telomere-associated sequences.

  3. Collection and Extraction of Saliva DNA for Next Generation Sequencing

    OpenAIRE

    Goode, Michael R.; Cheong, Soo Yeon; Li, Ning; Ray, William C.; Bartlett, Christopher W

    2014-01-01

    DNA extraction from saliva can provide a readily available source of high molecular weight DNA, with little to no degradation/fragmentation. This protocol provides optimized parameters for saliva collection/storage and DNA extraction to be of sufficient quality and quantity for downstream DNA assays with high quality requirements.

  4. Technology for Anonymity: Names By Other Nyms.

    Science.gov (United States)

    Wayner, Peter

    1999-01-01

    Provides a summary of some of the technical solutions for producing anonymous communication on the Internet and presents an argument that anonymity is as much a part of crime prevention as requiring people to provide their names. Discusses identity theft; the three major techniques that make anonymous cash possible; and anonymizing Internet…

  5. DNA supercoiling enables the Type IIS restriction enzyme BspMI to recognise the relative orientation of two DNA sequences

    OpenAIRE

    Kingston, Isabel J.; Gormley, Niall A.; Halford, Stephen E.

    2003-01-01

    Many proteins can sense the relative orientations of two sequences at distant locations in DNA: some require sites in inverted (head-to-head) orientation, others in repeat (head-to-tail) orientation. Like many restriction enzymes, the BspMI endonuclease binds two copies of its target site before cleaving DNA. Its target is an asymmetric sequence so two sites in repeat orientation differ from sites in inverted orientation. When tested against supercoiled plasmids with two sites 700 bp apart in...

  6. Anonymity and Historical-Anonymity in Location-Based Services

    Science.gov (United States)

    Bettini, Claudio; Mascetti, Sergio; Wang, X. Sean; Freni, Dario; Jajodia, Sushil

    The problem of protecting user’s privacy in Location-Based Services (LBS) has been extensively studied recently and several defense techniques have been proposed. In this contribution, we first present a categorization of privacy attacks and related defenses. Then, we consider the class of defense techniques that aim at providing privacy through anonymity and in particular algorithms achieving “historical k- anonymity” in the case of the adversary obtaining a trace of requests recognized as being issued by the same (anonymous) user. Finally, we investigate the issues involved in the experimental evaluation of anonymity based defense techniques; we show that user movement simulations based on mostly random movements can lead to overestimate the privacy protection in some cases and to overprotective techniques in other cases. The above results are obtained by comparison to a more realistic simulation with an agent-based simulator, considering a specific deployment scenario.

  7. Brain tubulin and actin cDNA sequences: isolation of recombinant plasmids.

    OpenAIRE

    Ginzburg, I.(Sobolev Institute of Mathematics and Novosibirsk State University, 630090, Novosibirsk, Russia); de Baetselier, A; Walker, M D; Behar, L; Lehrach, H; Frischauf, A M; Littauer, U Z

    1980-01-01

    Rat brain mRNA enriched for tubulin and actin sequences was used to prepare double stranded cDNA. A library of recombinant clones was constructed by inserting the dsDNA into the Pst1 site of pBR322 plasmid and transformation of E. coli chi 1776 host. Clones bearing sequences coding for tubulin and actin were identified and characterized.

  8. DNA sequence-dependent mechanics and protein-assisted bending in repressor-mediated loop formation

    International Nuclear Information System (INIS)

    As the chief informational molecule of life, DNA is subject to extensive physical manipulations. The energy required to deform double-helical DNA depends on sequence, and this mechanical code of DNA influences gene regulation, such as through nucleosome positioning. Here we examine the sequence-dependent flexibility of DNA in bacterial transcription factor-mediated looping, a context for which the role of sequence remains poorly understood. Using a suite of synthetic constructs repressed by the Lac repressor and two well-known sequences that show large flexibility differences in vitro, we make precise statistical mechanical predictions as to how DNA sequence influences loop formation and test these predictions using in vivo transcription and in vitro single-molecule assays. Surprisingly, sequence-dependent flexibility does not affect in vivo gene regulation. By theoretically and experimentally quantifying the relative contributions of sequence and the DNA-bending protein HU to DNA mechanical properties, we reveal that bending by HU dominates DNA mechanics and masks intrinsic sequence-dependent flexibility. Such a quantitative understanding of how mechanical regulatory information is encoded in the genome will be a key step towards a predictive understanding of gene regulation at single-base pair resolution. (paper)

  9. Optimized Protocol for Simple Extraction of High-Quality Genomic DNA from Clostridium difficile for Whole-Genome Sequencing

    OpenAIRE

    Sim, James Heng Chiak; Anikst, Victoria; Lohith, Akshar; Pourmand, Nader; Banaei, Niaz

    2015-01-01

    Successful sequencing of the Clostridium difficile genome requires high-quality genomic DNA (gDNA) as the starting material. gDNA extraction using conventional methods is laborious. We describe here an optimized method for the simple extraction of C. difficile gDNA using the QIAamp DNA minikit, which yielded high-quality sequence reads on the Illumina MiSeq platform.

  10. Sequence analysis of a cDNA coding for a pancreatic precursor to somatostatin.

    OpenAIRE

    Taylor, W.L.; Collier, K J; Deschenes, R J; Weith, H L; Dixon, J. E.

    1981-01-01

    A synthetic oligonucleotide having the sequence d(T-T-C-C-A-G-A-A-G-A-A) deduced from the amino acid sequence Phe-Phe-Trp-Lys of somatostatin-14 was used to prime the synthesis of a cDNA from channel catfish (Ictalurus punctatus) pancreatic poly(A)-RNA. The major product of this reaction was a cDNA fragment of 565 nucleotides. Chemical sequence analysis of the cDNA fragment revealed that it was complementary to a mRNA coding for somatostatin. The 565-nucleotide cDNA hybridizes strongly with a...

  11. Sequence-Dependent Fluorescence of Cy3- and Cy5-Labeled Double-Stranded DNA.

    Science.gov (United States)

    Kretschy, Nicole; Sack, Matej; Somoza, Mark M

    2016-03-16

    The fluorescent intensity of Cy3 and Cy5 dyes is strongly dependent on the nucleobase sequence of the labeled oligonucleotides. Sequence-dependent fluorescence may significantly influence the data obtained from many common experimental methods based on fluorescence detection of nucleic acids, such as sequencing, PCR, FRET, and FISH. To quantify sequence dependent fluorescence, we have measured the fluorescence intensity of Cy3 and Cy5 bound to the 5' end of all 1024 possible double-stranded DNA 5mers. The fluorescence intensity was also determined for these dyes bound to the 5' end of fixed-sequence double-stranded DNA with a variable sequence 3' overhang adjacent to the dye. The labeled DNA oligonucleotides were made using light-directed, in situ microarray synthesis. The results indicate that the fluorescence intensity of both dyes is sensitive to all five bases or base pairs, that the sequence dependence is stronger for double- (vs single-) stranded DNA, and that the dyes are sensitive to both the adjacent dsDNA sequence and the 3'-ssDNA overhang. Purine-rich sequences result in higher fluorescence. The results can be used to estimate measurement error in experiments with fluorescent-labeled DNA, as well as to optimize the fluorescent signal by considering the nucleobase environment of the labeling cyanine dye. PMID:26895222

  12. A Microbiome DNA Enrichment Method for Next-Generation Sequencing Sample Preparation.

    Science.gov (United States)

    Yigit, Erbay; Feehery, George R; Langhorst, Bradley W; Stewart, Fiona J; Dimalanta, Eileen T; Pradhan, Sriharsa; Slatko, Barton; Gardner, Andrew F; McFarland, James; Sumner, Christine; Davis, Theodore B

    2016-01-01

    "Microbiome" is used to describe the communities of microorganisms and their genes in a particular environment, including communities in association with a eukaryotic host or part of a host. One challenge in microbiome analysis concerns the presence of host DNA in samples. Removal of host DNA before sequencing results in greater sequence depth of the intended microbiome target population. This unit describes a novel method of microbial DNA enrichment in which methylated host DNA such as human genomic DNA is selectively bound and separated from microbial DNA before next-generation sequencing (NGS) library construction. This microbiome enrichment technique yields a higher fraction of microbial sequencing reads and improved read quality resulting in a reduced cost of downstream data generation and analysis. © 2016 by John Wiley & Sons, Inc. PMID:27366894

  13. Wavelet Based Lossless DNA Sequence Compression for Faster Detection of Eukaryotic Protein Coding Regions

    Directory of Open Access Journals (Sweden)

    G. N. Dash

    2012-07-01

    Full Text Available Discrimination of protein coding regions called exons from noncoding regions called introns or junk DNA in eukaryotic cell is a computationally intensive task. But the dimension of the DNA string is huge; hence it requires large computation time. Further the DNA sequences are inherently random and have vast redundancy, hidden regularities, long repeats and complementary palindromes and therefore cannot be compressed efficiently. The objective of this study is to present an integrated signal processing algorithm that considerably reduces the computational load by compressing the DNA sequence effectively and aids the problem of searching for coding regions in DNA sequences. The presented algorithm is based on the Discrete Wavelet Transform (DWT, a very fast and effective method used for data compression and followed by comb filter for effective prediction of protein coding period-3 regions in DNA sequences. This algorithm is validated using standard dataset such as HMR195, Burset and Guigo and KEGG.

  14. The DNA sequence and biology of human chromosome 19

    Energy Technology Data Exchange (ETDEWEB)

    Grimwood, J; Gordon, L A; Olsen, A; Terry, A; Schmutz, J; Lamerdin, J; Hellsten, U; Goodstein, D; Couronne, O; Tran-Gyamfi, M

    2004-04-06

    Chromosome 19 has the highest gene density of all human chromosomes, more than double the genome-wide average. The large clustered gene families, corresponding high GC content, CpG islands and density of repetitive DNA indicate a chromosome rich in biological and evolutionary significance. Here we describe 55.8 million base pairs of highly accurate finished sequence representing 99.9% of the euchromatin portion of the chromosome. Manual curation of gene loci reveals 1,461 protein-coding genes and 321 pseudogenes. Among these are genes directly implicated in Mendelian disorders, including familial hypercholesterolemia and insulin-resistant diabetes. Nearly one quarter of these genes belong to tandemly arranged families, encompassing more than 25% of the chromosome. Comparative analyses show a fascinating picture of conservation and divergence, revealing large blocks of gene orthology with rodents, scattered regions with more recent gene family expansions and deletions, and segments of coding and non-coding conservation with the distant fish species Takifugu.

  15. Carrier molecules and extraction of circulating tumor DNA for next generation sequencing in colorectal cancer.

    Science.gov (United States)

    Beránek, Martin; Sirák, Igor; Vošmik, Milan; Petera, Jiří; Drastíková, Monika; Palička, Vladimír

    2016-01-01

    The aims of the study were: i) to compare circulating tumor DNA (ctDNA) yields obtained by different manual extraction procedures, ii) to evaluate the addition of various carrier molecules into the plasma to improve ctDNA extraction recovery, and iii) to use next generation sequencing (NGS) technology to analyze KRAS, BRAF, and NRAS somatic mutations in ctDNA from patients with metastatic colorectal cancer. Venous blood was obtained from patients who suffered from metastatic colorectal carcinoma. For plasma ctDNA extraction, the following carriers were tested: carrier RNA, polyadenylic acid, glycogen, linear acrylamide, yeast tRNA, salmon sperm DNA, and herring sperm DNA. Each extract was characterized by quantitative real-time PCR and next generation sequencing. The addition of polyadenylic acid had a significant positive effect on the amount of ctDNA eluted. The sequencing data revealed five cases of ctDNA mutated in KRAS and one patient with a BRAF mutation. An agreement of 86% was found between tumor tissues and ctDNA. Testing somatic mutations in ctDNA seems to be a promising tool to monitor dynamically changing genotypes of tumor cells circulating in the body. The optimized process of ctDNA extraction should help to obtain more reliable sequencing data in patients with metastatic colorectal cancer. PMID:27526306

  16. mapDamage: testing for damage patterns in ancient DNA sequences

    DEFF Research Database (Denmark)

    Ginolhac, Aurelien; Rasmussen, Morten; Gilbert, M Thomas P;

    2011-01-01

    Ancient DNA extracts consist of a mixture of contaminant DNA molecules, most often originating from environmental microbes, and endogenous fragments exhibiting substantial levels of DNA damage. The latter introduce specific nucleotide misincorporations and DNA fragmentation signatures in sequencing...... embedded R script in order to detect typical patterns of genuine ancient DNA sequences. Availability and implementation: The Perl script mapDamage is freely available with documentation and example files at http://geogenetics.ku.dk/all_literature/mapdamage/. The script requires prior installation of the...

  17. Mitochondrial cardiomyopathies: how to identify candidate pathogenic mutations by mitochondrial DNA sequencing, MITOMASTER and phylogeny

    OpenAIRE

    Zaragoza, Michael V; Brandon, Martin C; Diegoli, Marta; Arbustini, Eloisa; Wallace, Douglas C.

    2010-01-01

    Pathogenic mitochondrial DNA (mtDNA) mutations leading to mitochondrial dysfunction can cause cardiomyopathy and heart failure. Owing to a high mutation rate, mtDNA defects may occur at any nucleotide in its 16 569 bp sequence. Complete mtDNA sequencing may detect pathogenic mutations, which can be difficult to interpret because of normal ethnic/geographic-associated haplogroup variation. Our goal is to show how to identify candidate mtDNA mutations by sorting out polymorphisms using readily ...

  18. Systematic sequencing of cDNA clones using the transposon Tn5

    OpenAIRE

    Shevchenko, Yuriy; Bouffard, Gerard G.; Butterfield, Yaron S.N.; Blakesley, Robert W.; Hartley, James L.; Young, Alice C.; Marco A. Marra; Jones, Steven J M; Touchman, Jeffrey W.; Green, Eric D.

    2002-01-01

    In parallel with the production of genomic sequence data, attention is being focused on the generation of comprehensive cDNA-sequence resources. Such efforts are increasingly emphasizing the production of high-accuracy sequence corresponding to the entire insert of cDNA clones, especially those presumed to reflect the full-length mRNA. The complete sequencing of cDNA clones on a large scale presents unique challenges because of the generally small, yet heterogeneous, sizes of the cloned inser...

  19. A Comparison of DNA Purification Methods for Sanger Sequencing and Library Size Selection

    OpenAIRE

    Martin, S.; McCoy, A.; Zianni, Michael

    2013-01-01

    Purification of DNA is a critical process for many aspects of molecular biology including DNA sequencing by automated capillary electrophoresis and library preparation for Next Generation DNA sequencing. Towards this end there are many options including alcohol precipitation, size exclusion chromatography, and solid phase reversible immobilization (SPRI). Two new SPRI reagents were tested for effectiveness and ease of use as compared to these other techniques and a previously used SPRI reagen...

  20. cDNA sequencing improves the detection of P53 missense mutations in colorectal cancer

    International Nuclear Information System (INIS)

    Recently published data showed discrepancies beteween P53 cDNA and DNA sequencing in glioblastomas. We hypothesised that similar discrepancies may be observed in other human cancers. To this end, we analyzed 23 colorectal cancers for P53 mutations and gene expression using both DNA and cDNA sequencing, real-time PCR and immunohistochemistry. We found P53 gene mutations in 16 cases (15 missense and 1 nonsense). Two of the 15 cases with missense mutations showed alterations based only on cDNA, and not DNA sequencing. Moreover, in 6 of the 15 cases with a cDNA mutation those mutations were difficult to detect in the DNA sequencing, so the results of DNA analysis alone could be misinterpreted if the cDNA sequencing results had not also been available. In all those 15 cases, we observed a higher ratio of the mutated to the wild type template by cDNA analysis, but not by the DNA analysis. Interestingly, a similar overexpression of P53 mRNA was present in samples with and without P53 mutations. In terms of colorectal cancer, those discrepancies might be explained under three conditions: 1, overexpression of mutated P53 mRNA in cancer cells as compared with normal cells; 2, a higher content of cells without P53 mutation (normal cells and cells showing K-RAS and/or APC but not P53 mutation) in samples presenting P53 mutation; 3, heterozygous or hemizygous mutations of P53 gene. Additionally, for heterozygous mutations unknown mechanism(s) causing selective overproduction of mutated allele should also be considered. Our data offer new clues for studying discrepancy in P53 cDNA and DNA sequencing analysis

  1. How effective is graphene nanopore geometry on DNA sequencing?

    OpenAIRE

    Satarifard, Vahid; Foroutan, Masumeh; Ejtehadi, Mohammad Reza

    2015-01-01

    In this paper we investigate the effects of graphene nanopore geometry on homopolymer ssDNA pulling process through nanopore using steered molecular dynamic (SMD) simulations. Different graphene nanopores are examined including axially symmetric and asymmetric monolayer graphene nanopores as well as five layer graphene polyhedral crystals (GPC). The pulling force profile, moving fashion of ssDNA, work done in irreversible DNA pulling and orientations of DNA bases near the nanopore are assesse...

  2. The organisation and evolution of a repeated DNA sequence family in related Allium species

    OpenAIRE

    Evans, Ian Jeffrey

    1983-01-01

    A large proportion of the genomes of species belonging to the genus Allium comprises repetitive sequence DNA, a component implicated as a cause of the large variation in C-values between even closely related species. The work presented here represents part of the first phase in the characterisation of some of these repetitive sequences in a number of Allium species. One repetitive DNA sequence family, BIOOO, isolated from the genome of A. sativum, has been characterised with respect to the...

  3. Computational optimisation of targeted DNA sequencing for cancer detection

    DEFF Research Database (Denmark)

    Martinez, Pierre; McGranahan, Nicholas; Birkbak, Nicolai Juul;

    2013-01-01

    circulating tumour DNA (ctDNA) might represent a non-invasive method to detect mutations in patients, facilitating early detection. In this article, we define reduced gene panels from publicly available datasets as a first step to assess and optimise the potential of targeted ctDNA scans for early tumour...

  4. Data Retention and Anonymity Services

    Science.gov (United States)

    Berthold, Stefan; Böhme, Rainer; Köpsell, Stefan

    The recently introduced legislation on data retention to aid prosecuting cyber-related crime in Europe also affects the achievable security of systems for anonymous communication on the Internet. We argue that data retention requires a review of existing security evaluations against a new class of realistic adversary models. In particular, we present theoretical results and first empirical evidence for intersection attacks by law enforcement authorities. The reference architecture for our study is the anonymity service AN.ON, from which we also collect empirical data. Our adversary model reflects an interpretation of the current implementation of the EC Directive on Data Retention in Germany.

  5. Analysis of T-DNA/Host-Plant DNA Junction Sequences in Single-Copy Transgenic Barley Lines

    Directory of Open Access Journals (Sweden)

    Joanne G. Bartlett

    2014-01-01

    Full Text Available Sequencing across the junction between an integrated transfer DNA (T-DNA and a host plant genome provides two important pieces of information. The junctions themselves provide information regarding the proportion of T-DNA which has integrated into the host plant genome, whilst the transgene flanking sequences can be used to study the local genetic environment of the integrated transgene. In addition, this information is important in the safety assessment of GM crops and essential for GM traceability. In this study, a detailed analysis was carried out on the right-border T-DNA junction sequences of single-copy independent transgenic barley lines. T-DNA truncations at the right-border were found to be relatively common and affected 33.3% of the lines. In addition, 14.3% of lines had rearranged construct sequence after the right border break-point. An in depth analysis of the host-plant flanking sequences revealed that a significant proportion of the T-DNAs integrated into or close to known repetitive elements. However, this integration into repetitive DNA did not have a negative effect on transgene expression.

  6. Replication of cloned DNA containing the Alu family sequence during cell extract-promoting simian virus 40 DNA synthesis.

    OpenAIRE

    Ariga, H

    1984-01-01

    The replicating activity of several cloned DNAs containing putative origin sequences was examined in a cell-free extract that absolutely depends on simian virus 40 (SV40) T antigen promoting initiation of SV40 DNA replication in vitro. Of the three DNAs containing the human Alu family sequence (BLUR8), the origin of (Saccharomyces cerevisiae plasmid 2 micron DNA (pJD29), and the yeast autonomous replicating sequence (YRp7), only BLUR8 was active as a template. Replication in a reaction mixtur...

  7. Compilation of human mtDNA control region sequences.

    OpenAIRE

    Handt, O.; Meyer, S.; von Haeseler, A

    1998-01-01

    This paper describes the organisation of a database for human mitochondrial control-region sequences. The data are divided into three ASCII files that contain aligned sequences from the hypervariable region I (HVRI), from the hypervariable region II (HVRII), and the available information about the individuals, from whom the sequences stem. The current collection comprises 4079 HVRI and 969 HVRII sequences. From 728 individuals sequences of both HVRI and HVRII are available. For easy access, t...

  8. SERS-melting: a new method for discriminating mutations in dna sequences

    OpenAIRE

    Mahajan, Sumeet; Richardson, James; Brown, Tom; Bartlett, Philip N

    2008-01-01

    The reliable discrimination of mutations, single nucleotide polymorphisms (SNPs), and other differences in genomic sequence is an essential part of DNA diagnostics and forensics. It is commonly achieved using fluorescently labeled DNA probes and thermal gradients to distinguish between the matched and mismatched DNA. Here, we describe a novel method that uses surface enhanced (resonance) Raman spectroscopy (SER(R)S) to follow denaturation of dsDNA attached to a structured gold surface. T...

  9. The complete nucleotide sequence of the mitochondrial DNA of the dogfish, Scyliorhinus canicula.

    OpenAIRE

    Delarbre, C; Spruyt, N; Delmarre, C; Gallut, C; Barriel, V.; Janvier, P.; Laudet, V; Gachelin, G

    1998-01-01

    We have determined the complete nucleotide sequence of the mitochondrial DNA (mtDNA) of the dogfish, Scyliorhinus canicula. The 16,697-bp-long mtDNA possesses a gene organization identical to that of the Osteichthyes, but different from that of the sea lamprey Petromyzon marinus. The main features of the mtDNA of osteichthyans were thus established in the common ancestor to chondrichthyans and osteichthyans. The phylogenetic analysis confirms that the Chondrichthyes are the sister group of th...

  10. Rapid isolation and sequencing of purified plasmid DNA from Bacillus subtilis.

    OpenAIRE

    Voskuil, M. I.; Chambliss, G H

    1993-01-01

    We report two methods for isolation of plasmid DNA from the gram-positive bacterium Bacillus subtilis. The protoplast alkaline lysis procedure was developed for general use, and the protoplast alkaline lysis magic procedure was developed for isolation of DNA for sequencing. Both procedures yielded large amounts of high-quality DNA in less than 1 h, while current protocols require 4 to 7 h to perform and give lower yields and quality. Plasmid DNA was obtained from strains containing either hig...

  11. Global matrilineal population structure in sperm whales as indicated by mitochondrial DNA sequences.

    OpenAIRE

    Lyrholm, T; Gyllensten, U

    1998-01-01

    The genetic variability and population structure of worldwide populations of the sperm whale was investigated by sequence analysis of the first 5'L 330 base pairs in the mitochondrial DNA (mtDNA) control region. The study included a total of 231 individuals from three major oceanic regions, the North Atlantic, the North Pacific and the Southern Hemisphere. Fifteen segregating nucleotide sites defined 16 mtDNA haplotypes (lineages). The most common mtDNA types were present in more than one oce...

  12. Thermoelectric effect and its dependence on molecular length and sequence in single DNA molecules

    OpenAIRE

    Li, Yueqi; Xiang, Limin; Palma, Julio L.; ASAI, Yoshihiro; Tao, Nongjian

    2016-01-01

    Studying the thermoelectric effect in DNA is important for unravelling charge transport mechanisms and for developing relevant applications of DNA molecules. Here we report a study of the thermoelectric effect in single DNA molecules. By varying the molecular length and sequence, we tune the charge transport in DNA to either a hopping- or tunnelling-dominated regimes. The thermoelectric effect is small and insensitive to the molecular length in the hopping regime. In contrast, the thermoelect...

  13. High-throughput sequencing of nematode communities from total soil DNA extractions

    DEFF Research Database (Denmark)

    Sapkota, Rumakanta; Nicolaisen, Mogens

    2015-01-01

    nematodes without the need for enrichment was developed. Using this strategy on DNA templates from a set of 22 agricultural soils, we obtained 64.4% sequences of nematode origin in total, whereas the remaining sequences were almost entirely from other metazoans. The nematode sequences were derived from a...

  14. Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications

    Science.gov (United States)

    Analysis of DNA methylation patterns relies increasingly on sequencing-based profiling methods. The four most frequently used sequencing-based technologies are the bisulfite-based methods MethylC-seq and reduced representation bisulfite sequencing (RRBS), and the enrichment-based techniques methylat...

  15. cDNA sequence of human transforming gene hst and identification of the coding sequence required for transforming activity

    International Nuclear Information System (INIS)

    The hst gene was originally identified as a transforming gene in DNAs from human stomach cancers and from a noncancerous portion of stomach mucosa by DNA-mediated transfection assay using NIH3T3 cells. cDNA clones of hst were isolated from the cDNA library constructed from poly(A)+ RNA of a secondary transformant induced by the DNA from a stomach cancer. The sequence analysis of the hst cDNA revealed the presence of two open reading frames. When this cDNA was inserted into an expression vector containing the simian virus 40 promoter, it efficiently induced the transformation of NIH3T3 cells upon transfection. It was found that one of the reading frames, which coded for 206 amino acids, was responsible for the transforming activity

  16. Molecular Phylogeny of Asian Meconopsis Based on Nuclear Ribosomal and Chloroplast DNA Sequence Data

    OpenAIRE

    Liu, Yu-cheng; Liu, Ya-Nan; Yang, Fu-Sheng; Wang, Xiao-Quan

    2014-01-01

    The taxonomy and phylogeny of Asian Meconopsis (Himalayan blue poppy) remain largely unresolved. We used the internal transcribed spacer (ITS) region of nuclear ribosomal DNA (nrDNA) and the chloroplast DNA (cpDNA) trnL-F region for phylogenetic reconstruction of Meconopsis and its close relatives Papaver, Roemeria, and Stylomecon. We identified five main clades, which were well-supported in the gene trees reconstructed with the nrDNA ITS and cpDNA trnL-F sequences. We found that 41 species o...

  17. Optimization of asymmetric polymerase chain reaction for rapid fluorescent DNA sequencing.

    Science.gov (United States)

    Wilson, R K; Chen, C; Hood, L

    1990-02-01

    A high-throughput method for the preparation of single-stranded template DNA, which is suitable for sequence analysis using fluorescent labeling chemistry, is described here. In this procedure, the asymmetric polymerase chain reaction is employed to amplify recombinant plasmid or bacteriophage DNA directly from colonies or plaques. The use of amplification primers located at least 200 base pairs 5' to the site of sequencing primer annealing removes the need for extensive purification of the asymmetric polymerase chain reaction product. Instead, the single-stranded product DNA is purified by a simple isopropanol precipitation step and then directly sequenced using fluorescent dye-labeled oligonucleotides. This method significantly reduces the time and labor required for template preparation and improves fluorescent DNA sequencing strategies by providing a much more uniform yield of single-stranded DNA. PMID:2317375

  18. Cell-free DNA next-generation sequencing in pancreatobiliary carcinomas

    Science.gov (United States)

    Zill, Oliver A.; Greene, Claire; Sebisanovic, Dragan; Siew, LaiMun; Leng, Jim; Vu, Mary; Hendifar, Andrew E.; Wang, Zhen; Atreya, Chloe E.; Kelley, Robin K.; Van Loon, Katherine; Ko, Andrew H.; Tempero, Margaret A.; Bivona, Trever G.; Munster, Pamela N.; Talasaz, AmirAli; Collisson, Eric A.

    2015-01-01

    Patients with pancreatic and biliary carcinomas lack personalized treatment options, in part because biopsies are often inadequate for molecular characterization. Cell-free DNA (cfDNA) sequencing may enable a precision oncology approach in this setting. We attempted to prospectively analyze 54 genes in tumor and cfDNA for 26 patients. Tumor sequencing failed in nine patients (35%). In the remaining 17, 90.3% (95% CI: 73.1–97.5%) of mutations detected in tumor biopsies were also detected in cfDNA. The diagnostic accuracy of cfDNA sequencing was 97.7%, with 92.3% average sensitivity and 100% specificity across five informative genes. Changes in cfDNA correlated well with tumor marker dynamics in serial sampling (r=0.93). We demonstrate that cfDNA sequencing is feasible, accurate, and sensitive in identifying tumor-derived mutations without prior knowledge of tumor genotype or the abundance of circulating tumor DNA. cfDNA sequencing should be considered in pancreatobiliary cancer trials where tissue sampling is unsafe, infeasible, or otherwise unsuccessful. PMID:26109333

  19. DNA sequencing method using laser-induced fluorescence and capillary gel electrophoresis

    International Nuclear Information System (INIS)

    A postelectrophoresis capillary scanning method for increasing the throughput of DNA sequencing has been developed. The method features a spatially and temporally separated arrangement between capillary gel electrophoresis separation of DNA sequencing fragments and the visualization of the separation pattern. Fluorescently labeled DNA sequencing fragments are produced in enzymatic chain-termination reactions and separated by capillary with a transparent polymer coating. The capillary containing all bands of the fragments is then scanned longitudinally with laser beams. The DNA sequence is determined by analyzing the four-color band patterns. The innerwall of the capillary is coated with linear polyacrylamide. The capillary can be used repeatedly by refilling it with crosslinked polyacrylamide gel which can be easily removed out using a HPLC pump. Scanning time of less than 7 s has been achieved and a sequence of about 400 bases can be determined per scan.

  20. System for rapid DNA sequencing with fluorescent chain-terminating dideoxynucleotides

    Energy Technology Data Exchange (ETDEWEB)

    Prober, J.M.; Trainor, G.L.; Dam, R.J.; Hobbs, F.W.; Robertson, C.W.; Zagursky, R.J.; Cocuzza, A.J.; Jensen, M.A.; Baumeister, K.

    1987-10-16

    A DNA sequencing system based on the use of a novel set of four chain-terminating dideoxynucleotides, each carrying a different chemically tuned succinylfluorescein dye distinguished by its fluorescent emission is described. Avian myeloblastosis virus reverse transcriptase is used in a modified dideoxy DNA sequencing protocol to produce a complete set of fluorescence-tagged fragments in one reaction mixture. These DNA fragments are resolved by polyacrylamide gel electrophoresis in one sequencing lane and are identified by a fluorescence detection system specifically matched to the emission characteristics of this dye set. A scanning system allows multiple samples to be run simultaneously and computer-based automatic base sequence identifications to be made. The sequence analysis of M13 and DNA made with this system is described.

  1. Nanopore DNA sequencing and epigenetic detection with a MspA nanopore

    Science.gov (United States)

    Laszlo, Andrew H.

    DNA forms the molecular basis for all known life. Widespread DNA sequencing has the potential to revolutionize healthcare and our understanding of the life sciences. Sequencing has already had a profound effect on our understanding of the molecular basis of life and underpinnings of disease. Current DNA sequencing technologies require costly reagents, can sequence only short DNA strands, and take too long to complete entire genomes. Furthermore, the required DNA sample size limits the types of experiments that can be run. For instance sequencing single cells is extremely difficult. New technologies are key to making DNA sequencing as cheap and accessible as possible and for making new experiments possible. One such new technology is nanopore sequencing. In nanopore sequencing, a thin membrane is used to divide a salt solution into two wells: cis and trans. This membrane contains a single nanometer sized hole that forms the only electrical connection between the two wells. When a voltage is applied across the membrane, ion current flows through the nanopore. This ion current is the primary signal for nanopore sequencing. DNA is negatively charged and can be pulled into the pore. When DNA is pulled into the pore, it occludes the pore and reduces the ion current that can pass through the pore. Individual DNA nucleotides along the DNA strand block the pore to varying degrees. One can measure the degree to which the pore is blocked as DNA passes through the pore and use the ion current signal to read off the DNA sequence. This thesis chronicles recent advances in the Gundlach laboratory in which I have played a leading role. It describes our work testing the biological nanopore Mycobacterium smegmatis porin A (MspA) for nanopore sequencing. The thesis consists of five chapters and three appendices which contain supplemental information for Chapters 2, 3, and 4. Chapter 1 begins with some motivation and defines the current challenges in DNA sequencing. I also introduce

  2. TRX-LOGOS - a graphical tool to demonstrate DNA information content dependent upon backbone dynamics in addition to base sequence

    OpenAIRE

    Fortin, Connor H.; Schulze, Katharina V.; Babbitt, Gregory A.

    2015-01-01

    Background It is now widely-accepted that DNA sequences defining DNA-protein interactions functionally depend upon local biophysical features of DNA backbone that are important in defining sites of binding interaction in the genome (e.g. DNA shape, charge and intrinsic dynamics). However, these physical features of DNA polymer are not directly apparent when analyzing and viewing Shannon information content calculated at single nucleobases in a traditional sequence logo plot. Thus, sequence lo...

  3. Ecological niche modelling and nDNA sequencing support a new, morphologically cryptic beetle species unveiled by DNA barcoding.

    Directory of Open Access Journals (Sweden)

    Oliver Hawlitschek

    Full Text Available BACKGROUND: DNA sequencing techniques used to estimate biodiversity, such as DNA barcoding, may reveal cryptic species. However, disagreements between barcoding and morphological data have already led to controversy. Species delimitation should therefore not be based on mtDNA alone. Here, we explore the use of nDNA and bioclimatic modelling in a new species of aquatic beetle revealed by mtDNA sequence data. METHODOLOGY/PRINCIPAL FINDINGS: The aquatic beetle fauna of Australia is characterised by high degrees of endemism, including local radiations such as the genus Antiporus. Antiporus femoralis was previously considered to exist in two disjunct, but morphologically indistinguishable populations in south-western and south-eastern Australia. We constructed a phylogeny of Antiporus and detected a deep split between these populations. Diagnostic characters from the highly variable nuclear protein encoding arginine kinase gene confirmed the presence of two isolated populations. We then used ecological niche modelling to examine the climatic niche characteristics of the two populations. All results support the status of the two populations as distinct species. We describe the south-western species as Antiporus occidentalis sp.n. CONCLUSION/SIGNIFICANCE: In addition to nDNA sequence data and extended use of mitochondrial sequences, ecological niche modelling has great potential for delineating morphologically cryptic species.

  4. Sequencing strategy of mitochondrial HV1 and HV2 DNA with length heteroplasmy

    DEFF Research Database (Denmark)

    Rasmussen, Erik Michael; Sørensen, E; Eriksen, Birthe;

    2002-01-01

    We describe a method to obtain reliable mitochondrial DNA (mtDNA) sequences downstream of the homopolymeric stretches with length heteroplasmy in the sequencing direction. The method is based on the use of junction primers that bind to a part of the homopolymeric stretch and the first 2-4 bases...... downstream of the homopolymeric region. This junction primer method gave clear and unambiguous results using samples from 21 individuals with length heteroplasmy in the hypervariable regions HV1, HV2 or both. The method is of special value for forensic casework, because sequencing of both strands of an mtDNA...

  5. Divergence between samples of chimpanzee and human DNA sequences is 5%, counting indels

    OpenAIRE

    Britten, Roy J.

    2002-01-01

    Five chimpanzee bacterial artificial chromosome (BAC) sequences (described in GenBank) have been compared with the best matching regions of the human genome sequence to assay the amount and kind of DNA divergence. The conclusion is the old saw that we share 98.5% of our DNA sequence with chimpanzee is probably in error. For this sample, a better estimate would be that 95% of the base pairs are exactly shared between chimpanzee and human DNA. In this sample of 779 kb, the divergence due to bas...

  6. Repetitive Sequences in Plant Nuclear DNA:Types, Distribution, Evolution and Function

    Institute of Scientific and Technical Information of China (English)

    Shweta Mehrotra; Vinod Goyal

    2014-01-01

    Repetitive DNA sequences are a major component of eukaryotic genomes and may account for up to 90% of the genome size. They can be divided into minisatellite, microsatellite and satellite sequences. Satellite DNA sequences are considered to be a fast-evolving component of eukaryotic genomes, comprising tandemly-arrayed, highly-repetitive and highly-conserved monomer sequences. The monomer unit of satellite DNA is 150-400 base pairs (bp) in length. Repetitive sequences may be species- or genus-specific, and may be centromeric or subtelomeric in nature. They exhibit cohesive and concerted evolution caused by molecular drive, leading to high sequence homogeneity. Repetitive sequences accumulate variations in sequence and copy number during evolution, hence they are important tools for taxonomic and phylogenetic studies, and are known as‘‘tuning knobs’’ in the evolution. Therefore, knowledge of repetitive sequences assists our understanding of the organization, evolution and behavior of eukaryotic genomes. Repetitive sequences have cytoplasmic, cellular and developmental effects and play a role in chromosomal recombination. In the post-genomics era, with the introduction of next-generation sequencing tech-nology, it is possible to evaluate complex genomes for analyzing repetitive sequences and decipher-ing the yet unknown functional potential of repetitive sequences.

  7. Analysis of proteins encoded by full-length cDNA sequence from IRM-2 mouse

    International Nuclear Information System (INIS)

    Objective: To screen and isolate radioresistance-related genes from IRM-2 mouse. Methods: Full-length cDNA products were amplified by PCR from IRM-2 mouse cDNA library according to twenty-one pieces of expressed sequence tags. The property of proteins encoded by full-length cDNA were analyzed by comparing with GenBank database. Results: Five pieces of full-length cDNA which were not the same source as the known mice genes were found out from IRM-2 mouse cDNA library.Amino acid sequence and property of proteins encoded by these five pieces of full-length cDNA were obtained. Conclusion: Proteins encoded by full-length cDNA imply that unknown radioresistance-related genes may exist in IR M-2 mouse. (authors)

  8. Sequence-specific Hydrolysis of Single-stranded DNA by PNA-Cerium (Ⅳ) Adduct

    Institute of Scientific and Technical Information of China (English)

    He Bai SHEN; Feng WANG; Yong Tao YANG

    2005-01-01

    A novel artificial site specific cleavage reagent, with peptide nucleic acid (PNA) as sequence-recognizing moiety and cerium (Ⅳ) ions as "scissors" for cleaving target DNA, was synthesized. Subsequently, it was employed in the cleavage of target 26-mer single-stranded DNA (ssDNA), which has 10-mer sequence complementary with PNA recognizer in the hybrids,under physiological conditions. Reversed-phase high-performance liquid chromatogram (RPHPLC) experiments indicated that the artificial site specific cleavage reagent could cleave the target DNA specifically.

  9. cDNA sequence of a new chicken embryonic rho-globin.

    OpenAIRE

    Roninson, I B; Ingram, V M

    1981-01-01

    In order to use specific DNA probes for the study of developmentally regulated gene expression, we have prepared cDNA clones corresponding to chicken embryonic globins by inserting cDNA.mRNA hybrids into the Pst I site of the plasmid pBR322 by using poly(dG) and poly(dC) linkers. The nucleotide sequence of the insert of one clone, representing a nearly full-length copy of an embryonic beta-like globin cDNA, has been determined. The amino acid sequence of the globin encoded by this insert is i...

  10. Targeting DNA with triplex-forming oligonucleotides to modify gene sequence.

    Science.gov (United States)

    Simon, Philippe; Cannata, Fabio; Concordet, Jean-Paul; Giovannangeli, Carine

    2008-08-01

    Molecules that interact with DNA in a sequence-specific manner are attractive tools for manipulating gene sequence and expression. For example, triplex-forming oligonucleotides (TFOs), which bind to oligopyrimidine.oligopurine sequences via Hoogsteen hydrogen bonds, have been used to inhibit gene expression at the DNA level as well as to induce targeted mutagenesis in model systems. Recent advances in using oligonucleotides and analogs to target DNA in a sequence-specific manner will be discussed. In particular, chemical modification of TFOs has been used to improve binding to chromosomal target sequences in living cells. Various oligonucleotide analogs have also been found to expand the range of sequences amenable to manipulation, including so-called "Zorro" locked nucleic acids (LNAs) and pseudo-complementary peptide nucleic acids (pcPNAs). Finally, we will examine the potential of TFOs for directing targeted gene sequence modification and propose that synthetic nucleases, based on conjugation of sequence-specific DNA ligands to DNA damaging molecules, are a promising alternative to protein-based endonucleases for targeted gene sequence modification. PMID:18460344

  11. Bisulfite sequencing reveals that Aspergillus flavus holds a hollow in DNA methylation.

    Directory of Open Access Journals (Sweden)

    Si-Yang Liu

    Full Text Available Aspergillus flavus first gained scientific attention for its production of aflatoxin. The underlying regulation of aflatoxin biosynthesis has been serving as a theoretical model for biosynthesis of other microbial secondary metabolites. Nevertheless, for several decades, the DNA methylation status, one of the important epigenomic modifications involved in gene regulation, in A. flavus remains to be controversial. Here, we applied bisulfite sequencing in conjunction with a biological replicate strategy to investigate the DNA methylation profiling of A. flavus genome. Both the bisulfite sequencing data and the methylome comparisons with other fungi confirm that the DNA methylation level of this fungus is negligible. Further investigation into the DNA methyltransferase of Aspergillus uncovers its close relationship with RID-like enzymes as well as its divergence with the methyltransferase of species with validated DNA methylation. The lack of repeat contents of the A. flavus' genome and the high RIP-index of the small amount of remanent repeat potentially support our speculation that DNA methylation may be absent in A. flavus or that it may possess de novo DNA methylation which occurs very transiently during the obscure sexual stage of this fungal species. This work contributes to our understanding on the DNA methylation status of A. flavus, as well as reinforces our views on the DNA methylation in fungal species. In addition, our strategy of applying bisulfite sequencing to DNA methylation detection in species with low DNA methylation may serve as a reference for later scientific investigations in other hypomethylated species.

  12. Noninvasive diagnosis of fetal aneuploidy by shotgun sequencing DNA from maternal blood.

    Science.gov (United States)

    Fan, H Christina; Blumenfeld, Yair J; Chitkara, Usha; Hudgins, Louanne; Quake, Stephen R

    2008-10-21

    We directly sequenced cell-free DNA with high-throughput shotgun sequencing technology from plasma of pregnant women, obtaining, on average, 5 million sequence tags per patient sample. This enabled us to measure the over- and underrepresentation of chromosomes from an aneuploid fetus. The sequencing approach is polymorphism-independent and therefore universally applicable for the noninvasive detection of fetal aneuploidy. Using this method, we successfully identified all nine cases of trisomy 21 (Down syndrome), two cases of trisomy 18 (Edward syndrome), and one case of trisomy 13 (Patau syndrome) in a cohort of 18 normal and aneuploid pregnancies; trisomy was detected at gestational ages as early as the 14th week. Direct sequencing also allowed us to study the characteristics of cell-free plasma DNA, and we found evidence that this DNA is enriched for sequences from nucleosomes. PMID:18838674

  13. Discovery and genotyping of existing and induced DNA sequence variation in potato

    OpenAIRE

    Uitdewilligen, J.G.A.M.L.

    2012-01-01

    In this thesis natural and induced DNA sequence diversity in potato (Solanum tuberosum) for use in marker-trait analysis and potato breeding is assessed. The study addresses the challenges of reliable, high-throughput identification and genotyping of sequence variants in existing tetraploid potato cultivar panels using traditional Sanger sequencing and next-generation massively parallel sequencing (MPS), and the application of this knowledge in the form of genetic markers. Furthermore, it exp...

  14. Characterization of an Unusually Conserved Alui Highly Reiterated DNA Sequence Family from the Honeybee, Apis Mellifera

    OpenAIRE

    Tares, S.; Cornuet, J. M.; Abad, P.

    1993-01-01

    An AluI family of highly reiterated nontranscribed sequences has been found in the genome of the honeybee Apis mellifera. This repeated sequence is shown to be present at approximately 23,000 copies per haploid genome constituting about 2% of the total genomic DNA. The nucleotide sequence of 10 monomers was determined. The consensus sequence is 176 nucleotides long and has an A + T content of 58%. There are clusters of both direct and inverted repeats. Internal subrepeating units ranging from...

  15. Reproducibility of Illumina platform deep sequencing errors allows accurate determination of DNA barcodes in cells.

    OpenAIRE

    Beltman, J.B.; J. Urbanus; Velds, A.; de, Rooij, R.; Rohr, J.C.; S.H. Naik; T.N. Schumacher.

    2016-01-01

    BACKGROUND Next generation sequencing (NGS) of amplified DNA is a powerful tool to describe genetic heterogeneity within cell populations that can both be used to investigate the clonal structure of cell populations and to perform genetic lineage tracing. For applications in which both abundant and rare sequences are biologically relevant, the relatively high error rate of NGS techniques complicates data analysis, as it is difficult to distinguish rare true sequences from spurious sequences t...

  16. Molecular cloning of a family of retroviral sequences found in chimpanzee but not human DNA.

    OpenAIRE

    Bonner, T I; Birkenmeier, E. H.; Gonda, M A; Mark, G E; Searfoss, G H; Todaro, G J

    1982-01-01

    A number of retrovirus-like sequences have been cloned from chimpanzee DNA which constitute the chimpanzee homologs of the endogenous colobus type C virus CPC-1. One of the clones contains a nearly complete viral genome, but others have sustained deletions of 1 to 2 kilobases in the polymerase gene. The pattern of related sequences detected in other primate species is consistent with the genetic transmission of these sequences for millions of years. However, the appropriately related sequence...

  17. DNA Barcode Sequence Identification Incorporating Taxonomic Hierarchy and within Taxon Variability

    OpenAIRE

    Little, Damon P.

    2011-01-01

    For DNA barcoding to succeed as a scientific endeavor an accurate and expeditious query sequence identification method is needed. Although a global multiple-sequence alignment can be generated for some barcoding markers (e.g. COI, rbcL), not all barcoding markers are as structurally conserved (e.g. matK). Thus, algorithms that depend on global multiple-sequence alignments are not universally applicable. Some sequence identification methods that use local pairwise alignments (e.g. BLAST) are u...

  18. Noninvasive diagnosis of fetal aneuploidy by shotgun sequencing DNA from maternal blood

    OpenAIRE

    Fan, H. Christina; Blumenfeld, Yair J.; Chitkara, Usha; Hudgins, Louanne; Quake, Stephen R.

    2008-01-01

    We directly sequenced cell-free DNA with high-throughput shotgun sequencing technology from plasma of pregnant women, obtaining, on average, 5 million sequence tags per patient sample. This enabled us to measure the over- and underrepresentation of chromosomes from an aneuploid fetus. The sequencing approach is polymorphism-independent and therefore universally applicable for the noninvasive detection of fetal aneuploidy. Using this method, we successfully identified all nine cases of trisomy...

  19. Characterising the atypical 5'-CG DNA sequence specificity of 9-aminoacridine carboxamide Pt complexes.

    Science.gov (United States)

    Kava, Hieronimus W; Galea, Anne M; Md Jamil, Farhana; Feng, Yue; Murray, Vincent

    2014-08-01

    In this study, the DNA sequence specificity of four DNA-targeted 9-aminoacridine carboxamide Pt complexes was compared with cisplatin, using two specially constructed plasmid templates. One plasmid contained 5'-CG and 5'-GA insert sequences while the other plasmid contained a G-rich transferrin receptor gene promoter insert sequence. The damage profiles of each compound on the different DNA templates were quantified via a polymerase stop assay with fluorescently labelled primers and capillary electrophoresis. With the plasmid that contained 5'-CG and 5'-GA dinucleotides, the four 9-aminoacridine carboxamide Pt complexes produced distinctly different damage profiles as compared with cisplatin. These 9-aminoacridine complexes had greatly increased levels of DNA damage at CG and GA dinucleotides as compared with cisplatin. It was shown that the presence of a CG or GA dinucleotide was sufficient to reveal the altered DNA sequence selectivity of the 9-aminoacridine carboxamide Pt analogues. The DNA sequence specificity of the Pt complexes was also found to be similarly altered utilising the transferrin receptor DNA sequence. PMID:24827388

  20. Nucleotide sequence heterogeneity of alpha satellite repetitive DNA: a survey of alphoid sequences from different human chromosomes.

    OpenAIRE

    Waye, J S; Willard, H F

    1987-01-01

    The human alpha satellite DNA family is composed of diverse, tandemly reiterated monomer units of approximately 171 basepairs localized to the centromeric region of each chromosome. These sequences are organized in a highly chromosome-specific manner with many, if not all human chromosomes being characterized by individually distinct alphoid subsets. Here, we compare the nucleotide sequences of 153 monomer units, representing alphoid components of at least 12 different human chromosomes. Base...

  1. mtDNA-Server: next-generation sequencing data analysis of human mitochondrial DNA in the cloud.

    Science.gov (United States)

    Weissensteiner, Hansi; Forer, Lukas; Fuchsberger, Christian; Schöpf, Bernd; Kloss-Brandstätter, Anita; Specht, Günther; Kronenberg, Florian; Schönherr, Sebastian

    2016-07-01

    Next generation sequencing (NGS) allows investigating mitochondrial DNA (mtDNA) characteristics such as heteroplasmy (i.e. intra-individual sequence variation) to a higher level of detail. While several pipelines for analyzing heteroplasmies exist, issues in usability, accuracy of results and interpreting final data limit their usage. Here we present mtDNA-Server, a scalable web server for the analysis of mtDNA studies of any size with a special focus on usability as well as reliable identification and quantification of heteroplasmic variants. The mtDNA-Server workflow includes parallel read alignment, heteroplasmy detection, artefact or contamination identification, variant annotation as well as several quality control metrics, often neglected in current mtDNA NGS studies. All computational steps are parallelized with Hadoop MapReduce and executed graphically with Cloudgene. We validated the underlying heteroplasmy and contamination detection model by generating four artificial sample mix-ups on two different NGS devices. Our evaluation data shows that mtDNA-Server detects heteroplasmies and artificial recombinations down to the 1% level with perfect specificity and outperforms existing approaches regarding sensitivity. mtDNA-Server is currently able to analyze the 1000G Phase 3 data (n = 2,504) in less than 5 h and is freely accessible at https://mtdna-server.uibk.ac.at. PMID:27084948

  2. PCR-Free Enrichment of Mitochondrial DNA from Human Blood and Cell Lines for High Quality Next-Generation DNA Sequencing

    OpenAIRE

    Gould, Meetha P; Bosworth, Colleen M.; McMahon, Sarah; Grandhi, Sneha; Grimerg, Brian T.; LaFramboise, Thomas

    2015-01-01

    Recent advances in sequencing technology allow for accurate detection of mitochondrial sequence variants, even those in low abundance at heteroplasmic sites. Considerable sequencing cost savings can be achieved by enriching samples for mitochondrial (relative to nuclear) DNA. Reduction in nuclear DNA (nDNA) content can also help to avoid false positive variants resulting from nuclear mitochondrial sequences (numts). We isolate intact mitochondrial organelles from both human cell lines and blo...

  3. Efficient selection of biomineralizing DNA aptamers using deep sequencing and population clustering.

    Science.gov (United States)

    Bawazer, Lukmaan A; Newman, Aaron M; Gu, Qian; Ibish, Abdullah; Arcila, Mary; Cooper, James B; Meldrum, Fiona C; Morse, Daniel E

    2014-01-28

    DNA-based information systems drive the combinatorial optimization processes of natural evolution, including the evolution of biominerals. Advances in high-throughput DNA sequencing expand the power of DNA as a potential information platform for combinatorial engineering, but many applications remain to be developed due in part to the challenge of handling large amounts of sequence data. Here we employ high-throughput sequencing and a recently developed clustering method (AutoSOME) to identify single-stranded DNA sequence families that bind specifically to ZnO semiconductor mineral surfaces. These sequences were enriched from a diverse DNA library after a single round of screening, whereas previous screening approaches typically require 5-15 rounds of enrichment for effective sequence identification. The consensus sequence of the largest cluster was poly d(T)30. This consensus sequence exhibited clear aptamer behavior and was shown to promote the synthesis of crystalline ZnO from aqueous solution at near-neutral pH. This activity is significant, as the crystalline form of this wide-bandgap semiconductor is not typically amenable to solution synthesis in this pH range. High-resolution TEM revealed that this DNA synthesis route yields ZnO nanoparticles with an amorphous-crystalline core-shell structure, suggesting that the mechanism of mineralization involves nanoscale coacervation around the DNA template. We thus demonstrate that our new method, termed Single round Enrichment of Ligands by deep Sequencing (SEL-Seq), can facilitate biomimetic synthesis of technological nanomaterials by accelerating combinatorial selection of biomolecular-mineral interactions. Moreover, by enabling direct characterization of sequence family demographics, we anticipate that SEL-Seq will enhance aptamer discovery in applications employing additional rounds of screening. PMID:24341560

  4. Comparing the performance of three ancient DNA extraction methods for high-throughput sequencing

    DEFF Research Database (Denmark)

    Gamba, Cristina; Hanghøj, Kristian Ebbesen; Gaunitz, Charleen;

    2016-01-01

    The DNA molecules that can be extracted from archaeological and palaeontological remains are often degraded and massively contaminated with environmental microbial material. This reduces the efficacy of shotgun approaches for sequencing ancient genomes, despite the decreasing sequencing costs of...... high-throughput sequencing (HTS). Improving the recovery of endogenous molecules from the DNA extraction and purification steps could, thus, help advance the characterization of ancient genomes. Here, we apply the three most commonly used DNA extraction methods to five ancient bone samples spanning a...... ~30 thousand year temporal range and originating from a diversity of environments, from South America to Alaska. We show that methods based on the purification of DNA fragments using silica columns are more advantageous than in solution methods and increase not only the total amount of DNA molecules...

  5. Multi-modulus algorithm based on global artificial fish swarm intelligent optimization of DNA encoding sequences.

    Science.gov (United States)

    Guo, Y C; Wang, H; Wu, H P; Zhang, M Q

    2015-01-01

    Aimed to address the defects of the large mean square error (MSE), and the slow convergence speed in equalizing the multi-modulus signals of the constant modulus algorithm (CMA), a multi-modulus algorithm (MMA) based on global artificial fish swarm (GAFS) intelligent optimization of DNA encoding sequences (GAFS-DNA-MMA) was proposed. To improve the convergence rate and reduce the MSE, this proposed algorithm adopted an encoding method based on DNA nucleotide chains to provide a possible solution to the problem. Furthermore, the GAFS algorithm, with its fast convergence and global search ability, was used to find the best sequence. The real and imaginary parts of the initial optimal weight vector of MMA were obtained through DNA coding of the best sequence. The simulation results show that the proposed algorithm has a faster convergence speed and smaller MSE in comparison with the CMA, the MMA, and the AFS-DNA-MMA. PMID:26782395

  6. Anonymous Client Authentication for Transport Layer Security

    OpenAIRE

    Dietrich, Kurt

    2010-01-01

    Nowadays, anonymity and privacy protecting mechanisms are becoming more and more important. The anonymity of platforms and the privacy of users operating in the Internet are major concerns of current research activities. Although different techniques for protecting anonymity exist, standard protocols like Transport Layer Security are still missing adequate support for these technologies. In this paper, we analyze how Trusted Computing technologies and anonymous credential systems can be used ...

  7. [Name Withheld]: Anonymity and Its Implications

    OpenAIRE

    Weicher, Maureen

    2006-01-01

    Anonymity allows the individual to have a voice without having a name. Since the word “anonymous” entered the English language with the advent of the printing press, the implications of being anonymous - and its lexical offspring “anonymity” - have shifted with time, place, and circumstance. What are the perceived effects of being anonymous/anonymity on the individual and on society? In this paper, I will explore some of the shifting meanings and implications of this concept, first as i...

  8. Designing universal primers for the isolation of DNA sequences encoding Proanthocyanidins biosynthetic enzymes in Crataegus aronia

    Directory of Open Access Journals (Sweden)

    Zuiter Afnan

    2012-08-01

    Full Text Available Abstract Background Hawthorn is the common name of all plant species in the genus Crataegus, which belongs to the Rosaceae family. Crataegus are considered useful medicinal plants because of their high content of proanthocyanidins (PAs and other related compounds. To improve PAs production in Crataegus tissues, the sequences of genes encoding PAs biosynthetic enzymes are required. Findings Different bioinformatics tools, including BLAST, multiple sequence alignment and alignment PCR analysis were used to design primers suitable for the amplification of DNA fragments from 10 candidate genes encoding enzymes involved in PAs biosynthesis in C. aronia. DNA sequencing results proved the utility of the designed primers. The primers were used successfully to amplify DNA fragments of different PAs biosynthesis genes in different Rosaceae plants. Conclusion To the best of our knowledge, this is the first use of the alignment PCR approach to isolate DNA sequences encoding PAs biosynthetic enzymes in Rosaceae plants.

  9. Sequence-specific RNA Photocleavage by Single-stranded DNA in Presence of Riboflavin

    Science.gov (United States)

    Zhao, Yongyun; Chen, Gangyi; Yuan, Yi; Li, Na; Dong, Juan; Huang, Xin; Cui, Xin; Tang, Zhuo

    2015-10-01

    Constant efforts have been made to develop new method to realize sequence-specific RNA degradation, which could cause inhibition of the expression of targeted gene. Herein, by using an unmodified short DNA oligonucleotide for sequence recognition and endogenic small molecue, vitamin B2 (riboflavin) as photosensitizer, we report a simple strategy to realize the sequence-specific photocleavage of targeted RNA. The DNA strand is complimentary to the target sequence to form DNA/RNA duplex containing a G•U wobble in the middle. The cleavage reaction goes through oxidative elimination mechanism at the nucleoside downstream of U of the G•U wobble in duplex to obtain unnatural RNA terminal, and the whole process is under tight control by using light as switch, which means the cleavage could be carried out according to specific spatial and temporal requirements. The biocompatibility of this method makes the DNA strand in combination with riboflavin a promising molecular tool for RNA manipulation.

  10. A new technique for determining the distribution of N7-methylguanine using an automated DNA sequencer.

    Science.gov (United States)

    Shoukry, S; Anderson, M W; Glickman, B W

    1991-11-01

    We have developed a method to determine rapidly the sequence specificity of DNA alkylation resulting from chemical treatment. The utility of this approach is demonstrated here in a study of the sequence specificity of alkylation by dimethylsulphate (DMS). The method is independent of the sequence chosen and makes use of the polymerase chain reaction (PCR) to generate a fluorescently labelled DNA target. In this study, a 302 bp segment of the Escherichia coli lacI gene was amplified and the product purified by liquid chromatography on a Mono Q column. This DNA was alkylated with DMS and treated with hot piperidine to produce single-strand breaks at sites of N7 alkylation. The distribution of the break points, and hence the position and extent of alkylation, were determined on an Applied Biosystems 370A automated DNA sequencer. PMID:1682064

  11. Genomic Signal Processing Methods for Computation of Alignment-Free Distances from DNA Sequences

    Science.gov (United States)

    Borrayo, Ernesto; Mendizabal-Ruiz, E. Gerardo; Vélez-Pérez, Hugo; Romo-Vázquez, Rebeca; Mendizabal, Adriana P.; Morales, J. Alejandro

    2014-01-01

    Genomic signal processing (GSP) refers to the use of digital signal processing (DSP) tools for analyzing genomic data such as DNA sequences. A possible application of GSP that has not been fully explored is the computation of the distance between a pair of sequences. In this work we present GAFD, a novel GSP alignment-free distance computation method. We introduce a DNA sequence-to-signal mapping function based on the employment of doublet values, which increases the number of possible amplitude values for the generated signal. Additionally, we explore the use of three DSP distance metrics as descriptors for categorizing DNA signal fragments. Our results indicate the feasibility of employing GAFD for computing sequence distances and the use of descriptors for characterizing DNA fragments. PMID:25393409

  12. Investigation of mtDNA control region sequences in an Egyptian population sample.

    Science.gov (United States)

    Elmadawy, Mostafa Ali; Nagai, Atsushi; Gomaa, Ghada M; Hegazy, Hanaa M R; Shaaban, Fawzy Eid; Bunai, Yasuo

    2013-11-01

    The sequences of mitochondrial DNA (mtDNA) control region were investigated in 101 unrelated individuals living in the northern region of Nile delta (Gharbia, N=55 and Kafrelsheikh, N=46). DNA was extracted from blood stained filter papers or buccal swabs. HV1, HV2 and HV3 were PCR amplified and sequenced; the resulted sequences were aligned and compared with revised Cambridge sequence (rCRS). The results revealed presence of total 93 different haplotypes, 86 of them are unique and 7 are shared haplotypes, the most common haplotype, was observed with a frequency, 2.97% of population sample. High mtDNA diversity was observed with genetic diversity and power of discrimination, 0.9982 and 0.9883, respectively. In this dataset the west Eurasian haplogroups predominated over the African haplogroups. The results would be useful for forensic examinations and human genetic studies. PMID:23910099

  13. Whole genome sequencing of enriched chloroplast DNA using the Illumina GAII platform

    Directory of Open Access Journals (Sweden)

    Shepherd Lara D

    2010-09-01

    Full Text Available Abstract Background Complete chloroplast genome sequences provide a valuable source of molecular markers for studies in molecular ecology and evolution of plants. To obtain complete genome sequences, recent studies have made use of the polymerase chain reaction to amplify overlapping fragments from conserved gene loci. However, this approach is time consuming and can be more difficult to implement where gene organisation differs among plants. An alternative approach is to first isolate chloroplasts and then use the capacity of high-throughput sequencing to obtain complete genome sequences. We report our findings from studies of the latter approach, which used a simple chloroplast isolation procedure, multiply-primed rolling circle amplification of chloroplast DNA, Illumina Genome Analyzer II sequencing, and de novo assembly of paired-end sequence reads. Results A modified rapid chloroplast isolation protocol was used to obtain plant DNA that was enriched for chloroplast DNA, but nevertheless contained nuclear and mitochondrial DNA. Multiply-primed rolling circle amplification of this mixed template produced sufficient quantities of chloroplast DNA, even when the amount of starting material was small, and improved the template quality for Illumina Genome Analyzer II (hereafter Illumina GAII sequencing. We demonstrate, using independent samples of karaka (Corynocarpus laevigatus, that there is high fidelity in the sequence obtained from this template. Although less than 20% of our sequenced reads could be mapped to chloroplast genome, it was relatively easy to assemble complete chloroplast genome sequences from the mixture of nuclear, mitochondrial and chloroplast reads. Conclusions We report successful whole genome sequencing of chloroplast DNA from karaka, obtained efficiently and with high fidelity.

  14. Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases.

    Science.gov (United States)

    Schadt, Eric E; Banerjee, Onureena; Fang, Gang; Feng, Zhixing; Wong, Wing H; Zhang, Xuegong; Kislyuk, Andrey; Clark, Tyson A; Luong, Khai; Keren-Paz, Alona; Chess, Andrew; Kumar, Vipin; Chen-Plotkin, Alice; Sondheimer, Neal; Korlach, Jonas; Kasarskis, Andrew

    2013-01-01

    Current generation DNA sequencing instruments are moving closer to seamlessly sequencing genomes of entire populations as a routine part of scientific investigation. However, while significant inroads have been made identifying small nucleotide variation and structural variations in DNA that impact phenotypes of interest, progress has not been as dramatic regarding epigenetic changes and base-level damage to DNA, largely due to technological limitations in assaying all known and unknown types of modifications at genome scale. Recently, single-molecule real time (SMRT) sequencing has been reported to identify kinetic variation (KV) events that have been demonstrated to reflect epigenetic changes of every known type, providing a path forward for detecting base modifications as a routine part of sequencing. However, to date no statistical framework has been proposed to enhance the power to detect these events while also controlling for false-positive events. By modeling enzyme kinetics in the neighborhood of an arbitrary location in a genomic region of interest as a conditional random field, we provide a statistical framework for incorporating kinetic information at a test position of interest as well as at neighboring sites that help enhance the power to detect KV events. The performance of this and related models is explored, with the best-performing model applied to plasmid DNA isolated from Escherichia coli and mitochondrial DNA isolated from human brain tissue. We highlight widespread kinetic variation events, some of which strongly associate with known modification events, while others represent putative chemically modified sites of unknown types. PMID:23093720

  15. Revocable Anonymous Access to the Internet?

    Science.gov (United States)

    Claessens, Joris; Diaz, Claudia; Goemans, Caroline; Preneel, Bart; Vandewalle, Joos; Dumortier, Jos

    2003-01-01

    Users of telecommunications networks are concerned about privacy, and desire anonymous access, while some organizations are concerned about how this anonymous access might be abused. Proposes a solution for revocable anonymous access to the Internet. Presents some legal background and motivation for such a solution. Indicates some difficulties and…

  16. Anonymous Boh avatud kunsti maastikul / Raivo Kelomees

    Index Scriptorium Estoniae

    Kelomees, Raivo, 1960-

    2010-01-01

    Anonymous Bohi näitus Tartu Kunstimajas, avatud 30. juulini 2010. Anonymous Boh on koos Non Grataga läbi viinud performance´id Euroopas, Ameerikas ja Aasias. Anonymous Bohi vastused oma näituse ja loominguga seotud küsimustele

  17. Stochastic model of homogeneous coding and latent periodicity in DNA sequences.

    Science.gov (United States)

    Chaley, Maria; Kutyrkin, Vladimir

    2016-02-01

    The concept of latent triplet periodicity in coding DNA sequences which has been earlier extensively discussed is confirmed in the result of analysis of a number of eukaryotic genomes, where latent periodicity of a new type, called profile periodicity, is recognized in the CDSs. Original model of Stochastic Homogeneous Organization of Coding (SHOC-model) in textual string is proposed. This model explains the existence of latent profile periodicity and regularity in DNA sequences. PMID:26656186

  18. cDNA cloning, sequence analysis, and chromosomal localization of the gene for human carnitine palmitoyltransferase.

    OpenAIRE

    Finocchiaro, G; Taroni, F; Rocchi, M; Martin, A.L.; Colombo, I; Tarelli, G T; DiDonato, S

    1991-01-01

    We have cloned and sequenced a cDNA encoding human liver carnitine palmitoyltransferase (CPTase; palmitoyl-CoA:L-carnitine O-palmitoyltransferase, EC 2.3.1.21), an inner mitochondrial membrane enzyme that plays a major role in the fatty acid oxidation pathway. Mixed oligonucleotide primers whose sequences were deduced from one tryptic peptide obtained from purified CPTase were used in a polymerase chain reaction, allowing the amplification of a 0.12-kilobase fragment of human genomic DNA enco...

  19. Fast solid support detection of PCR amplified viral DNA sequences using radioiodinated or hapten labelled primers.

    OpenAIRE

    Sauvaigo, S; Fouqué, B; Roget, A; Livache, T; BAZIN, H.; Chypre, C; Téoule, R

    1990-01-01

    Oligonucleotides with novel modifications have been synthesized and incorporated into enzymatically amplified DNA sequences. They allow the fast detection of viral DNA sequences after two rounds of amplification. The hybrids formed are immobilized by affinity on coated tubes and detected by direct beta (32P) or gamma (125I) counting or by colorimetric revelation. The effect of a dilution step between the two amplifications is studied to obtain optimal sensitivity and specificity. This test is...

  20. Mitochondrial DNA Sequence and Body Size Variations in Turkish Sardine (Sardina pilchardus) Stocks

    OpenAIRE

    SARMAŞIK, Aliye; ÇOLAKOĞLU, Fatma ARIK; Altun, Tülay

    2008-01-01

    Sardine (Sardina pilchardus) is one of the most important species among Turkish fisheries and is broadly distributed along its coastal waters. In the present study, mitochondrial DNA sequences from the cytochrome b (cytb) gene were examined to assess the genetic diversity of sardines inhabiting Turkish coastal waters. A fragment of sardine cytb DNA from each sample collected from 8 representative regions along the coastal zones was amplified by PCR analysis and subsequently sequenced. The res...

  1. The use of permanganate as a sequencing reagent for identification of 5-methylcytosine residues in DNA.

    OpenAIRE

    Fritzsche, E; Hayatsu, H; Igloi, G L; Iida, S.; Kössel, H

    1987-01-01

    The use of permanganate as a reagent for DNA sequencing by chemical degradation has been studied with respect to its specificity for 5-methylcytosine residues. At weakly acidic pH and room temperature, 0.2 mM potassium permanganate reacts preferentially with thymine, 5-methylcytosine, and to a lesser extent with purine residues, while cytosine remains essentially intact. Permanganate oxidation is, therefore, a suitable DNA sequencing reaction for positive discrimination between 5-methylcytosi...

  2. Aspergillus and Penicillium identification using DNA sequences: Barcode or MLST?

    Science.gov (United States)

    Current methods in DNA technology can detect single nucleotide polymorphisms with measurable accuracy using several different approaches appropriate for different uses. If there are even single nucleotide differences that are invariant markers of the species, we can accomplish identification through...

  3. Draft versus finished sequence data for DNA and protein diagnostic signature development

    Energy Technology Data Exchange (ETDEWEB)

    Gardner, S N; Lam, M W; Smith, J R; Torres, C L; Slezak, T R

    2004-10-29

    Sequencing pathogen genomes is costly, demanding careful allocation of limited sequencing resources. We built a computational Sequencing Analysis Pipeline (SAP) to guide decisions regarding the amount of genomic sequencing necessary to develop high-quality diagnostic DNA and protein signatures. SAP uses simulations to estimate the number of target genomes and close phylogenetic relatives (near neighbors, or NNs) to sequence. We use SAP to assess whether draft data is sufficient or finished sequencing is required using Marburg and variola virus sequences. Simulations indicate that intermediate to high quality draft with error rates of 10{sup -3}-10{sup -5} ({approx} 8x coverage) of target organisms is suitable for DNA signature prediction. Low quality draft with error rates of {approx} 1% (3x to 6x coverage) of target isolates is inadequate for DNA signature prediction, although low quality draft of NNs is sufficient, as long as the target genomes are of high quality. For protein signature prediction, sequencing errors in target genomes substantially reduce the detection of amino acid sequence conservation, even if the draft is of high quality. In summary, high quality draft of target and low quality draft of NNs appears to be a cost-effective investment for DNA signature prediction, but may lead to underestimation of predicted protein signatures.

  4. Voucher specimens for DNA sequences of Phytoseiid mites (Acari: Mesostigmata)

    OpenAIRE

    Tixier, Marie-Stéphane; Okassa, Mireille; Liguori, Marialivia; Poinso, Alix; Salerno, Barbara; Kreiter, Serge

    2010-01-01

    Molecular approaches are increasingly used to help in species diagnostics. These approaches have been recently and successfully applied to assess some taxonomic questions within the mite family Phytoseiidae. However, many protocols for DNA extraction of such small specimens require crushing the entire sample, precluding deposition of the carcass as a museum voucher. This study aimed to determine the efficiency of a modified Qiagen DNeasy tissue kit extraction method to both extract enough DNA...

  5. Sequence-specific DNA purification by triplex affinity capture.

    OpenAIRE

    Ito, T.; Smith, C L; Cantor, C R

    1992-01-01

    A DNA isolation procedure was developed by using triple-helix formation and magnetic separation. In this procedure, target DNA is captured by a biotinylated oligonucleotide via intermolecular triplex formation, bound to streptavidin-coated magnetic beads, and recovered in double-stranded form by elution with a mild alkaline buffer that destabilizes the triple helix. The effectiveness of the procedure was demonstrated by a model experiment with an artificially reconstructed library and, also, ...

  6. cDNA cloning, sequence analysis, and chromosomal localization of the gene for human carnitine palmitoyltransferase

    Energy Technology Data Exchange (ETDEWEB)

    Finocchiaro, G.; Taroni, F.; Martin, A.L.; Colombo, I.; Tarelli, G.T.; DiDonato, S. (Istituto Nazionale Neurologico C. Besta, Milan (Italy)); Rocchi, M. (Istituto G. Gaslini, Genoa (Italy))

    1991-01-15

    The authors have cloned and sequenced a cDNA encoding human liver carnitine palmitoyltransferase an inner mitochondrial membrane enzyme that plays a major role in the fatty acid oxidation pathway. Mixed oligonucleotide primers whose sequences were deduced from one tryptic peptide obtained from purified CPTase were used in a polymerase chain reaction, allowing the amplification of a 0.12-kilobase fragment of human genomic DNA encoding such a peptide. A 60-base-pair (bp) oligonucleotide synthesized on the basis of the sequence from this fragment was used for the screening of a cDNA library from human liver and hybridized to a cDNA insert of 2255 bp. This cDNA contains an open reading frame of 1974 bp that encodes a protein of 658 amino acid residues including 25 residues of an NH{sub 2}-terminal leader peptide. The assignment of this open reading frame to human liver CPTase is confirmed by matches to seven different amino acid sequences of tryptic peptides derived from pure human CPTase and by the 82.2% homology with the amino acid sequence of rat CPTase. The NH{sub 2}-terminal region of CPTase contains a leucine-proline motif that is shared by carnitine acetyl- and octanoyltransferases and by choline acetyltransferase. The gene encoding CPTase was assigned to human chromosome 1, region 1q12-1pter, by hybridization of CPTase cDNA with a DNA panel of 19 human-hanster somatic cell hybrids.

  7. cDNA cloning, sequence analysis, and chromosomal localization of the gene for human carnitine palmitoyltransferase

    International Nuclear Information System (INIS)

    The authors have cloned and sequenced a cDNA encoding human liver carnitine palmitoyltransferase an inner mitochondrial membrane enzyme that plays a major role in the fatty acid oxidation pathway. Mixed oligonucleotide primers whose sequences were deduced from one tryptic peptide obtained from purified CPTase were used in a polymerase chain reaction, allowing the amplification of a 0.12-kilobase fragment of human genomic DNA encoding such a peptide. A 60-base-pair (bp) oligonucleotide synthesized on the basis of the sequence from this fragment was used for the screening of a cDNA library from human liver and hybridized to a cDNA insert of 2255 bp. This cDNA contains an open reading frame of 1974 bp that encodes a protein of 658 amino acid residues including 25 residues of an NH2-terminal leader peptide. The assignment of this open reading frame to human liver CPTase is confirmed by matches to seven different amino acid sequences of tryptic peptides derived from pure human CPTase and by the 82.2% homology with the amino acid sequence of rat CPTase. The NH2-terminal region of CPTase contains a leucine-proline motif that is shared by carnitine acetyl- and octanoyltransferases and by choline acetyltransferase. The gene encoding CPTase was assigned to human chromosome 1, region 1q12-1pter, by hybridization of CPTase cDNA with a DNA panel of 19 human-hanster somatic cell hybrids

  8. CLONING AND ANALYSIS OF THE GENOMIC DNA SEQUENCE OF AUGMENTER OF LIVER REGENERATION FROM RAT

    Institute of Scientific and Technical Information of China (English)

    董菁; 成军; 王勤环; 施双双; 王刚; 斯崇文

    2002-01-01

    Objective.To search for genomic DNA sequence of the augmenter of liver regeneration (ALR) of rat.Methods.Polymerase chain reaction (PCR) with specific primers was used to amplify the sequence from the rat genome.Results.A piece of genomic DNA sequence and a piece of pseudogene of rat ALR were identified.The lengths of the gene and pseudogene are 1508 bp and 442 bp,respectively.The ALR gene of rat includes 3 exons and 2 introns.The 442 bp DNA sequence may represent a pseudogene or a ALR related peptide.Predicted amino acid sequence analysis showed that there were 14 different amino acid residues between the gene and pseudogene.ALR related peptide is 84 amino acid residues in length and relates closely to ALR protein.Conclusion.There might be a multigene family of ALR in rat.

  9. Efficiency of ITS Sequences for DNA Barcoding in Passiflora (Passifloraceae)

    Science.gov (United States)

    Giudicelli, Giovanna Câmara; Mäder, Geraldo; de Freitas, Loreta Brandão

    2015-01-01

    DNA barcoding is a technique for discriminating and identifying species using short, variable, and standardized DNA regions. Here, we tested for the first time the performance of plastid and nuclear regions as DNA barcodes in Passiflora. This genus is a largely variable, with more than 900 species of high ecological, commercial, and ornamental importance. We analyzed 1034 accessions of 222 species representing the four subgenera of Passiflora and evaluated the effectiveness of five plastid regions and three nuclear datasets currently employed as DNA barcodes in plants using barcoding gap, applied similarity-, and tree-based methods. The plastid regions were able to identify less than 45% of species, whereas the nuclear datasets were efficient for more than 50% using “best match” and “best close match” methods of TaxonDNA software. All subgenera presented higher interspecific pairwise distances and did not fully overlap with the intraspecific distance, and similarity-based methods showed better results than tree-based methods. The nuclear ribosomal internal transcribed spacer 1 (ITS1) region presented a higher discrimination power than the other datasets and also showed other desirable characteristics as a DNA barcode for this genus. Therefore, we suggest that this region should be used as a starting point to identify Passiflora species. PMID:25837628

  10. Efficiency of ITS Sequences for DNA Barcoding in Passiflora (Passifloraceae

    Directory of Open Access Journals (Sweden)

    Giovanna Câmara Giudicelli

    2015-04-01

    Full Text Available DNA barcoding is a technique for discriminating and identifying species using short, variable, and standardized DNA regions. Here, we tested for the first time the performance of plastid and nuclear regions as DNA barcodes in Passiflora. This genus is a largely variable, with more than 900 species of high ecological, commercial, and ornamental importance. We analyzed 1034 accessions of 222 species representing the four subgenera of Passiflora and evaluated the effectiveness of five plastid regions and three nuclear datasets currently employed as DNA barcodes in plants using barcoding gap, applied similarity-, and tree-based methods. The plastid regions were able to identify less than 45% of species, whereas the nuclear datasets were efficient for more than 50% using “best match” and “best close match” methods of TaxonDNA software. All subgenera presented higher interspecific pairwise distances and did not fully overlap with the intraspecific distance, and similarity-based methods showed better results than tree-based methods. The nuclear ribosomal internal transcribed spacer 1 (ITS1 region presented a higher discrimination power than the other datasets and also showed other desirable characteristics as a DNA barcode for this genus. Therefore, we suggest that this region should be used as a starting point to identify Passiflora species.

  11. Sequence-specific nucleic acid mobility using a reversible block copolymer gel matrix and DNA amphiphiles (lipid-DNA) in capillary and microfluidic electrophoretic separations

    NARCIS (Netherlands)

    Wagler, Patrick; Minero, Gabriel Antonio S.; Tangen, Uwe; de Vries, Jan Willem; Prusty, Deepak; Kwak, Minseok; Herrmann, Andreas; McCaskill, John S.

    2015-01-01

    Reversible noncovalent but sequence-dependent attachment of DNA to gels is shown to allow programmable mobility processing of DNA populations. The covalent attachment of DNA oligomers to polyacrylamide gels using acrydite-modified oligonucleotides has enabled sequence-specific mobility assays for DN

  12. Cloning, sequencing and expression of cDNA encoding growth hormone from Indian catfish (Heteropneustes fossilis)

    Indian Academy of Sciences (India)

    Vikas Anathy; Thayanithy Venugopal; Ramanathan Koteeswaran; Thavamani J Pandian; Sinnakaruppan Mathavan

    2001-09-01

    A tissue-specific cDNA library was constructed using polyA+ RNA from pituitary glands of the Indian catfish Heteropneustes fossilis (Bloch) and a cDNA clone encoding growth hormone (GH) was isolated. Using polymerase chain reaction (PCR) primers representing the conserved regions of fish GH sequences the 3′ region of catfish GH cDNA (540 bp) was cloned by random amplification of cDNA ends and the clone was used as a probe to isolate recombinant phages carrying the full-length cDNA sequence. The full-length cDNA clone is 1132 bp in length, coding for an open reading frame (ORF) of 603 bp; the reading frame encodes a putative polypeptide of 200 amino acids including the signal sequence of 22 amino acids. The 5′ and 3′ untranslated regions of the cDNA are 58 bp and 456 bp long, respectively. The predicted amino acid sequence of H. fossils GH shared 98% homology with other catfishes. Mature GH protein was efficiently expressed in bacterial and zebrafish systems using appropriate expression vectors. The successful expression of the cloned GH cDNA of catfish confirms the functional viability of the clone.

  13. Cloning, sequencing and expression of cDNA encoding growth hormone from Indian catfish (Heteropneustes fossilis)

    Indian Academy of Sciences (India)

    Vikas Anathy; Thayanithy Venugopal; Ramanathan Koteeswaran; Thavamani J Pandian; Sinnakaruppan Mathavan

    2013-03-01

    A tissue-specific cDNA library was constructed using polyA+ RNA from pituitary glands of the Indian catfish Heteropneustes fossilis (Bloch) and a cDNA clone encoding growth hormone (GH) was isolated. Using polymerase chain reaction (PCR) primers representing the conserved regions of fish GH sequences the 3′ region of catfish GH cDNA (540 bp) was cloned by random amplification of cDNA ends and the clone was used as a probe to isolate recombinant phages carrying the full-length cDNA sequence. The full-length cDNA clone is 1132 bp in length, coding for an open reading frame (ORF) of 603 bp; the reading frame encodes a putative polypeptide of 200 amino acids including the signal sequence of 22 amino acids. The 5′ and 3′ untranslated regions of the cDNA are 58 bp and 456 bp long, respectively. The predicted amino acid sequence of H. fossils GH shared 98% homology with other catfishes. Mature GH protein was efficiently expressed in bacterial and zebrafish systems using appropriate expression vectors. The successful expression of the cloned GH cDNA of catfish confirms the functional viability of the clone.

  14. Mitochondrial DNA sequence variation in Finnish patients with matrilineal diabetes mellitus

    Directory of Open Access Journals (Sweden)

    Soini Heidi K

    2012-07-01

    Full Text Available Abstract Background The genetic background of type 2 diabetes is complex involving contribution by both nuclear and mitochondrial genes. There is an excess of maternal inheritance in patients with type 2 diabetes and, furthermore, diabetes is a common symptom in patients with mutations in mitochondrial DNA (mtDNA. Polymorphisms in mtDNA have been reported to act as risk factors in several complex diseases. Findings We examined the nucleotide variation in complete mtDNA sequences of 64 Finnish patients with matrilineal diabetes. We used conformation sensitive gel electrophoresis and sequencing to detect sequence variation. We analysed the pathogenic potential of nonsynonymous variants detected in the sequences and examined the role of the m.16189 T>C variant. Controls consisted of non-diabetic subjects ascertained in the same population. The frequency of mtDNA haplogroup V was 3-fold higher in patients with diabetes. Patients harboured many nonsynonymous mtDNA substitutions that were predicted to be possibly or probably damaging. Furthermore, a novel m.13762 T>G in MTND5 leading to p.Ser476Ala and several rare mtDNA variants were found. Haplogroup H1b harbouring m.16189 T > C and m.3010 G > A was found to be more frequent in patients with diabetes than in controls. Conclusions Mildly deleterious nonsynonymous mtDNA variants and rare population-specific haplotypes constitute genetic risk factors for maternally inherited diabetes.

  15. DNA sequence and structure recognition by Fe(II)[center dot]bleomycin

    Energy Technology Data Exchange (ETDEWEB)

    Kane, S.A.

    1993-01-01

    The bleomycins (BLMs) are a family of clinically-important antitumor antibiotics whose chemotherapeutic effects are believed to be expressed at the level of DNA degradation. Bleomycin-mediated DNA strand scission is sequence-selective, resulting in cleavage predominantly at [sup 5[prime

  16. Nucleotide sequence determination of the region in adenovirus 5 DNA involved in cell transformation

    International Nuclear Information System (INIS)

    A description is given of investigations into the primary structure of the transforming region of adenovirus type 5 DNA. The phenomenon of cell transformation is discussed in general terms and the principles of a number of fairly recent techniques, which have been in use for DNA sequence determination since 1975 are dealt with. A few of the author's own techniques are described which deal both with nucleotide sequence analysis and with the determination of DNA cleavage sites of restriction endonucleases. The results are given of the mapping of cleavage sites in the HpaI-E fragment of adenovirus DNA of HpaII, HaeIII, AluI, HinfI and TaqI and of the determination of the nucleotide sequence in the transforming region of adenovirus type 5 DNA. The results of the sequence determination of the Ad5 HindIII-G fragment are discussed in relation with the investigation on the transforming proteins isolated from in vitro and in vivo synthesizing systems. Labelling procedures of DNA are described including the exonuclease III/DNA polymerase 1 method and TA polynucleotide kinase labelling of DNA fragments. (Auth.)

  17. On the sequence selective bis-intercalation of a homodimeric thiazole orange dye in DNA

    DEFF Research Database (Denmark)

    Bunkenborg, Jakob; Stidsen, M M; Jacobsen, J P

    1998-01-01

    The thiazole orange dye 1,1'-(4,4,8,8-tetramethyl-4, 8-diazaundecamethylene)-bis-4-[(3-methyl-2,3-dihydro(benzo-1, 3-thiazolyl)-2-methylidene]quinolinium tetraiodide (TOTO) binds sequence selectively to double-stranded DNA (dsDNA) by bis-intercalation. Each chromophore is sandwiched between two...

  18. Sequence-specific nucleic acid mobility using a reversible block copolymer gel matrix and DNA amphiphiles (lipid-DNA) in capillary and microfluidic electrophoretic separations.

    Science.gov (United States)

    Wagler, Patrick; Minero, Gabriel Antonio S; Tangen, Uwe; de Vries, Jan Willem; Prusty, Deepak; Kwak, Minseok; Herrmann, Andreas; McCaskill, John S

    2015-10-01

    Reversible noncovalent but sequence-dependent attachment of DNA to gels is shown to allow programmable mobility processing of DNA populations. The covalent attachment of DNA oligomers to polyacrylamide gels using acrydite-modified oligonucleotides has enabled sequence-specific mobility assays for DNA in gel electrophoresis: sequences binding to the immobilized DNA are delayed in their migration. Such a system has been used for example to construct complex DNA filters facilitating DNA computations. However, these gels are formed irreversibly and the choice of immobilized sequences is made once off during fabrication. In this work, we demonstrate the reversible self-assembly of gels combined with amphiphilic DNA molecules, which exhibit hydrophobic hydrocarbon chains attached to the nucleobase. This amphiphilic DNA, which we term lipid-DNA, is synthesized in advance and is blended into a block copolymer gel to induce sequence-dependent DNA retention during electrophoresis. Furthermore, we demonstrate and characterize the programmable mobility shift of matching DNA in such reversible gels both in thin films and microchannels using microelectrode arrays. Such sequence selective separation may be employed to select nucleic acid sequences of similar length from a mixture via local electronics, a basic functionality that can be employed in novel electronic chemical cell designs and other DNA information-processing systems. PMID:26095642

  19. Cloning, nucleotide sequence, and engineered expression of Thermus thermophilus DNA ligase, a homolog of Escherichia coli DNA ligase.

    OpenAIRE

    Lauer, G; Rudd, E A; McKay, D L; Ally, A; Ally, D; Backman, K C

    1991-01-01

    We have cloned and sequenced the gene for DNA ligase from Thermus thermophilus. A comparison of this sequence and those of other ligases reveals significant homology only with that of Escherichia coli. The overall amino acid composition of the thermophilic ligase and the pattern of amino acid substitutions between the two proteins are consistent with compositional biases in other thermophilic enzymes. We have engineered the expression of the T. thermophilus gene in Escherichia coli, and we sh...

  20. Assessment of clone identity and sequence fidelity for 1189 IMAGE cDNA clones

    OpenAIRE

    Halgren, Robert G.; Fielden, Mark R.; Fong, Cora J.; Zacharewski, Timothy R

    2001-01-01

    This report documents the error rate in a commercially distributed subset of the IMAGE Consortium mouse cDNA clone collection. After isolation of plasmid DNA from 1189 bacterial stock cultures, only 62.2% were uncontaminated and contained cDNA inserts that had significant sequence identity to published data for the ordered clones. An agarose gel electrophoresis pre-screening strategy identified 361 stock cultures that appeared to contain two or more plasmid species. Is...

  1. Capillary electrophoresis as a technique to analyze sequence-induced anomalously migrating DNA fragments.

    OpenAIRE

    Wenz, H M

    1994-01-01

    Sequence-induced anomalous migration of double-stranded (ds) DNA in native gel electrophoresis is a well known phenomenon. The retardation of migration is more obvious in polyacrylamide compared with agarose gels, and is greatly affected by the concentration of the gel and the temperature. This anomalous migration results in a difference between calculated and actual sizes of the affected DNA fragments. A low viscosity polymer solution (DNA Fragment Analysis Reagent) under investigation for u...

  2. Analysis of domestic dog mitochondrial DNA sequence variation for forensic investigations

    OpenAIRE

    Angleby, Helen

    2005-01-01

    The first method for DNA analysis in forensics was presented in 1985. Since then, the introduction of the polymerase chain reaction (PCR) has rendered possible the analysis of small amounts of DNA and automated sequencing and fragment analysis techniques have facilitated the analyses. In most cases short tandemly repeated regions (STRs) of nuclear DNA are analysed in forensic investigations, but all samples cannot be successfully analysed using this method. For samples containing minute amoun...

  3. Digital Droplet Multiple Displacement Amplification (ddMDA) for Whole Genome Sequencing of Limited DNA Samples

    OpenAIRE

    Minsoung Rhee; Yooli K Light; Meagher, Robert J.; Anup K. Singh

    2016-01-01

    Multiple displacement amplification (MDA) is a widely used technique for amplification of DNA from samples containing limited amounts of DNA (e.g., uncultivable microbes or clinical samples) before whole genome sequencing. Despite its advantages of high yield and fidelity, it suffers from high amplification bias and non-specific amplification when amplifying sub-nanogram of template DNA. Here, we present a microfluidic digital droplet MDA (ddMDA) technique where partitioning of the template D...

  4. Sequence analysis of the ribosomal DNA ITS2 region in two Trichogramma species (Hymenoptera: Trichogrammatidae

    Directory of Open Access Journals (Sweden)

    Ercan Sumer Fahriye

    2011-01-01

    Full Text Available Two egg parasitoid wasps, Trichogramma euproctidis (Girault and Trichogramma brassicae (Bezdenko (Hymenoptera: Trichogrammatidae were identified in the study. The taxonomy of these wasps is problematic because of their small size and lack of distinguishable morphological characters. The DNA sequence variation from the internal transcribed spacer 2 (ITS2 region of nuclear ribosomal DNA (rDNA was analyzed from these two Trichogramma species. This technique provides quick, simple and reliable molecular identification of Trichogramma species.

  5. Protocols for 16S rDNA Array Analyses of Microbial Communities by Sequence-Specific Labeling of DNA Probes

    Directory of Open Access Journals (Sweden)

    Knut Rudi

    2003-01-01

    Full Text Available Analyses of complex microbial communities are becoming increasingly important. Bottlenecks in these analyses, however, are the tools to actually describe the biodiversity. Novel protocols for DNA array-based analyses of microbial communities are presented. In these protocols, the specificity obtained by sequence-specific labeling of DNA probes is combined with the possibility of detecting several different probes simultaneously by DNA array hybridization. The gene encoding 16S ribosomal RNA was chosen as the target in these analyses. This gene contains both universally conserved regions and regions with relatively high variability. The universally conserved regions are used for PCR amplification primers, while the variable regions are used for the specific probes. Protocols are presented for DNA purification, probe construction, probe labeling, and DNA array hybridizations.

  6. Ray Wu as Fifth Business: Deconstructing collective memory in the history of DNA sequencing.

    Science.gov (United States)

    Onaga, Lisa A

    2014-06-01

    The concept of 'Fifth Business' is used to analyze a minority standpoint and bring serious attention to the role of scientists who play a galvanizing role in a science but for multiple reasons appear less prominently in more common recounts of any particular development. Biochemist Ray Wu (1928-2008) published a DNA sequencing experiment in March 1970 using DNA polymerase catalysis and specific nucleotide labeling, both of which are foundational to general sequencing methods today. The scant mention of Wu's work from textbooks, research articles, and other accounts of DNA sequencing calls into question how scientific collective memory forms. This alternative history seeks to understand why a key figure in nucleic acid sequence analysis has remained less visibly connected or peripheral to solidifying narratives about the history of DNA sequencing. The study resists predictable dismissals of Wu's work in order to seriously examine the formation of his nucleic acid sequence analysis research program and how he shared his knowledge of sequencing during a period of rapid advancement in the field. An analysis of Wu's work on sequencing the cohesive ends of lambda bacteriophage in the 1960s and 1970s exemplifies how a variety of individuals and groups attempted to develop protocol for sequencing the order of nucleotide base pairs comprising DNA. This historical examination of the sociality of scientific research suggests a way to understand how Wu and others contributed to the very collective memory of DNA sequencing that Wu eventually tried to repair. The study of Wu, who was a Chinese immigrant to the United States, provides a foundation for further critical scholarship on the heterogeneous histories of Asian American bioscientists, the sociality of their scientific works, and how the resulting knowledge produced is preserved, if not evenly, in a scientific field's collective memory. PMID:24565976

  7. The genome-wide DNA sequence specificity of the anti-tumour drug bleomycin in human cells.

    Science.gov (United States)

    Murray, Vincent; Chen, Jon K; Tanaka, Mark M

    2016-07-01

    The cancer chemotherapeutic agent, bleomycin, cleaves DNA at specific sites. For the first time, the genome-wide DNA sequence specificity of bleomycin breakage was determined in human cells. Utilising Illumina next-generation DNA sequencing techniques, over 200 million bleomycin cleavage sites were examined to elucidate the bleomycin genome-wide DNA selectivity. The genome-wide bleomycin cleavage data were analysed by four different methods to determine the cellular DNA sequence specificity of bleomycin strand breakage. For the most highly cleaved DNA sequences, the preferred site of bleomycin breakage was at 5'-GT* dinucleotide sequences (where the asterisk indicates the bleomycin cleavage site), with lesser cleavage at 5'-GC* dinucleotides. This investigation also determined longer bleomycin cleavage sequences, with preferred cleavage at 5'-GT*A and 5'- TGT* trinucleotide sequences, and 5'-TGT*A tetranucleotides. For cellular DNA, the hexanucleotide DNA sequence 5'-RTGT*AY (where R is a purine and Y is a pyrimidine) was the most highly cleaved DNA sequence. It was striking that alternating purine-pyrimidine sequences were highly cleaved by bleomycin. The highest intensity cleavage sites in cellular and purified DNA were very similar although there were some minor differences. Statistical nucleotide frequency analysis indicated a G nucleotide was present at the -3 position (relative to the cleavage site) in cellular DNA but was absent in purified DNA. PMID:27188426

  8. Sequence-specific DNA breaks produced by triplex-directed decay of iodine-125

    International Nuclear Information System (INIS)

    Triplex forming oligonucleotides (TFO) labeled with Auger emitters could be ideal vehicles to deliver radioactive-decay energy to specific DNA sequences, causing DNA breaks and, subsequently, inactivation of these sequences. To demonstrate this approach we labeled with 125I (two 125I per molecule on average) a purine-rich 38-mer which forms a stable triplex with a polypurine x polypyrimidine stretch in the human HPRT gene. Decay of 125I in the bound TFO was shown to cause sequence-specific double strand breaks (DSB) in the target HPRT sequence cloned into plasmid DNA. No sequence-specific breaks were observed if 125I-labeled TFO were not bound to the plasmid DNA. After 60 days of decay accumulation (one 125I half-life) approximately a quarter of all plasmid molecules contained sequence-specific DSB, corresponding to 0.3 site-specific DSB per decay. Sequencing gel analysis shows that the DNA breaks are distributed within a few bases of the maxima at those bases opposite to the positions of 125I in the TFO. (orig.)

  9. Sequence-specific DNA breaks produced by triplex-directed decay of iodine-125

    Energy Technology Data Exchange (ETDEWEB)

    Panyutin, I.G. [National Institutes of Health, Bethesda, MD (United States). Dept. of Nuclear Medicine; Neumann, R.D. [National Institutes of Health, Bethesda, MD (United States). Dept. of Nuclear Medicine

    1996-12-31

    Triplex forming oligonucleotides (TFO) labeled with Auger emitters could be ideal vehicles to deliver radioactive-decay energy to specific DNA sequences, causing DNA breaks and, subsequently, inactivation of these sequences. To demonstrate this approach we labeled with {sup 125}I (two {sup 125}I per molecule on average) a purine-rich 38-mer which forms a stable triplex with a polypurine x polypyrimidine stretch in the human HPRT gene. Decay of {sup 125}I in the bound TFO was shown to cause sequence-specific double strand breaks (DSB) in the target HPRT sequence cloned into plasmid DNA. No sequence-specific breaks were observed if {sup 125}I-labeled TFO were not bound to the plasmid DNA. After 60 days of decay accumulation (one {sup 125}I half-life) approximately a quarter of all plasmid molecules contained sequence-specific DSB, corresponding to 0.3 site-specific DSB per decay. Sequencing gel analysis shows that the DNA breaks are distributed within a few bases of the maxima at those bases opposite to the positions of {sup 125}I in the TFO. (orig.).

  10. Genetic alterations of hepatocellular carcinoma by random amplified polymorphic DNA analysis and cloning sequencing of tumor differential DNA fragment

    Institute of Scientific and Technical Information of China (English)

    Zhi-Hong Xian; Wen-Ming Cong; Shu-Hui Zhang; Meng-Chao Wu

    2005-01-01

    AIM: To study the genetic alterations and their association with clinicopathological characteristics of hepatocellular carcinoma (HCC), and to find the tumor related DNA fragments.METHODS: DNA isolated from tumors and corresponding noncancerous liver tissues of 56 HCC patients was amplified by random amplified polymorphic DNA (RAPD)with 10 random 10-mer arbitrary primers. The RAPD bands showing obvious differences in tumor tissue DNA corresponding to that of normal tissue were separated,purified, cloned and sequenced. DNA sequences were analyzed and compared with GenBank data.RESULTS: A total of 56 cases of HCC were demonstrated to have genetic alterations, which were detected by at least one primer. The detestability of genetic alterations ranged from 20% to 70% in each case, and 17.9% to 50% in each primer. Serum HBV infection, tumor size,histological grade, tumor capsule, as well as tumor intrahepatic metastasis, might be correlated with genetic alterations on certain primers. A band with a higher intensity of 480 bp or so amplified fragments in tumor DNA relative to normal DNA could be seen in 27 of 56 tumor samples using primer 4. Sequence analysis of these fragments showed 91% homology with Homo sapiens double homeobox protein DUX10 gene.CONCLUSION: Genetic alterations are a frequent event in HCC, and tumor related DNA fragments have been found in this study, which may be associated with hepatocarcinogenesis. RAPD is an effective method for the identification and analysis of genetic alterations in HCC, and may provide new information for further evaluating the molecular mechanism of hepatocarcinogenesis.

  11. Introduction of restriction enzyme sites in protein-coding DNA sequences by site-specific mutagenesis not affecting the amino acid sequence: a computer program.

    OpenAIRE

    Arentzen, R; Ripka, W. C.

    1984-01-01

    Structure/function relationship studies of proteins are greatly facilitated by recombinant DNA technology which allows specific amino acid mutations to be made at the DNA sequence level by site-specific mutagenesis employing synthetic oligonucleotides. This technique has been successfully used to alter one or two amino acids in a protein. Replacement of existing DNA sequence coding for several amino acids with new synthetic DNA fragments would be facilitated by the presence of unique restrict...

  12. DNA Sequence Duplication in Rhodobacter sphaeroides 2.4.1: Evidence of an Ancient Partnership between Chromosomes I and II†

    OpenAIRE

    Choudhary, Madhusudan; Fu, Yun-Xin; Mackenzie, Chris; Kaplan, Samuel

    2004-01-01

    The complex genome of Rhodobacter sphaeroides 2.4.1, composed of chromosomes I (CI) and II (CII), has been sequenced and assembled. We present data demonstrating that the R. sphaeroides genome possesses an extensive amount of exact DNA sequence duplication, 111 kb or ∼2.7% of the total chromosomal DNA. The chromosomal DNA sequence duplications were aligned to each other by using MUMmer. Frequency and size distribution analyses of the exact DNA duplications revealed that the interchromosomal d...

  13. Discovery and genotyping of existing and induced DNA sequence variation in potato

    NARCIS (Netherlands)

    Uitdewilligen, J.G.A.M.L.

    2012-01-01

    In this thesis natural and induced DNA sequence diversity in potato (Solanum tuberosum) for use in marker-trait analysis and potato breeding is assessed. The study addresses the challenges of reliable, high-throughput identification and genotyping of sequence variants in existing tetraploid potato c

  14. Identification of Rhizoctonia solani associated with soybean in Brazil by rDNA-ITS sequences

    Directory of Open Access Journals (Sweden)

    Fenille Roseli C.

    2003-01-01

    Full Text Available The aim of this study was to identify isolates of Rhizoctonia solani causing hypocotyl rot and foliar blight in soybean (Glycine max in Brazil by the nucleotide sequences of ITS-5.8S regions of rDNA. The 5.8S rDNA gene sequence (155 bp was highly conserved among all isolates but differences in length and nucleotide sequence of the ITS1 and ITS2 regions were observed between soybean isolates and AG testers. The similarity of the nucleotide sequence among AG-1 IA isolates, causing foliar blight, was 95.1-100% and 98.5-100% in the ITS1 and ITS2 regions, respectively. The nucleotide sequence similarity among subgroups IA, IB and IC ranged from 84.3 to 89% in ITS1 and from 93.3 to 95.6% in ITS2. Nucleotide sequence similarity of 99.1% and 99.3-100% for ITS1 and ITS2, respectively, was observed between AG-4 soybean isolates causing hypocotyl rots and the AG-4 HGI tester. The similarity of the nucleotide sequence of the ITS-5.8S rDNA region confirmed that the R. solani Brazilian isolates causing foliar blight are AG-1 IA and isolates causing hypocotyl rot symptoms are AG-4 HGI. The ITS-5.8S rDNA sequence was not determinant for the identification of the AG-2-2 IIIB R. solani soybean isolate.

  15. Differential DNA and RNA sequence discrimination by PNA having charged side chains.

    Science.gov (United States)

    De Costa, N Tilani S; Heemstra, Jennifer M

    2014-05-15

    PNA sequences modified with charged side chains were evaluated for base-pairing sequence selectivity under physiological conditions. PNA having negatively charged aspartic acid side chains shows higher selectivity with RNA, while PNA having positively charged lysine side chains shows higher selectivity with DNA. These observations provide insight into the binding selectivity of modified PNA in antisense and antigene applications. PMID:24731279

  16. Open source tools to exploit DNA sequence data from livestock species

    Science.gov (United States)

    Next-Generation Sequencing (NGS) is a recent technological development that allows researchers to rapidly determine the DNA sequence of an individual. The decrease in cost of NGS has brought the technology into the realm of practical applications in livestock genomics, where it can be used to genera...

  17. A likelihood ratio test for species membership based on DNA sequence data

    DEFF Research Database (Denmark)

    Matz, Mikhail V.; Nielsen, Rasmus

    2005-01-01

    sequence is a member of an a priori specified species. We investigate the performance of the test using coalescence simulations, as well as using the real data from butterflies and frogs representing two kinds of challenge for DNA barcoding: extremely low and extremely high levels of sequence variability....

  18. Complete DNA sequence of the linear mitochondrial genome of the pathogenic yeast Candida parapsilosis

    DEFF Research Database (Denmark)

    Nosek, J.; Novotna, M.; Hlavatovicova, Z.;

    2004-01-01

    The complete sequence of the mitochondrial DNA of the opportunistic yeast pathogen Candida parapsilosis was determined. The mitochondrial genome is represented by linear DNA molecules terminating with tandem repeats of a 738-bp unit. The number of repeats varies, thus generating a population...... of linear DNA molecules that are heterogeneous in size. The length of the shortest molecules is 30,922 bp, whereas the longer molecules have expanded terminal tandem arrays (n x 738 bp). The mitochondrial genome is highly compact., with less than 8% of the sequence corresponding to non-coding intergenic...

  19. Cloning, nucleotide sequence, and regulatory analysis of the Lactococcus lactis dnaJ gene.

    OpenAIRE

    van Asseldonk, M; Simons, A.; Visser, H.; DE VOS W.M.; Simons, G

    1993-01-01

    The dnaJ gene of Lactococcus lactis was isolated from a genomic library of L. lactis NIZO R5 and cloned into pUC19. Nucleotide sequencing revealed an open reading frame of 1,137 bp in length, encoding a protein of 379 amino acids. The deduced amino acid sequence showed homology to the DnaJ proteins of Escherichia coli, Mycobacterium tuberculosis, Bacillus subtilis, and Clostridium acetobutylicum. The level of the dnaJ monocistronic mRNA increased approximately threefold after heat shock. The ...

  20. Strong physical constraints on sequence-specific target location by proteins on DNA molecules

    DEFF Research Database (Denmark)

    Flyvbjerg, H.; Keatch, S.A.; Dryden, D.T.F

    2006-01-01

    Sequence-specific binding to DNA in the presence of competing non-sequence-specific ligands is a problem faced by proteins in all organisms. It is akin to the problem of parking a truck at a loading bay by the side of a road in the presence of cars parked at random along the road. Cars even...... required for function rather than the more commonly measured physical footprint. Assaying the complex type I restriction enzyme, EcoKI, gives an activity footprint of similar to 66 bp for ATP hydrolysis and 300 bp for the DNA cleavage function which is intimately linked with translocation of DNA by Eco...

  1. Bisulfite sequencing reveals that Aspergillus flavus holds a hollow in DNA methylation

    DEFF Research Database (Denmark)

    Liu, Si-Yang; Lin, Jian-Qing; Wu, Hong-Long;

    2012-01-01

    Aspergillus flavus first gained scientific attention for its production of aflatoxin. The underlying regulation of aflatoxin biosynthesis has been serving as a theoretical model for biosynthesis of other microbial secondary metabolites. Nevertheless, for several decades, the DNA methylation status......, one of the important epigenomic modifications involved in gene regulation, in A. flavus remains to be controversial. Here, we applied bisulfite sequencing in conjunction with a biological replicate strategy to investigate the DNA methylation profiling of A. flavus genome. Both the bisulfite sequencing...... detection in species with low DNA methylation may serve as a reference for later scientific investigations in other hypomethylated species....

  2. A database of mitochondrial DNA hypervariable regions I and II sequences of individuals from Slovakia.

    Science.gov (United States)

    Lehocký, Ivan; Baldovic, Marian; Kádasi, Ludevít; Metspalu, Ene

    2008-09-01

    In order to identify polymorphic positions and to determine their frequencies and the frequency of haplotypes in the human mitochondrial control region, two hypervariable regions (HV1 and HV2) of the mitochondrial DNA (mtDNA) of 374 unrelated individuals from Slovakia were amplified and sequenced. Sequence comparison led to the identification of 284 mitochondrial lineages as defined by 163 variable sites. Genetic diversity (GD) was estimated at 0.997 and the probability of two randomly selected individuals from population having identical mtDNA types (random match probability, RMP) for the both regions is 0.60%. PMID:19083829

  3. Cell-free DNA next-generation sequencing in pancreatobiliary carcinomas

    OpenAIRE

    Zill, Oliver A.; Greene, Claire; Sebisanovic, Dragan; Siew, LaiMun; Leng, Jim; Vu, Mary; HENDIFAR, ANDREW E.; Zhen WANG; Atreya, Chloe E.; Kelley, Robin K.; Van Loon, Katherine; Ko, Andrew H.; Tempero, Margaret A.; Bivona, Trever G; Munster, Pamela N.

    2015-01-01

    Patients with pancreatic and biliary carcinomas lack personalized treatment options, in part because biopsies are often inadequate for molecular characterization. Cell-free DNA (cfDNA) sequencing may enable a precision oncology approach in this setting. We attempted to prospectively analyze 54 genes in tumor and cfDNA for 26 patients. Tumor sequencing failed in nine patients (35%). In the remaining 17, 90.3% (95% CI: 73.1–97.5%) of mutations detected in tumor biopsies were also detected in cf...

  4. Nanopores in suspended WS2 membranes for DNA sequencing

    Science.gov (United States)

    Danda, Gopinath; Masih Das, Paul; Chou, Yung-Chien; Mlack, Jerome; Naylor, Carl; Perea-Lopez, Nestor; Lin, Zhong; Fulton, Laura Beth; Terrones, Mauricio; Johnson, A. T. Charlie; Drndic, Marija

    Recent advances in solid-state nanopore sensor systems for DNA detection and analysis have been supported by using increasingly thinner materials to the point of utilizing atomically thin two-dimensional materials such as graphene and MoS2. However, these materials still have issues with pore wettability and signal-to-noise ratios displayed in DNA translocation measurements. Recently, the fabrication and operation of nanopores in MoS2 have been demonstrated, but the wetting properties and signal-to-noise ratios of transition metal dichalcogenides are yet to be understood and further improved. Here we fabricate suspended WS2 nanopore devices with sub-10 nm pore diameters using a novel nanomaterial transfer method and TEM nanosculpting to study and better understand nanopore wetting properties and performance in DNA translocation measurements.

  5. Sequence-specific DNA purification by triplex affinity capture

    Energy Technology Data Exchange (ETDEWEB)

    Ito, Takashi; Smith, C.L.; Cantor, C.R. (Lawrence Berkeley Lab., CA (United States))

    1992-01-15

    A DNA isolation procedure was developed by using triple-helix formation and magnetic separation. In this procedure, target DNA is captured by a biotinylated oligonucleotide via intermolecular triplex formation, bound to streptavidin-coated magnetic beads, and recovered in double-stranded form by elution with a mild alkaline buffer that destabilizes the triple helix. The effectiveness of the procedure was demonstrated by a model experiment with an artificially reconstructed library and, also, by the isolation of (dT-dC){sub n}{center dot}(dG-dA){sub n} dinucleotide repeats from a human genomic library. This procedure provides a prototype for other triplex mediated DNA isolation technologies.

  6. Oxidation by DNA Charge Transport Damages Conserved Sequence Block II, a Regulatory Element in Mitochondrial DNA

    OpenAIRE

    Merino, Edward J.; Barton, Jacqueline K.

    2007-01-01

    Sites of oxidative damage in mitochondrial DNA have been identified on the basis of DNA-mediated charge transport. Our goal is to understand which sites in mitochondrial DNA are prone to oxidation at long range and whether such oxidative damage correlates with cancerous transformation. Here we show that a primer extension reaction can be used to monitor directly oxidative damage to authentic mitochondrial DNA through photoreactions with a rhodium intercalator. The complex [Rh(phi)_2bpy]Cl_3 (...

  7. Sequence Dependent Interactions Between DNA and Single-Walled Carbon Nanotubes

    Science.gov (United States)

    Roxbury, Daniel

    It is known that single-stranded DNA adopts a helical wrap around a single-walled carbon nanotube (SWCNT), forming a water-dispersible hybrid molecule. The ability to sort mixtures of SWCNTs based on chirality (electronic species) has recently been demonstrated using special short DNA sequences that recognize certain matching SWCNTs of specific chirality. This thesis investigates the intricacies of DNA-SWCNT sequence-specific interactions through both experimental and molecular simulation studies. The DNA-SWCNT binding strengths were experimentally quantified by studying the kinetics of DNA replacement by a surfactant on the surface of particular SWCNTs. Recognition ability was found to correlate strongly with measured binding strength, e.g. DNA sequence (TAT)4 was found to bind 20 times stronger to the (6,5)-SWCNT than sequence (TAT)4T. Next, using replica exchange molecular dynamics (REMD) simulations, equilibrium structures formed by (a) single-strands and (b) multiple-strands of 12-mer oligonucleotides adsorbed on various SWCNTs were explored. A number of structural motifs were discovered in which the DNA strand wraps around the SWCNT and 'stitches' to itself via hydrogen bonding. Great variability among equilibrium structures was observed and shown to be directly influenced by DNA sequence and SWCNT type. For example, the (6,5)-SWCNT DNA recognition sequence, (TAT)4, was found to wrap in a tight single-stranded right-handed helical conformation. In contrast, DNA sequence T12 forms a beta-barrel left-handed structure on the same SWCNT. These are the first theoretical indications that DNA-based SWCNT selectivity can arise on a molecular level. In a biomedical collaboration with the Mayo Clinic, pathways for DNA-SWCNT internalization into healthy human endothelial cells were explored. Through absorbance spectroscopy, TEM imaging, and confocal fluorescence microscopy, we showed that intracellular concentrations of SWCNTs far exceeded those of the incubation

  8. DNA sequence and analysis of human chromosome 18.

    Science.gov (United States)

    Nusbaum, Chad; Zody, Michael C; Borowsky, Mark L; Kamal, Michael; Kodira, Chinnappa D; Taylor, Todd D; Whittaker, Charles A; Chang, Jean L; Cuomo, Christina A; Dewar, Ken; FitzGerald, Michael G; Yang, Xiaoping; Abouelleil, Amr; Allen, Nicole R; Anderson, Scott; Bloom, Toby; Bugalter, Boris; Butler, Jonathan; Cook, April; DeCaprio, David; Engels, Reinhard; Garber, Manuel; Gnirke, Andreas; Hafez, Nabil; Hall, Jennifer L; Norman, Catherine Hosage; Itoh, Takehiko; Jaffe, David B; Kuroki, Yoko; Lehoczky, Jessica; Lui, Annie; Macdonald, Pendexter; Mauceli, Evan; Mikkelsen, Tarjei S; Naylor, Jerome W; Nicol, Robert; Nguyen, Cindy; Noguchi, Hideki; O'Leary, Sinéad B; O'Neill, Keith; Piqani, Bruno; Smith, Cherylyn L; Talamas, Jessica A; Topham, Kerri; Totoki, Yasushi; Toyoda, Atsushi; Wain, Hester M; Young, Sarah K; Zeng, Qiandong; Zimmer, Andrew R; Fujiyama, Asao; Hattori, Masahira; Birren, Bruce W; Sakaki, Yoshiyuki; Lander, Eric S

    2005-09-22

    Chromosome 18 appears to have the lowest gene density of any human chromosome and is one of only three chromosomes for which trisomic individuals survive to term. There are also a number of genetic disorders stemming from chromosome 18 trisomy and aneuploidy. Here we report the finished sequence and gene annotation of human chromosome 18, which will allow a better understanding of the normal and disease biology of this chromosome. Despite the low density of protein-coding genes on chromosome 18, we find that the proportion of non-protein-coding sequences evolutionarily conserved among mammals is close to the genome-wide average. Extending this analysis to the entire human genome, we find that the density of conserved non-protein-coding sequences is largely uncorrelated with gene density. This has important implications for the nature and roles of non-protein-coding sequence elements. PMID:16177791

  9. A new approach for detecting riboswitches in DNA sequences

    OpenAIRE

    Havill, Jessen T.; Bhatiya, Chinmoy; Johnson, Steven M.; Sheets, Joseph D.; Thompson, Jeffrey S.

    2014-01-01

    Motivation: Riboswitches are short sequences of messenger RNA that can change their structural conformation to regulate the expression of adjacent genes. Computational prediction of putative riboswitches can provide direction to molecular biologists studying riboswitch-mediated gene expression.

  10. DNA sequencing leads to genomics progress in China

    Institute of Scientific and Technical Information of China (English)

    WU JiaYan; XIAO JingFa; ZHANG RuoSi; YU Jun

    2011-01-01

    1 Science in the large-scale sequencing era Ten years ago,the first draft sequence assembly of the human genome was completed [1],bringing biomedical research one-step closer toward the goal of revolutionizing diagnosis,prevention,and treatment of human diseases.Recently,journalists from the journal Nature surveyed more than 1000 life scientists regarding this laudable aim [2],obtaining substantially negative responses [3].However,almost all of those surveyed had been influenced,in one way or another,by the availability of the human genome sequence,and they also agreed with the notion that the "sequence is the start." The complexity of genome biology and almost every aspect of human biology is far greater than previously thought [4].

  11. A New Revised DNA Cramp Tool Based Approach of Chopping DNA Repetitive and Non-Repetitive Genome Sequences

    Directory of Open Access Journals (Sweden)

    V.Hari Prasad

    2012-11-01

    Full Text Available In vogue tremendous amount of data generated day by day by the living organism of genetic sequences and its accumulation in database, their size is growing in an exponential manner. Due to excessive storage of DNA sequences in public databases like NCBI, EMBL and DDBJ archival maintenance is tedious task. Transmission of information from one place to another place in network management systems is also a critical task. So To improve the efficiency and to reduce the overhead of the database need of compression arises in database optimization. In this connection different techniques were bloomed, but achieved results are not bountiful. Many classical algorithms are fails to compress genetic sequences due to the specificity of text encoded in dna and few of the existing techniques achieved positive results. DNA is repetitive and non repetitive in nature. Our proposed technique DNACRAMP is applicable on repetitive and non repetitive sequences of dna and it yields better compression ratio in terms of bits per bases. This is compared with existing techniques and observed that our one is the optimum technique and compression results are on par with existing techniques.

  12. Mixed-Sequence Recognition of Double-Stranded DNA Using Enzymatically Stable Phosphorothioate Invader Probes

    Directory of Open Access Journals (Sweden)

    Brooke A. Anderson

    2015-07-01

    Full Text Available Development of probes that allow for sequence-unrestricted recognition of double-stranded DNA (dsDNA continues to attract much attention due to the prospect for molecular tools that enable detection, regulation, and manipulation of genes. We have recently introduced so-called Invader probes as alternatives to more established approaches such as triplex-forming oligonucleotides, peptide nucleic acids and polyamides. These short DNA duplexes are activated for dsDNA recognition by installment of +1 interstrand zippers of intercalator-functionalized nucleotides such as 2′-N-(pyren-1-ylmethyl-2′-N-methyl-2′-aminouridine and 2′-O-(pyren-1-ylmethyluridine, which results in violation of the nearest neighbor exclusion principle and duplex destabilization. The individual probes strands have high affinity toward complementary DNA strands, which generates the driving force for recognition of mixed-sequence dsDNA regions. In the present article, we characterize Invader probes that are based on phosphorothioate backbones (PS-DNA Invaders. The change from the regular phosphodiester backbone furnishes Invader probes that are much more stable to nucleolytic degradation, while displaying acceptable dsDNA-recognition efficiency. PS-DNA Invader probes therefore present themselves as interesting probes for dsDNA-targeting applications in cellular environments and living organisms.

  13. Mixed-Sequence Recognition of Double-Stranded DNA Using Enzymatically Stable Phosphorothioate Invader Probes.

    Science.gov (United States)

    Anderson, Brooke A; Karmakar, Saswata; Hrdlicka, Patrick J

    2015-01-01

    Development of probes that allow for sequence-unrestricted recognition of double-stranded DNA (dsDNA) continues to attract much attention due to the prospect for molecular tools that enable detection, regulation, and manipulation of genes. We have recently introduced so-called Invader probes as alternatives to more established approaches such as triplex-forming oligonucleotides, peptide nucleic acids and polyamides. These short DNA duplexes are activated for dsDNA recognition by installment of +1 interstrand zippers of intercalator-functionalized nucleotides such as 2'-N-(pyren-1-yl)methyl-2'-N-methyl-2'-aminouridine and 2'-O-(pyren-1-yl)methyluridine, which results in violation of the nearest neighbor exclusion principle and duplex destabilization. The individual probes strands have high affinity toward complementary DNA strands, which generates the driving force for recognition of mixed-sequence dsDNA regions. In the present article, we characterize Invader probes that are based on phosphorothioate backbones (PS-DNA Invaders). The change from the regular phosphodiester backbone furnishes Invader probes that are much more stable to nucleolytic degradation, while displaying acceptable dsDNA-recognition efficiency. PS-DNA Invader probes therefore present themselves as interesting probes for dsDNA-targeting applications in cellular environments and living organisms. PMID:26230684

  14. Identification of Chinese Herbs Using a Sequencing-Free Nanostructured Electrochemical DNA Biosensor

    Directory of Open Access Journals (Sweden)

    Yan Lei

    2015-11-01

    Full Text Available Due to the nearly identical phenotypes and chemical constituents, it is often very challenging to accurately differentiate diverse species of a Chinese herbal genus. Although technologies including DNA barcoding have been introduced to help address this problem, they are generally time-consuming and require expensive sequencing. Herein, we present a simple sequencing-free electrochemical biosensor, which enables easy differentiation between two closely related Fritillaria species. To improve its differentiation capability using trace amounts of DNA sample available from herbal extracts, a stepwise electrochemical deposition of reduced graphene oxide (RGO and gold nanoparticles (AuNPs was adopted to engineer a synergistic nanostructured sensing interface. By using such a nanofeatured electrochemical DNA (E-DNA biosensor, two Chinese herbal species of Fritillaria (F. thunbergii and F. cirrhosa were successfully discriminated at the DNA level, because a fragment of 16-mer sequence at the spacer region of the 5S-rRNA only exists in F. thunbergii. This E-DNA sensor was capable of identifying the target sequence in the range from 100 fM to 10 nM, and a detection limit as low as 11.7 fM (S/N = 3 was obtained. Importantly, this sensor was applied to detect the unique fragment of the PCR products amplified from F. thunbergii and F. cirrhosa, respectively. We anticipate that such a direct, sequencing-free sensing mode will ultimately pave the way towards a new generation of herb-identification strategies.

  15. Unique nucleotide sequence-guided assembly of repetitive DNA parts for synthetic biology applications

    Energy Technology Data Exchange (ETDEWEB)

    Torella, JP; Lienert, F; Boehm, CR; Chen, JH; Way, JC; Silver, PA

    2014-08-07

    Recombination-based DNA construction methods, such as Gibson assembly, have made it possible to easily and simultaneously assemble multiple DNA parts, and they hold promise for the development and optimization of metabolic pathways and functional genetic circuits. Over time, however, these pathways and circuits have become more complex, and the increasing need for standardization and insulation of genetic parts has resulted in sequence redundancies-for example, repeated terminator and insulator sequences-that complicate recombination-based assembly. We and others have recently developed DNA assembly methods, which we refer to collectively as unique nucleotide sequence (UNS)-guided assembly, in which individual DNA parts are flanked with UNSs to facilitate the ordered, recombination-based assembly of repetitive sequences. Here we present a detailed protocol for UNS-guided assembly that enables researchers to convert multiple DNA parts into sequenced, correctly assembled constructs, or into high-quality combinatorial libraries in only 2-3 d. If the DNA parts must be generated from scratch, an additional 2-5 d are necessary. This protocol requires no specialized equipment and can easily be implemented by a student with experience in basic cloning techniques.

  16. Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments.

    Science.gov (United States)

    Dabney, Jesse; Knapp, Michael; Glocke, Isabelle; Gansauge, Marie-Theres; Weihmann, Antje; Nickel, Birgit; Valdiosera, Cristina; García, Nuria; Pääbo, Svante; Arsuaga, Juan-Luis; Meyer, Matthias

    2013-09-24

    Although an inverse relationship is expected in ancient DNA samples between the number of surviving DNA fragments and their length, ancient DNA sequencing libraries are strikingly deficient in molecules shorter than 40 bp. We find that a loss of short molecules can occur during DNA extraction and present an improved silica-based extraction protocol that enables their efficient retrieval. In combination with single-stranded DNA library preparation, this method enabled us to reconstruct the mitochondrial genome sequence from a Middle Pleistocene cave bear (Ursus deningeri) bone excavated at Sima de los Huesos in the Sierra de Atapuerca, Spain. Phylogenetic reconstructions indicate that the U. deningeri sequence forms an early diverging sister lineage to all Western European Late Pleistocene cave bears. Our results prove that authentic ancient DNA can be preserved for hundreds of thousand years outside of permafrost. Moreover, the techniques presented enable the retrieval of phylogenetically informative sequences from samples in which virtually all DNA is diminished to fragments shorter than 50 bp. PMID:24019490

  17. Cloning and sequencing of a DNA fragment encoding N37 apoptotic peptide derived from p53

    Institute of Scientific and Technical Information of China (English)

    Yan-xia Bai; Qing-yong Ma; Guang-xiao Yang

    2009-01-01

    Objective It was reported that p53 apoptotic peptide (N37) could inhibit p73 gene through being bound with iASPP, which could induce tumor cell apoptosis. To further explore the function of N37, we constructed the cloning plasmid of DNA fragment encoding p53 (N37) apoptotic peptide by using DNA synthesis and molecular biology methods. Methods According to human p53 sequence from the GenBank database, the primer of p53(N37) gene was designed using Primer V7.0 software. The DNA fragment encoding p53 (N37) apoptotic peptide was amplified by using self-complementation polymerase chain reaction (PCR) method and cloned into the pGEM-T Easy vector. The constructed plasmid was confirmed by endonuclease analysis and sequencing. Results The insertion of objective DNA fragment was confirmed by plasmid DNA enzyme spectrum analysis, p53 (N37) gene was successfully synthesized chemically in vitro. The sequencing result of positive clone was completely identical to the human p53(N37) sequence in GenBank using BLAST software (http://www. ncbi. him. nih. gov/cgi-bin /BLASTn). Conclusion The cloning of DNA fragment encoding p53(N37) apoptotic peptide was constructed by using DNA synthesis and pGEM-T Easy cloning methods. With the constructed plasmid, we could further investigate the function of N37 peptide.

  18. Multiple gene sequence analysis using genes of the bacterial DNA repair pathway

    Directory of Open Access Journals (Sweden)

    Miguel Rotelok Neto

    2015-06-01

    Full Text Available The ability to recognize and repair abnormal DNA structures is common to all forms of life. Physiological studies and genomic sequencing of a variety of bacterial species have identified an incredible diversity of DNA repair pathways. Despite the amount of available genes in public database, the usual method to place genomes in a taxonomic context is based mainly on the 16S rRNA or housekeeping genes. Thus, the relationships among genomes remain poorly understood. In this work, an approach of multiple gene sequence analysis based on genes of DNA repair pathway was used to compare bacterial genomes. Housekeeping and DNA repair genes were searched in 872 completely sequenced bacterial genomes. Seven DNA repair and housekeeping genes from distinct metabolic pathways were selected, aligned, edited and concatenated head-to-tail to form a super-gene. Results showed that the multiple gene sequence analysis using DNA repair genes had better resolution at class level than the housekeeping genes. As housekeeping genes, the DNA repair genes were advantageous to separate bacterial groups at low taxonomic levels and also sensitive to genes derived from horizontal transfer.

  19. Phylogeny and genetic diversity of Bridgeoporus nobilissimus inferred using mitochondrial and nuclear rDNA sequences

    Science.gov (United States)

    Redberg, G.L.; Hibbett, D.S.; Ammirati, J.F., Jr.; Rodriguez, R.J.

    2003-01-01

    The genetic diversity and phylogeny of Bridgeoporus nobilissimus have been analyzed. DNA was extracted from spores collected from individual fruiting bodies representing six geographically distinct populations in Oregon and Washington. Spore samples collected contained low levels of bacteria, yeast and a filamentous fungal species. Using taxon-specific PCR primers, it was possible to discriminate among rDNA from bacteria, yeast, a filamentous associate and B. nobilissimus. Nuclear rDNA internal transcribed spacer (ITS) region sequences of B. nobilissimus were compared among individuals representing six populations and were found to have less than 2% variation. These sequences also were used to design dual and nested PCR primers for B. nobilissimus-specific amplification. Mitochondrial small-subunit rDNA sequences were used in a phylogenetic analysis that placed B. nobilissimus in the hymenochaetoid clade, where it was associated with Oxyporus and Schizopora.

  20. Sequence-selective targeting of duplex DNA by peptide nucleic acids

    DEFF Research Database (Denmark)

    Nielsen, Peter E

    2010-01-01

    nucleic acid (PNA) can recognize duplex DNA with high sequence specificity and affinity in triplex, duplex and double-duplex invasive modes or non-invasive triplex modes. Novel PNA modification has improved the affinity for DNA recognition via duplex invasion, double-duplex invasion and triplex......Sequence-selective gene targeting constitutes an attractive drug-discovery approach for genetic therapy, with the aim of reducing or enhancing the activity of specific genes at the transcriptional level, or as part of a methodology for targeted gene repair. The pseudopeptide DNA mimic peptide...... recognition considerably. Such modifications have also resulted in new approaches to targeted gene repair and sequence-selective double-strand cleavage of genomic DNA....

  1. A Model of Sequence Dependent Rna-Polymerase Diffusion Along Dna

    CERN Document Server

    Barbi, M; Popkov, V; Salerno, M; Barbi, Maria; Place, Christophe; Popkov, Vladislav; Salerno, Mario

    2001-01-01

    We introduce a probabilistic model for the RNA-polymerase sliding motion along DNA during the promoter search. The model accounts for possible effects due to sequence-dependent interactions between the nonspecific DNA and the enzyme. We focus on T7 RNA-polymerase and exploit the available information about its interaction at the promoter site in order to investigate the influence of bacteriophage T7 DNA sequence on the dynamics of the sliding process. Hydrogen bonds in the major groove are used as the main sequence-dependent interaction between the RNA-polymerase and the DNA. The resulting dynamical properties and the possibility of an experimental validation are discussed in details. We show that, while at large times the process reaches a pure diffusive regime, it initially displays a sub-diffusive behavior. The crossover from anomalous to normal diffusion may occur at times large enough to be of biological interest.

  2. Statistical Algorithms for Long DNA Sequences: Oligonucleotide Distributions and Homogeneity Maps

    Directory of Open Access Journals (Sweden)

    P. Katsaloulis

    2005-01-01

    Full Text Available The statistical properties of oligonucleotide appearances within long DNA sequences often reveal useful characteristics of the corresponding DNA areas. Two algorithms to statistically analyze oligonucleotide appearances within long DNA sequences in genome banks are presented. The first algorithm determines statistical indices for arbitrary length oligonucleotides within arbitrary length DNA sequences. The critical exponent μ of the distance distribution between consecutive occurrences of the same oligonucleotide is calculated and its value is shown to characterize the functionality of the oligonucleotide. The second algorithm searches for areas with variable homogeneity, based on the density of oligonucleotides. The two algorithms have been applied to representative eucaryotes (the animal Mus musculusand the plant Arabidopsis thaliana and interesting results were obtained, confirmed by biological observations. All programs are open source and publicly available on our web site.

  3. 5'-end sequences of budding yeast full-length cDNA clones and quality scores - Budding yeast cDNA sequencing project | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available Budding yeast cDNA sequencing project 5'-end sequences of budding yeast full-length cDNA clones and quality ...scores Data detail Data name 5'-end sequences of budding yeast full-length cDNA clones and quality scores De...from the budding yeast full-length cDNA library by the vector-capping method, the sequence quality score gen...s accession only. Sequence 5'-end sequence data of budding yeast full-length cDNA clones. FASTA format. Quality Phred's quality... Update History of This Database Site Policy | Contact Us 5'-end sequences of budding yeast full-length cDNA clones and quality

  4. Plant or fungal sequences? An alternative optimized PCR protocol to avoid ITS (nrDNA) misamplification

    OpenAIRE

    Vitor Fernandes Oliveira de Miranda; Vanderlei Geraldo Martins; Antonio Furlan; Maurício Bacci Jr.

    2010-01-01

    The nuclear ribosomal DNA internal transcribed spacers (ITS1 and ITS2) from leaves of Drosera (Droseraceae) were amplified using "universal" primers. The analysis of the products demonstrated most samples were a molecular mixture as a result of unsuccessful and non-specific amplifications. Among the obtained sequences, two were from Basidiomycota fungi. Homologous sequences of Basidiomycota were obtained from GenBank database and added to a data set with sequences from Drosera leaves. Parsimo...

  5. WebGMAP: a web service for mapping and aligning cDNA sequences to genomes

    OpenAIRE

    Liang, Chun; Liu, Lin; Ji, Guoli

    2009-01-01

    The genomes of thousands of organisms are being sequenced, often with accompanying sequences of cDNAs or ESTs. One of the great challenges in bioinformatics is to make these genomic sequences and genome annotations accessible in a user-friendly manner to general biologists to address interesting biological questions. We have created an open-access web service called WebGMAP (http://www.bioinfolab.org/software/webgmap) that seamlessly integrates cDNA-genome alignment tools, such as GMAP, with ...

  6. Genetic organization of a repeated DNA sequence family in the rice blast fungus.

    OpenAIRE

    Romao, J; Hamer, J E

    1992-01-01

    The fungal rice pathogen Magnaporthe grisea contains repetitive DNA sequences called MGR. We have used a DNA probe, MGR586, derived from these sequences and crosses between rice-pathogenic and non-rice-pathogenic laboratory strains of M. grisea to rapidly map genes in this organism. The rice-pathogenic strain contained 57 EcoRI restriction fragments that hybridize to the MGR586 probe; the other five non-rice-pathogenic parent strains contained a single MGR586 sequence. Genetic analysis of MGR...

  7. Human insulin genome sequence map, biochemical structure of insulin for recombinant DNA insulin.

    Science.gov (United States)

    Chakraborty, Chiranjib; Mungantiwar, Ashish A

    2003-08-01

    Insulin is a essential molecule for type I diabetes that is marketed by very few companies. It is the first molecule, which was made by recombinant technology; but the commercialization process is very difficult. Knowledge about biochemical structure of insulin and human insulin genome sequence map is pivotal to large scale manufacturing of recombinant DNA Insulin. This paper reviews human insulin genome sequence map, the amino acid sequence of porcine insulin, crystal structure of porcine insulin, insulin monomer, aggregation surfaces of insulin, conformational variation in the insulin monomer, insulin X-ray structures for recombinant DNA technology in the synthesis of human insulin in Escherichia coli. PMID:12769691

  8. Sequence-Dependent Configurational Entropy Change of DNA upon Intercalation

    Czech Academy of Sciences Publication Activity Database

    Kolář, Michal; Kubař, T.; Hobza, Pavel

    2010-01-01

    Roč. 114, č. 42 (2010), s. 13446-13454. ISSN 1520-6106 R&D Projects: GA MŠk LC512; GA ČR GA203/06/1727 Institutional research plan: CEZ:AV0Z40550506 Keywords : configurational entropy * dna...ligand binding * molecular dynamic Subject RIV: CC - Organic Chemistry Impact factor: 3.603, year: 2010

  9. Genomic DNA enrichment using sequence capture microarrays: a novel approach to discover sequence nucleotide polymorphisms (SNP in Brassica napus L.

    Directory of Open Access Journals (Sweden)

    Wayne E Clarke

    Full Text Available Targeted genomic selection methodologies, or sequence capture, allow for DNA enrichment and large-scale resequencing and characterization of natural genetic variation in species with complex genomes, such as rapeseed canola (Brassica napus L., AACC, 2n=38. The main goal of this project was to combine sequence capture with next generation sequencing (NGS to discover single nucleotide polymorphisms (SNPs in specific areas of the B. napus genome historically associated (via quantitative trait loci -QTL- analysis to traits of agronomical and nutritional importance. A 2.1 million feature sequence capture platform was designed to interrogate DNA sequence variation across 47 specific genomic regions, representing 51.2 Mb of the Brassica A and C genomes, in ten diverse rapeseed genotypes. All ten genotypes were sequenced using the 454 Life Sciences chemistry and to assess the effect of increased sequence depth, two genotypes were also sequenced using Illumina HiSeq chemistry. As a result, 589,367 potentially useful SNPs were identified. Analysis of sequence coverage indicated a four-fold increased representation of target regions, with 57% of the filtered SNPs falling within these regions. Sixty percent of discovered SNPs corresponded to transitions while 40% were transversions. Interestingly, fifty eight percent of the SNPs were found in genic regions while 42% were found in intergenic regions. Further, a high percentage of genic SNPs was found in exons (65% and 64% for the A and C genomes, respectively. Two different genotyping assays were used to validate the discovered SNPs. Validation rates ranged from 61.5% to 84% of tested SNPs, underpinning the effectiveness of this SNP discovery approach. Most importantly, the discovered SNPs were associated with agronomically important regions of the B. napus genome generating a novel data resource for research and breeding this crop species.

  10. Merging Two Strategies for Mixed-Sequence Recognition of Double-Stranded DNA: Pseudocomplementary Invader Probes.

    Science.gov (United States)

    Anderson, Brooke A; Hrdlicka, Patrick J

    2016-04-15

    The development of molecular strategies that enable recognition of specific double-stranded DNA (dsDNA) regions has been a longstanding goal as evidenced by the emergence of triplex-forming oligonucleotides, peptide nucleic acids (PNAs), minor groove binding polyamides, and-more recently-engineered proteins such as CRISPR/Cas9. Despite this progress, an unmet need remains for simple hybridization-based probes that recognize specific mixed-sequence dsDNA regions under physiological conditions. Herein, we introduce pseudocomplementary Invader probes as a step in this direction. These double-stranded probes are chimeras between pseudocomplementary DNA (pcDNA) and Invader probes, which are activated for mixed-sequence dsDNA-recognition through the introduction of pseudocomplementary base pairs comprised of 2-thiothymine and 2,6-diaminopurine, and +1 interstrand zipper arrangements of intercalator-functionalized nucleotides, respectively. We demonstrate that certain pseudocomplementary Invader probe designs result in very efficient and specific recognition of model dsDNA targets in buffers of high ionic strength. These chimeric probes, therefore, present themselves as a promising strategy for mixed-sequence recognition of dsDNA targets for applications in molecular biology and nucleic acid diagnostics. PMID:26998918

  11. Assembly of long DNA sequences using a new synthetic Escherichia coli-yeast shuttle vector.

    Science.gov (United States)

    Hou, Zheng; Zhou, Zheng; Wang, Zonglin; Xiao, Gengfu

    2016-04-01

    Synthetic biology is a newly developed field of research focused on designing and rebuilding novel biomolecular components, circuits, and networks. Synthetic biology can also help understand biological principles and engineer complex artificial metabolic systems. DNA manipulation on a large genome-wide scale is an inevitable challenge, but a necessary tool for synthetic biology. To improve the methods used for the synthesis of long DNA fragments, here we constructed a novel shuttle vector named pGF (plasmid Genome Fast) for DNA assembly in vivo. The BAC plasmid pCC1BAC, which can accommodate large DNA molecules, was chosen as the backbone. The sequence of the yeast artificial chromosome (YAC) regulatory element CEN6-ARS4 was synthesized and inserted into the plasmid to enable it to replicate in yeast. The selection sequence HIS3, obtained by polymerase chain reaction (PCR) from the plasmid pBS313, was inserted for screening. This new synthetic shuttle vector can mediate the transformation-associated recombination (TAR) assembly of large DNA fragments in yeast, and the assembled products can be transformed into Escherichia coli for further amplification. We also conducted in vivo DNA assembly using pGF and yeast homologous recombination and constructed a 31-kb long DNA sequence from the cyanophage PP genome. Our findings show that this novel shuttle vector would be a useful tool for efficient genome-scale DNA reconstruction. PMID:27113243

  12. The determination of the DNA sequence specificity of bleomycin-induced abasic sites.

    Science.gov (United States)

    Chen, Jon K; Murray, Vincent

    2016-06-01

    The DNA sequence specificity of the cancer chemotherapeutic agent, bleomycin, was determined with high precision in purified plasmid DNA using an improved technique. This improved technique involved the labelling of the 5'- and 3'-ends of DNA with different fluorescent tags, followed by simultaneous cleavage by bleomycin and capillary electrophoresis with laser-induced fluorescence. This permitted the determination of bleomycin cleavage specificity with high accuracy since end-label bias was greatly reduced. Bleomycin produces single- and double-strand breaks, abasic sites and other base damage in DNA. This high-precision method was utilised to elucidate, for the first time, the DNA sequence specificity of bleomycin-induced DNA damage at abasic sites. This was accomplished using endonuclease IV that cleaves DNA at abasic sites after bleomycin damage. It was found that bleomycin-induced abasic sites formed at 5'-GC and 5'-GT sites while bleomycin-induced phosphodiester strand breaks formed mainly at 5'-GT dinucleotides. Since bleomycin-induced abasic sites are produced in the absence of molecular oxygen, this difference in DNA sequence specificity could be important in hypoxic tumour cells. PMID:26940956

  13. Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites.

    Science.gov (United States)

    Serrao, Erik; Cherepanov, Peter; Engelman, Alan N

    2016-01-01

    Retroviruses exhibit signature integration preferences on both the local and global scales. Here, we present a detailed protocol for (1) generation of diverse libraries of retroviral integration sites using ligation-mediated PCR (LM-PCR) amplification and next-generation sequencing (NGS), (2) mapping the genomic location of each virus-host junction using BEDTools, and (3) analyzing the data for statistical relevance. Genomic DNA extracted from infected cells is fragmented by digestion with restriction enzymes or by sonication. After suitable DNA end-repair, double-stranded linkers are ligated onto the DNA ends, and semi-nested PCR is conducted using primers complementary to both the long terminal repeat (LTR) end of the virus and the ligated linker DNA. The PCR primers carry sequences required for DNA clustering during NGS, negating the requirement for separate adapter ligation. Quality control (QC) is conducted to assess DNA fragment size distribution and adapter DNA incorporation prior to NGS. Sequence output files are filtered for LTR-containing reads, and the sequences defining the LTR and the linker are cropped away. Trimmed host cell sequences are mapped to a reference genome using BLAT and are filtered for minimally 97% identity to a unique point in the reference genome. Unique integration sites are scrutinized for adjacent nucleotide (nt) sequence and distribution relative to various genomic features. Using this protocol, integration site libraries of high complexity can be constructed from genomic DNA in three days. The entire protocol that encompasses exogenous viral infection of susceptible tissue culture cells to integration site analysis can therefore be conducted in approximately one to two weeks. Recent applications of this technology pertain to longitudinal analysis of integration sites from HIV-infected patients. PMID:27023428

  14. rDNA-ITS sequence analysis of pathogens of cucumber downy mildew and cucumber powdery mildew

    Institute of Scientific and Technical Information of China (English)

    Na WANG; Yajun MA; Cuiyun YANG; Guanghui DAI; Zhezhi WANG

    2008-01-01

    To determine the pathogens of cucumber downy mildew and cucumber powdery mildew by molecular marker,we amplified and sequenced the rDNA-ITS region of the pathogens of cucumber downy mildew and cucumber powdery mildew collected from the Shanghai region.The intra-/interspecific sequence difference was analyzed by rDNA-ITS sequence.The results show that the length of rDNA-ITS1 and rDNA-ITS2 of cucumber downy mildew's pathogen was 141 bp and 406 bp,respectively,with GC contents of 41.13% in ITS1 and 46.8% (Minhang and Jinshan District,sml and sm2) or 46.55% (Pudong District,sm3) in ITS2.The rDNA-ITS sequence was intraspecific conservation.The interspecific difference was related with their kin relationship.The pathogen of cucumber downy mildew was identified as Pseudoperonospora cubensis by molecular marker.The length of rDNA-ITS1 and rDNA-ITS2 of cucumber powdery mildew's pathogen was 136 bp and 89 bp,respectively,with GC contents being 59.56% and 66.29%,and rDNA-ITS sequence being highly conservative in this study that was the same as Sphaerotheca cucurbitae.But the sequence difference between the strains in the Shanghai region in this study with S.fuliginea was 4.5%,which was identified by morphology.It is suggested that the pathogen of cucumber powdery mildew should be further clarified and determined.

  15. Sequence-specific protection of duplex DNA against restriction and methylation enzymes by pseudocomplementary PNAs

    DEFF Research Database (Denmark)

    Izvolsky, K I; Demidov, V V; Nielsen, P E; Frank-Kamenetskii, M D

    2000-01-01

    A new generation of PNAs, so-called pseudocomplementary PNAs (pcPNAs), which are able to target the designated sites on duplex DNA with mixed sequence of purines and pyrimidines via double-duplex invasion mode, has recently been introduced. It has been demonstrated that appropriate pairs of...... sequence-specific complexes with duplex DNA in a very salt-dependent manner. In accord with a strand-invasion mode of complex formation, the pcPNA binding proceeds much faster with supercoiled than with linear plasmids. The double-duplex invasion complexes selectively shield specific DNA sites from Bcl...... decameric pcPNAs block an access of RNA polymerase to the corresponding promoter. Here, we show that this type of PNAs protects selected DNA sites containing all four nucleobases from the action of restriction enzymes and DNA methyltransferases. We have found that pcPNAs as short as octamers form stable and...

  16. Sequence analysis of three mitochondrial DNA molecules reveals interesting differences among Saccharomyces yeasts

    DEFF Research Database (Denmark)

    Langkjær, Rikke Breinhold; Casaregola, S.; Ussery, David;

    2003-01-01

    The complete sequences of mitochondrial DNA ( mtDNA) from the two budding yeasts Saccharomyces castellii and Saccharomyces servazzii, consisting of 25 753 and 30 782 bp, respectively, were analysed and compared to Saccharomyces cerevisiae mtDNA. While some of the traits are very similar among...... Saccharomyces yeasts, others have highly diverged. The two mtDNAs are much more compact than that of S. cerevisiae and contain fewer introns and intergenic sequences, although they have almost the same coding potential. A few genes contain group I introns, but group II introns, otherwise found in S. cerevisiae...... mtDNA, are not present. Surprisingly, four genes (ATP6, COX2, COX3 and COB) in the mtDNA of S. servazzii contain, in total, five + 1 frameshifts. mtDNAs of S. castellii, S. servazzii and S. cerevisiae contain all genes on the same strand, except for one tRNA gene. On the other hand, the gene order is...

  17. Rapid detection and purification of sequence specific DNA binding proteins using magnetic separation

    Directory of Open Access Journals (Sweden)

    TIJANA SAVIC

    2006-02-01

    Full Text Available In this paper, a method for the rapid identification and purification of sequence specific DNA binding proteins based on magnetic separation is presented. This method was applied to confirm the binding of the human recombinant USF1 protein to its putative binding site (E-box within the human SOX3 protomer. It has been shown that biotinylated DNA attached to streptavidin magnetic particles specifically binds the USF1 protein in the presence of competitor DNA. It has also been demonstrated that the protein could be successfully eluted from the beads, in high yield and with restored DNA binding activity. The advantage of these procedures is that they could be applied for the identification and purification of any high-affinity sequence-specific DNA binding protein with only minor modifications.

  18. DNA sequencing with capillary electrophoresis and single cell analysis with mass spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Fung, N.

    1998-03-27

    Since the first demonstration of the laser in the 1960`s, lasers have found numerous applications in analytical chemistry. In this work, two different applications are described, namely, DNA sequencing with capillary gel electrophoresis and single cell analysis with mass spectrometry. Two projects are described in which high-speed DNA separations with capillary gel electrophoresis were demonstrated. In the third project, flow cytometry and mass spectrometry were coupled via a laser vaporization/ionization interface and individual mammalian cells were analyzed. First, DNA Sanger fragments were separated by capillary gel electrophoresis. A separation speed of 20 basepairs per minute was demonstrated with a mixed poly(ethylene oxide) (PEO) sieving solution. In addition, a new capillary wall treatment protocol was developed in which bare (or uncoated) capillaries can be used in DNA sequencing. Second, a temperature programming scheme was used to separate DNA Sanger fragments. Third, flow cytometry and mass spectrometry were coupled with a laser vaporization/ionization interface.

  19. Thermoelectric effect and its dependence on molecular length and sequence in single DNA molecules

    Science.gov (United States)

    Li, Yueqi; Xiang, Limin; Palma, Julio L.; Asai, Yoshihiro; Tao, Nongjian

    2016-04-01

    Studying the thermoelectric effect in DNA is important for unravelling charge transport mechanisms and for developing relevant applications of DNA molecules. Here we report a study of the thermoelectric effect in single DNA molecules. By varying the molecular length and sequence, we tune the charge transport in DNA to either a hopping- or tunnelling-dominated regimes. The thermoelectric effect is small and insensitive to the molecular length in the hopping regime. In contrast, the thermoelectric effect is large and sensitive to the length in the tunnelling regime. These findings indicate that one may control the thermoelectric effect in DNA by varying its sequence and length. We describe the experimental results in terms of hopping and tunnelling charge transport models.

  20. Characteristics of palindromic sequences in DNA of the sea urchin Stronglyocentrotus intermedius

    International Nuclear Information System (INIS)

    The fraction of palindromic sequences in the nuclear DNA of the sea urchin S. intermedius was characterized. Using chromatography on hydroxyapatite and treatment with S1 nuclease, it was shown that the fraction of palindromic sequences more than doubles when the sodium concentration in solution is increased or the temperature of reassociation is lowered. The increase is due to the involvement of inverted repeats in reassociation, which are characterized by a substantial nonhomologous character and/or the presence of an extended intervening DNA sequence. It was found by the method of reassociation of a nicked palindrome fraction with an excess of total homologous DNA that most of the inverted repeats in the sea urchin genome are unique sequences. The complexity of the palindrome fraction was estimated at 8.2 x 107 nucleotide pairs, and the number of palindromes per haploid genome ∼ 500,000

  1. Designing and Building a Framework for DNA Sequence Alignment Using Grid Computing

    Directory of Open Access Journals (Sweden)

    EL-Sayed Orabi

    2014-09-01

    Full Text Available Deoxyribonucleic acid (DNA is a molecule that encodes unique genetic instructions used in the development and functioning of all known living organisms and many viruses. This Genetic information is encoded as a sequence of nucleotides (adenine, cytosine, guanine, and thymine recorded using the letters A, C, G, and T.DNA querying or alignment of these sequences required dynamic programming tools and very complex matrices and some heuristic methods like FASTA and BLAST that use massive force of processing and highly time consuming. We present a parallel solution to reduce the processing time. Smith waterman algorithm, Needleman-Wunsch, some weighting matrices and a grid of computers are used to find field of similarity between these sequences in large DNA datasets. This grid consists of master computer and unlimited number of agents. The master computer is the user interface for insert the queried sequence and coordinates the processing between the grid agents.

  2. Base J glucosyltransferase does not regulate the sequence specificity of J synthesis in trypanosomatid telomeric DNA.

    Science.gov (United States)

    Bullard, Whitney; Cliffe, Laura; Wang, Pengcheng; Wang, Yinsheng; Sabatini, Robert

    2015-12-01

    Telomeric DNA of trypanosomatids possesses a modified thymine base, called base J, that is synthesized in a two-step process; the base is hydroxylated by a thymidine hydroxylase forming hydroxymethyluracil (hmU) and a glucose moiety is then attached by the J-associated glucosyltransferase (JGT). To examine the importance of JGT in modifiying specific thymine in DNA, we used a Leishmania episome system to demonstrate that the telomeric repeat (GGGTTA) stimulates J synthesis in vivo while mutant telomeric sequences (GGGTTT, GGGATT, and GGGAAA) do not. Utilizing an in vitro GT assay we find that JGT can glycosylate hmU within any sequence with no significant change in Km or kcat, even mutant telomeric sequences that are unable to be J-modified in vivo. The data suggests that JGT possesses no DNA sequence specificity in vitro, lending support to the hypothesis that the specificity of base J synthesis is not at the level of the JGT reaction. PMID:26815240

  3. Mitochondrial DNA control region sequences study in Saraiki population from Pakistan.

    Science.gov (United States)

    Hayat, Sikandar; Akhtar, Tanveer; Siddiqi, Muhammad Hassan; Rakha, Allah; Haider, Naeem; Tayyab, Muhammad; Abbas, Ghazanfar; Ali, Azam; Bokhari, Syed Yassir Abbas; Tariq, Muhammad Akram; Khan, Fazle Majid

    2015-03-01

    The analysis of mitochondrial DNA (mtDNA) control region was carried in 85 unrelated Sariki individuals living in the different provinces of Pakistan. DNA was extracted from blood preserved in EDTA vacutainers. Hypervariable regions (HV1, HV2 & HV3) were PCR amplified and sequenced. Sequencing results were aligned and compared with revised Cambridge reference sequence (rCRS). The sequencing results showed presence of total 63 different haplotypes, 58 of them are unique and 05 are common haplotypes shared by more than one individual. The most common haplotype observed was (W6) with a frequency 12.9% of population sample. The Saraiki population was detected with genetic diversity (0.9570) and power of discrimination (0.9458). This study will be beneficial for forensic casework. PMID:25465675

  4. Molecular phylogeny of endophytic isolates of Ampelomyces from Iran based on rDNA ITS sequences.

    Science.gov (United States)

    Jamali, Samad

    2015-01-01

    During 2012, five isolates of pycnidial fungi were recovered from roots of tomato (Solanum lycopersicum) plants in Iran. Based on morphological characteristics the presence of Ampelomyces was documented. To confirm morphological identification and clarify the placement of endophytic isolates of Ampelomyces, DNA was extracted from isolates using a genomic DNA purification Kit. Region of internal transcribed spacers 1, 2 and 5.8S genes of rDNA were amplified using ITS4 and ITS1 universal primer set. Amplicons were purified, sequenced and submitted to the GenBank. The resulting sequence (600 bp) was submitted to a BLAST search to find most similar sequences in GenBank. The ITS sequences of isolates obtained in Iran were compared to those of other related authentic sequences obtained from GenBank. Iranian endophytic isolates had 100 % similarity of among themselves, while all isolates of Ampelomyces sequences analyzed had an average of 95.2 % (range 87-100 %) similarity. When Ampelomyces ITS sequences were analyzed by both distance-based and maximum parsimony methods, the Ampelomyces isolates were segregate into 11 distinct clades. The ITS sequences of endophytic isolates obtained in Iran were identical with endophytic isolates from other country including USA, Australia, Hungary and Spain. Our analyses of phylogenetic data showed that endophytic isolates from Iran and other countries are distinct group. The high ITS sequence-divergence values and the phylogenetic analysis suggested the isolates of Ampelomyces in the clades are not closely related and indeed a problematic species complex. PMID:25245955

  5. Characterization and assessment of an avian repetitive DNA sequence as an icterid phylogenetic marker.

    Science.gov (United States)

    Quinn, J S; Guglich, E; Seutin, G; Lau, R; Marsolais, J; Parna, L; Boag, P T; White, B N

    1992-02-01

    The first tandemly repeated sequence examined in a passerine bird, a 431-bp PstI fragment named pMAT1, has been cloned from the genome of the brown-headed cowbird (Molothrus ater). The sequence represents about 5-10% of the genome (about 4 x 10(5) copies) and yields prominent ethidium bromide stained bands when genomic DNA cut with a variety of restriction enzymes is electrophoresed in agarose gels. A particularly striking ladder of fragments is apparent when the DNA is cut with HinfI, indicative of a tandem arrangement of the monomer. The cloned PstI monomer has been sequenced, revealing no internal repeated structure. There are sequences that hybridize with pMAT1 found in related nine-primaried oscines but not in more distantly related oscines, suboscines, or nonpasserine species. Little sequence similarity to tandemly repeated PstI cut sequences from the merlin (Falco columbarius), saurus crane (Grus antigone), or Puerto Rican parrot (Amazona vittata) or to HinfI digested sequence from the Toulouse goose (Anser anser) was detected. The isolated sequence was used as a probe to examine DNA samples of eight members of the tribe Icterini. This examination revealed phylogenetically informative characters. The repeat contains cutting sites from a number of restriction enzymes, which, if sufficiently polymorphic, would provide new phylogenetic characters. Sequences like these, conserved within a species, but variable between closely related species, may be very useful for phylogenetic studies of closely related taxa. PMID:1572527

  6. Predicting DNA-binding sites of proteins from amino acid sequence

    Directory of Open Access Journals (Sweden)

    Wu Feihong

    2006-05-01

    Full Text Available Abstract Background Understanding the molecular details of protein-DNA interactions is critical for deciphering the mechanisms of gene regulation. We present a machine learning approach for the identification of amino acid residues involved in protein-DNA interactions. Results We start with a Naïve Bayes classifier trained to predict whether a given amino acid residue is a DNA-binding residue based on its identity and the identities of its sequence neighbors. The input to the classifier consists of the identities of the target residue and 4 sequence neighbors on each side of the target residue. The classifier is trained and evaluated (using leave-one-out cross-validation on a non-redundant set of 171 proteins. Our results indicate the feasibility of identifying interface residues based on local sequence information. The classifier achieves 71% overall accuracy with a correlation coefficient of 0.24, 35% specificity and 53% sensitivity in identifying interface residues as evaluated by leave-one-out cross-validation. We show that the performance of the classifier is improved by using sequence entropy of the target residue (the entropy of the corresponding column in multiple alignment obtained by aligning the target sequence with its sequence homologs as additional input. The classifier achieves 78% overall accuracy with a correlation coefficient of 0.28, 44% specificity and 41% sensitivity in identifying interface residues. Examination of the predictions in the context of 3-dimensional structures of proteins demonstrates the effectiveness of this method in identifying DNA-binding sites from sequence information. In 33% (56 out of 171 of the proteins, the classifier identifies the interaction sites by correctly recognizing at least half of the interface residues. In 87% (149 out of 171 of the proteins, the classifier correctly identifies at least 20% of the interface residues. This suggests the possibility of using such classifiers to identify

  7. Cloning, sequencing, and expression of cDNA for human β-glucuronidase

    International Nuclear Information System (INIS)

    The authors report here the cDNA sequence for human placental β-glucuronidase (β-D-glucuronoside glucuronosohydrolase, EC 3.2.1.31) and demonstrate expression of the human enzyme in transfected COS cells. They also sequenced a partial cDNA clone from human fibroblasts that contained a 153-base-pair deletion within the coding sequence and found a second type of cDNA clone from placenta that contained the same deletion. Nuclease S1 mapping studies demonstrated two types of mRNAs in human placenta that corresponded to the two types of cDNA clones isolated. The NH2-terminal amino acid sequence determined for human spleen β-glucuronidase agreed with that inferred from the DNA sequence of the two placental clones, beginning at amino acid 23, suggesting a cleaved signal sequence of 22 amino acids. When transfected into COS cells, plasmids containing either placental clone expressed an immunoprecipitable protein that contained N-linked oligosaccharides as evidenced by sensitivity to endoglycosidase F. However, only transfection with the clone containing the 153-base-pair segment led to expression of human β-glucuronidase activity. These studies provide the sequence for the full-length cDNA for human β-glucuronidase, demonstrate the existence of two populations of mRNA for β-glucuronidase in human placenta, only one of which specifies a catalytically active enzyme, and illustrate the importance of expression studies in verifying that a cDNA is functionally full-length

  8. A rapid method for sequencing of rRNA gene(s) amplified by polymerase chain reaction using an automated DNA sequencer

    OpenAIRE

    Dwivedi, P.P.; Patel, B.K.C.; Rees, G.N.; Ollivier, Bernard

    1996-01-01

    A method for DNA sequencing of ribosomal RNA (rRNA) genes, amplified by polymerase chain reaction (PCR), using internal primers, designed on the basis of conserved regions of rRNA genes for determining a near complete sequence (99%) of the gene using an automated DNA sequencer (Applied Biosystem Incorporation, USA) is described. The procedure is extremely rapid as cloning of the gene is not required for sequence determination. In addition time consuming steps such as ethanol precipitation and...

  9. Mycobacterial DNA Extraction for Whole-Genome Sequencing from Early Positive Liquid (MGIT) Cultures

    OpenAIRE

    Votintseva, Antonina A.; Pankhurst, Louise J.; Anson, Luke W.; Morgan, Marcus R.; Gascoyne-Binzi, Deborah; Walker, Timothy M; Quan, T. Phuong; Wyllie, David H; Del Ojo Elias, Carlos; Wilcox, Mark; Walker, A. Sarah; Peto, Tim E A; Crook, Derrick W.

    2015-01-01

    We developed a low-cost and reliable method of DNA extraction from as little as 1 ml of early positive mycobacterial growth indicator tube (MGIT) cultures that is suitable for whole-genome sequencing to identify mycobacterial species and predict antibiotic resistance in clinical samples. The DNA extraction method is based on ethanol precipitation supplemented by pretreatment steps with a MolYsis kit or saline wash for the removal of human DNA and a final DNA cleanup step with solid-phase reve...

  10. Mycobacterial DNA extraction for whole-genome sequencing from early positive liquid (MGIT) cultures

    OpenAIRE

    Votintseva, AA; Pankhurst, LJ; Anson, LW; Morgan, *; Gascoyne-Binzi, D.; Walker, TM; quan, TP; Wyllie, DH; Del Ojo Elias, C; Wilcox, M; Walker, AS; Peto, TE; Crook, DW

    2015-01-01

    We developed a low-cost and reliable method of DNA extraction from as little as 1 ml of early positive mycobacterial growth indicator tube (MGIT) cultures that is suitable for whole-genome sequencing to identify mycobacterial species and predict antibiotic resistance in clinical samples. The DNA extraction method is based on ethanol precipitation supplemented by pretreatment steps with a MolYsis kit or saline wash for the removal of human DNA and a final DNA cleanup step with solid-phase reve...

  11. The linear plastid chromosomes of maize: terminal sequences, structures, and implications for DNA replication.

    Science.gov (United States)

    Oldenburg, Delene J; Bendich, Arnold J

    2016-05-01

    The structure of a chromosomal DNA molecule may influence the way in which it is replicated and inherited. For decades plastid DNA (ptDNA) was believed to be circular, with breakage invoked to explain linear forms found upon extraction from the cell. Recent evidence indicates that ptDNA in vivo consists of linear molecules with discrete termini, although these ends were not characterized. We report the sequences of two terminal regions, End1 and End2, for maize (Zea mays L.) ptDNA. We describe structural features of these terminal regions and similarities found in other plant ptDNAs. The terminal sequences are within inverted repeat regions (leading to four genomic isomers) and adjacent to origins of replication. Conceptually, stem-loop structures may be formed following melting of the double-stranded DNA ends. Exonuclease digestion indicates that the ends in maize are unobstructed, but tobacco (Nicotiana tabacum L.) ends may have a 5'-protein. If the terminal structure of ptDNA molecules influences the retention of ptDNA, the unprotected molecular ends in mature leaves of maize may be more susceptible to degradation in vivo than the protected ends in tobacco. The terminal sequences and cumulative GC skew profiles are nearly identical for maize, wheat (Triticum aestivum L.) and rice (Oryza sativa L.), with less similarity among other plants. The linear structure is now confirmed for maize ptDNA and inferred for other plants and suggests a virus-like recombination-dependent replication mechanism for ptDNA. Plastid transformation vectors containing the terminal sequences may increase the chances of success in generating transplastomic cereals. PMID:26650613

  12. Sequence conservation of an avian centromeric repeated DNA component.

    Science.gov (United States)

    Madsen, C S; Brooks, J E; de Kloet, E; de Kloet, S R

    1994-06-01

    The approximately 190-bp centromeric repeat monomers of the spur-winged lapwing (Vanellus spinosus, Charadriidae), the Chilean flamingo (Phoenicopterus chilensis, Phoenicopteridae), the sarus crane (Grus antigone, Gruidae), parrots (Psittacidae), waterfowl (Anatidae), and the merlin (Falco columbarius, Falconidae) contain elements that are interspecifically highly variable, as well as elements (trinucleotides and higher order oligonucleotides) that are highly conserved in sequence and relative location within the repeat. Such conservation suggests that the centromeric repeats of these avian species have evolved from a common ancestral sequence that may date from very early stages of avian radiation. PMID:8034177

  13. Correcting sequencing errors in DNA coding regions using a dynamic programming approach

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Y.; Mural, R.J.; Uberbacher, E.C.

    1994-12-01

    This paper presents an algorithm for detecting and ``correcting`` sequencing errors that occur in DNA coding regions. The types of sequencing error addressed include insertions and deletions (indels) of DNA bases. The goal is to provide a capability which makes single-pass or low-redundancy sequence data more informative, reducing the need for high-redundancy sequencing for gene identification and characterization purposes. The algorithm detects sequencing errors by discovering changes in the statistically preferred reading frame within a putative coding region and then inserts a number of ``neutral`` bases at a perceived reading frame transition point to make the putative exon candidate frame consistent. The authors have implemented the algorithm as a front-end subsystem of the GRAIL DNA sequence analysis system to construct a version which is very error tolerant and also intend to use this as a testbed for further development of sequencing error-correction technology. On a test set consisting of 68 Human DNA sequences with 1% randomly generated indels in coding regions, the algorithm detected and corrected 76% of the indels. The average distance between the position of an indel and the predicted one was 9.4 bases. With this subsystem in place, GRAIL correctly predicted 89% of the coding messages with 10% false message on the ``corrected`` sequences, compared to 69% correctly predicted coding messages and 11% falsely predicted messages on the ``corrupted`` sequences using standard GRAIL II method. The method uses a dynamic programming algorithm, and runs in time and space linear to the size of the input sequence.

  14. Sequence Searcher: A Java tool to perform regular expression and fuzzy searches of multiple DNA and protein sequences

    Directory of Open Access Journals (Sweden)

    Upton Chris

    2009-01-01

    Full Text Available Abstract Background Many sequence-searching tools have limiting factors for their use. For example, they may be platform specific, enforce restrictive size limits and sequences to be searched, or only allow searches of one of DNA or protein. Findings We present an easy-to-use, fast, platform-independent tool to search for amino acid or nucleotide patterns within one or many protein or nucleic acid sequences. The user can choose to search for regular expressions or perform a fuzzy search in which a particular number of errors is accepted during matching of a sequence. Positions of mismatches in fuzzy searches are displayed graphically the user. Conclusion SeqS provides an improved feature set and functions as a stand-alone tool or could be integrated into other bioinformatics platforms.

  15. Different ways of providing anonymity

    OpenAIRE

    Glavač, Vesna

    2012-01-01

    The aim of this thesis is to show the importance of security and anonymity on the internet by demonstrating the use of a SOCKS proxy. In theoretical part, properties of various security mechanisms are explored with focus on SOCKS protocol as one of the most widely used systems. Presented are the inner workings and different versions as well as advantages and drawbacks of the protocol. The paper tries to identify the simplest way of encrypting data traffic by using SOCKS protocol with SSH tunn...

  16. An Anonymous Credit Card System

    Science.gov (United States)

    Androulaki, Elli; Bellovin, Steven

    Credit cards have many important benefits; however, these same benefits often carry with them many privacy concerns. In particular, the need for users to be able to monitor their own transactions, as well as bank’s need to justify its payment requests from cardholders, entitle the latter to maintain a detailed log of all transactions its credit card customers were involved in. A bank can thus build a profile of each cardholder even without the latter’s consent. In this paper, we present a practical and accountable anonymous credit system based on ecash, with a privacy preserving mechanism for error correction and expense-reporting.

  17. DNA sequence and analysis of human chromosome 8.

    Science.gov (United States)

    Nusbaum, Chad; Mikkelsen, Tarjei S; Zody, Michael C; Asakawa, Shuichi; Taudien, Stefan; Garber, Manuel; Kodira, Chinnappa D; Schueler, Mary G; Shimizu, Atsushi; Whittaker, Charles A; Chang, Jean L; Cuomo, Christina A; Dewar, Ken; FitzGerald, Michael G; Yang, Xiaoping; Allen, Nicole R; Anderson, Scott; Asakawa, Teruyo; Blechschmidt, Karin; Bloom, Toby; Borowsky, Mark L; Butler, Jonathan; Cook, April; Corum, Benjamin; DeArellano, Kurt; DeCaprio, David; Dooley, Kathleen T; Dorris, Lester; Engels, Reinhard; Glöckner, Gernot; Hafez, Nabil; Hagopian, Daniel S; Hall, Jennifer L; Ishikawa, Sabine K; Jaffe, David B; Kamat, Asha; Kudoh, Jun; Lehmann, Rüdiger; Lokitsang, Tashi; Macdonald, Pendexter; Major, John E; Matthews, Charles D; Mauceli, Evan; Menzel, Uwe; Mihalev, Atanas H; Minoshima, Shinsei; Murayama, Yuji; Naylor, Jerome W; Nicol, Robert; Nguyen, Cindy; O'Leary, Sinéad B; O'Neill, Keith; Parker, Stephen C J; Polley, Andreas; Raymond, Christina K; Reichwald, Kathrin; Rodriguez, Joseph; Sasaki, Takashi; Schilhabel, Markus; Siddiqui, Roman; Smith, Cherylyn L; Sneddon, Tam P; Talamas, Jessica A; Tenzin, Pema; Topham, Kerri; Venkataraman, Vijay; Wen, Gaiping; Yamazaki, Satoru; Young, Sarah K; Zeng, Qiandong; Zimmer, Andrew R; Rosenthal, Andre; Birren, Bruce W; Platzer, Matthias; Shimizu, Nobuyoshi; Lander, Eric S

    2006-01-19

    The International Human Genome Sequencing Consortium (IHGSC) recently completed a sequence of the human genome. As part of this project, we have focused on chromosome 8. Although some chromosomes exhibit extreme characteristics in terms of length, gene content, repeat content and fraction segmentally duplicated, chromosome 8 is distinctly typical in character, being very close to the genome median in each of these aspects. This work describes a finished sequence and gene catalogue for the chromosome, which represents just over 5% of the euchromatic human genome. A unique feature of the chromosome is a vast region of approximately 15 megabases on distal 8p that appears to have a strikingly high mutation rate, which has accelerated in the hominids relative to other sequenced mammals. This fast-evolving region contains a number of genes related to innate immunity and the nervous system, including loci that appear to be under positive selection--these include the major defensin (DEF) gene cluster and MCPH1, a gene that may have contributed to the evolution of expanded brain size in the great apes. The data from chromosome 8 should allow a better understanding of both normal and disease biology and genome evolution. PMID:16421571

  18. An editing environment for DNA sequence analysis and annotation

    Energy Technology Data Exchange (ETDEWEB)

    Uberbacher, E.C.; Xu, Y.; Shah, M.B.; Olman, V.; Parang, M.; Mural, R.

    1998-12-31

    This paper presents a computer system for analyzing and annotating large-scale genomic sequences. The core of the system is a multiple-gene structure identification program, which predicts the most probable gene structures based on the given evidence, including pattern recognition, EST and protein homology information. A graphics-based user interface provides an environment which allows the user to interactively control the evidence to be used in the gene identification process. To overcome the computational bottleneck in the database similarity search used in the gene identification process, the authors have developed an effective way to partition a database into a set of sub-databases of related sequences, and reduced the search problem on a large database to a signature identification problem and a search problem on a much smaller sub-database. This reduces the number of sequences to be searched from N to O({radical}N) on average, and hence greatly reduces the search time, where N is the number of sequences in the original database. The system provides the user with the ability to facilitate and modify the analysis and modeling in real time.

  19. Engineering the DNA cytosine-5 methyltransferase reaction for sequence-specific labeling of DNA

    OpenAIRE

    Lukinavičius, Gražvydas; Lapinaitė, Audronė; Urbanavičiūtė, Giedrė; Gerasimaitė, Rūta; Klimašauskas, Saulius

    2012-01-01

    DNA methyltransferases catalyse the transfer of a methyl group from the ubiquitous cofactor S-adenosyl-L-methionine (AdoMet) onto specific target sites on DNA and play important roles in organisms from bacteria to humans. AdoMet analogs with extended propargylic side chains have been chemically produced for methyltransferase-directed transfer of activated groups (mTAG) onto DNA, although the efficiency of reactions with synthetic analogs remained low. We performed steric engineering of the co...

  20. Direct evidence for sequence-dependent attraction between double-stranded DNA controlled by methylation

    Science.gov (United States)

    Yoo, Jejoong; Kim, Hajin; Aksimentiev, Aleksei; Ha, Taekjip

    2016-03-01

    Although proteins mediate highly ordered DNA organization in vivo, theoretical studies suggest that homologous DNA duplexes can preferentially associate with one another even in the absence of proteins. Here we combine molecular dynamics simulations with single-molecule fluorescence resonance energy transfer experiments to examine the interactions between duplex DNA in the presence of spermine, a biological polycation. We find that AT-rich DNA duplexes associate more strongly than GC-rich duplexes, regardless of the sequence homology. Methyl groups of thymine acts as a steric block, relocating spermine from major grooves to interhelical regions, thereby increasing DNA-DNA attraction. Indeed, methylation of cytosines makes attraction between GC-rich DNA as strong as that between AT-rich DNA. Recent genome-wide chromosome organization studies showed that remote contact frequencies are higher for AT-rich and methylated DNA, suggesting that direct DNA-DNA interactions that we report here may play a role in the chromosome organization and gene regulation.

  1. Integration of hepatitis B virus DNA in chromosome-specific satellite sequences

    International Nuclear Information System (INIS)

    The authors previously reported the cloning and detailed analysis of the integrated hepatitis B virus sequences in a human hepatoma cell line. They report here the integration of at least one of hepatitis B virus at human satellite DNA sequences. The majority of the cellular sequences identified by this satellite were organized as a multimeric composition of a 0.6-kilobase EcoRI fragment. This clone hybridized in situ almost exclusively to the centromeric heterochromatin of chromosomes 1 and 16 and to a lower extent to chromosome 2 and to the heterochromatic region of the Y chromosome. The immediate flanking host sequence appeared as a hierarchy of repeating units which were almost identical to a previously reported human satellite III DNA sequence

  2. Application of cytochrome b DNA sequences for the authentication of endangered snake species.

    Science.gov (United States)

    Wong, Ka-Lok; Wang, Jun; But, Paul Pui-Hay; Shaw, Pang-Chui

    2004-01-01

    In order to enforce the conservation program and curbing the illegal trading and consumption of endangered snake species, the value of cytochrome b sequence in the authentication of snake species was evaluated. As an illustration, DNA was extracted, selected cytochrome b DNA sequences amplified and sequenced from six snakes commonly consumed in Hong Kong. Cataloging with sequences available in public, a cytochrome b database containing 90 species of snakes was constructed. In this database, sequence homology between snakes ranged from 70.68 to 95.11%. On the other hand, intraspecific variation of three tested snakes was 0-0.98%. Using the database, we were able to determine the identity of six meat samples confiscated by the Agriculture, Fisheries and Conservation Department, HKSAR. PMID:14687773

  3. Comparison of microbial DNA enrichment tools for metagenomic whole genome sequencing.

    Science.gov (United States)

    Thoendel, Matthew; Jeraldo, Patricio R; Greenwood-Quaintance, Kerryl E; Yao, Janet Z; Chia, Nicholas; Hanssen, Arlen D; Abdel, Matthew P; Patel, Robin

    2016-08-01

    Metagenomic whole genome sequencing for detection of pathogens in clinical samples is an exciting new area for discovery and clinical testing. A major barrier to this approach is the overwhelming ratio of human to pathogen DNA in samples with low pathogen abundance, which is typical of most clinical specimens. Microbial DNA enrichment methods offer the potential to relieve this limitation by improving this ratio. Two commercially available enrichment kits, the NEBNext Microbiome DNA Enrichment Kit and the Molzym MolYsis Basic kit, were tested for their ability to enrich for microbial DNA from resected arthroplasty component sonicate fluids from prosthetic joint infections or uninfected sonicate fluids spiked with Staphylococcus aureus. Using spiked uninfected sonicate fluid there was a 6-fold enrichment of bacterial DNA with the NEBNext kit and 76-fold enrichment with the MolYsis kit. Metagenomic whole genome sequencing of sonicate fluid revealed 13- to 85-fold enrichment of bacterial DNA using the NEBNext enrichment kit. The MolYsis approach achieved 481- to 9580-fold enrichment, resulting in 7 to 59% of sequencing reads being from the pathogens known to be present in the samples. These results demonstrate the usefulness of these tools when testing clinical samples with low microbial burden using next generation sequencing. PMID:27237775

  4. CLONING AND EXPRESSION OF A cDNA SEQUENCE FOR HUMAN THIOREDOXIN

    Institute of Scientific and Technical Information of China (English)

    Liu Qingyong(刘庆勇); Ruan Xiyun(阮喜云); Liu Xiaogong(刘效恭); Ji Zongzheng(纪宗正); Dang Jiangong; Nan Xunyi(南勋义); Wang Quanying(王全颖); Yang Guangxiao(杨广笑)

    2003-01-01

    Objective To clone and determine the sequence and expression of a cDNA segment for human thioredoxin. Methods The cDNA segment of thioredoxin was obtained through amplification by RT-PCR cloning from 143 (TK-) human osteosarcoma cell. The amplified products were cloned into pGEM-T Easy vector and sequenced. Then the expressed vector pBV220-hTRX was constructed and transformed into E.coli strain DH5α for hTRX expression. The hTRX was purified by DEAE-Sephadex A-50 column and the activity of recombinant hTRX was determined by the insulin disulfide reduction assay. Results Comparison of cDNA sequence of the cloned fragments with that of the reported hTRX (GenBank J04026) demonstrated that there were two differences compared to the reported cDNA sequence for hTRX at bp180 and bp284, and the amino acids enceoded altered respectively, but motif of the sequence was identical to that of the reported hTRX. The recombinant hTRX can catalyze insulin reduction by DTT. Conclusion The successful cloning and expression of hTRX cDNA formed a basis for further study on biological functions and utilization of hTRX.

  5. Inhibition of hepatitis B virus replication with linear DNA sequences expressing antiviral micro-RNA shuttles

    Energy Technology Data Exchange (ETDEWEB)

    Chattopadhyay, Saket; Ely, Abdullah; Bloom, Kristie; Weinberg, Marc S. [Antiviral Gene Therapy Research Unit, University of the Witwatersrand (South Africa); Arbuthnot, Patrick, E-mail: Patrick.Arbuthnot@wits.ac.za [Antiviral Gene Therapy Research Unit, University of the Witwatersrand (South Africa)

    2009-11-20

    RNA interference (RNAi) may be harnessed to inhibit viral gene expression and this approach is being developed to counter chronic infection with hepatitis B virus (HBV). Compared to synthetic RNAi activators, DNA expression cassettes that generate silencing sequences have advantages of sustained efficacy and ease of propagation in plasmid DNA (pDNA). However, the large size of pDNAs and inclusion of sequences conferring antibiotic resistance and immunostimulation limit delivery efficiency and safety. To develop use of alternative DNA templates that may be applied for therapeutic gene silencing, we assessed the usefulness of PCR-generated linear expression cassettes that produce anti-HBV micro-RNA (miR) shuttles. We found that silencing of HBV markers of replication was efficient (>75%) in cell culture and in vivo. miR shuttles were processed to form anti-HBV guide strands and there was no evidence of induction of the interferon response. Modification of terminal sequences to include flanking human adenoviral type-5 inverted terminal repeats was easily achieved and did not compromise silencing efficacy. These linear DNA sequences should have utility in the development of gene silencing applications where modifications of terminal elements with elimination of potentially harmful and non-essential sequences are required.

  6. Inhibition of hepatitis B virus replication with linear DNA sequences expressing antiviral micro-RNA shuttles

    International Nuclear Information System (INIS)

    RNA interference (RNAi) may be harnessed to inhibit viral gene expression and this approach is being developed to counter chronic infection with hepatitis B virus (HBV). Compared to synthetic RNAi activators, DNA expression cassettes that generate silencing sequences have advantages of sustained efficacy and ease of propagation in plasmid DNA (pDNA). However, the large size of pDNAs and inclusion of sequences conferring antibiotic resistance and immunostimulation limit delivery efficiency and safety. To develop use of alternative DNA templates that may be applied for therapeutic gene silencing, we assessed the usefulness of PCR-generated linear expression cassettes that produce anti-HBV micro-RNA (miR) shuttles. We found that silencing of HBV markers of replication was efficient (>75%) in cell culture and in vivo. miR shuttles were processed to form anti-HBV guide strands and there was no evidence of induction of the interferon response. Modification of terminal sequences to include flanking human adenoviral type-5 inverted terminal repeats was easily achieved and did not compromise silencing efficacy. These linear DNA sequences should have utility in the development of gene silencing applications where modifications of terminal elements with elimination of potentially harmful and non-essential sequences are required.

  7. A universal DNA extraction and PCR amplification method for fungal rDNA sequence-based identification.

    Science.gov (United States)

    Romanelli, A M; Fu, J; Herrera, M L; Wickes, B L

    2014-10-01

    Accurate identification of fungal pathogens using a sequence-based approach requires an extraction method that yields template DNA pure enough for polymerase chain reaction (PCR) or other types of amplification. Therefore, the objective of this study was to develop and standardise a rapid, inexpensive DNA extraction protocol applicable to the major fungal phyla, which would yield sufficient template DNA pure enough for PCR and sequencing. A total of 519 clinical and culture collection strains, comprised of both yeast and filamentous fungi, were prepared using our extraction method to determine its applicability for PCR, which targeted the ITS and D1/D2 regions in a single PCR amplicon. All templates were successfully amplified and found to yield the correct strain identification when sequenced. This protocol could be completed in approximately 30 min and utilised a combination of physical and chemical extraction methods but did not require organic solvents nor ethanol precipitation. The method reduces the number of tube manipulations and yielded suitable template DNA for PCR amplification from all phyla that were tested. PMID:24865530

  8. Electrochemical direct immobilization of DNA sequences for label-free herpes virus detection

    International Nuclear Information System (INIS)

    DNA sequences/bio-macromolecules of herpes virus (5'-AT CAC CGA CCC GGA GAG GGA C-3') were directly immobilized into polypyrrole matrix by using the cyclic voltammetry method, and grafted onto arrays of interdigitated platinum microelectrodes. The morphology surface of the obtained PPy/DNA of herpes virus composite films was investigated by a FESEM Hitachi-S 4800. Fourier transform infrared spectroscopy (FTIR) was used to characterize the PPy/DNA film and to study the specific interactions that may exist between DNA biomacromolecules and PPy chains. Attempts are made to use these PPy/DNA composite films for label-free herpes virus detection revealed a response time of 60 s in solutions containing as low as 2 nM DNA concentration, and self life of six months when emerged in double distilled water and kept refrigerated.

  9. Structural basis for sequence-specific recognition of DNA by TAL effectors

    KAUST Repository

    Deng, Dong

    2012-01-05

    TAL (transcription activator-like) effectors, secreted by phytopathogenic bacteria, recognize host DNA sequences through a central domain of tandem repeats. Each repeat comprises 33 to 35 conserved amino acids and targets a specific base pair by using two hypervariable residues [known as repeat variable diresidues (RVDs)] at positions 12 and 13. Here, we report the crystal structures of an 11.5-repeat TAL effector in both DNA-free and DNA-bound states. Each TAL repeat comprises two helices connected by a short RVD-containing loop. The 11.5 repeats form a right-handed, superhelical structure that tracks along the sense strand of DNA duplex, with RVDs contacting the major groove. The 12th residue stabilizes the RVD loop, whereas the 13th residue makes a base-specific contact. Understanding DNA recognition by TAL effectors may facilitate rational design of DNA-binding proteins with biotechnological applications.

  10. DNA Sequencing by Capillary Electrophoresis Using Quasi-inter penetrating Network Formed by Polyacrylamide and Poly(N-hydroxymethylacrylamide)

    Institute of Scientific and Technical Information of China (English)

    Wen Long ZHANG; Yan Mei WANG

    2006-01-01

    Quasi-interpenetrating network formed by polyacrylamide and poly (N-hydroxymethylacrylamide) was designed, synthesized, and tested for DNA sequencing by capillary electrophoresis. The performance of quasi-IPN on DNA sequencing was determined by the acrylamide to N-hydroxymethylacrylamide molar ratio and sequencing temperature.

  11. Mechanism of sequence-specific template binding by the DNA primase of bacteriophage T7

    KAUST Repository

    Lee, Seung-Joo

    2010-03-28

    DNA primases catalyze the synthesis of the oligoribonucleotides required for the initiation of lagging strand DNA synthesis. Biochemical studies have elucidated the mechanism for the sequence-specific synthesis of primers. However, the physical interactions of the primase with the DNA template to explain the basis of specificity have not been demonstrated. Using a combination of surface plasmon resonance and biochemical assays, we show that T7 DNA primase has only a slightly higher affinity for DNA containing the primase recognition sequence (5\\'-TGGTC-3\\') than for DNA lacking the recognition site. However, this binding is drastically enhanced by the presence of the cognate Nucleoside triphosphates (NTPs), Adenosine triphosphate (ATP) and Cytosine triphosphate (CTP) that are incorporated into the primer, pppACCA. Formation of the dimer, pppAC, the initial step of sequence-specific primer synthesis, is not sufficient for the stable binding. Preformed primers exhibit significantly less selective binding than that observed with ATP and CTP. Alterations in subdomains of the primase result in loss of selective DNA binding. We present a model in which conformational changes induced during primer synthesis facilitate contact between the zinc-binding domain and the polymerase domain. The Author(s) 2010. Published by Oxford University Press.

  12. Sequence-specific interactions of drugs interfering with the topoisomerase-DNA cleavage complex.

    Science.gov (United States)

    Palumbo, Manlio; Gatto, Barbara; Moro, Stefano; Sissi, Claudia; Zagotto, Giuseppe

    2002-07-18

    DNA-processing enzymes, such as the topoisomerases (tops), represent major targets for potent anticancer (and antibacterial) agents. The drugs kill cells by poisoning the enzymes' catalytic cycle. Understanding the molecular details of top poisoning is a fundamental requisite for the rational development of novel, more effective antineoplastic drugs. In this connection, sequence-specific recognition of the top-DNA complex is a key step to preferentially direct the action of the drugs onto selected genomic sequences. In fact, the (reversible) interference of drugs with the top-DNA complex exhibits well-defined preferences for DNA bases in the proximity of the cleavage site, each drug showing peculiarities connected to its structural features. A second level of selectivity can be observed when chemically reactive groups are present in the structure of the top-directed drug. In this case, the enzyme recognizes or generates a unique site for covalent drug-DNA binding. This will further subtly modulate the drug's efficiency in stimulating DNA damage at selected sites. Finally, drugs can discriminate not only among different types of tops, but also among different isoenzymes, providing an additional level of specific selection. Once the molecular basis for DNA sequence-dependent recognition has been established, the above-mentioned modes to generate selectivity in drug poisoning can be rationally exploited, alone or in combination, to develop tailor-made drugs targeted at defined loci in cancer cells. PMID:12084456

  13. Whole genome bisulfite sequencing of cell-free DNA and its cellular contributors uncovers placenta hypomethylated domains

    OpenAIRE

    Jensen, Taylor J.; Kim, Sung K; Zhu, Zhanyang; Chin, Christine; Gebhard, Claudia; Lu, Tim; Deciu, Cosmin; Van den Boom, Dirk; Ehrich, Mathias

    2015-01-01

    Background Circulating cell-free fetal DNA has enabled non-invasive prenatal fetal aneuploidy testing without direct discrimination of the maternal and fetal DNA. Testing may be improved by specifically enriching the sample material for fetal DNA. DNA methylation may allow for such a separation of DNA; however, this depends on knowledge of the methylomes of circulating cell-free DNA and its cellular contributors. Results We perform whole genome bisulfite sequencing on a set of unmatched sampl...

  14. Sequencing cDNAs: An Introduction to DNA Sequence Analysis in the Undergraduate Molecular Genetics Course.

    Science.gov (United States)

    Galewsky, Samuel

    2000-01-01

    Introduces a series of molecular genetics laboratories where students pick a single colony from a Drosophila melanogester embryo cDNA library and purify the plasmid, then analyze the insert through restriction digests and gel electrophoresis. (Author/YDS)

  15. Wavelet-based multifractal analysis of DNA sequences by using chaos-game representation

    International Nuclear Information System (INIS)

    Chaos game representation (CGR) is proposed as a scale-independent representation for DNA sequences and provides information about the statistical distribution of oligonucleotides in a DNA sequence. CGR images of DNA sequences represent some kinds of fractal patterns, but the common multifractal analysis based on the box counting method cannot deal with CGR images perfectly. Here, the wavelet transform modulus maxima (WTMM) method is applied to the multifractal analysis of CGR images. The results show that the scale-invariance range of CGR edge images can be extended to three orders of magnitude, and complete singularity spectra can be calculated. Spectrum parameters such as the singularity spectrum span are extracted to describe the statistical character of DNA sequences. Compared with the singularity spectrum span, exon sequences with a minimal spectrum span have the most uniform fractal structure. Also, the singularity spectrum parameters are related to oligonucleotide length, sequence component and species, thereby providing a method of studying the length polymorphism of repeat oligonucleotides. (general)

  16. Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays.

    Science.gov (United States)

    Drmanac, Radoje; Sparks, Andrew B; Callow, Matthew J; Halpern, Aaron L; Burns, Norman L; Kermani, Bahram G; Carnevali, Paolo; Nazarenko, Igor; Nilsen, Geoffrey B; Yeung, George; Dahl, Fredrik; Fernandez, Andres; Staker, Bryan; Pant, Krishna P; Baccash, Jonathan; Borcherding, Adam P; Brownley, Anushka; Cedeno, Ryan; Chen, Linsu; Chernikoff, Dan; Cheung, Alex; Chirita, Razvan; Curson, Benjamin; Ebert, Jessica C; Hacker, Coleen R; Hartlage, Robert; Hauser, Brian; Huang, Steve; Jiang, Yuan; Karpinchyk, Vitali; Koenig, Mark; Kong, Calvin; Landers, Tom; Le, Catherine; Liu, Jia; McBride, Celeste E; Morenzoni, Matt; Morey, Robert E; Mutch, Karl; Perazich, Helena; Perry, Kimberly; Peters, Brock A; Peterson, Joe; Pethiyagoda, Charit L; Pothuraju, Kaliprasad; Richter, Claudia; Rosenbaum, Abraham M; Roy, Shaunak; Shafto, Jay; Sharanhovich, Uladzislau; Shannon, Karen W; Sheppy, Conrad G; Sun, Michel; Thakuria, Joseph V; Tran, Anne; Vu, Dylan; Zaranek, Alexander Wait; Wu, Xiaodi; Drmanac, Snezana; Oliphant, Arnold R; Banyai, William C; Martin, Bruce; Ballinger, Dennis G; Church, George M; Reid, Clifford A

    2010-01-01

    Genome sequencing of large numbers of individuals promises to advance the understanding, treatment, and prevention of human diseases, among other applications. We describe a genome sequencing platform that achieves efficient imaging and low reagent consumption with combinatorial probe anchor ligation chemistry to independently assay each base from patterned nanoarrays of self-assembling DNA nanoballs. We sequenced three human genomes with this platform, generating an average of 45- to 87-fold coverage per genome and identifying 3.2 to 4.5 million sequence variants per genome. Validation of one genome data set demonstrates a sequence accuracy of about 1 false variant per 100 kilobases. The high accuracy, affordable cost of $4400 for sequencing consumables, and scalability of this platform enable complete human genome sequencing for the detection of rare variants in large-scale genetic studies. PMID:19892942

  17. Plasmid P1 replication: negative control by repeated DNA sequences.

    OpenAIRE

    Chattoraj, D; Cordes, K.; Abeles, A

    1984-01-01

    The incompatibility locus, incA, of the unit-copy plasmid P1 is contained within a fragment that is essentially a set of nine 19-base-pair repeats. One or more copies of the fragment destabilizes the plasmid when present in trans. Here we show that extra copies of incA interfere with plasmid DNA replication and that a deletion of most of incA increases plasmid copy number. Thus, incA is not essential for replication but is required for its control. When cloned in a high-copy-number vector, pi...

  18. Interference of Co-Amplified Nuclear Mitochondrial DNA Sequences on the Determination of Human mtDNA Heteroplasmy by Using the SURVEYOR Nuclease and the WAVE HS System

    OpenAIRE

    Yen, Hsiu-Chuan; Li, Shiue-Li; Hsu, Wei-Chien; Tang, Petrus

    2014-01-01

    High-sensitivity and high-throughput mutation detection techniques are useful for screening the homoplasmy or heteroplasmy status of mitochondrial DNA (mtDNA), but might be susceptible to interference from nuclear mitochondrial DNA sequences (NUMTs) co-amplified during polymerase chain reaction (PCR). In this study, we first evaluated the platform of SURVEYOR Nuclease digestion of heteroduplexed DNA followed by the detection of cleaved DNA by using the WAVE HS System (SN/WAVE-HS) for detectin...

  19. Temporal stability of epigenetic markers: sequence characteristics and predictors of short-term DNA methylation variations.

    Directory of Open Access Journals (Sweden)

    Hyang-Min Byun

    Full Text Available BACKGROUND: DNA methylation is an epigenetic mechanism that has been increasingly investigated in observational human studies, particularly on blood leukocyte DNA. Characterizing the degree and determinants of DNA methylation stability can provide critical information for the design and conduction of human epigenetic studies. METHODS: We measured DNA methylation in 12 gene-promoter regions (APC, p16, p53, RASSF1A, CDH13, eNOS, ET-1, IFNγ, IL-6, TNFα, iNOS, and hTERT and 2 of non-long terminal repeat elements, i.e., L1 and Alu in blood samples obtained from 63 healthy individuals at baseline (Day 1 and after three days (Day 4. DNA methylation was measured by bisulfite-PCR-Pyrosequencing. We calculated intraclass correlation coefficients (ICCs to measure the within-individual stability of DNA methylation between Day 1 and 4, subtracted of pyrosequencing error and adjusted for multiple covariates. RESULTS: Methylation markers showed different temporal behaviors ranging from high (IL-6, ICC = 0.89 to low stability (APC, ICC = 0.08 between Day 1 and 4. Multiple sequence and marker characteristics were associated with the degree of variation. Density of CpG dinucleotides nearby the sequence analyzed (measured as CpG(o/e or G+C content within ±200 bp was positively associated with DNA methylation stability. The 3' proximity to repeat elements and range of DNA methylation on Day 1 were also positively associated with methylation stability. An inverted U-shaped correlation was observed between mean DNA methylation on Day 1 and stability. CONCLUSIONS: The degree of short-term DNA methylation stability is marker-dependent and associated with sequence characteristics and methylation levels.

  20. Identification and isolation of full-length cDNA sequences by sequencing and analysis of expressed sequence tags from guarana (Paullinia cupana).

    Science.gov (United States)

    Figueirêdo, L C; Faria-Campos, A C; Astolfi-Filho, S; Azevedo, J L

    2011-01-01

    The current intense production of biological data, generated by sequencing techniques, has created an ever-growing volume of unanalyzed data. We reevaluated data produced by the guarana (Paullinia cupana) transcriptome sequencing project to identify cDNA clones with complete coding sequences (full-length clones) and complete sequences of genes of biotechnological interest, contributing to the knowledge of biological characteristics of this organism. We analyzed 15,490 ESTs of guarana in search of clones with complete coding regions. A total of 12,402 sequences were analyzed using BLAST, and 4697 full-length clones were identified, responsible for the production of 2297 different proteins. Eighty-four clones were identified as full-length for N-methyltransferase and 18 were sequenced in both directions to obtain the complete genome sequence, and confirm the search made in silico for full-length clones. Phylogenetic analyses were made with the complete genome sequences of three clones, which showed only 0.017% dissimilarity; these are phylogenetically close to the caffeine synthase of Theobroma cacao. The search for full-length clones allowed the identification of numerous clones that had the complete coding region, demonstrating this to be an efficient and useful tool in the process of biological data mining. The sequencing of the complete coding region of identified full-length clones corroborated the data from the in silico search, strengthening its efficiency and utility. PMID:21732283

  1. Security Analysis of Accountable Anonymity in Dissent

    OpenAIRE

    Syta, Ewa; Johnson, Aaron; Corrigan-Gibbs, Henry; Weng, Shu-Chun; Wolinsky, David; Ford, Bryan

    2014-01-01

    Users often wish to communicate anonymously on the Internet, for example in group discussion or instant messaging forums. Existing solutions are vulnerable to misbehaving users, however, who may abuse their anonymity to disrupt communication. Dining Cryptographers Networks (DC-nets) leave groups vulnerable to denial-of-service and Sybil attacks, mix networks are difficult to protect against traffic analysis, and accountable voting schemes are unsuited to general anonymous messaging. DISSENT ...

  2. Internet and the right of anonymity

    OpenAIRE

    Voorhoof, Dirk

    2011-01-01

    This articles explores the ratio and characteristics of the right of anonymity on the Internet. A right of anonymity is considered as a shield against oppression, harassment, retaliation, censorship or discrimination and therefore it is considered as a vital component of freedom of speech or freedom of expression. Reference is made to several existing types of rights of anonymity in relation to freedom of expression, such as the right to protect (confidential) journalistic sources, free elec...

  3. Privacy-Preserving Updates to Anonymous Databases

    OpenAIRE

    Sivasubramanian, R.; K.P. KALIYAMURTHIE

    2013-01-01

    Suppose a medical facility connected with a research institution and the researchers can use themedical details of a patient without knowing the personal details. Thus the research data base used by theresearchers must be anonymized (Sanitized). We can consider another problem in the area of census.Individuals give the private information to a trusted party (Census Bureau) and the census bureau mustpublish anonymized or sanitized version of data. So anonymization is done for privacy. Our work...

  4. Amplification of a transcriptionally active DNA sequence in the human brain

    International Nuclear Information System (INIS)

    The authors present their findings of tissue-specific amplification of a DNA fragment actively transcribed in the human brain. This genome fragment was found in the library complement of cDNA of the human brain and evidently belongs to a new class of moderate repetitions of DNA with an unstable copying capacity in the human genome. The authors isolated total cell RNA from various human tissues (brain, placenta), and rat tissues (brain, liver), by the method of hot phenol extraction with guanidine thiocynate. The poly(A+) RNA fraction was isolated by chromatography. Synthesis of cDNA was done on a matrix of poly(A+) RNA of human brain. The cDNA obtained was cloned in plasmid pBR322 for the PstI site using (dC/dG) sequences synthesized on the 3' ends of the vector molecule and cDNA respectively. In cloning 75 ng cDNA, the authors obtained approximately 105 recombinant. This library was analyzed by the hybridization method on columns with two radioactive (32P) probes: the total cDNA preparation and the total nuclear DNA from the human brain. The number of copies of the cloned DNA fragment in the genome was determined by dot hybridization. Restricting fragments of human and rat DNA genomes homologous to the cloned cDNA were identified on radio-autographs. In each case, 10 micrograms of EcoRI DNA hydrolyzate was fractionated in 1% agarose gel. The probe was also readied with RNA samples fractionated in agarose gel with formaldehyde and transferred to a nitrocellulose filter under weak vacuum. The filter was hybridized with 0.1 micrograms DNA pAG 02, labeled with (32P) to a specific activity of 0.5-1 x 109 counts/min x microgram. The autograph was exposed with amplifying screens at -700C for 2 days

  5. Comparison of the Personality Profiles of Inmate Anonymous and Non-Anonymous Male Addicts

    Directory of Open Access Journals (Sweden)

    Nasrolah Erfani

    2013-05-01

    Full Text Available Aim: This study compared the personality profiles of inmate anonymous and non-anonymous male addicts. Method: The participants of study were anonymous and non-anonymous male addicts of the prisons of the Hamadan province in 1391. The population was 3130 addicts, including 627 anonymous and 2503 non-anonymous addicts. The 310 addicts were selected by stratified random sampling the sample size was determined by Cochran formula.The short-form NEO Five Factor personality questionnaire administered among selected sample. Data analyzed by descriptive statistic as frequency and percentage, also, inferential statistic as multivariate analysis of variance was run. Results: The results showed that personality profiles of anonymous and non-anonymous addicts were significantly different. That is, mean score of neuroticism in anonymous addicts was less than non anonymous. Also, mean score of extraversion was higher in anonymous addicts. Conclusion: It can be concluded that the anonymous male addicts are differ with non-anonymous male addicts in personality traits.

  6. More of an Art than a Science: Using Microbial DNA Sequences to Compose Music†

    Science.gov (United States)

    Larsen, Peter E.

    2016-01-01

    Bacteria are everywhere. Microbial ecology is emerging as a critical field for understanding the relationships between these ubiquitous bacterial communities, the environment, and human health. Next generation DNA sequencing technology provides us a powerful tool to indirectly observe the communities by sequencing and analyzing all of the bacterial DNA present in an environment. The results of the DNA sequencing experiments can generate gigabytes to terabytes of information, however, making it difficult for the citizen scientist to grasp and the educator to convey this data. Here, we present a method for interpreting massive amounts of microbial ecology data as musical performances, easily generated on any computer and using only commonly available or freely available software and the ‘Microbial Bebop’ algorithm. Using this approach, citizen scientists and biology educators can sonify complex data in a fun and interactive format, making it easier to communicate both the importance and the excitement of exploring the planet earth’s largest ecosystem. PMID:27047609

  7. More of an Art than a Science: Using Microbial DNA Sequences to Compose Music

    Directory of Open Access Journals (Sweden)

    Peter E. Larsen

    2015-12-01

    Full Text Available Bacteria are everywhere. Microbial ecology is emerging as a critical field for understanding the relationships between these ubiquitous bacterial communities, the environment, and human health. Next generation DNA sequencing technology provides us a powerful tool to indirectly observe the communities by sequencing and analyzing all of the bacterial DNA present in an environment. The results of the DNA sequencing experiments can generate gigabytes to terabytes of information, however, making it difficult for the citizen scientist to grasp and the educator to convey this data. Here, we present a method for interpreting massive amounts of microbial ecology data as musical performances, easily generated on any computer and using only commonly available or freely available software and the ‘Microbial Bebop’ algorithm. Using this approach, citizen scientists and biology educators can sonify complex data in a fun and interactive format, making it easier to communicate both the importance and the excitement of exploring the planet earth’s largest ecosystem.

  8. Sequences with high propensity to form G-quartet structures in kinetoplast DNA from Phytomonas serpens.

    Science.gov (United States)

    Sá-Carvalho, D; Traub-Cseko, Y M

    1995-06-01

    Naturally occurring sequences containing repetitive guanine motifs have the potential to form tetraplex DNA. Phytomonas serpens minicircle DNA shows some regions where one strand is composed mainly of G and T (GT regions). These regions contain several stretches of contiguous guanines. An oligonucleotide was constructed with the sequence corresponding to one of these regions (Phyto-GT). It was demonstrated by native gel electrophoresis and methylation protection that Phyto-GT forms tetramolecular (G4), bimolecular (G'2) and unimolecular (G4') structures stabilized through G-quartets. Tetraplex DNA formation by this sequence could have biological relevance as it can be formed in physiological conditions and GT regions comprise approximately one-third of P. serpens and Crithidia oncopelti minicircles. PMID:8538680

  9. Sequence polymorphism of mitochondrial DNA in Japanese individuals from Gifu Prefecture.

    Science.gov (United States)

    Nagai, Atsushi; Nakamura, Isao; Shiraki, Futoru; Bunai, Yasuo; Ohya, Isao

    2003-03-01

    Sequence polymorphisms of the hypervariable region HV1 in mitochondrial DNA (mtDNA) were analyzed in a sample of 137 unrelated Japanese individuals living in Gifu Prefecture (central region of Japan) using polymerase chain reaction amplification and direct sequencing. Eighty-two different haplotypes resulting from 81 variable sites were found in the mtDNA HV1 region between positions 16061 and 16450. The most frequent haplotype (16223T, 16362C) was shared by ten individuals. The genetic diversity and the genetic identity were 0.985 and 0.022, respectively. The C-stretch region located around position 16189 was observed in 23.4% of this population sample. Sequence heteroplasmy at the position 16103 (A/G) was found in one individual. PMID:12935592

  10. Sequence-specific cleavage of single-stranded DNA: Oligodeoxynucleotide-EDTA·Fe(II)

    OpenAIRE

    1985-01-01

    The synthesis of a DNA hybridization probe 19 nucleotides in length, equipped with the metal chelator EDTA at C-5 of thymidine in position 10 (indicated by T*) is described. DNA-EDTA 1 has the sequence 5'-T-A-A-C-G-C-A-G-T*-C-A-G-G-C-A-C-C-G-T-3', which is complementary to a 19-nucleotide sequence in the plasmid pBR322. In the presence of Fe(II), O2, and dithiothreitol, DNA-EDTA 1 affords specific cleavage (25 degrees C, pH 7.4, 60 min) at its complementary sequence in a heat-denatured 167-ba...

  11. Multi-scale coding of genomic information: From DNA sequence to genome structure and function

    International Nuclear Information System (INIS)

    Understanding how chromatin is spatially and dynamically organized in the nucleus of eukaryotic cells and how this affects genome functions is one of the main challenges of cell biology. Since the different orders of packaging in the hierarchical organization of DNA condition the accessibility of DNA sequence elements to trans-acting factors that control the transcription and replication processes, there is actually a wealth of structural and dynamical information to learn in the primary DNA sequence. In this review, we show that when using concepts, methodologies, numerical and experimental techniques coming from statistical mechanics and nonlinear physics combined with wavelet-based multi-scale signal processing, we are able to decipher the multi-scale sequence encoding of chromatin condensation-decondensation mechanisms that play a fundamental role in regulating many molecular processes involved in nuclear functions.

  12. Sequence Effect on the Topology of 3 + 1 Interlocked Bimolecular DNA G-Quadruplexes.

    Science.gov (United States)

    Gao, Shang; Cao, Yanwei; Yan, Yuting; Guo, Xinhua

    2016-05-17

    Electrospray ionization mass spectrometry (ESI-MS) combined with fluorescence, circular dichroism, UV spectrophotometer, and native polyacrylamide gel electrophoresis techniques are used to study structural features of interlocked dimers formed by DNA sequence 93del (GGGGTGGGAGGAGGGT) and its derivatives. Herein, we demonstrate that the interlocked dimers can be distinguished from stacked dimers formed by sequences T30923 (GGGTGGGTGGGTGGGT) and T30177 (GTGGTGGGTGGGTGGGT). In addition, loop length, the base at 5'-end, and the isolation of T and TT to the first 4G tract do significantly influence the formation and topologies of interlocked dimers. Furthermore, our results suggest that the 4G tract and the 2G tract in various locations in the 93del derivative sequence can form interlocked structure. This work not only provides new insight into the assembly of 3 + 1 interlocked DNA conformations but also demonstrates that ESI-MS combined with other analytical methods is rapid and useful for DNA structural studies. PMID:27027538

  13. More of an Art than a Science: Using Microbial DNA Sequences to Compose Music.

    Science.gov (United States)

    Larsen, Peter E

    2016-03-01

    Bacteria are everywhere. Microbial ecology is emerging as a critical field for understanding the relationships between these ubiquitous bacterial communities, the environment, and human health. Next generation DNA sequencing technology provides us a powerful tool to indirectly observe the communities by sequencing and analyzing all of the bacterial DNA present in an environment. The results of the DNA sequencing experiments can generate gigabytes to terabytes of information, however, making it difficult for the citizen scientist to grasp and the educator to convey this data. Here, we present a method for interpreting massive amounts of microbial ecology data as musical performances, easily generated on any computer and using only commonly available or freely available software and the 'Microbial Bebop' algorithm. Using this approach, citizen scientists and biology educators can sonify complex data in a fun and interactive format, making it easier to communicate both the importance and the excitement of exploring the planet earth's largest ecosystem. PMID:27047609

  14. Gold electrode modified by self-assembled monolayers of thiols to determine DNA sequences hybridization

    Indian Academy of Sciences (India)

    Mízia M S Silva; Igor T Cavalcanti; M Fátima Barroso; M Goreti F Sales; Rosa Fireman Dutra

    2010-11-01

    The process of immobilization of biological molecules is one of the most important steps in the construction of a biosensor. In the case of DNA, the way it exposes its bases can result in electrochemical signals to acceptable levels. The use of self-assembled monolayer that allows a connection to the gold thiol group and DNA binding to an aldehydic ligand resulted in the possibility of determining DNA hybridization. Immobilized single strand of DNA (ssDNA) from calf thymus pre-formed from alkanethiol film was formed by incubating a solution of 2-aminoethanothiol (Cys) followed by glutaraldehyde (Glu). Cyclic voltammetry (CV) was used to characterize the self-assembled monolayer on the gold electrode and, also, to study the immobilization of ssDNA probe and hybridization with the complementary sequence (target ssDNA). The ssDNA probe presents a well-defined oxidation peak at +0.158 V. When the hybridization occurs, this peak disappears which confirms the efficacy of the annealing and the DNA double helix performing without the presence of electroactive indicators. The use of SAM resulted in a stable immobilization of the ssDNA probe, enabling the hybridization detection without labels. This study represents a promising approach for molecular biosensor with sensible and reproducible results.

  15. A Real-Time de novo DNA Sequencing Assembly Platform Based on an FPGA Implementation.

    Science.gov (United States)

    Hu, Yuanqi; Georgiou, Pantelis

    2016-01-01

    This paper presents an FPGA based DNA comparison platform which can be run concurrently with the sensing phase of DNA sequencing and shortens the overall time needed for de novo DNA assembly. A hybrid overlap searching algorithm is applied which is scalable and can deal with incremental detection of new bases. To handle the incomplete data set which gradually increases during sequencing time, all-against-all comparisons are broken down into successive window-against-window comparison phases and executed using a novel dynamic suffix comparison algorithm combined with a partitioned dynamic programming method. The complete system has been designed to facilitate parallel processing in hardware, which allows real-time comparison and full scalability as well as a decrease in the number of computations required. A base pair comparison rate of 51.2 G/s is achieved when implemented on an FPGA with successful DNA comparison when using data sets from real genomes. PMID:27045828

  16. Obesity risk gene TMEM18 encodes a sequence-specific DNA-binding protein.

    Directory of Open Access Journals (Sweden)

    Jaana M Jurvansuu

    Full Text Available Transmembrane protein 18 (TMEM18 has previously been connected to cell migration and obesity. However, the molecular function of the protein has not yet been described. Here we show that TMEM18 localises to the nuclear membrane and binds to DNA in a sequence-specific manner. The protein binds DNA with its positively charged C-terminus that contains also a nuclear localisation signal. Increase in the amount of TMEM18 in cells suppresses expression from a reporter vector with the TMEM18 target sequence. TMEM18 is a small protein of 140 residues and is predicted to be mostly alpha-helical with three transmembrane parts. As a consequence the DNA binding by TMEM18 would bring the chromatin very near to nuclear membrane. We speculate that this closed perinuclear localisation of TMEM18-bound DNA might repress transcription from it.

  17. An Effective Identification of Species from DNA Sequence: A Classification Technique by Integrating DM and ANN

    Directory of Open Access Journals (Sweden)

    Sathish Kumar S

    2012-08-01

    Full Text Available Species classification from DNA sequences remains as an open challenge in the area of bioinformatics, which deals with the collection, processing and analysis of DNA and proteomic sequence. Though incorporation of data mining can guide the process to perform well, poor definition, and heterogeneous nature of gene sequence remains as a barrier. In this paper, an effective classification technique to identify the organism from its gene sequence is proposed. The proposed integrated technique is mainly based on pattern mining and neural network-based classification. In pattern mining, the technique mines nucleotide patterns and their support from selected DNA sequence. The high dimension of the mined dataset is reduced using Multilinear Principal Component Analysis (MPCA. In classification, a well-trained neural network classifies the selected gene sequence and so the organism is identified even from a part of the sequence. The proposed technique is evaluated by performing 10-fold cross validation, a statistical validation measure, and the obtained results prove the efficacy of the technique.

  18. Isolation and sequence analysis of a cDNA clone encoding the fifth complement component

    DEFF Research Database (Denmark)

    Lundwall, Åke B; Wetsel, Rick A; Kristensen, Torsten;

    1985-01-01

    clone of 1.85 kilobase pairs was isolated. Hybridization of the mixed-sequence probe to the complementary strand of the plasmid insert and sequence analysis by the dideoxy method predicted the expected protein sequence of C5a (positions 1-12), amino-terminal to the anticipated priming site. The sequence......We have used available protein sequence data for the anaphylatoxin (C5a) portion of the fifth component of human complement (residues 19-25) to synthesize a mixed-sequence oligonucleotide probe. The labeled oligonucleotide was then used to screen a human liver cDNA library, and a single candidate cDNA...... obtained further predicted an arginine-rich sequence (RPRR) immediately upstream of the N-terminal threonine of C5a, indicating that the promolecule form of C5 is synthesized with a beta alpha-chain orientation as previously shown for pro-C3 and pro-C4. The C5 cDNA clone was sheared randomly by sonication...

  19. cDNA-derived amino acid sequences of myoglobins from nine species of whales and dolphins.

    Science.gov (United States)

    Iwanami, Kentaro; Mita, Hajime; Yamamoto, Yasuhiko; Fujise, Yoshihiro; Yamada, Tadasu; Suzuki, Tomohiko

    2006-10-01

    We determined the myoglobin (Mb) cDNA sequences of nine cetaceans, of which six are the first reports of Mb sequences: sei whale (Balaenoptera borealis), Bryde's whale (Balaenoptera edeni), pygmy sperm whale (Kogia breviceps), Stejneger's beaked whale (Mesoplodon stejnegeri), Longman's beaked whale (Indopacetus pacificus), and melon-headed whale (Peponocephala electra), and three confirm the previously determined chemical amino acid sequences: sperm whale (Physeter macrocephalus), common minke whale (Balaenoptera acutorostrata) and pantropical spotted dolphin (Stenella attenuata). We found two types of Mb in the skeletal muscle of pantropical spotted dolphin: Mb I with the same amino acid sequence as that deposited in the protein database, and Mb II, which differs at two amino acid residues compared with Mb I. Using an alignment of the amino acid or cDNA sequences of cetacean Mb, we constructed a phylogenetic tree by the NJ method. Clustering of cetacean Mb amino acid and cDNA sequences essentially follows the classical taxonomy of cetaceans, suggesting that Mb sequence data is valid for classification of cetaceans at least to the family level. PMID:16962803

  20. cDNA cloning, sequence analysis, and chromosomal localization of the gene for human carnitine palmitoyltransferase.

    Science.gov (United States)

    Finocchiaro, G; Taroni, F; Rocchi, M; Martin, A L; Colombo, I; Tarelli, G T; DiDonato, S

    1991-01-01

    We have cloned and sequenced a cDNA encoding human liver carnitine palmitoyltransferase (CPTase; palmitoyl-CoA:L-carnitine O-palmitoyltransferase, EC 2.3.1.21), an inner mitochondrial membrane enzyme that plays a major role in the fatty acid oxidation pathway. Mixed oligonucleotide primers whose sequences were deduced from one tryptic peptide obtained from purified CPTase were used in a polymerase chain reaction, allowing the amplification of a 0.12-kilobase fragment of human genomic DNA encoding such a peptide. A 60-base-pair (bp) oligonucleotide synthesized on the basis of the sequence from this fragment was used for the screening of a cDNA library from human liver and hybridized to a cDNA insert of 2255 bp. This cDNA contains an open reading frame of 1974 bp that encodes a protein of 658 amino acid residues including 25 residues of an NH2-terminal leader peptide. The assignment of this open reading frame to human liver CPTase is confirmed by matches to seven different amino acid sequences of tryptic peptides derived from pure human CPTase and by the 82.2% homology with the amino acid sequence of rat CPTase. The NH2-terminal region of CPTase contains a leucine-proline motif that is shared by carnitine acetyl- and octanoyltransferases and by choline acetyltransferase. The gene encoding CPTase was assigned to human chromosome 1, region 1q12-1pter, by hybridization of CPTase cDNA with a DNA panel of 19 human-hamster somatic cell hybrids. Images PMID:1988962