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Sample records for dna base cg

  1. Universal spectrum for DNA base CG frequency distribution in Takifugu rubripes (Puffer fish) genome

    CERN Document Server

    Selvam, A M

    2007-01-01

    The frequency distribution of DNA bases A, C, G, T exhibit fractal fluctuations, namely a zigzag pattern of an increase followed by a decrease of all orders of magnitude along the length of the DNA molecule. Selfsimilar fractal fluctuations are ubiquitous to space-time fluctuations of dynamical systems in nature. The power spectra of fractal fluctuations exhibit inverse power law form signifying long-range space-time correlations such that there is two-way communication between local (small-scale) and global (large-scale) perturbations. In this paper it is shown that DNA base CG frequency distribution in Takifugu rubripes (Puffer fish) Genome Release 4 exhibit universal inverse power law form of the statistical normal distribution consistent with a general systems theory model prediction of quantumlike chaos governing fractal space-time distributions. The model predictions are (i) quasicrystalline Penrose tiling pattern for the nested coiled structure thereby achieving maximum packing efficiency for the DNA m...

  2. Universal spectrum for DNA base C+G frequency distribution in Human chromosomes 1 to 24

    CERN Document Server

    Selvam, A M

    2007-01-01

    Power spectra of human DNA base C+G frequency distribution in all available contiguous sections exhibit the universal inverse power law form of the statistical normal distribution for the 24 chromosomes. Inverse power law form for power spectra of space-time fluctuations is generic to dynamical systems in nature and indicate long-range space-time correlations. A recently developed general systems theory predicts the observed non-local connections as intrinsic to quantumlike chaos governing space-time fluctuations of dynamical systems. The model predicts the following. (1) The quasiperiodic Penrose tiling pattern for the nested coiled structure of the DNA molecule in the chromosome resulting in maximum packing efficiency. (2) The DNA molecule functions as a unified whole fuzzy logic network with ordered two-way signal transmission between the coding and non-coding regions. Recent studies indicate influence of non-coding regions on functions of coding regions in the DNA molecule.

  3. Universal spectrum for DNA base C+G concentration variability in Human chromosome Y

    CERN Document Server

    Selvam, A M

    2004-01-01

    The spatial distribution of DNA base sequence A, C, G and T exhibit selfsimilar fractal fluctuations and the corresponding power spectra follow inverse power law form, which implies the following: (1) A scale invariant eddy continuum, namely, the amplitudes of component eddies are related to each other by a scale factor alone. In general, the scale factor is different for different scale ranges and indicates a multifractal structure for the spatial distribution of DNA base sequence. (2) Long-range spatial correlations of the eddy fluctuations. Multifractal structure to space-time fluctuations and the associated inverse power law form for power spectra is generic to spatially extended dynamical systems in nature and is a signature of self-organized criticality. The exact physical mechanism for the observed self-organized criticality is not yet identified. The author has developed a general systems theory where quantum mechanical laws emerge as self-consistent explanations for the observed long-range space-time...

  4. CG methylation in DNA transcription

    Science.gov (United States)

    Chela-Flores, J.; Migoni, R. L.

    1990-08-01

    A simple model of DNA is considered in which the nucleotides cytosine (C) and guanine (G) are not assumed to be identical, and in which macroscopic thermodynamic quantities may be calculated exactly. The H bonds between the C and G nucleotides are assumed to be Morse potentials. We discuss the statistical mechanics of the DNA molecule in the configuration (5'...GGG ...3'; 3'...CCC ...5'), which may be copied by RNA polymerase into a messenger RNA (mRNA) strand (5'...CCC ...3'). This model suggests that replacements of C by 5-methylcytosine (5mC) may be a secondary effect in the inhibition of genetic expression, not interfering directly with the formation of an open state. An experimental test is suggested. The implications of this result are discussed for a related system, in which the enzyme methylase is known to methylate almost exclusively those Cs that are followed by Gs as a regulatory strategy employed by some eukaryotes.

  5. cgDNA: a software package for the prediction of sequence-dependent coarse-grain free energies of B-form DNA.

    Science.gov (United States)

    Petkevičiūtė, D; Pasi, M; Gonzalez, O; Maddocks, J H

    2014-11-10

    cgDNA is a package for the prediction of sequence-dependent configuration-space free energies for B-form DNA at the coarse-grain level of rigid bases. For a fragment of any given length and sequence, cgDNA calculates the configuration of the associated free energy minimizer, i.e. the relative positions and orientations of each base, along with a stiffness matrix, which together govern differences in free energies. The model predicts non-local (i.e. beyond base-pair step) sequence dependence of the free energy minimizer. Configurations can be input or output in either the Curves+ definition of the usual helical DNA structural variables, or as a PDB file of coordinates of base atoms. We illustrate the cgDNA package by comparing predictions of free energy minimizers from (a) the cgDNA model, (b) time-averaged atomistic molecular dynamics (or MD) simulations, and (c) NMR or X-ray experimental observation, for (i) the Dickerson-Drew dodecamer and (ii) three oligomers containing A-tracts. The cgDNA predictions are rather close to those of the MD simulations, but many orders of magnitude faster to compute. Both the cgDNA and MD predictions are in reasonable agreement with the available experimental data. Our conclusion is that cgDNA can serve as a highly efficient tool for studying structural variations in B-form DNA over a wide range of sequences.

  6. NICE CG178 Psychosis and Schizophrenia in Adults: Treatment and Management - an evidence-based guideline?

    Science.gov (United States)

    Taylor, Mark; Perera, Udayanga

    2015-05-01

    National Institute for Health and Care Excellence (NICE) clinical guideline (CG)178 was published in 2014. NICE guidelines occupy an important international position. We argue that CG178 overemphasises the use of cognitive-behavioural therapy for schizophrenia and those 'at risk' of psychosis, with recommendations that do not always reflect the evidence base. The CG178 recommendations on medications are limited.

  7. Evidence for DAPI intercalation in CG sites of DNA oligomer [d(CGACGTCG)]2: a 1H NMR study.

    Science.gov (United States)

    Trotta, E; D'Ambrosio, E; Ravagnan, G; Paci, M

    1995-01-01

    The interaction between 4',6-diamidino-2-phenylindole (DAPI) and the DNA oligomer [d(CGACGTCG)]2 has been investigated by proton one- and two-dimensional NMR spectroscopy in solution. Compared with the minor groove binding of the drug to [d(GCGATCGC)]2, previously studied by NMR spectroscopy, the interaction of DAPI with [d(CGACGTCG)]2 appears markedly different and gives results typical of a binding mechanism by intercalation. C:G imino proton signals of the [d(CGACGTCG)]2 oligomer as well as DAPI resonances appear strongly upfield shifted and sequential dipolar connectivities between cytosine and guanine residues show a clear decrease upon binding. Moreover, protons lying in both the minor and major grooves of the DNA double helix appear involved in the interaction, as evidenced principally by intermolecular drug-DNA NOEs. In particular, the results indicate the existence of two stereochemically non-equivalent intercalation binding sites located in the central and terminal adjacent C:G base pairs of the palindromic DNA sequence. Different lifetimes of the complexes were also observed for the two sites of binding. Moreover, due to the fast exchange on the NMR timescale between free and bound species, different interactions in dynamic equilibrium with the observed intercalative bindings were not excluded. PMID:7753623

  8. visualization of reaction mechanism by cg based on quantum ...

    African Journals Online (AJOL)

    IICBA01

    in MOPAC for vibration analysis. If the peak was observed, .... A student is expected to obtain the image of an umbrella reversal like motion in Walden's inversion. ... This manual control feature provides “Hands-on” feeling to student. This CG.

  9. RNAi, DRD1, and histone methylation actively target developmentally important non-CG DNA methylation in arabidopsis.

    Directory of Open Access Journals (Sweden)

    Simon W-L Chan

    2006-06-01

    Full Text Available Cytosine DNA methylation protects eukaryotic genomes by silencing transposons and harmful DNAs, but also regulates gene expression during normal development. Loss of CG methylation in the Arabidopsis thaliana met1 and ddm1 mutants causes varied and stochastic developmental defects that are often inherited independently of the original met1 or ddm1 mutation. Loss of non-CG methylation in plants with combined mutations in the DRM and CMT3 genes also causes a suite of developmental defects. We show here that the pleiotropic developmental defects of drm1 drm2 cmt3 triple mutant plants are fully recessive, and unlike phenotypes caused by met1 and ddm1, are not inherited independently of the drm and cmt3 mutations. Developmental phenotypes are also reversed when drm1 drm2 cmt3 plants are transformed with DRM2 or CMT3, implying that non-CG DNA methylation is efficiently re-established by sequence-specific signals. We provide evidence that these signals include RNA silencing though the 24-nucleotide short interfering RNA (siRNA pathway as well as histone H3K9 methylation, both of which converge on the putative chromatin-remodeling protein DRD1. These signals act in at least three partially intersecting pathways that control the locus-specific patterning of non-CG methylation by the DRM2 and CMT3 methyltransferases. Our results suggest that non-CG DNA methylation that is inherited via a network of persistent targeting signals has been co-opted to regulate developmentally important genes.

  10. Classification of pregnancies of unknown location according to four different hCG-based protocols.

    Science.gov (United States)

    Fistouris, J; Bergh, C; Strandell, A

    2016-10-01

    How do four protocols based on serial human chorionic gonadotropin (hCG) measurements perform when classifying pregnancies of unknown location (PULs) as low or high risk of being an ectopic pregnancy (EP)? The use of cut-offs in hCG level changes published by NICE, and a logistic regression model, M4, correctly classify more PULs as high risk, compared with two other protocols. A logistic regression model, M4, based on the mean of two consecutive hCG values and the hCG ratio (hCG 48 h/hCG 0 h) that classify PULs into low- and high-risk groups for triage purposes, identifies more EPs than a protocol using the cut-offs between a 13% decline and a 66% rise in hCG levels over 48 h. A retrospective comparative study of four different hCG-based protocols classifying PULs as low or high risk of being an EP was performed at a gynaecological emergency unit over 3 years. We identified 915 women with a PUL. Initial transvaginal ultrasonography (TVS) findings categorised 187 of the PULs as probable intrauterine pregnancies (IUPs) and 16 as probable EPs. The rate of change in hCG levels over 48 h was calculated for each patient and subjected to three different hCG threshold intervals and a logistic regression model for outcome prediction. Each PUL was subsequently dichotomised to either low-risk (i.e. failed PUL/IUP) or high-risk (i.e. EP) classification, which allowed us to compare the diagnostic performance. In 'Protocol A', a PUL was classified as low risk if >13% hCG level decline or >66% hCG level rise was achieved; otherwise, the PUL was classified as high risk of being an EP. 'Protocol B' classified a PUL as low or high risk using cut-offs of 35-50% declining hCG levels and of 53% rising hCG levels. Similarly, 'Protocol C' used hCG level cut-offs published by NICE, 50% for declining hCG levels and 63% for rising hCG levels. Finally, if a logistic regression model 'Protocol M4' calculated a ≥5% risk of the PUL being an EP, it was classified as high risk, and otherwise

  11. Effects of Pronunciation Practice System Based on Personalized CG Animations of Mouth Movement Model

    Directory of Open Access Journals (Sweden)

    Kohei Arai

    2012-06-01

    Full Text Available Pronunciation practice system based on personalized Computer Graphics: CG animation of mouth movement model is proposed. The system enables a learner to practice pronunciation by looking at personalized CG animations of mouth movement model , and allows him/her to compare them with his/her own mouth movements. In order to evaluate the effectiveness of the system by using personalized CG animation of mouth movement model, Japanese vowel and consonant sounds were read by 8 infants before and after practicing with the proposed system, and their pronunciations were examined. Remarkable improvement on their pronunciations is confirmed through a comparison to their pronunciation without the proposed system based on identification test by subjective basis.

  12. Early hCG addition to rFSH for ovarian stimulation in IVF provides better results and the cDNA copies of the hCG receptor may be an indicator of successful stimulation

    Directory of Open Access Journals (Sweden)

    Paraskevis Dimitris

    2009-10-01

    Full Text Available Abstract A simple, safe and cost-effective treatment protocol in ovarian stimulation is of great importance in IVF practice, especially in the case of previous unsuccessful attempts. hCG has been used as a substitute of LH because of the degree of homology between the two hormones. The main aim of this prospective randomized study was to determine, for the first time, whether low dose hCG added to rFSH for ovarian stimulation could produce better results compared to the addition of rLH in women entering IVF-ET, especially in those women that had previous IVF failures. An additional aim was to find an indicator that would allow us to follow-up ovarian stimulation and, possibly, modify it in order to achieve a better IVF outcome; and that indicator may be the cDNA copies of the LH/hCG receptor. Group A patients (n = 58 were administered hCG and Group B rLH (n = 56 in addition to rFSH in the first days of ovarian stimulation. The number of follicles and oocytes and, most importantly, implantation and pregnancy rates were shown to be statistically significantly higher in the hCG group. This study has also determined, for the first time to our best knowledge, m-RNA for LH/hCG receptors in the lymphocytes of peripheral blood 40 h before ovum pick-up. cDNA levels of the hCG receptor after ovarian stimulation were significantly higher among women receiving hCG compared to those receiving LH. In addition, higher levels were encountered among women with pregnancy compared to those without, although this was not statistically significant due to the small number of pregnancies. It seems that hCG permits a highly effective and more stable occupancy of rLH/hCG receptors and gives more follicles and more oocytes. The determination of cDNA copies could be, in the future, a marker during ovulation induction protocols and of course a predictor for the outcome of ART in the special subgroup of patients with previous failures.

  13. Hyperrecombination in pneumococcus: A/G to C.G repair and requirement for DNA polymerase I.

    Science.gov (United States)

    Pasta, F; Sicard, M A

    1994-09-01

    During pneumococcal transformation, we had previously described that the ami36 mutation, which results from a C.G to A.T transversion, induces a large excess of wild-type recombinants in two point crosses. Upon donor-recipient DNA recombination, two heteroduplexes are generated by this mutation: A36/G+ and C+/T36. In two point crosses, hyperrecombination is observed only when transformation leads to the A/G mismatch. Here, we have studied the separate evolution of A36/G+ and C+/T36 heterozygotes created upon transformation of an ami36 mutant strain with artificial heteroduplex DNAs. We found that the A36/G+ mismatch leads to a preferential generation of wild-type progeny as compared with the complementary C+/T36 mismatch. This result suggests that A/G carrying transformants partly behave as wild-type homozygotes. The only way to account for such behavior is an excision repair correcting some A/G mispairs created upon transformation into C.G pairs. Moreover, we show that hyperrecombination triggered by ami36 is strongly reduced in a DNA polymerase I deficient strain. This strengthens the fact of DNA repair synthesis, which should be therefore prominently due to DNA polymerase I.

  14. MeCP2 binds to non-CG methylated DNA as neurons mature, influencing transcription and the timing of onset for Rett syndrome.

    Science.gov (United States)

    Chen, Lin; Chen, Kaifu; Lavery, Laura A; Baker, Steven Andrew; Shaw, Chad A; Li, Wei; Zoghbi, Huda Y

    2015-04-28

    Epigenetic mechanisms, such as DNA methylation, regulate transcriptional programs to afford the genome flexibility in responding to developmental and environmental cues in health and disease. A prime example involving epigenetic dysfunction is the postnatal neurodevelopmental disorder Rett syndrome (RTT), which is caused by mutations in the gene encoding methyl-CpG binding protein 2 (MeCP2). Despite decades of research, it remains unclear how MeCP2 regulates transcription or why RTT features appear 6-18 months after birth. Here we report integrated analyses of genomic binding of MeCP2, gene-expression data, and patterns of DNA methylation. In addition to the expected high-affinity binding to methylated cytosine in the CG context (mCG), we find a distinct epigenetic pattern of substantial MeCP2 binding to methylated cytosine in the non-CG context (mCH, where H = A, C, or T) in the adult brain. Unexpectedly, we discovered that genes that acquire elevated mCH after birth become preferentially misregulated in mouse models of MeCP2 disorders, suggesting that MeCP2 binding at mCH loci is key for regulating neuronal gene expression in vivo. This pattern is unique to the maturing and adult nervous system, as it requires the increase in mCH after birth to guide differential MeCP2 binding among mCG, mCH, and nonmethylated DNA elements. Notably, MeCP2 binds mCH with higher affinity than nonmethylated identical DNA sequences to influence the level of Bdnf, a gene implicated in the pathophysiology of RTT. This study thus provides insight into the molecular mechanism governing MeCP2 targeting and sheds light on the delayed onset of RTT symptoms.

  15. CG Chair

    OpenAIRE

    Pedro, Catarina

    2013-01-01

    Neste relatório de estágio damos conta da nossa integração e actividades desenvolvidas e, mais especificamente, relativa ao projeto final da cadeira empilhavel denominada CG Chair. O estágio desenvolveu-se na empresa de mobiliário escolar e de escritório VS - Vereinigte Spezialmobelfabriken GmbH Co. KG, em Tauberbischöfsheim - Alemanha. É uma empresa que existe há 114 anos, domina o mercado mobiliário escolar na Europa e está a investir ainda no mobiliár...

  16. Stochastic Finite Element Method for Mechanical Vibration Based on Conjugate Gradient(CG)

    Institute of Scientific and Technical Information of China (English)

    MO Wen-hui

    2008-01-01

    When material properties, geometry parameters and applied loads are assumed to be stochastic, the vibration equation of a system is transformed to static problem by using Newmark method. In order to improve the computational efficiency and to save storage, the Conjugate Gradient (CG) method is presented. The CG is an effective method for solving a large system of linear equations and belongs to the method of iteration with rapid convergence and high precision. An example is given and calculated results are compared to validate the proposed methods.

  17. Effect of the 3-halo substitution of the 2'-deoxy aminopyridinyl-pseudocytidine derivatives on the selectivity and stability of antiparallel triplex DNA with a CG inversion site.

    Science.gov (United States)

    Wang, Lei; Taniguchi, Yosuke; Okamura, Hidenori; Sasaki, Shigeki

    2017-07-15

    Triplex formation against a target duplex DNA has the potential to become a tool for the genome research. However, there is an intrinsic restriction on the duplex DNA sequences capable of forming the triplex DNA. Recently, we demonstrated the selective formation of the stable antiparallel triplexes containing the CG inversion sites using the 2'-deoxy-1-methylpseudocytidine derivative (ΨdC), whose amino group was conjugated with the 2-aminopyridine at its 5-position as an additional hydrogen bonding unit (AP-ΨdC). The 1-N of 2-aminopyridine was supposed to be protonated to form the hydrogen bond with the guanine of the CG inversion site. In this study, to test the effect of the 3-substitution of the 2-aminopyridine unit of AP-ΨdC on the triplex stability, we synthesized the 3-halogenated 2-aminopyridine derivatives of AP-ΨdC. The pKa values 1-N of the 2-aminopyridine unit of AP-ΨdC as the monomer nucleoside were determined to be 6.3 for 3-CH3 ((Me)AP-ΨdC), 6.1 for 3-H (AP-ΨdC), 4.3 for 3-Cl ((Cl)AP-ΨdC), 4.4 for 3-Br ((Br)AP-ΨdC), and 4.7 for 3-I ((I)AP-ΨdC), suggesting that all the halogenated AP-ΨdCs are not protonated under neutral conditions. Interestingly, although the recognition selectivity depends on the sequence context, the TFO having the sequence of the 3'-G-((I)AP-ΨdC)-A-5' context showed the selective triplex formation with the CG inversion site. These results suggest that the protonation at the 1-N position plays an important role in the stable and selective triplex formation of AP-ΨdC derivatives in any sequences. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. Sharp switches between regular and swinger mitochondrial replication: 16S rDNA systematically exchanging nucleotides AT+CG in the mitogenome of Kamimuria wangi.

    Science.gov (United States)

    Seligmann, Hervé

    2016-07-01

    Swinger DNAs are sequences whose homology with known sequences is detected only by assuming systematic exchanges between nucleotides. Nine symmetric (XY, i.e. AC) and fourteen asymmetric (X->Y->Z, i.e. A->C->G) exchanges exist. All swinger DNA previously detected in GenBank follow the AT+CG exchange, while mitochondrial swinger RNAs distribute among different swinger types. Here different alignment criteria detect 87 additional swinger mitochondrial DNAs (86 from insects), including the first swinger gene embedded within a complete genome, corresponding to the mitochondrial 16S rDNA of the stonefly Kamimuria wangi. Other Kamimuria mt genome regions are "regular", stressing unanswered questions on (a) swinger polymerization regulation; (b) swinger 16S rDNA functions; and (c) specificity to rDNA, in particular 16S rDNA. Sharp switches between regular and swinger replication, together with previous observations on swinger transcription, suggest that swinger replication might be due to a switch in polymerization mode of regular polymerases and the possibility of swinger-encoded information, predicted in primordial genes such as rDNA.

  19. Determination of biological activity of gonadotropins hCG and FSH by Förster resonance energy transfer based biosensors.

    Science.gov (United States)

    Mazina, Olga; Allikalt, Anni; Tapanainen, Juha S; Salumets, Andres; Rinken, Ago

    2017-02-09

    Determination of biological activity of gonadotropin hormones is essential in reproductive medicine and pharmaceutical manufacturing of the hormonal preparations. The aim of the study was to adopt a G-protein coupled receptor (GPCR)-mediated signal transduction pathway based assay for quantification of biological activity of gonadotropins. We focussed on studying human chorionic gonadotropin (hCG) and follicle-stimulating hormone (FSH), as these hormones are widely used in clinical practice. Receptor-specific changes in cellular cyclic adenosine monophosphate (cAMP, second messenger in GPCR signalling) were monitored by a Förster resonance energy transfer (FRET) biosensor protein (T)Epac(VV) in living cells upon activation of the relevant gonadotropin receptor. The BacMam gene delivery system was used for biosensor protein expression in target cells. In the developed assay only biologically active hormones initiated GPCR-mediated cellular signalling. High assay sensitivities were achieved for detection of hCG (limit of detection, LOD: 5 pM) and FSH (LOD: 100 pM). Even the small-scale conformational changes caused by thermal inactivation and reducing the biological activity of the hormones were registered. In conclusion, the proposed assay is suitable for quantification of biological activity of gonadotropins and is a good alternative to antibody- and animal-testing-based assays used in pharmaceutical industry and clinical research.

  20. Determination of biological activity of gonadotropins hCG and FSH by Förster resonance energy transfer based biosensors

    Science.gov (United States)

    Mazina, Olga; Allikalt, Anni; Tapanainen, Juha S.; Salumets, Andres; Rinken, Ago

    2017-01-01

    Determination of biological activity of gonadotropin hormones is essential in reproductive medicine and pharmaceutical manufacturing of the hormonal preparations. The aim of the study was to adopt a G-protein coupled receptor (GPCR)-mediated signal transduction pathway based assay for quantification of biological activity of gonadotropins. We focussed on studying human chorionic gonadotropin (hCG) and follicle-stimulating hormone (FSH), as these hormones are widely used in clinical practice. Receptor-specific changes in cellular cyclic adenosine monophosphate (cAMP, second messenger in GPCR signalling) were monitored by a Förster resonance energy transfer (FRET) biosensor protein TEpacVV in living cells upon activation of the relevant gonadotropin receptor. The BacMam gene delivery system was used for biosensor protein expression in target cells. In the developed assay only biologically active hormones initiated GPCR-mediated cellular signalling. High assay sensitivities were achieved for detection of hCG (limit of detection, LOD: 5 pM) and FSH (LOD: 100 pM). Even the small-scale conformational changes caused by thermal inactivation and reducing the biological activity of the hormones were registered. In conclusion, the proposed assay is suitable for quantification of biological activity of gonadotropins and is a good alternative to antibody- and animal-testing-based assays used in pharmaceutical industry and clinical research. PMID:28181555

  1. DNA based computers II

    CERN Document Server

    Landweber, Laura F; Baum, Eric B

    1998-01-01

    The fledgling field of DNA computers began in 1994 when Leonard Adleman surprised the scientific community by using DNA molecules, protein enzymes, and chemicals to solve an instance of a hard computational problem. This volume presents results from the second annual meeting on DNA computers held at Princeton only one and one-half years after Adleman's discovery. By drawing on the analogy between DNA computing and cutting-edge fields of biology (such as directed evolution), this volume highlights some of the exciting progress in the field and builds a strong foundation for the theory of molecular computation. DNA computing is a radically different approach to computing that brings together computer science and molecular biology in a way that is wholly distinct from other disciplines. This book outlines important advances in the field and offers comprehensive discussion on potential pitfalls and the general practicality of building DNA based computers.

  2. 广东地区土壤中分离的棘阿米巴CG/S 1株的18 S rDNA基因分析%Analysis of 18 S rDNA gene of Acanthamoeba sp. CG/S 1 isolated from Guangdong soil

    Institute of Scientific and Technical Information of China (English)

    王月华; 玄英花; 郑善子; 崔春权

    2007-01-01

    [目的]从广东地区土壤中分离棘阿米巴CG/S 1株,测定其18 S rDNA基因序列. [方法]从土壤中分离棘阿米巴CG/S 1株,提取基因组18 S rDNA,应用棘阿米巴属特异性引物进行PCR扩增,测定序列,用分子生物学软件Clustal X进行序列分析,并与其他棘阿米巴分离株进行比较分析. [结果]棘阿米巴CG/S 1的18 S rDNA全基因序列为2 292 bp,基因型为T 5型;CG/S 1与A.lenticulata 7327株的序列差异率为0.61%,与CB/S 1株的序列差异率为0.74%. [结论]广东地区土壤中分离的棘阿米巴Acanthamoeba sp. CG/S 1为A. lenticulata株.

  3. Studies of the B-Z transition of DNA: The temperature dependence of the free-energy difference, the composition of the counterion sheath in mixed salt, and the preparation of a sample of the 5'-d[T-(m(5) C-G)12 -T] duplex in pure B-DNA or Z-DNA form.

    Science.gov (United States)

    Guéron, Maurice; Plateau, Pierre; Filoche, Marcel

    2016-07-01

    It is often envisioned that cations might coordinate at specific sites of nucleic acids and play an important structural role, for instance in the transition between B-DNA and Z-DNA. However, nucleic acid models explicitly devoid of specific sites may also exhibit features previously considered as evidence for specific binding. Such is the case of the "composite cylinder" (or CC) model which spreads out localized features of DNA structure and charge by cylindrical averaging, while sustaining the main difference between the B and Z structures, namely the better immersion of the B-DNA phosphodiester charges in the solution. Here, we analyze the non-electrostatic component of the free-energy difference between B-DNA and Z-DNA. We also compute the composition of the counterion sheath in a wide range of mixed-salt solutions and of temperatures: in contrast with the large difference of composition between the B-DNA and Z-DNA forms, the temperature dependence of sheath composition, previously unknown, is very weak. In order to validate the model, the mixed-salt predictions should be compared to experiment. We design a procedure for future measurements of the sheath composition based on Anomalous Small-Angle X-ray Scattering and complemented by (31) P NMR. With due consideration for the kinetics of the B-Z transition and for the capacity of generating at will the B or Z form in a single sample, the 5'-d[T-(m(5) C-G)12 -T] 26-mer emerges as a most suitable oligonucleotide for this study. Finally, the application of the finite element method to the resolution of the Poisson-Boltzmann equation is described in detail. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 369-384, 2016.

  4. DNA Based Molecular Scale Nanofabrication

    Science.gov (United States)

    2015-12-04

    water adsorption on DNA origami template and its impact on DNA- mediated chemical reactions. We also extended the concept of DNA- mediated reaction to...addition, we have expanded our efforts to include DNA- mediated HF etching of SiÜ2, DNA- mediated nanoimprinting lithography, DNA-based patterning of self...detailed kinetics study of DNA- mediated chemical reactions. Examples of such reactions include chemical vapor deposition (CVD) of inorganic oxide and HF

  5. Reuse of norgestomet implants in an eCG-based superovulation protocol administered to Nelore (Bos taurus indicus) cows

    OpenAIRE

    Sudano, Mateus Jose [UNESP; Landim-Alvarenga, Fernanda da Cruz [UNESP; Sartori, Roberto; Machado, Rui

    2011-01-01

    This study assessed the reuse of norgestomet implants in Nelore cows that were superstimulated with eCG. In a crossover design trial, eight cows were randomly divided into two experimental groups and twice superstimulated: Group 1 - half of the cows received a new norgestomet implant and 2 mg estradiol benzoate (EB) on Day 0; Group 2 - remaining cows received two once-used norgestomet implants and 2 mg EB also on Day 0. on Day 4 all cows received a single dose of 2000 IU eCG, and on Day 6 cow...

  6. Martini Coarse-Grained Force Field : Extension to DNA

    NARCIS (Netherlands)

    Uusitalo, Jaakko J.; Ingolfsson, Helgi I.; Akhshi, Parisa; Tieleman, D. Peter; Marrink, Siewert J.

    2015-01-01

    We systematically parameterized a coarsegrained (CG) model for DNA that is compatible with the Martini force field. The model maps each nucleotide into six to seven CG beads and is parameterized following the Martini philosophy. The CG nonbonded interactions are based on partitioning of the nudeobas

  7. Martini Coarse-Grained Force Field : Extension to DNA

    NARCIS (Netherlands)

    Uusitalo, Jaakko J.; Ingolfsson, Helgi I.; Akhshi, Parisa; Tieleman, D. Peter; Marrink, Siewert J.

    2015-01-01

    We systematically parameterized a coarsegrained (CG) model for DNA that is compatible with the Martini force field. The model maps each nucleotide into six to seven CG beads and is parameterized following the Martini philosophy. The CG nonbonded interactions are based on partitioning of the nudeobas

  8. DNA methylation-based age prediction from saliva: High age predictability by combination of 7 CpG markers.

    Science.gov (United States)

    Hong, Sae Rom; Jung, Sang-Eun; Lee, Eun Hee; Shin, Kyoung-Jin; Yang, Woo Ick; Lee, Hwan Young

    2017-07-01

    DNA methylation is currently one of the most promising age-predictive biomarkers. Many studies have reported DNA methylation-based age predictive models, but most of these are based on DNA methylation patterns from blood. Only a few studies have examined age-predictive DNA patterns in saliva, which is one of the most frequently-encountered body fluids at crime scenes. In this study, we generated genome-wide DNA methylation profiles of saliva from 54 individuals and identified CpG markers that showed a high correlation between methylation and age. Because the age-associated marker candidates from saliva differed from those of blood, we investigated DNA methylation patterns of 6 age-associated CpG marker candidates (cg00481951, cg19671120, cg14361627, cg08928145, cg12757011, and cg07547549 of the SST, CNGA3, KLF14, TSSK6, TBR1, and SLC12A5 genes, respectively) in addition to a cell type-specific CpG marker (cg18384097 of the PTPN7 gene) in an independent set of saliva samples obtained from 226 individuals aged 18 to 65 years. Multiplex methylation SNaPshot reactions were used to generate the data. We then generated a linear regression model with age information and the methylation profile from the 113 training samples. The model exhibited a 94.5% correlation between predicted and chronological age with a mean absolute deviation (MAD) from chronological age of 3.13 years. In subsequent validation using 113 test samples, we also observed a high correlation between predicted and chronological age (Spearman's rho=0.952, MAD from chronological age=3.15years). The model composed of 7 selected CpG sites enabled age prediction in saliva with high accuracy, which will be useful in saliva analysis for investigative leads. Copyright © 2017 Elsevier B.V. All rights reserved.

  9. Triaging pregnancies of unknown location: the performance of protocols based on single serum progesterone or repeated serum hCG levels.

    Science.gov (United States)

    Guha, S; Ayim, F; Ludlow, J; Sayasneh, A; Condous, G; Kirk, E; Stalder, C; Timmerman, D; Bourne, T; Van Calster, B

    2014-05-01

    How does a protocol based on a single serum progesterone measurement perform as a triage tool in women with pregnancy of unknown location (PUL) in comparison to protocols based on serial hCG measurement? Triage based on the logistic regression model M4 (using initial hCG and hCG ratio (48 h/0 h)) classifies the majority of PUL into low and high risk groups, in contrast to a progesterone protocol based on a serum level threshold of 10 nmol/l. Low progesterone has been shown to identify failing pregnancies and those at low risk of complications. A prediction model (M4) based on the initial hCG and the hCG ratio at 0 and 48 h can successfully classify PUL into low and high risk groups. A multi-centre diagnostic accuracy study of 1271 women was performed retrospectively on data from women at St. George's Hospital (SGH, London, UK) between February 2005 and 2006, Queen Charlottes & Chelsea Hospital (QCCH, London, UK) between April 2009 and August 2012, and the Royal Prince Alfred Hospital (RPAH, Sydney, Australia) between February 2008 and October 2011. The end-points were the final observed outcome for each pregnancy as a failed PUL (low risk), intrauterine pregnancy (IUP, low risk), or ectopic pregnancy (EP, high risk), and any interventions or complications for EP during the follow-up period. Complete data were available for initial progesterone, 0/48 h hCG and final outcome in 431 of 534 women (81%) at SGH, 396/585 (68%) at QCCH and 96/152 (63%) at RPAH. Missing values were handled using multiple imputation. Three diagnostic approaches were used to classify PUL as high risk: a range of serum progesterone levels were evaluated (>10, 16 and 20 nmol/l) for the progesterone protocol, risk of EP given by the M4 model ≥5% for the M4-based protocol, and hCG ratio was between 0.87 and 1.66 for hCG cut-offs as previously published. Results were analysed using random intercept models or stratified analysis to account for variability between centres. The progesterone

  10. Development of a GnRH-PGF2α-progesterone-based synchronization protocol with eCG for inducing single and double ovulations in beef cattle.

    Science.gov (United States)

    Martinez, M F; Tutt, D; Quirke, L D; Tattersfield, G; Juengel, J L

    2014-11-01

    Experiments were designed to investigate the effect of different doses and timing of an eCG treatment given during GnRH-based synchronization protocols on follicular dynamics and fertility in cattle. In Exp. 1, Angus heifers (n = 50) received a 7-d Ovsynch + progesterone protocol (on d 0, GnRH and progesterone insert were administered; on d 7, progesterone insert was removed and PGF2α was injected; and on d 9.5, GnRH was injected 56 h after progesterone removal) with eCG (0, 300, 500, 700, or 1,000 IU) administered on d 7. In Exp. 2, Angus cows (n = 27) received the same protocol as Exp. 1 and were assigned randomly to receive 0 or 400 IU eCG i.m. on d 2 or 7. In Exp. 3, Angus cows (n = 18) received a 6-d Ovsynch + progesterone protocol and were randomly assigned to receive 0 or 800 IU eCG on d 3 of the protocol (Exp. 3a). A pilot field trial was also performed using the same treatments in suckled Angus-cross cows (n = 72; Exp. 3b). In Exp. 4, beef heifers (n = 200) were assigned randomly to the same treatments as in Exp. 3, but the second GnRH was not given, with Holstein bulls introduced on d 6. In Exp. 5, Angus cows (n = 12) received the same treatment as in Exp. 3, but were not inseminated. Progesterone concentrations were assessed in plasma collected during the estrous cycle following synchronization. Ultrasonography was used to monitor ovarian dynamics and to diagnose pregnancy. In Exp. 1, the mean number of ovulations was affected (P reproductive performance through increased pregnancy rates in single ovulating animals as well as the induction of twin ovulations for twinning.

  11. ShCG 245

    Directory of Open Access Journals (Sweden)

    Hrant M. Tovmassian

    2007-01-01

    Full Text Available Los grupos compactos de galaxias Shakhbazian son las configuraciones más densas que se conocen. Hace algunos años iniciamos un estudio fotométrico y espectroscópico de estos grupos. En este artículo presentamos los resultados de la investigación en los grupos ShCG 104, ShCG 120, ShCG 243 y ShCG 245. Presentamos los corrimientos al rojo de las galaxias miembro, los resultados de la fotometría R, las curvas de brillo superficial-radio efectivo, las masas estimadas, las luminosidades y las razones masa-luminosidad de los grupos, además de algunos parámetros dinámicos como la dispersión de velocidad radial y el tiempo de cruce. Los ShCGs estudiados consisten principalmente de galaxias elípticas y lenticulares. Se muestra que algunas galaxias en estos grupos están en proceso de interacción.

  12. DNA-based hybrid catalysis.

    Science.gov (United States)

    Rioz-Martínez, Ana; Roelfes, Gerard

    2015-04-01

    In the past decade, DNA-based hybrid catalysis has merged as a promising novel approach to homogeneous (asymmetric) catalysis. A DNA hybrid catalysts comprises a transition metal complex that is covalently or supramolecularly bound to DNA. The chiral microenvironment and the second coordination sphere interactions provided by the DNA are key to achieve high enantioselectivities and, often, additional rate accelerations in catalysis. Nowadays, current efforts are focused on improved designs, understanding the origin of the enantioselectivity and DNA-induced rate accelerations, expanding the catalytic scope of the concept and further increasing the practicality of the method for applications in synthesis. Herein, the recent developments will be reviewed and the perspectives for the emerging field of DNA-based hybrid catalysis will be discussed.

  13. DNA-Based Nanopore Sensing.

    Science.gov (United States)

    Liu, Lei; Wu, Hai-Chen

    2016-12-05

    Nanopore sensing is an attractive, label-free approach that can measure single molecules. Although initially proposed for rapid and low-cost DNA sequencing, nanopore sensors have been successfully employed in the detection of a wide variety of substrates. Early successes were mostly achieved based on two main strategies by 1) creating sensing elements inside the nanopore through protein mutation and chemical modification or 2) using molecular adapters to enhance analyte recognition. Over the past five years, DNA molecules started to be used as probes for sensing rather than substrates for sequencing. In this Minireview, we highlight the recent research efforts of nanopore sensing based on DNA-mediated characteristic current events. As nanopore sensing is becoming increasingly important in biochemical and biophysical studies, DNA-based sensing may find wider applications in investigating DNA-involving biological processes. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. SU-E-T-64: CG-Based Radiation Therapy Simulator with Physical Modeling for Avoidance of Collisions Between Gantry and Couch Or Patient

    Energy Technology Data Exchange (ETDEWEB)

    Yamanouchi, M; Arimura, H; Yuda, I [Kokura Memorial Hospital, Kitakyushu-shi, Fukuoka (Japan)

    2014-06-01

    Purpose: It is time-consuming and might cause re-planning to check couch-gantry and patient-gantry collisions on a radiotherapy machine when using couch rotations for non-coplanar beam angles. The aim of this study was to develop a computer-graphics (CG)-based radiation therapy simulator with physical modeling for avoidance of collisions between gantry and couch or patient on a radiotherapy machine. Methods: The radiation therapy simulator was three-dimensionally constructed including a radiotherapy machine (Clinac iX, Varian Medical Systems), couch, and radiation treatment room according to their designs by using a physical-modeling-based computer graphics software (Blender, free and open-source). Each patient was modeled by applying a surface rendering technique to their planning computed tomography (CT) images acquired from 16-slice CT scanner (BrightSpeed, GE Healthcare). Immobilization devices for patients were scanned by the CT equipment, and were rendered as the patient planning CT images. The errors in the collision angle of the gantry with the couch or patient between gold standards and the estimated values were obtained by fixing the gantry angle for the evaluation of the proposed simulator. Results: The average error of estimated collision angles to the couch head side was -8.5% for gantry angles of 60 to 135 degree, and -5.5% for gantry angles of 225 to 300 degree. Moreover, the average error of estimated collision angles to the couch foot side was -1.1% for gantry angles of 60 to 135 degree, and 1.4% for gantry angles of 225 to 300 degree. Conclusion: The CG-based radiation therapy simulator could make it possible to estimate the collision angle between gantry and couch or patient on the radiotherapy machine without verifying the collision angles in the radiation treatment room.

  15. Chiroplasmonic DNA-based nanostructures

    Science.gov (United States)

    Cecconello, Alessandro; Besteiro, Lucas V.; Govorov, Alexander O.; Willner, Itamar

    2017-09-01

    Chiroplasmonic properties of nanoparticles, organized using DNA-based nanostructures, have attracted both theoretical and experimental interest. Theory suggests that the circular dichroism spectra accompanying chiroplasmonic nanoparticle assemblies are controlled by the sizes, shapes, geometries and interparticle distances of the nanoparticles. In this Review, we present different methods to assemble chiroplasmonic nanoparticle or nanorod systems using DNA scaffolds, and we discuss the operations of dynamically reconfigurable chiroplasmonic nanostructures. The chiroplasmonic properties of the different systems are characterized by circular dichroism and further supported by high-resolution transmission electron microscopy or cryo-transmission electron microscopy imaging and theoretical modelling. We also outline the applications of chiroplasmonic assemblies, including their use as DNA-sensing platforms and as functional systems for information processing and storage. Finally, future perspectives in applying chiroplasmonic nanoparticles as waveguides for selective information transfer and their use as ensembles for chiroselective synthesis are discussed. Specifically, we highlight the upscaling of the systems to device-like configurations.

  16. DNA Microarray-Based Diagnostics.

    Science.gov (United States)

    Marzancola, Mahsa Gharibi; Sedighi, Abootaleb; Li, Paul C H

    2016-01-01

    The DNA microarray technology is currently a useful biomedical tool which has been developed for a variety of diagnostic applications. However, the development pathway has not been smooth and the technology has faced some challenges. The reliability of the microarray data and also the clinical utility of the results in the early days were criticized. These criticisms added to the severe competition from other techniques, such as next-generation sequencing (NGS), impacting the growth of microarray-based tests in the molecular diagnostic market.Thanks to the advances in the underlying technologies as well as the tremendous effort offered by the research community and commercial vendors, these challenges have mostly been addressed. Nowadays, the microarray platform has achieved sufficient standardization and method validation as well as efficient probe printing, liquid handling and signal visualization. Integration of various steps of the microarray assay into a harmonized and miniaturized handheld lab-on-a-chip (LOC) device has been a goal for the microarray community. In this respect, notable progress has been achieved in coupling the DNA microarray with the liquid manipulation microsystem as well as the supporting subsystem that will generate the stand-alone LOC device.In this chapter, we discuss the major challenges that microarray technology has faced in its almost two decades of development and also describe the solutions to overcome the challenges. In addition, we review the advancements of the technology, especially the progress toward developing the LOC devices for DNA diagnostic applications.

  17. Model-Based Least Squares Reconstruction of Coded Source Neutron Radiographs: Integrating the ORNL HFIR CG1D Source Model

    Energy Technology Data Exchange (ETDEWEB)

    Santos-Villalobos, Hector J [ORNL; Gregor, Jens [University of Tennessee, Knoxville (UTK); Bingham, Philip R [ORNL

    2014-01-01

    At the present, neutron sources cannot be fabricated small and powerful enough in order to achieve high resolution radiography while maintaining an adequate flux. One solution is to employ computational imaging techniques such as a Magnified Coded Source Imaging (CSI) system. A coded-mask is placed between the neutron source and the object. The system resolution is increased by reducing the size of the mask holes and the flux is increased by increasing the size of the coded-mask and/or the number of holes. One limitation of such system is that the resolution of current state-of-the-art scintillator-based detectors caps around 50um. To overcome this challenge, the coded-mask and object are magnified by making the distance from the coded-mask to the object much smaller than the distance from object to detector. In previous work, we have shown via synthetic experiments that our least squares method outperforms other methods in image quality and reconstruction precision because of the modeling of the CSI system components. However, the validation experiments were limited to simplistic neutron sources. In this work, we aim to model the flux distribution of a real neutron source and incorporate such a model in our least squares computational system. We provide a full description of the methodology used to characterize the neutron source and validate the method with synthetic experiments.

  18. Targeting DNA base pair mismatch with artificial nucleobases. Advances and perspectives in triple helix strategy.

    Science.gov (United States)

    Malnuit, Vincent; Duca, Maria; Benhida, Rachid

    2011-01-21

    This review, divided into three sections, describes the contribution of the chemists' community to the development and application of triple helix strategy by using artificial nucleic acids, particularly for the recognition of DNA sequences incorporating base pair inversions. Firstly, the development of nucleobases that recognise CG inversion is surveyed followed secondly by specific recognition of TA inverted base pair. Finally, we point out in the last section recent perspectives and applications, driven from knowledge in nucleic acids interactions, in the growing field of nanotechnology and supramolecular chemistry at the border area of physics, chemistry and molecular biology.

  19. GnRH agonist ovulation trigger and hCG-based, progesterone-free luteal support: a proof of concept study

    DEFF Research Database (Denmark)

    Kol, Shahar; Humaidan, Peter; Itskovitz-Eldor, Joseph

    2011-01-01

    BACKGROUND It is now well established that a GnRH agonist (GnRHa) ovulation trigger completely prevents ovarian hyperstimulation syndrome. However, early studies, using conventional luteal support, showed inferior clinical results following a GnRHa trigger compared with a conventional hCG trigger...

  20. Metallic Nanostructures Based on DNA Nanoshapes

    Directory of Open Access Journals (Sweden)

    Boxuan Shen

    2016-08-01

    Full Text Available Metallic nanostructures have inspired extensive research over several decades, particularly within the field of nanoelectronics and increasingly in plasmonics. Due to the limitations of conventional lithography methods, the development of bottom-up fabricated metallic nanostructures has become more and more in demand. The remarkable development of DNA-based nanostructures has provided many successful methods and realizations for these needs, such as chemical DNA metallization via seeding or ionization, as well as DNA-guided lithography and casting of metallic nanoparticles by DNA molds. These methods offer high resolution, versatility and throughput and could enable the fabrication of arbitrarily-shaped structures with a 10-nm feature size, thus bringing novel applications into view. In this review, we cover the evolution of DNA-based metallic nanostructures, starting from the metallized double-stranded DNA for electronics and progress to sophisticated plasmonic structures based on DNA origami objects.

  1. Reversible Data Hiding Based on DNA Computing

    Directory of Open Access Journals (Sweden)

    Bin Wang

    2017-01-01

    Full Text Available Biocomputing, especially DNA, computing has got great development. It is widely used in information security. In this paper, a novel algorithm of reversible data hiding based on DNA computing is proposed. Inspired by the algorithm of histogram modification, which is a classical algorithm for reversible data hiding, we combine it with DNA computing to realize this algorithm based on biological technology. Compared with previous results, our experimental results have significantly improved the ER (Embedding Rate. Furthermore, some PSNR (peak signal-to-noise ratios of test images are also improved. Experimental results show that it is suitable for protecting the copyright of cover image in DNA-based information security.

  2. Studies of base pair sequence effects on DNA solvation based on all-atom molecular dynamics simulations

    Indian Academy of Sciences (India)

    Surjit B Dixit; Mihaly Mezei; David L Beveridge

    2012-07-01

    Detailed analyses of the sequence-dependent solvation and ion atmosphere of DNA are presented based on molecular dynamics (MD) simulations on all the 136 unique tetranucleotide steps obtained by the ABC consortium using the AMBER suite of programs. Significant sequence effects on solvation and ion localization were observed in these simulations. The results were compared to essentially all known experimental data on the subject. Proximity analysis was employed to highlight the sequence dependent differences in solvation and ion localization properties in the grooves of DNA. Comparison of the MD-calculated DNA structure with canonical A- and B-forms supports the idea that the G/C-rich sequences are closer to canonical A- than B-form structures, while the reverse is true for the poly A sequences, with the exception of the alternating ATAT sequence. Analysis of hydration density maps reveals that the flexibility of solute molecule has a significant effect on the nature of observed hydration. Energetic analysis of solute–solvent interactions based on proximity analysis of solvent reveals that the GC or CG base pairs interactmore strongly with watermolecules in the minor groove of DNA that the AT or TA base pairs, while the interactions of the AT or TA pairs in the major groove are stronger than those of the GC or CG pairs. Computation of solvent-accessible surface area of the nucleotide units in the simulated trajectories reveals that the similarity with results derived from analysis of a database of crystallographic structures is excellent. The MD trajectories tend to follow Manning’s counterion condensation theory, presenting a region of condensed counterions within a radius of about 17 Å from the DNA surface independent of sequence. The GC and CG pairs tend to associate with cations in the major groove of the DNA structure to a greater extent than the AT and TA pairs. Cation association is more frequent in the minor groove of AT than the GC pairs. In general

  3. DNA intercalation without flipping in the specific ThaI-DNA complex.

    Science.gov (United States)

    Firczuk, Malgorzata; Wojciechowski, Marek; Czapinska, Honorata; Bochtler, Matthias

    2011-01-01

    The PD-(D/E)XK type II restriction endonuclease ThaI cuts the target sequence CG/CG with blunt ends. Here, we report the 1.3 Å resolution structure of the enzyme in complex with substrate DNA and a sodium or calcium ion taking the place of a catalytic magnesium ion. The structure identifies Glu54, Asp82 and Lys93 as the active site residues. This agrees with earlier bioinformatic predictions and implies that the PD and (D/E)XK motifs in the sequence are incidental. DNA recognition is very unusual: the two Met47 residues of the ThaI dimer intercalate symmetrically into the CG steps of the target sequence. They approach the DNA from the minor groove side and penetrate the base stack entirely. The DNA accommodates the intercalating residues without nucleotide flipping by a doubling of the CG step rise to twice its usual value, which is accompanied by drastic unwinding. Displacement of the Met47 side chains from the base pair midlines toward the downstream CG steps leads to large and compensating tilts of the first and second CG steps. DNA intercalation by ThaI is unlike intercalation by HincII, HinP1I or proteins that bend or repair DNA.

  4. Low pressure microfluidic-based DNA fragmentation

    NARCIS (Netherlands)

    Shui, Lingling; Sparreboom, Wouter; Bomer, Johan G.; Jin, Mingliang; Carlen, Edwin; van den Berg, Albert

    2011-01-01

    We report a low-pressure microfluidic deoxyribonucleic acid (DNA) fragmentation device based on a combination of me-chanical hydrodynamic shearing and low temperature sample heating. Conventional DNA fragmentation based on hydrody-namic shearing is capable of achieving fragment lengths (FL) < 10k bp

  5. DNA-based applications in nanobiotechnology.

    Science.gov (United States)

    Abu-Salah, Khalid M; Ansari, Anees A; Alrokayan, Salman A

    2010-01-01

    Biological molecules such as deoxyribonucleic acid (DNA) have shown great potential in fabrication and construction of nanostructures and devices. The very properties that make DNA so effective as genetic material also make it a very suitable molecule for programmed self-assembly. The use of DNA to assemble metals or semiconducting particles has been extended to construct metallic nanowires and functionalized nanotubes. This paper highlights some important aspects of conjugating the unique physical properties of dots or wires with the remarkable recognition capabilities of DNA which could lead to miniaturizing biological electronics and optical devices, including biosensors and probes. Attempts to use DNA-based nanocarriers for gene delivery are discussed. In addition, the ecological advantages and risks of nanotechnology including DNA-based nanobiotechnology are evaluated.

  6. DNA-based assembly lines and nanofactories.

    Science.gov (United States)

    Simmel, Friedrich C

    2012-08-01

    With the invention of the DNA origami technique, DNA self-assembly has reached a new level of sophistication. DNA can now be used to arrange molecules and other nanoscale components into almost arbitrary geometries-in two and even three dimensions and with nanometer precision. One exciting prospect is the realization of dynamic systems based on DNA, in which chemical reactions are precisely controlled by the spatial arrangement of components, ultimately resulting in nanoscale analogs of molecular assembly lines or 'nanofactories'. This review will discuss recent progress toward this goal, ranging from DNA-templated synthesis over artificial DNA-based enzyme cascades to first examples of 'molecular robots'. Copyright © 2012. Published by Elsevier Ltd.

  7. Reduced representation bisulphite sequencing of the cattle genome reveals DNA methylation patterns

    Science.gov (United States)

    Using reduced representation bisulphite sequencing (RRBS), we obtained the first single-base-resolution maps of bovine DNA methylation in ten somatic tissues. In total, we observed 1,868,049 cytosines in the CG-enriched regions. Similar to the methylation patterns in other species, the CG context wa...

  8. Alternative DNA base pairing through metal coordination.

    Science.gov (United States)

    Clever, Guido H; Shionoya, Mitsuhiko

    2012-01-01

    Base-pairing in the naturally occurring DNA and RNA oligonucleotide duplexes is based on π-stacking, hydrogen bonding, and shape complementarity between the nucleobases adenine, thymine, guanine, and cytosine as well as on the hydrophobic-hydrophilic balance in aqueous media. This complex system of multiple supramolecular interactions is the product of a long-term evolutionary process and thus highly optimized to serve its biological functions such as information storage and processing. After the successful implementation of automated DNA synthesis, chemists have begun to introduce artificial modifications inside the core of the DNA double helix in order to study various aspects of base pairing, generate new base pairs orthogonal to the natural ones, and equip the biopolymer with entirely new functions. The idea to replace the hydrogen bonding interactions with metal coordination between ligand-like nucleosides and suitable transition metal ions culminated in the development of a plethora of artificial base-pairing systems termed "metal base-pairs" which were shown to strongly enhance the DNA duplex stability. Furthermore, they show great potential for the use of DNA as a molecular wire in nanoscale electronic architectures. Although single electrons have proven to be transmitted by natural DNA over a distance of several base pairs, the high ohmic resistance of unmodified oligonucleotides was identified as a serious obstacle. By exchanging some or all of the Watson-Crick base pairs in DNA with metal complexes, this problem may be solved. In the future, these research efforts are supposed to lead to DNA-like materials with superior conductivity for nano-electronic applications. Other fields of potential application such as DNA-based supramolecular architecture and catalysis may be strongly influenced by these developments as well. This text is meant to illustrate the basic concepts of metal-base pairing and give an outline over recent developments in this field.

  9. QPSO-based adaptive DNA computing algorithm.

    Science.gov (United States)

    Karakose, Mehmet; Cigdem, Ugur

    2013-01-01

    DNA (deoxyribonucleic acid) computing that is a new computation model based on DNA molecules for information storage has been increasingly used for optimization and data analysis in recent years. However, DNA computing algorithm has some limitations in terms of convergence speed, adaptability, and effectiveness. In this paper, a new approach for improvement of DNA computing is proposed. This new approach aims to perform DNA computing algorithm with adaptive parameters towards the desired goal using quantum-behaved particle swarm optimization (QPSO). Some contributions provided by the proposed QPSO based on adaptive DNA computing algorithm are as follows: (1) parameters of population size, crossover rate, maximum number of operations, enzyme and virus mutation rate, and fitness function of DNA computing algorithm are simultaneously tuned for adaptive process, (2) adaptive algorithm is performed using QPSO algorithm for goal-driven progress, faster operation, and flexibility in data, and (3) numerical realization of DNA computing algorithm with proposed approach is implemented in system identification. Two experiments with different systems were carried out to evaluate the performance of the proposed approach with comparative results. Experimental results obtained with Matlab and FPGA demonstrate ability to provide effective optimization, considerable convergence speed, and high accuracy according to DNA computing algorithm.

  10. QPSO-Based Adaptive DNA Computing Algorithm

    Directory of Open Access Journals (Sweden)

    Mehmet Karakose

    2013-01-01

    Full Text Available DNA (deoxyribonucleic acid computing that is a new computation model based on DNA molecules for information storage has been increasingly used for optimization and data analysis in recent years. However, DNA computing algorithm has some limitations in terms of convergence speed, adaptability, and effectiveness. In this paper, a new approach for improvement of DNA computing is proposed. This new approach aims to perform DNA computing algorithm with adaptive parameters towards the desired goal using quantum-behaved particle swarm optimization (QPSO. Some contributions provided by the proposed QPSO based on adaptive DNA computing algorithm are as follows: (1 parameters of population size, crossover rate, maximum number of operations, enzyme and virus mutation rate, and fitness function of DNA computing algorithm are simultaneously tuned for adaptive process, (2 adaptive algorithm is performed using QPSO algorithm for goal-driven progress, faster operation, and flexibility in data, and (3 numerical realization of DNA computing algorithm with proposed approach is implemented in system identification. Two experiments with different systems were carried out to evaluate the performance of the proposed approach with comparative results. Experimental results obtained with Matlab and FPGA demonstrate ability to provide effective optimization, considerable convergence speed, and high accuracy according to DNA computing algorithm.

  11. Serum hCG Levels following the Ovulatory Injection: Associations with Patient Weight and Implantation Time

    Science.gov (United States)

    Noorhasan, Dorette J.; McGovern, Peter G.; Cho, Michael; Seungdamrong, Aimee; Ahmad, Khaliq; McCulloh, David H.

    2015-01-01

    Objective. To test if serum hCG levels the morning after the ovulatory hCG injection correlate with (1) retrieval efficiency, (2) oocyte maturity, (3) embryo quality, (4) pregnancy, and/or (5) time to implantation in patients undergoing in vitro fertilization (IVF) with intracytoplasmic sperm injection (ICSI). Design. Retrospective cohort analysis. Setting. University-based IVF clinic. Patient(s). All IVF/ICSI cycles from April 2005 to February 2008 whose hCG administration was confirmed (n = 472 patients). Intervention(s). Serum hCG was measured the morning following the ovulatory injection, on the 16th day following retrieval, and repeated on day 18 for those with positive results. Main Outcome Measure(s). Number of follicles on the day of hCG injection, number of oocytes retrieved, maturity of oocytes, embryo quality, pregnancy outcome, and time to implantation. Result(s). hCG levels did not correlate with retrieval efficiency, oocyte maturity, embryo quality, or pregnancy. Postinjection hCG levels were inversely associated with patient weight and time to implantation. Conclusion(s). No correlation was found between hCG level and any parameter of embryo quality. Patient weight affected hCG levels following hCG injection and during the early period of pregnancy following implantation. No association between postinjection hCG level and time of implantation (adjusted for patient weight) was apparent. PMID:26587025

  12. Reproductive performance of woolly and hairless crossbred ewes treated with an exogenous progestagen and eCG hormone during the non-breeding seasonDesempenho reprodutivo de ovelhas mestiças lanadas e deslanadas submetidas a protocolo hormonal a base de progestágeno e eCG, durante a contraestação reprodutiva

    Directory of Open Access Journals (Sweden)

    Gustavo Martins Gomes dos Santos

    2011-07-01

    Full Text Available The aim of this study was to evaluate the reproductive performance of woolly and hairless crossbred ewes treated with an exogenous progestagen and eCG hormone during the non-breeding season. Mixed breed ewes (n = 48 were assigned into two treatments considering the presence (G-Woolly, n = 25 or absence of wool (G-Hairless, n = 23. The ewes underwent hormone treatment to induction/synchronization of estrus, which consisted of the insertion of an intravaginal device randomly at the estrous cycle (D0. On Day 7, ewes were injected with eCG and d-cloprostenol. On Day 9, the device was removed and males were introduced into the herd (proportion of 1:6 twelve hours later during days 10, 11 and 12. After Day 12, males were separated from females for ten days and later reintroduced into the herd for 45 days. The rate of onset of estrus and the pregnancy rate from the synchronization was 84.0 and 36.0% vs. 87.0 and 56.6%, G-Woolly vs. G-Hairless (p> 0.05. The total pregnancy rate after male reintroduction was 68.0 vs. 91.3%, G-Woolly vs. G-Hairless (pEste trabalho teve como objetivo avaliar o desempenho reprodutivo de ovelhas mestiças lanadas e deslanadas submetidas a um protocolo hormonal a base de progestágeno e eCG durante a contraestação reprodutiva. Ovelhas mestiças (n=48, sem raça definida, foram divididas em dois tratamentos, considerando-se a presença (G-Lanada, n=25 ou ausência de lã (G-Deslanada, n=23. As ovelhas foram submetidas a um tratamento hormonal de indução/sincronização de estro, que consistiu na colocação do dispositivo intravaginal em dia aleatório do ciclo estral (D0. No D7, foi administrado eCG e d-cloprostenol. No D9, o dispositivo foi retirado e após 12 h os machos foram introduzidos no lote (proporção 1:6, nos dias 10, 11 e 12. Posteriormente, os machos foram separados das fêmeas por dez dias e então reintroduzidos no lote por mais 45 dias. A taxa de apresentação de estro e de prenhez resultantes da

  13. DNA Coding Based Knowledge Discovery Algorithm

    Institute of Scientific and Technical Information of China (English)

    LI Ji-yun; GENG Zhao-feng; SHAO Shi-huang

    2002-01-01

    A novel DNA coding based knowledge discovery algorithm was proposed, an example which verified its validity was given. It is proved that this algorithm can discover new simplified rules from the original rule set efficiently.

  14. Analytical sensitivity of four commonly used hCG point of care devices.

    Science.gov (United States)

    Kamer, Sandy M; Foley, Kevin F; Schmidt, Robert L; Greene, Dina N

    2015-04-01

    Point of care (POC) hCG assays are often used to rule-out pregnancy and therefore diagnostic sensitivity, especially at low concentrations of hCG, is important. There are very few studies in the literature that seek to verify the claimed analytical sensitivity of hCG POC devices. The analytical sensitivity of four commonly used hCG POC devices (Alere hCG Combo Cassette, ICON 20 hCG, OSOM hCG Combo Test, and Sure-Vue Serum/Urine hCG-STAT) was challenged using urine samples (n=50) selected based on quantitative hCG concentrations. The majority of these specimens (n=40) had an hCG concentration between 20 and 200 U/L. Each specimen/device combination was reviewed by three individuals. Statistical calculations were performed using Stata 12. The analytical sensitivity of the OSOM was significantly lower inferior than that of the other POC devices. There was no significant difference in the sensitivity of the Alere, ICON 20 and Sure-Vue devices. There was no significant difference in the individual interpretation of the hCG POC results. All hCG POC devices evaluated in this study were susceptible to false negative results at low concentrations of urine hCG. Laboratorians and clinicians should be aware that there are limitations when using urine hCG POC devices to rule out early pregnancy. Copyright © 2014 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

  15. Transgenerational stability of the Arabidopsis epigenome is coordinated by CG methylation.

    Science.gov (United States)

    Mathieu, Olivier; Reinders, Jon; Caikovski, Marian; Smathajitt, Chotika; Paszkowski, Jerzy

    2007-09-01

    Maintenance of CG methylation ((m)CG) patterns is essential for chromatin-mediated epigenetic regulation of transcription in plants and mammals. However, functional links between (m)CG and other epigenetic mechanisms in vivo remain obscure. Using successive generations of an Arabidopsis thaliana mutant deficient in maintaining (m)CG, we find that (m)CG loss triggers genome-wide activation of alternative epigenetic mechanisms. However, these mechanisms, which involve RNA-directed DNA methylation, inhibiting expression of DNA demethylases, and retargeting of histone H3K9 methylation, act in a stochastic and uncoordinated fashion. As a result, new and aberrant epigenetic patterns are progressively formed over several plant generations in the absence of (m)CG. Interestingly, the unconventional redistribution of epigenetic marks is necessary to "rescue" the loss of (m)CG, since mutant plants impaired in rescue activities are severely dwarfed and sterile. Our results provide evidence that (m)CG is a central coordinator of epigenetic memory that secures stable transgenerational inheritance in plants.

  16. Sequence dependency of canonical base pair opening in the DNA double helix.

    Science.gov (United States)

    Lindahl, Viveca; Villa, Alessandra; Hess, Berk

    2017-04-01

    The flipping-out of a DNA base from the double helical structure is a key step of many cellular processes, such as DNA replication, modification and repair. Base pair opening is the first step of base flipping and the exact mechanism is still not well understood. We investigate sequence effects on base pair opening using extensive classical molecular dynamics simulations targeting the opening of 11 different canonical base pairs in two DNA sequences. Two popular biomolecular force fields are applied. To enhance sampling and calculate free energies, we bias the simulation along a simple distance coordinate using a newly developed adaptive sampling algorithm. The simulation is guided back and forth along the coordinate, allowing for multiple opening pathways. We compare the calculated free energies with those from an NMR study and check assumptions of the model used for interpreting the NMR data. Our results further show that the neighboring sequence is an important factor for the opening free energy, but also indicates that other sequence effects may play a role. All base pairs are observed to have a propensity for opening toward the major groove. The preferred opening base is cytosine for GC base pairs, while for AT there is sequence dependent competition between the two bases. For AT opening, we identify two non-canonical base pair interactions contributing to a local minimum in the free energy profile. For both AT and CG we observe long-lived interactions with water and with sodium ions at specific sites on the open base pair.

  17. DNA watermarks: A proof of concept

    Directory of Open Access Journals (Sweden)

    Barnekow Angelika

    2008-04-01

    Full Text Available Abstract Background DNA-based watermarks are helpful tools to identify the unauthorized use of genetically modified organisms (GMOs protected by patents. In silico analyses showed that in coding regions synonymous codons can be used to insert encrypted information into the genome of living organisms by using the DNA-Crypt algorithm. Results We integrated an authenticating watermark in the Vam7 sequence. For our investigations we used a mutant Saccharomyces cerevisiae strain, called CG783, which has an amber mutation within the Vam7 sequence. The CG783 cells are unable to sporulate and in addition display an abnormal vacuolar morphology. Transformation of CG783 with pRS314 Vam7 leads to a phenotype very similar to the wildtype yeast strain CG781. The integrated watermark did not influence the function of Vam7 and the resulting phenotype of the CG783 cells transformed with pRS314 Vam7-TB shows no significant differences compared to the CG783 cells transformed with pRS314 Vam7. Conclusion From our experiments we conclude that the DNA watermarks produced by DNA-Crypt do not influence the translation from mRNA into protein. By analyzing the vacuolar morphology, growth rate and ability to sporulate we confirmed that the resulting Vam7 protein was functionally active.

  18. DNA-Based Enzyme Reactors and Systems

    Directory of Open Access Journals (Sweden)

    Veikko Linko

    2016-07-01

    Full Text Available During recent years, the possibility to create custom biocompatible nanoshapes using DNA as a building material has rapidly emerged. Further, these rationally designed DNA structures could be exploited in positioning pivotal molecules, such as enzymes, with nanometer-level precision. This feature could be used in the fabrication of artificial biochemical machinery that is able to mimic the complex reactions found in living cells. Currently, DNA-enzyme hybrids can be used to control (multi-enzyme cascade reactions and to regulate the enzyme functions and the reaction pathways. Moreover, sophisticated DNA structures can be utilized in encapsulating active enzymes and delivering the molecular cargo into cells. In this review, we focus on the latest enzyme systems based on novel DNA nanostructures: enzyme reactors, regulatory devices and carriers that can find uses in various biotechnological and nanomedical applications.

  19. A Coarse-Grained DNA Model Parameterized from Atomistic Simulations by Inverse Monte Carlo

    Directory of Open Access Journals (Sweden)

    Nikolay Korolev

    2014-05-01

    Full Text Available Computer modeling of very large biomolecular systems, such as long DNA polyelectrolytes or protein-DNA complex-like chromatin cannot reach all-atom resolution in a foreseeable future and this necessitates the development of coarse-grained (CG approximations. DNA is both highly charged and mechanically rigid semi-flexible polymer and adequate DNA modeling requires a correct description of both its structural stiffness and salt-dependent electrostatic forces. Here, we present a novel CG model of DNA that approximates the DNA polymer as a chain of 5-bead units. Each unit represents two DNA base pairs with one central bead for bases and pentose moieties and four others for phosphate groups. Charges, intra- and inter-molecular force field potentials for the CG DNA model were calculated using the inverse Monte Carlo method from all atom molecular dynamic (MD simulations of 22 bp DNA oligonucleotides. The CG model was tested by performing dielectric continuum Langevin MD simulations of a 200 bp double helix DNA in solutions of monovalent salt with explicit ions. Excellent agreement with experimental data was obtained for the dependence of the DNA persistent length on salt concentration in the range 0.1–100 mM. The new CG DNA model is suitable for modeling various biomolecular systems with adequate description of electrostatic and mechanical properties.

  20. 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.

  1. Presence of. beta. hCG mRNA in the human pituitary

    Energy Technology Data Exchange (ETDEWEB)

    van Strien, A.; van Wezenbeek, P. (Organon International BV, Oss (Netherlands))

    1989-07-11

    A strong structural and biological similarity exist between human chorionic gonadotropin (hCG) and luteinizing hormone (LH). They share the same {alpha} subunit and have evolutionary related {beta} subunits. hCG is synthesized in first trimester placenta, whereas LH is synthesized in the pituitary. Substances with immunological, physical and biological properties of hCG have, however, been observed in postmenopausal urinary gonadotropin preparations as well as in pituitary extracts. Despite this finding it has not yet been proven that the hCG-like material is identical to placental hCG. This report describes the presence of a minor messenger RNA species in the human pituitary. RNA was isolated from five human pituitary glands and an amplified cDNA library was prepared.

  2. Parallel preconditioning techniques for sparse CG solvers

    Energy Technology Data Exchange (ETDEWEB)

    Basermann, A.; Reichel, B.; Schelthoff, C. [Central Institute for Applied Mathematics, Juelich (Germany)

    1996-12-31

    Conjugate gradient (CG) methods to solve sparse systems of linear equations play an important role in numerical methods for solving discretized partial differential equations. The large size and the condition of many technical or physical applications in this area result in the need for efficient parallelization and preconditioning techniques of the CG method. In particular for very ill-conditioned matrices, sophisticated preconditioner are necessary to obtain both acceptable convergence and accuracy of CG. Here, we investigate variants of polynomial and incomplete Cholesky preconditioners that markedly reduce the iterations of the simply diagonally scaled CG and are shown to be well suited for massively parallel machines.

  3. Evidence for Base Substitutions and Repair of DNA Mismatch Damage Induced by Low Energy N+ Ion Beam Implantation in E. coli

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    Ever since the low energy N+ ion beam has been accepted, the mutations of ionizing radiation are attributable mainly to avoidance of DNA damages repair. Evidences based on in vivo proof results are limited. Using the E.coli wild type and mutator strains, the mutant frequencies suggest that base substitutions in rpoB gene are induced by the N+ implantation. A highly conserved region is selected to get the direct evidence for base substitutions by sequence of the high fidelity PCR amplification products in mutants. Most of the mutants (90.9%, 40/44) have at least one base substitution in the amplification region. The evidences for CG to TA (55%, 22/40), AT to GC (20%, 8/40) and TA to CG (5%, 2/40) transitions are identified. The transversions are AT to TA (15%, 6/40) and GC to CG (5%, 2/40). It is suggested that DNA cytosine methylase might play an important role in mismatch repair of DNA damage induced by N+ implantation by analysis of the mutant frequencies of mutator strains.

  4. Development of a recombinant hCG-specific single chain immunotoxin cytotoxic to hCG expressing cancer cells.

    Science.gov (United States)

    Nand, Kripa N; Gupta, Jagdish C; Panda, A K; Jain, S K

    2015-02-01

    A large number of cancers express human chorionic gonadotropin (hCG) or its subunits ectopically. Patients harboring such cancers have poor prognosis and adverse survival. PiPP is a monoclonal antibody of high affinity and specificity for hCGβ/hCG. Work was carried out to develop a PiPP based recombinant immunotoxin for the immunotherapy of hCG expressing cancers. Recombinant PiPP antibody was constructed in scFv format in which gene encoding the VH and VL domains were joined through a linker. This scFv gene was fused to the gene expressing Pseudomonas exotoxin (PE38), and cloned in a Escherichia coli based expression vector under the control of strong bacteriophage T7 promoter. Immunotoxin conjugating scFv(PiPP) and PE38, was expressed in E. coli as recombinant protein. Recombinant PiPP immunotoxin was purified from the bacterial cell lysate and tested for binding and killing of hCGβ expressing lymphoma, T-lymphoblastic leukemia and lung carcinoma cells in vitro. Immunotoxin showed nearly 90% killing on the cells. This is the first ever report on recombinant immunotoxin for binding and cytotoxicity to hCG expressing cancer cells, and thus can be a potential candidate for the immunotherapy of hCG expressing cells. Copyright © 2014 Elsevier Inc. All rights reserved.

  5. Luminescent DNA- and agar-based membranes.

    Science.gov (United States)

    Leones, R; Fernandes, M; Ferreira, R A S; Cesarino, I; Lima, J F; Carlos, L D; Bermudez, V de Zea; Magon, C J; Donoso, J P; Silva, M M; Pawlicka, A

    2014-09-01

    Luminescent materials containing europium ions are investigated for different optical applications. They can be obtained using bio-macromolecules, which are promising alternatives to synthetic polymers based on the decreasing oil resources. This paper describes studies of the DNA- and Agar-europium triflate luminescent membranes and its potential technological applications are expanded to electroluminescent devices. Polarized optical microscopy demonstrated that the samples are birefringent with submicrometer anisotropy. The X-ray diffraction analysis revealed predominantly amorphous nature of the samples and the atomic force microscopy images showed a roughness of the membranes of 409.0 and 136.1 nm for the samples of DNA10Eu and Agar1.11Eu, respectively. The electron paramagnetic resonance spectra of the DNA(n)Eu membranes with the principal lines at g ≈ 2.0 and g ≈ 4.8 confirmed uniform distribution of rare earth ions in a disordered matrix. Moreover, these strong and narrow resonance lines for the samples of DNA(n)Eu when compared to the Agar(n)Eu suggested a presence of paramagnetic radicals arising from the DNA matrix. The emission spectra suggested that the Eu3+ ions occupy a single local environment in both matrices and the excitation spectra monitored around the Eu emission lines pointed out that the Eu3+ ions in the Agar host were mainly excited via the broad band component rather than by direct intra-4f(6) excitation, whereas the opposite case occurred for the DNA-based sample.

  6. Reference ranges and determinants of total hCG levels during pregnancy: the Generation R Study.

    Science.gov (United States)

    Korevaar, Tim I M; Steegers, Eric A P; de Rijke, Yolanda B; Schalekamp-Timmermans, Sarah; Visser, W Edward; Hofman, Albert; Jaddoe, Vincent W V; Tiemeier, Henning; Visser, Theo J; Medici, Marco; Peeters, Robin P

    2015-09-01

    Human chorionic gonadotropin (hCG) is a pregnancy hormone secreted by the placental synctiotrophoblast cell layer that has been linked to fetal growth and various placental, uterine and fetal functions. In order to investigate the effects of hCG on clinical endpoints, knowledge on reference range (RR) methodology and determinants of gestational hCG levels is crucial. Moreover, a better understanding of gestational hCG physiology can improve current screening programs and future clinical management. Serum total hCG levels were determined in 8195 women participating in the Generation R Study. Gestational age specific RRs using 'ultrasound derived gestational age' (US RRs) were calculated and compared with 'last menstrual period derived gestational age' (LMP RRs) and a model-based RR. We also investigated which pregnancy characteristics were associated with hCG levels. Compared to the US RRs, the LMP RRs were lower, most notably for the median and lower limit levels. No considerable differences were found between RRs calculated in the general population or in uncomplicated pregnancies only. Maternal smoking, BMI, parity, ethnicity, fetal gender, placental weight and hyperemesis gravidarum symptoms were associated with total hCG. We provide gestational RRs for total hCG and show that total hCG values and RR cut-offs during pregnancy vary depending on pregnancy dating methodology. This is likely due to the influence of hCG on embryonic growth, suggesting that ultrasound based pregnancy dating might be less reliable in women with high/low hCG levels. Furthermore, we identify different pregnancy characteristics that influence total hCG levels considerably and should therefore be accounted for in clinical studies.

  7. Transcription factor CgMTF-1 regulates CgZnT1 and CgMT expression in Pacific oyster (Crassostrea gigas) under zinc stress

    Energy Technology Data Exchange (ETDEWEB)

    Meng, Jie; Zhang, Linlin [Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, Shandong (China); Li, Li, E-mail: lili@qdio.ac.cn [Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, Shandong (China); Li, Chunyan; Wang, Ting [Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, Shandong (China); University of Chinese Academy of Sciences, Beijing 100039 (China); Zhang, Guofan, E-mail: gfzhang@qdio.ac.cn [Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, Shandong (China)

    2015-08-15

    Highlights: • CgMTF-1 and CgZnT1 were first identified in oysters. • CgMTF-1 localized in cell nucleus under unstressed conditions. • CgMTF-1 proteins could bind with the typical MRE motif. • CgMTF-1 activated CgZnT1, CgMT1 and CgMT4 promoters and regulated their expressions under zinc exposure. - Abstract: Oysters accumulate zinc at high tissue concentrations, and the metal response element (MRE)-binding transcription factor (MTF) functions as the cellular zinc sensor that coordinates the expression of genes involved in zinc efflux and storage, as well as those that protect against metal toxicity. In this study, we cloned MTF-1 in oysters and examined its regulation mechanism for its classic target genes, including MTs and ZnT1 under zinc exposure conditions. We cloned CgMTF-1 and determined the subcellular locations of its protein product in HEK293 cells. CgMTF-1 has a 2826 bp open reading frame that encodes a predicted polypeptide with 707 amino acid residues, showing six well-conserved zinc finger domains that are required for metal binding. In HEK293 cell lines, CgMTF-1 primarily localizes in the cell nucleus under unstressed conditions and nuclear translocation was not critical for the activation of this gene. We searched for CgMTF-1-regulated genes in oysters using RNA interference. Decreased expression levels of CgMT1, CgMT4, and CgZnT1 were observed after CgMTF-1 interference (>70% inhibition) under zinc exposure, indicating the critical role of CgMTF-1 in the regulation of these genes. We searched for a direct regulation mechanism involving CgMTF-1 for CgMT1, CgMT4, and CgZnT1 in vitro. EMSA experiments indicated that CgMTF-1 can bind with the MREs found in the CgZnT1, CgMT1 and CgMT4 promoter regions. Additionally, luciferase reporter gene experiments indicated that CgMTF-1 could activate the CgMT1, CgMT4, and CgZnT1 promoters. Overall, our results suggest that CgMTF-1 directly coordinates the regulation of CgMTs and CgZnT1 expression and plays

  8. Micro-dose hCG as luteal phase support without exogenous progesterone administration: mathematical modelling of the hCG concentration in circulation and initial clinical experience.

    Science.gov (United States)

    Andersen, C Yding; Fischer, R; Giorgione, V; Kelsey, Thomas W

    2016-10-01

    For the last two decades, exogenous progesterone administration has been used as luteal phase support (LPS) in connection with controlled ovarian stimulation combined with use of the human chorionic gonadotropin (hCG) trigger for the final maturation of follicles. The introduction of the GnRHa trigger to induce ovulation showed that exogenous progesterone administration without hCG supplementation was insufficient to obtain satisfactory pregnancy rates. This has prompted development of alternative strategies for LPS. Augmenting the local endogenous production of progesterone by the multiple corpora lutea has been one focus with emphasis on one hand to avoid development of ovarian hyper-stimulation syndrome and, on the other hand, to provide adequate levels of progesterone to sustain implantation. The present study evaluates the use of micro-dose hCG for LPS support and examines the potential advances and disadvantages. Based on the pharmacokinetic characteristics of hCG, the mathematical modelling of the concentration profiles of hCG during the luteal phase has been evaluated in connection with several different approaches for hCG administration as LPS. It is suggested that the currently employed LPS provided in connection with the GnRHa trigger (i.e. 1.500 IU) is too strong, and that daily micro-dose hCG administration is likely to provide an optimised LPS with the current available drugs. Initial clinical results with the micro-dose hCG approach are presented.

  9. Random Coding Bounds for DNA Codes Based on Fibonacci Ensembles of DNA Sequences

    Science.gov (United States)

    2008-07-01

    COVERED (From - To) 6 Jul 08 – 11 Jul 08 4. TITLE AND SUBTITLE RANDOM CODING BOUNDS FOR DNA CODES BASED ON FIBONACCI ENSEMBLES OF DNA SEQUENCES ... sequences which are generalizations of the Fibonacci sequences . 15. SUBJECT TERMS DNA Codes, Fibonacci Ensembles, DNA Computing, Code Optimization 16...coding bound on the rate of DNA codes is proved. To obtain the bound, we use some ensembles of DNA sequences which are generalizations of the Fibonacci

  10. Communication: Electron ionization of DNA bases

    Science.gov (United States)

    Rahman, M. A.; Krishnakumar, E.

    2016-04-01

    No reliable experimental data exist for the partial and total electron ionization cross sections for DNA bases, which are very crucial for modeling radiation damage in genetic material of living cell. We have measured a complete set of absolute partial electron ionization cross sections up to 500 eV for DNA bases for the first time by using the relative flow technique. These partial cross sections are summed to obtain total ion cross sections for all the four bases and are compared with the existing theoretical calculations and the only set of measured absolute cross sections. Our measurements clearly resolve the existing discrepancy between the theoretical and experimental results, thereby providing for the first time reliable numbers for partial and total ion cross sections for these molecules. The results on fragmentation analysis of adenine supports the theory of its formation in space.

  11. Hyperglycosylated hCG: a Unique Human Implantation and Invasion Factor.

    Science.gov (United States)

    Evans, Jemma

    2016-03-01

    Human chorionic gonadotropin (hCG), as one of the first embryonic products, has been extensively investigated for its role in implantation and placental development. Discovery of an over-glycosylated form of this hormone, hyperglycosylated hCG (hCG-H), has provided an additional level of complexity in our understanding of the implantation and placentation process; the structure, activity and functional implications of alterations in hCG isoforms throughout pregnancy are still being characterized. HCG-H comprises up to 90% of total hCG measurable in serum and urine during the first 2-3 weeks of pregnancy when invasive trophoblast activity is high, dropping to negligible proportions, less than 5%, of total hCG at the end of the first trimester. Functionally, hCG-H promotes trophoblast invasion during early pregnancy and has potential roles in immune cell modulation and endothelial function within the uterus at the time of pregnancy initiation. Altered levels of hCG-H are characteristics of pregnancy complications of altered trophoblast function and inadequate placentation, such as pre-eclampsia, and also over-abundance of invasive cytotrophoblasts, such as Down's syndrome. Improving our basic knowledge of the functional role-specific hCG isoforms plays in the complex cascade of events involved in implantation and placental development, and determining dynamic changes in the structure and activity of hCG isoforms throughout gestation will facilitate evidence-based decisions in assisted reproduction/in vitro fertilization based on the potential of embryos to implant, provide biomarkers for diagnosis of pregnancy complications associated with altered placental development and enhance understanding of how hCG isoforms may influence receptivity of the endometrium. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  12. DNA methylation profiling using bisulfite-based epityping of pooled genomic DNA.

    Science.gov (United States)

    Docherty, Sophia J; Davis, Oliver S P; Haworth, Claire M A; Plomin, Robert; Mill, Jonathan

    2010-11-01

    DNA methylation plays a vital role in normal cellular function, with aberrant methylation signatures being implicated in a growing number of human pathologies and complex human traits. Methods based on the modification of genomic DNA with sodium bisulfite are considered the 'gold-standard' for DNA methylation profiling on genomic DNA; however they require large amounts of DNA and may be prohibitively expensive when used on the large sample sizes necessary to detect small effects. DNA pooling approaches are already widely used in large-scale studies of DNA sequence and gene expression. In this paper, we describe the application of this economical DNA pooling technique to the study of DNA methylation profiles. This method generates accurate quantitative assessments of group DNA methylation averages, reducing the time, cost and amount of DNA starting material required for large-scale epigenetic investigation of disease phenotypes.

  13. Coast Guard Spectrum Management (CG-652)

    Science.gov (United States)

    2012-01-01

    Deepwater Horizon Response, Gulf of Mexico , BP Oil Platform (Greatly Reduced Foot Print)  USCG Deployment Basra, Iraq, Port Advisory Coordination...652 (HQ/FT MEADE) Dan Freedman ENGINEER Coast Guard Spectrum Management Flow Chart for Proposals USCG SPECTRUM INBOX USCG FAO LANT...USCG FAO LANT 01 USCG FAO D5 CG HQ LANT (RESCUE 21) CG HQ (NAIS) USCG FAO D14 USCG FAO D8 USCG FAO D9 USCG

  14. DNA-Based Vaccine Protects Against Zika in Animal Study

    Science.gov (United States)

    ... page: https://medlineplus.gov/news/fullstory_161959.html DNA-Based Vaccine Protects Against Zika in Animal Study ... In animals infected with Zika virus, the synthetic DNA-based vaccine was 100 percent effective in protecting ...

  15. DNA-Based Vaccine Guards Against Zika in Monkey Study

    Science.gov (United States)

    ... page: https://medlineplus.gov/news/fullstory_161106.html DNA-Based Vaccine Guards Against Zika in Monkey Study ... THURSDAY, Sept. 22, 2016 (HealthDay News) -- An experimental DNA-based vaccine protected monkeys from infection with the ...

  16. Spectroscopic (UV/VIS, Raman) and Electrophoresis Study of Cytosine-Guanine Oligonucleotide DNA Influenced by Magnetic Field.

    Science.gov (United States)

    Banihashemian, Seyedeh Maryam; Periasamy, Vengadesh; Boon Tong, Goh; Abdul Rahman, Saadah

    2016-01-01

    Studying the effect of a magnetic field on oligonucleotide DNA can provide a novel DNA manipulation technique for potential application in bioengineering and medicine. In this work, the optical and electrochemical response of a 100 bases oligonucleotides DNA, cytosine-guanine (CG100), is investigated via exposure to different magnetic fields (250, 500, 750, and 1000 mT). As a result of the optical response of CG100 to the magnetic field, the ultra-violet-visible spectrum indicated a slight variation in the band gap of CG100 of about 0.3 eV. Raman spectroscopy showed a significant deviation in hydrogen and phosphate bonds' vibration after exposure to the magnetic field. Oligonucleotide DNA mobility was investigated in the external electric field using the gel electrophoresis technique, which revealed a small decrease in the migration of CG100 after exposure to the magnetic field.

  17. Sequence dependency of canonical base pair opening in the DNA double helix.

    Directory of Open Access Journals (Sweden)

    Viveca Lindahl

    2017-04-01

    Full Text Available The flipping-out of a DNA base from the double helical structure is a key step of many cellular processes, such as DNA replication, modification and repair. Base pair opening is the first step of base flipping and the exact mechanism is still not well understood. We investigate sequence effects on base pair opening using extensive classical molecular dynamics simulations targeting the opening of 11 different canonical base pairs in two DNA sequences. Two popular biomolecular force fields are applied. To enhance sampling and calculate free energies, we bias the simulation along a simple distance coordinate using a newly developed adaptive sampling algorithm. The simulation is guided back and forth along the coordinate, allowing for multiple opening pathways. We compare the calculated free energies with those from an NMR study and check assumptions of the model used for interpreting the NMR data. Our results further show that the neighboring sequence is an important factor for the opening free energy, but also indicates that other sequence effects may play a role. All base pairs are observed to have a propensity for opening toward the major groove. The preferred opening base is cytosine for GC base pairs, while for AT there is sequence dependent competition between the two bases. For AT opening, we identify two non-canonical base pair interactions contributing to a local minimum in the free energy profile. For both AT and CG we observe long-lived interactions with water and with sodium ions at specific sites on the open base pair.

  18. DNA & Protein detection based on microbead agglutination

    KAUST Repository

    Kodzius, Rimantas

    2012-06-06

    We report a simple and rapid room temperature assay for point-of-care (POC) testing that is based on specific agglutination. Agglutination tests are based on aggregation of microparticles in the presence of a specific analyte thus enabling the macroscopic observation. Agglutination-based tests are most often used to explore the antibody-antigen reactions. Agglutination has been used for mode protein assays using a biotin/streptavidin two-component system, as well as a hybridization based two-component assay; however, as our work shows, two-component systems are prone to self-termination of the linking analyte and thus have a lower sensitivity. Three component systems have also been used with DNA hybridization, as in our work; however, their assay requires 48 hours for incubation, while our assay is performed in 5 minutes making it a real candidate for POC testing. We demonstrate three assays: a two-component biotin/streptavidin assay, a three-component hybridization assay using single stranded DNA (ssDNA) molecules and a stepped three-component hybridization assay. The comparison of these three assays shows our simple stepped three-component agglutination assay to be rapid at room temperature and more sensitive than the two-component version by an order of magnitude. An agglutination assay was also performed in a PDMS microfluidic chip where agglutinated beads were trapped by filter columns for easy observation. We developed a rapid (5 minute) room temperature assay, which is based on microbead agglutination. Our three-component assay solves the linker self-termination issue allowing an order of magnitude increase in sensitivity over two–component assays. Our stepped version of the three-component assay solves the issue with probe site saturation thus enabling a wider range of detection. Detection of the agglutinated beads with the naked eye by trapping in microfluidic channels has been shown.

  19. Biological functions of hCG and hCG-related molecules

    Directory of Open Access Journals (Sweden)

    Cole Laurence A

    2010-08-01

    Full Text Available Abstract Background hCG is a term referring to 4 independent molecules, each produced by separate cells and each having completely separate functions. These are hCG produced by villous syncytiotrophoblast cells, hyperglycosylated hCG produced by cytotrophoblast cells, free beta-subunit made by multiple primary non-trophoblastic malignancies, and pituitary hCG made by the gonadotrope cells of the anterior pituitary. Results and discussion hCG has numerous functions. hCG promotes progesterone production by corpus luteal cells; promotes angiogenesis in uterine vasculature; promoted the fusion of cytotrophoblast cell and differentiation to make syncytiotrophoblast cells; causes the blockage of any immune or macrophage action by mother on foreign invading placental cells; causes uterine growth parallel to fetal growth; suppresses any myometrial contractions during the course of pregnancy; causes growth and differentiation of the umbilical cord; signals the endometrium about forthcoming implantation; acts on receptor in mother's brain causing hyperemesis gravidarum, and seemingly promotes growth of fetal organs during pregnancy. Hyperglycosylated hCG functions to promote growth of cytotrophoblast cells and invasion by these cells, as occurs in implantation of pregnancy, and growth and invasion by choriocarcinoma cells. hCG free beta-subunit is produced by numerous non-trophoblastic malignancies of different primaries. The detection of free beta-subunit in these malignancies is generally considered a sign of poor prognosis. The free beta-subunit blocks apoptosis in cancer cells and promotes the growth and malignancy of the cancer. Pituitary hCG is a sulfated variant of hCG produced at low levels during the menstrual cycle. Pituitary hCG seems to mimic luteinizing hormone actions during the menstrual cycle.

  20. Biological functions of hCG and hCG-related molecules

    Science.gov (United States)

    2010-01-01

    Background hCG is a term referring to 4 independent molecules, each produced by separate cells and each having completely separate functions. These are hCG produced by villous syncytiotrophoblast cells, hyperglycosylated hCG produced by cytotrophoblast cells, free beta-subunit made by multiple primary non-trophoblastic malignancies, and pituitary hCG made by the gonadotrope cells of the anterior pituitary. Results and discussion hCG has numerous functions. hCG promotes progesterone production by corpus luteal cells; promotes angiogenesis in uterine vasculature; promoted the fusion of cytotrophoblast cell and differentiation to make syncytiotrophoblast cells; causes the blockage of any immune or macrophage action by mother on foreign invading placental cells; causes uterine growth parallel to fetal growth; suppresses any myometrial contractions during the course of pregnancy; causes growth and differentiation of the umbilical cord; signals the endometrium about forthcoming implantation; acts on receptor in mother's brain causing hyperemesis gravidarum, and seemingly promotes growth of fetal organs during pregnancy. Hyperglycosylated hCG functions to promote growth of cytotrophoblast cells and invasion by these cells, as occurs in implantation of pregnancy, and growth and invasion by choriocarcinoma cells. hCG free beta-subunit is produced by numerous non-trophoblastic malignancies of different primaries. The detection of free beta-subunit in these malignancies is generally considered a sign of poor prognosis. The free beta-subunit blocks apoptosis in cancer cells and promotes the growth and malignancy of the cancer. Pituitary hCG is a sulfated variant of hCG produced at low levels during the menstrual cycle. Pituitary hCG seems to mimic luteinizing hormone actions during the menstrual cycle. PMID:20735820

  1. A rare nucleotide base tautomer in the structure of an asymmetric DNA junction.

    Science.gov (United States)

    Khuu, Patricia; Ho, P Shing

    2009-08-25

    The single-crystal structure of a DNA Holliday junction assembled from four unique sequences shows a structure that conforms to the general features of models derived from similar constructs in solution. The structure is a compact stacked-X form junction with two sets of stacked B-DNA-type arms that coaxially stack to form semicontinuous duplexes interrupted only by the crossing of the junction. These semicontinuous helices are related by a right-handed rotation angle of 56.5 degrees, which is nearly identical to the 60 degree angle in the solution model but differs from the more shallow value of approximately 40 degrees for previous crystal structures of symmetric junctions that self-assemble from single identical inverted-repeat sequences. This supports the model in which the unique set of intramolecular interactions at the trinucleotide core of the crossing strands, which are not present in the current asymmetric junction, affects both the stability and geometry of the symmetric junctions. An unexpected result, however, is that a highly wobbled A.T base pair, which is ascribed here to a rare enol tautomer form of the thymine, was observed at the end of a CCCC/GGGG sequence within the stacked B-DNA arms of this 1.9 A resolution structure. We suggest that the junction itself is not responsible for this unusual conformation but served as a vehicle for the study of this CG-rich sequence as a B-DNA duplex, mimicking the form that would be present in a replication complex. The existence of this unusual base lends credence to and defines a sequence context for the "rare tautomer hypothesis" as a mechanism for inducing transition mutations during DNA replication.

  2. Envisioning the molecular choreography of DNA base excision repair.

    Science.gov (United States)

    Parikh, S S; Mol, C D; Hosfield, D J; Tainer, J A

    1999-02-01

    Recent breakthroughs integrate individual DNA repair enzyme structures, biochemistry and biology to outline the structural cell biology of the DNA base excision repair pathways that are essential to genome integrity. Thus, we are starting to envision how the actions, movements, steps, partners and timing of DNA repair enzymes, which together define their molecular choreography, are elegantly controlled by both the nature of the DNA damage and the structural chemistry of the participating enzymes and the DNA double helix.

  3. Single-Base DNA Discrimination via Transverse Ionic Transport

    CERN Document Server

    Wilson, James

    2013-01-01

    We suggest to discriminate single DNA bases via transverse ionic transport, namely by detecting the ionic current that flows in a channel while a single-stranded DNA is driven through an intersecting nanochannel. Our all-atom molecular dynamics simulations indeed show that the ionic currents of the four bases are statistically distinct, thus offering another possible approach to sequence DNA.

  4. DNA nanostructure-based imaging probes and drug carriers.

    Science.gov (United States)

    Zhan, Pengfei; Jiang, Qiao; Wang, Zhen-Gang; Li, Na; Yu, Haiyin; Ding, Baoquan

    2014-09-01

    Self-assembled DNA nanostructures are well-defined nanoscale shapes, with uniform sizes, precise spatial addressability, and excellent biocompatibility. With these features, DNA nanostructures show great potential for biomedical applications; various DNA-based biomedical imaging probes or payload delivery carriers have been developed. In this review, we summarize the recent developments of DNA-based nanostructures as tools for diagnosis and cancer therapy. The biological effects that are brought about by DNA nanostructures are highlighted by in vitro and in vivo imaging, antitumor drug delivery, and immunostimulatory therapy. The challenges and perspectives of DNA nanostructures in the field of nanomedicine are discussed.

  5. Hepatitis B virus DNA polymerase gene polymorphism based ...

    African Journals Online (AJOL)

    2017-09-03

    Sep 3, 2017 ... HBV is distributed into various genotypes based on nucleic acid sequence variation. ... compared to genotype B and higher incidence of HCC in genotype D ... DNA sequencing technology to sequence HBV DNA polymerase ...

  6. Updated Physical Parameters of SN 2012cg

    Science.gov (United States)

    Marion, G. H.; Challis, P.; Hicken, M.; Mandel, K.; Meyer, S.; Kirshner, R. P.; Foley, R. J.; Friedman, A.; Irwin, J.; Wood-Vasey, W. M.; Wheeler, J. C.; Vinko, J.; Rines, K.; Wilhelmy, S.; Macri, L.

    2012-06-01

    The Harvard-Smithsonian Center for Astrophysics Supernova Group reports photometric and spectroscopic observations of SN 2012cg (ATEL #4115, #4159). We find that SN 2012cg has a slow decline rate and low expansion velocities. BayeSN fits to the data show that SN 2012cg has significant dust extinction (A_v ~ 0.67 mag). We find R_v = 2.7 +/- 0.5, which is consistent with the Milky Way value of 3.1 and mildly inconsistent with the extremely low values reported for some highly reddened SN (e.g., R_v = 1.59 +/- 0.07 for SN 2002cv; Elias-Rosa et al.

  7. Large-scale genomic 2D visualization reveals extensive CG-AT skew correlation in bird genomes

    Directory of Open Access Journals (Sweden)

    Deng Xuemei

    2007-11-01

    Full Text Available Abstract Background Bird genomes have very different compositional structure compared with other warm-blooded animals. The variation in the base skew rules in the vertebrate genomes remains puzzling, but it must relate somehow to large-scale genome evolution. Current research is inclined to relate base skew with mutations and their fixation. Here we wish to explore base skew correlations in bird genomes, to develop methods for displaying and quantifying such correlations at different scales, and to discuss possible explanations for the peculiarities of the bird genomes in skew correlation. Results We have developed a method called Base Skew Double Triangle (BSDT for exhibiting the genome-scale change of AT/CG skew as a two-dimensional square picture, showing base skews at many scales simultaneously in a single image. By this method we found that most chicken chromosomes have high AT/CG skew correlation (symmetry in 2D picture, except for some microchromosomes. No other organisms studied (18 species show such high skew correlations. This visualized high correlation was validated by three kinds of quantitative calculations with overlapping and non-overlapping windows, all indicating that chicken and birds in general have a special genome structure. Similar features were also found in some of the mammal genomes, but clearly much weaker than in chickens. We presume that the skew correlation feature evolved near the time that birds separated from other vertebrate lineages. When we eliminated the repeat sequences from the genomes, the AT and CG skews correlation increased for some mammal genomes, but were still clearly lower than in chickens. Conclusion Our results suggest that BSDT is an expressive visualization method for AT and CG skew and enabled the discovery of the very high skew correlation in bird genomes; this peculiarity is worth further study. Computational analysis indicated that this correlation might be a compositional characteristic

  8. Circulating Cell Free DNA in the Diagnosis of Trophoblastic Tumors

    Science.gov (United States)

    Openshaw, Mark R.; Harvey, Richard A.; Sebire, Neil J.; Kaur, Baljeet; Sarwar, Naveed; Seckl, Michael J.; Fisher, Rosemary A.

    2015-01-01

    Gestational trophoblastic neoplasia (GTN) represents a group of diseases characterized by production of human chorionic gonadotropin (hCG). Since non-gestational tumors may occasionally secrete hCG, histopathological diagnosis is important for appropriate clinical management. However, a histopathological diagnosis is not always available. We therefore investigated the feasibility of extracting cell free DNA (cfDNA) from the plasma of women with GTN for use as a “liquid biopsy” in patients without histopathological diagnosis. cfDNA was prepared from the plasma of 20 women with a diagnosis of GTN and five with hCG-secreting tumors of unknown origin. Genotyping of cfDNA from the patient, genomic DNA from her and her partner and DNA from the tumor tissue identified circulating tumor DNA (ctDNA) (from 9% to 53% of total cfDNA) in 12 of 20 patients with GTN. In one case without a tissue diagnosis, ctDNA enabled a diagnosis of GTN originating in a non-molar conception and in another a diagnosis of non-gestational tumor, based on the high degree of allelic instability and loss of heterozygosity in the ctDNA. In summary ctDNA can be detected in the plasma of women with GTN and can facilitate the diagnosis of both gestational and non-gestational trophoblastic tumors in cases without histopathological diagnosis. PMID:26981554

  9. Circulating Cell Free DNA in the Diagnosis of Trophoblastic Tumors

    Directory of Open Access Journals (Sweden)

    Mark R. Openshaw

    2016-02-01

    Full Text Available Gestational trophoblastic neoplasia (GTN represents a group of diseases characterized by production of human chorionic gonadotropin (hCG. Since non-gestational tumors may occasionally secrete hCG, histopathological diagnosis is important for appropriate clinical management. However, a histopathological diagnosis is not always available. We therefore investigated the feasibility of extracting cell free DNA (cfDNA from the plasma of women with GTN for use as a “liquid biopsy” in patients without histopathological diagnosis. cfDNA was prepared from the plasma of 20 women with a diagnosis of GTN and five with hCG-secreting tumors of unknown origin. Genotyping of cfDNA from the patient, genomic DNA from her and her partner and DNA from the tumor tissue identified circulating tumor DNA (ctDNA (from 9% to 53% of total cfDNA in 12 of 20 patients with GTN. In one case without a tissue diagnosis, ctDNA enabled a diagnosis of GTN originating in a non-molar conception and in another a diagnosis of non-gestational tumor, based on the high degree of allelic instability and loss of heterozygosity in the ctDNA. In summary ctDNA can be detected in the plasma of women with GTN and can facilitate the diagnosis of both gestational and non-gestational trophoblastic tumors in cases without histopathological diagnosis.

  10. 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.

  11. Prolog+CG: A Maintainer's Perspective

    DEFF Research Database (Denmark)

    Petersen, Ulrik

    2006-01-01

    Prolog+CG is an implementation of Prolog with Conceptual Graphs as first-class datastructures, on a par with terms. As such, it lends itself well to applications in which reasoning with Conceptual Graphs and/or ontologies plays a role. It  as originally developed by Prof. Dr. Adil Kabbaj, who in ...

  12. Photometric and Spectroscopic Study of the Shakhbazian Compact Galaxy Groups ShCG 31, ShCG 38, ShCG 43, and ShCG 282

    Directory of Open Access Journals (Sweden)

    H. M. Tovmassian

    2003-01-01

    Full Text Available Los grupos compactos de galaxias Shakhbazian son las configuraciones más densas que se conocen. Hace unos pocos años iniciamos un estudio fotométrico y espectroscópico de estos grupos. En este artículo presentamos los resultados de la investigación en los grupos ShCG 31, ShCG 38, ShCG 43 y ShCG 282. Presentamos los corrimientos al rojo de las galaxias miembro, los resultados de la fonometría BV R, las curvas de brillo superficial-radio efectivo, las masas estimadas, luminosidades y las razones masa-luminosidad de los grupos, además de algunos parámetros dinámicos como la dispersión de velocidades radiales y el tiempo de cruce. Los ShCGs estudiados consisten principalmente de galaxias elípticas y lenticulares. Se muestra que algunas galaxias en estos grupos están en proceso de interacción.

  13. The Drosophila gene CG9918 codes for a pyrokinin-1 receptor

    DEFF Research Database (Denmark)

    Cazzamali, Giuseppe; Torp, Malene; Hauser, Frank

    2005-01-01

    The database from the Drosophila Genome Project contains a gene, CG9918, annotated to code for a G protein-coupled receptor. We cloned the cDNA of this gene and functionally expressed it in Chinese hamster ovary cells. We tested a library of about 25 Drosophila and other insect neuropeptides, and...

  14. High tilt susceptibility of the Scintrex CG-5 relative gravimeters

    Science.gov (United States)

    Reudink, R.; Klees, R.; Francis, O.; Kusche, J.; Schlesinger, R.; Shabanloui, A.; Sneeuw, N.; Timmen, L.

    2014-06-01

    We report on the susceptibility of the Scintrex CG-5 relative gravimeters to tilting, that is the tendency of the instrument of providing incorrect readings after being tilted (even by small angles) for a moderate period of time. Tilting of the instrument can occur when in transit between sites usually on the backseat of a car even using the specially designed transport case. Based on a series of experiments with different instruments, we demonstrate that the readings may be offset by tens of Gal. In addition, it may take hours before the first reliable readings can be taken, with the actual time depending on how long the instrument had been tilted. This sensitivity to tilt in combination with the long time required for the instrument to provide reliable readings has not yet been reported in the literature and is not addressed adequately in the Scintrex CG-5 user manual. In particular, the inadequate instrument state cannot easily be detected by checking the readings during the observation or by reviewing the final data before leaving a site, precautions suggested by Scintrex Ltd. In regional surveys with car transportation over periods of tens of minutes to hours, the gravity measurements can be degraded by some 10 Gal. To obtain high-quality results in line with the CG-5 specifications, the gravimeters must remain in upright position to within a few degrees during transits. This requirement may often be unrealistic during field observations, particularly when observing in hilly terrain or when walking with the instrument in a backpack.

  15. Analytical Devices Based on Direct Synthesis of DNA on Paper.

    Science.gov (United States)

    Glavan, Ana C; Niu, Jia; Chen, Zhen; Güder, Firat; Cheng, Chao-Min; Liu, David; Whitesides, George M

    2016-01-01

    This paper addresses a growing need in clinical diagnostics for parallel, multiplex analysis of biomarkers from small biological samples. It describes a new procedure for assembling arrays of ssDNA and proteins on paper. This method starts with the synthesis of DNA oligonucleotides covalently linked to paper and proceeds to assemble microzones of DNA-conjugated paper into arrays capable of simultaneously capturing DNA, DNA-conjugated protein antigens, and DNA-conjugated antibodies. The synthesis of ssDNA oligonucleotides on paper is convenient and effective with 32% of the oligonucleotides cleaved and eluted from the paper substrate being full-length by HPLC for a 32-mer. These ssDNA arrays can be used to detect fluorophore-linked DNA oligonucleotides in solution, and as the basis for DNA-directed assembly of arrays of DNA-conjugated capture antibodies on paper, detect protein antigens by sandwich ELISAs. Paper-anchored ssDNA arrays with different sequences can be used to assemble paper-based devices capable of detecting DNA and antibodies in the same device and enable simple microfluidic paper-based devices.

  16. Enhanced base excision repair capacity in carotid atherosclerosis may protect nuclear DNA but not mitochondrial DNA

    DEFF Research Database (Denmark)

    Skarpengland, Tonje; B. Dahl, Tuva; Skjelland, Mona

    2016-01-01

    Lesional and systemic oxidative stress has been implicated in the pathogenesis of atherosclerosis, potentially leading to accumulation of DNA base lesions within atherosclerotic plaques. Although base excision repair (BER) is a major pathway counteracting oxidative DNA damage, our knowledge on BER...... and accumulation of DNA base lesions in clinical atherosclerosis is scarce. Here, we evaluated the transcriptional profile of a wide spectrum of BER components as well as DNA damage accumulation in atherosclerotic and non-atherosclerotic arteries. BER gene expression levels were analyzed in 162 carotid plaques, 8...... genes in atherosclerosis may contribute to lesional nuclear DNA stability but appears insufficient to maintain mtDNA integrity, potentially influencing mitochondrial function in cells within the atherosclerotic lesion....

  17. Methods for sequencing GC-rich and CCT repeat DNA templates

    Science.gov (United States)

    Robinson, Donna L.

    2007-02-20

    The present invention is directed to a PCR-based method of cycle sequencing DNA and other polynucleotide sequences having high CG content and regions of high GC content, and includes for example DNA strands with a high Cytosine and/or Guanosine content and repeated motifs such as CCT repeats.

  18. DNA chip based sensor for amperometric detection of infectious pathogens.

    Science.gov (United States)

    Singh, Swati; Kaushal, Ankur; Khare, Shashi; Kumar, Ashok

    2017-10-01

    Several infectious pathogens are found in human whose detection is essential for rapid cure of diseases. The most commonly found pathogen in human is Streptococcus pyogenes which leads to a wide range of infections from mild pharyngitis to rheumatic heart disease. An ultrasensitive DNA chip based sensor was developed for quick identification of pathogen S. pyogenes from patient throat swab samples. The amperometric response was measured after hybridization of specific probe with single stranded genomic DNA (ssG-DNA) from the patient samples. The DNA chip was characterized by FTIR, SEM and validated with suspected patient real samples. The sensitivity of the DNA chip based sensor was found 951.34(μA/cm(2))/ng DNA and lower limit of detection (LOD) was 130fg/6μL samples. The DNA chip based sensor is highly specific and takes only 30min for identification of specific pathogen. Copyright © 2017 Elsevier B.V. All rights reserved.

  19. Detecting Chemically Modified DNA Bases Using Surface Enhanced Raman Spectroscopy.

    Science.gov (United States)

    Barhoumi, Aoune; Halas, Naomi J

    2011-12-15

    Post-translational modifications of DNA- changes in the chemical structure of individual bases that occur without changes in the DNA sequence- are known to alter gene expression. They are believed to result in frequently deleterious phenotypic changes, such as cancer. Methylation of adenine, methylation and hydroxymethylation of cytosine, and guanine oxidation are the primary DNA base modifications identified to date. Here we show it is possible to use surface enhanced Raman spectroscopy (SERS) to detect these primary DNA base modifications. SERS detection of modified DNA bases is label-free and requires minimal additional sample preparation, reducing the possibility of additional chemical modifications induced prior to measurement. This approach shows the feasibility of DNA base modification assessment as a potentially routine analysis that may be further developed for clinical diagnostics.

  20. How to make DNA count: DNA-based diagnostic tools in veterinary parasitology.

    Science.gov (United States)

    Hunt, P W; Lello, J

    2012-05-04

    Traditional methods for the diagnosis of parasitic helminth infections of livestock have a number of limitations, such as the inability to distinguish mixed-species infections, a heavy reliance on technical experience and also sub-sampling errors. Some of these limitations may be overcome through the development of rapid and accurate DNA-based tests. For example, DNA-based tests can specifically detect individual species in a mixed infection at either the larval or egg stages, in the absence of morphological differences among species. Even so, some diagnostic problems remain the same, irrespective of whether a DNA-based or traditional method is used. For example, sub-sampling errors from an aggregated distribution are likely to persist. It is proposed, however, that DNA-based diagnostic technologies offer an opportunity to expand diagnostic capabilities, and are discussed in the current review. The future introduction of DNA-based diagnostic technologies into routine diagnostic settings will also be discussed.

  1. DNA Based Electrochromic and Photovoltaic Cells

    Science.gov (United States)

    2012-01-01

    and biodegradable material, has low cost and good film forming properties, is not toxic and forms transparent solutions with high viscosity [17]. An...applications requires fundamental studies on DNA in solid state, in which the behavior is expected to be different than that in solution. DNA is an acid , but...function of temperature of the blends samples of DNA with poly(ethylene dioxythiophene):poly(styrene sulphonate ) (PEDOT:PSS), poly(orthoethoxy aniline

  2. A novel bio-sensor based on DNA strand displacement.

    Directory of Open Access Journals (Sweden)

    Xiaolong Shi

    Full Text Available DNA strand displacement technology performs well in sensing and programming DNA segments. In this work, we construct DNA molecular systems based on DNA strand displacement performing computation of logic gates. Specifically, a class of so-called "DNA neurons" are achieved, in which a "smart" way inspired by biological neurons encoding information is developed to encode and deliver information using DNA molecules. The "DNA neuron" is bistable, that is, it can sense DNA molecules as input signals, and release "negative" or "positive" signals DNA molecules. We design intelligent DNA molecular systems that are constructed by cascading some particularly organized "DNA neurons", which could perform logic computation, including AND, OR, XOR logic gates, automatically. Both simulation results using visual DSD (DNA strand displacement software and experimental results are obtained, which shows that the proposed systems can detect DNA signals with high sensitivity and accretion; moreover, the systems can process input signals automatically with complex nonlinear logic. The method proposed in this work may provide a new way to construct a sensitive molecular signal detection system with neurons spiking behavior in vitro, and can be used to develop intelligent molecular processing systems in vivo.

  3. DNA duplex membrane effect for the electrochemical detection of single-base DNA mutations

    Institute of Scientific and Technical Information of China (English)

    Luo Chunxiong; Mao Yongdong; Ouyang Qi

    2006-01-01

    Here we report a new method to detect DNA point mutations.The method is based on the formation and deformation of double-stranded DNA(dsDNA)membranes on a gold surface.It can encage reporter molecules between the gold surface and the double-stranded DNA or keep them away from the gold surface.In these systems,Fe(CN)63- was used as the reporter.As the temperature increases,a sharp electrochemical signal change in the melting curve of wild-type dsDNA appears.At a special temperature,the and single base mutation target.Thus,the system provides a simple and sensitive method to detect DNA point mutations without labeling targets.

  4. Electroporation-based DNA delivery technology

    DEFF Research Database (Denmark)

    Gothelf, A; Gehl, Julie

    2014-01-01

    DNA delivery to for example skin and muscle can easily be performed with electroporation. The method is efficient, feasible, and inexpensive and the future possibilities are numerous. Here we present our protocol for gene transfection to mouse skin using naked plasmid DNA and electric pulses....

  5. Carbon-based electrode materials for DNA electroanalysis.

    Science.gov (United States)

    Kato, Dai; Niwa, Osamu

    2013-01-01

    This review addresses recent studies of newly developed carbon-based electrode materials and their use for DNA electroanalysis. Recently, new carbon materials including carbon nanotubes (CNT), graphene and diamond-based nanocarbon electrodes have been actively developed as sensing platforms for biomolecules, such as DNA and proteins. Electrochemical techniques using these new material-based electrodes can provide very simple and inexpensive sensing platforms, and so are expected to be used as one of the "post-light" DNA analysis methods, which include coulometric detection, amperometric detection with electroactive tags or intercalators, and potentiometric detection. DNA electroanalysis using these new carbon materials is summarized in view of recent advances on electrodes.

  6. hCG - related molecules and their measurement.

    Science.gov (United States)

    Szczerba, Anna; Białas, Piotr; Pięta, Paweł Piotr; Jankowska, Anna

    2016-01-01

    Measurements of human chorionic gonadotropin (hCG) synthesized by trophoblast cells is a powerful tool of pregnancy monitoring. It was showed that similarly to pregnancy also trophoblastic and nontrophoblastic malignancies produce variety of hCG molecules. In urine and serum of both pregnant women and tumors patients a fifteen various forms of hCG, such as: regular hCG, hyperglycosylated hCG and predominant hyperglycosylated hCG free β, were identified. These forms might be useful in order to recognize between physiological and pathological pregnancies as well as cancers. Even the presence of these different hormone variants is well documented the commercially available biochemical tests detecting hCG failed to identified and distinguish among these forms. Especially hard is to identify glycan chains linked to heterodimer. Thus, a detailed analysis of hCG-related molecules produced during physiological and pathological condition, together with a new tests development are needed.

  7. Star formation, structure, and formation mechanism of cometary globules: NIR observations of CG 1 and CG 2

    CERN Document Server

    Mäkelä, M M

    2012-01-01

    Cometary globule (CG) 1 and CG 2 are "classic" CGs in the Gum Nebula. They have compact heads and long dusty tails that point away from the centre of the Gum Nebula. We study the structure of CG 1 and CG 2 and the star formation in them to find clues to the CG formation mechanism. The two possible mechanisms, radiation-driven implosion (RDI) and a supernova (SN) blast wave, produce a characteristic mass distribution where the major part of the mass is situated in either the head (RDI) or the tail (SN). CG 1 and CG 2 were imaged in the near infrared (NIR) JsHKs bands. NIR photometry was used to locate NIR excess objects and to create extinction maps of the CGs. The A_V maps allow us to analyse the large-scale structure of CG 1 and CG 2. Archival images from the WISE and Spitzer satellites and HIRES-processed IRAS images were used to study the small-scale structure. In addition to the previously known CG 1 IRS 1 we discovered three new NIR-excess objects, two in CG 1 and one in CG 2. CG 2 IRS 1 is the first det...

  8. Recycling BiCG for Model Reduction

    CERN Document Server

    Ahuja, Kapil; Chang, Eun R; Gugercin, Serkan

    2010-01-01

    Science and engineering problems frequently require solving a sequence of dual linear systems. Two examples are the Iterative Rational Krylov Algorithm (IRKA) for model reduction and Quantum Monte Carlo (QMC) methods in electronic structure calculations. This paper introduces Recycling BiCG, a BiCG method that recycles two Krylov subspaces from one pair of linear systems to the next pair. We develop an augmented bi-Lanczos algorithm and a modified two-term recurrence to include recycling in the iteration. The recycle spaces are approximate left and right invariant subspaces corresponding to the eigenvalues close to the origin. These recycle spaces are found by solving a small generalized eigenvalue problem alongside the dual linear systems being solved in the sequence. We test our algorithm in two application areas. First, we solve a discretized partial differential equation of convection-diffusion type, because these are well-known model problems. Second, we use Recycling BiCG for the linear systems arising ...

  9. DNA base excision repair nanosystem engineering: model development.

    Science.gov (United States)

    Sokhansanj, B A

    2005-01-01

    DNA base damage results from a combination of endogenous sources, (normal metabolism, increased metabolism due to obesity, stress from diseases such as arthritis and diabetes, and ischemia) and the environment (ingested toxins, ionizing radiation, etc.). If unrepaired DNA base damage can lead to diminished cell function, and potentially diseases and eventually mutations that lead to cancer. Sophisticated DNA repair mechanisms have evolved in all living cells to preserve the integrity of inherited genetic information and transcriptional control. Understanding a system like DNA repair is greatly enhanced by using engineering methods, in particular modeling interactions and using predictive simulation to analyze the impact of perturbations. We describe the use of such a "nanosystem engineering" approach to analyze the DNA base excision repair pathway in human cells, and use simulation to predict the impact of varying enzyme concentration on DNA repair capacity.

  10. Hamilton Graph Based on DNA Computing

    Institute of Scientific and Technical Information of China (English)

    ZHANGJia-xiu

    2004-01-01

    DNA computing is a novel method for solving a class of intractable computationalproblems in which the computing can grow exponentially with problem size. Up to now, manyaccomplishments have been achieved to improve its performance and increase its reliability.Hamilton Graph Problem has been solved by means of molecular biology techniques. A smallgraph was encoded in molecules of DNA, and the “operations” of the computation wereperformed with standard protocols and enzymes. This work represents further evidence forthe ability of DNA computing to solve NP-complete search problems.

  11. [Uracil-DNA glycosylases].

    Science.gov (United States)

    Pytel, Dariusz; Słupianek, Artur; Ksiazek, Dominika; Skórski, Tomasz; Błasiak, Janusz

    2008-01-01

    Uracil is one of four nitrogen bases, most frequently found in normal RNA. Uracyl can be found also in DNA as a result of enzymatic or non-enzymatic deamination of cytosine as well as misincorporation of dUMP instead of dTMP during DNA replication. Uracil from DNA can be removed by DNA repair enzymes with apirymidine site as an intermediate. However, if uracil is not removed from DNA a pair C:G in parental DNA can be changed into a T:A pair in the daughter DNA molecule. Therefore, uracil in DNA may lead to a mutation. Uracil in DNA, similarly to thymine, forms energetically most favorable hydrogen bonds with adenine, therefore uracil does not change the coding properties of DNA. Uracil in DNA is recognized by uracil DNA glycosylase (UDGs), which initiates DNA base excision repair, leading to removing of uracil from DNA and replacing it by thymine or cytosine, when arose as a result of cytosine deamination. Eukaryotes have at least four nuclear UDGs: UNG2, SMUG1, TDG i MBD4, while UNG1 operates in the mitochondrium. UNG2 is involved in DNA repair associated with DNA replication and interacts with PCNA and RPA proteins. Uracil can also be an intermediate product in the process of antigen-dependent antibody diversification in B lymphocytes. Enzymatic deamination of viral DNA by host cells can be a defense mechanism against viral infection, including HIV-1. UNG2, MBD4 and TDG glycosylases may cooperate with mismatch repair proteins and TDG can be involved in nucleotide excision repair system.

  12. Controlling charge current through a DNA based molecular transistor

    Science.gov (United States)

    Behnia, S.; Fathizadeh, S.; Ziaei, J.

    2017-01-01

    Molecular electronics is complementary to silicon-based electronics and may induce electronic functions which are difficult to obtain with conventional technology. We have considered a DNA based molecular transistor and study its transport properties. The appropriate DNA sequence as a central chain in molecular transistor and the functional interval for applied voltages is obtained. I-V characteristic diagram shows the rectifier behavior as well as the negative differential resistance phenomenon of DNA transistor. We have observed the nearly periodic behavior in the current flowing through DNA. It is reported that there is a critical gate voltage for each applied bias which above it, the electrical current is always positive.

  13. Antibody-controlled actuation of DNA-based molecular circuits

    Science.gov (United States)

    Engelen, Wouter; Meijer, Lenny H. H.; Somers, Bram; de Greef, Tom F. A.; Merkx, Maarten

    2017-02-01

    DNA-based molecular circuits allow autonomous signal processing, but their actuation has relied mostly on RNA/DNA-based inputs, limiting their application in synthetic biology, biomedicine and molecular diagnostics. Here we introduce a generic method to translate the presence of an antibody into a unique DNA strand, enabling the use of antibodies as specific inputs for DNA-based molecular computing. Our approach, antibody-templated strand exchange (ATSE), uses the characteristic bivalent architecture of antibodies to promote DNA-strand exchange reactions both thermodynamically and kinetically. Detailed characterization of the ATSE reaction allowed the establishment of a comprehensive model that describes the kinetics and thermodynamics of ATSE as a function of toehold length, antibody-epitope affinity and concentration. ATSE enables the introduction of complex signal processing in antibody-based diagnostics, as demonstrated here by constructing molecular circuits for multiplex antibody detection, integration of multiple antibody inputs using logic gates and actuation of enzymes and DNAzymes for signal amplification.

  14. Modulation of DNA base excision repair during neuronal differentiation

    DEFF Research Database (Denmark)

    Sykora, Peter; Yang, Jenq-Lin; Ferrarelli, Leslie K

    2013-01-01

    Neurons are terminally differentiated cells with a high rate of metabolism and multiple biological properties distinct from their undifferentiated precursors. Previous studies showed that nucleotide excision DNA repair is downregulated in postmitotic muscle cells and neurons. Here, we characterize...... DNA damage susceptibility and base excision DNA repair (BER) capacity in undifferentiated and differentiated human neural cells. The results show that undifferentiated human SH-SY5Y neuroblastoma cells are less sensitive to oxidative damage than their differentiated counterparts, in part because...

  15. Serum human chorionic gonadotropin (hCG) trend within the first few days after medical abortion: a prospective study.

    Science.gov (United States)

    Pocius, Katherine D; Bartz, Deborah; Maurer, Rie; Stenquist, Asha; Fortin, Jennifer; Goldberg, Alisa B

    2017-03-01

    To prospectively describe the decline in serum human chorionic gonadotropin (hCG) in the first 5 days after complete medical abortion and evaluate the influence of initial hCG and gestational duration. We conducted a prospective, physiologic study of women ≤63 days gestation who underwent medical abortion with 200 mg mifepristone and 800 mcg buccal misoprostol. We stratified enrollment into two gestational cohorts, hCG values on Day 1 (day of mifepristone), Day 3, Day 5 and a routine follow up hCG on Days 7-14. We calculated the percent hCG decline from Day 1 to each repeat measure and evaluated trends based on initial serum hCG level and gestation. We enrolled 66 women; 59 were protocol-adherent and included in our analysis. Mean gestation on Day 1 was 49 days and mean baseline hCG was 72,332 IU. Fifty-seven subjects (97%) had a complete medical abortion without further intervention. The mean serum hCG decline among subjects with complete medical abortion was 70.0±10.6% [range 36.9-98.6%] on Day 3 and 91.4±4.4% [range 68.4-97.7%] on Day 5. The mean serum hCG decline from Day 1 to routine follow-up on Days 7-9 was 97.1±1.7% [range 92.4-99.2%], from Day 1 to Day 10-11 was 98.5±1.4% [range 94.7-99.6%] and from Day 1 to Day 12-14 was 98.7±2.8% [range 86.7-99.9%]. There was no difference in percent hCG decline stratified by initial hCG or gestation. There is a rapid and predictable decline in serum hCG as early as Day 5 after complete medical abortion through 63 days gestation. Rate of hCG decline is not affected by initial hCG or gestational duration. For women who require confirmation of complete abortion sooner than 1 week after mifepristone, due to patient preference, logistical constraints or in the setting of pregnancy of unconfirmed location, a single repeat hCG on Day 5 may be clinically useful. Copyright © 2016 Elsevier Inc. All rights reserved.

  16. Analysis list: CG8478 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available CG8478 Cell line,Embryo,Pupae + dm3 http://dbarchive.biosciencedbc.jp/kyushu-u/dm3/target/CG8478.1.tsv http:...//dbarchive.biosciencedbc.jp/kyushu-u/dm3/target/CG8478.5.tsv http://dbarchive.bios...ciencedbc.jp/kyushu-u/dm3/target/CG8478.10.tsv http://dbarchive.biosciencedbc.jp/kyushu-u/dm3/colo/CG8478.Cell_line.tsv,http:...//dbarchive.biosciencedbc.jp/kyushu-u/dm3/colo/CG8478.Embryo.tsv,http:...//dbarchive.biosciencedbc.jp/kyushu-u/dm3/colo/CG8478.Pupae.tsv http://dbarchive.biosciencedbc.jp/kyus

  17. Pregnancy testing with hCG--future prospects.

    Science.gov (United States)

    Berger, Peter; Sturgeon, Catharine

    2014-12-01

    Pregnancy tests for human chorionic gonadotrophin (hCG) are used widely in hospital and home settings. Assays measuring hCG also have uses in prenatal screening and oncology. The output from three recent international workshops provides a framework for reliable measurement of hCG. Requirements for future hCG assays include use of clear descriptive nomenclature, informed selection of antibodies of well-defined epitope specificities, and design of robust methods. Tests will be precisely characterized and calibrated in SI units using six International Reference Reagents (IRR) for hCG and variants, and the Fifth International Standard for hCG 07/364, making it possible to report clinical results in molar units. These measures will help to increase patient safety by reducing the risk of erroneous or misleading hCG results.

  18. HERBIG-HARO OBJECTS AROUND CG 30

    Directory of Open Access Journals (Sweden)

    P. Kajdic

    2010-01-01

    Full Text Available En este trabajo estudiamos objetos Herbig-Haro ubicados en la región alrededor de la cabeza del glóbulo cometario CG 30. Se presentan dos conjuntos de imágenes ópticas. El primero consta de imágenes obtenidas con el New Technology Telescope de 3.5 m en 1995 en tres líneas de emisión: H¿, [SII]¿¿6731,6716 ¿A y [O II]¿3729 ¿A. El segundo conjunto es la imagen en H¿ del complejo CG 30/31/38 obtenida en 2006 con el Telescopio Subaru de 8 m. Se ha estudiado los movimientos propios usando las imágenes en H¿ de ambas épocas. Debido a la alta resolución de nuestras imágenes hemos podido, por primera vez, resolver el objeto HH 120 en diez nudos y medir movimientos propios para algunos de ellos. Hemos descubierto varios nuevos objetos HH que se ven mejor en nuestra imagen en [S II], como también un gran chorro bipolar, HH 950, que sale de la cabeza de CG 30. Proponemos que dos fuentes submilimétricas previamente conocidas emiten los flujos HH 120 y HH 950. Las dos fuentes podrían ser objetos binarios. Esto se debe a que (1 los vectores de movimiento propio de los nudos de HH 120 sugieren que este objeto está compuesto de dos flujos y (2 la estructura del flujo HH 950 sugiere que la dirección del eje del chorro ha cambiado en el pasado.

  19. The effect of base pair mismatch on DNA strand displacement

    CERN Document Server

    Broadwater, Bo

    2016-01-01

    DNA strand displacement is a key reaction in DNA homologous recombination and DNA mismatch repair and is also heavily utilized in DNA-based computation and locomotion. Despite its ubiquity in science and engineering, sequence-dependent effects of displacement kinetics have not been extensively characterized. Here, we measured toehold-mediated strand displacement kinetics using single-molecule fluorescence in the presence of a single base pair mismatch. The apparent displacement rate varied significantly when the mismatch was introduced in the invading DNA strand. The rate generally decreased as the mismatch in the invader was encountered earlier in displacement. Our data indicate that a single base pair mismatch in the invader stalls branch migration, and displacement occurs via direct dissociation of the destabilized incumbent strand from the substrate strand. We combined both branch migration and direct dissociation into a model, which we term, the concurrent displacement model, and used the first passage t...

  20. qPCR-based mitochondrial DNA quantification: Influence of template DNA fragmentation on accuracy

    Energy Technology Data Exchange (ETDEWEB)

    Jackson, Christopher B., E-mail: Christopher.jackson@insel.ch [Division of Human Genetics, Departements of Pediatrics and Clinical Research, Inselspital, University of Berne, Freiburgstrasse, CH-3010 Berne (Switzerland); Gallati, Sabina, E-mail: sabina.gallati@insel.ch [Division of Human Genetics, Departements of Pediatrics and Clinical Research, Inselspital, University of Berne, Freiburgstrasse, CH-3010 Berne (Switzerland); Schaller, Andre, E-mail: andre.schaller@insel.ch [Division of Human Genetics, Departements of Pediatrics and Clinical Research, Inselspital, University of Berne, Freiburgstrasse, CH-3010 Berne (Switzerland)

    2012-07-06

    Highlights: Black-Right-Pointing-Pointer Serial qPCR accurately determines fragmentation state of any given DNA sample. Black-Right-Pointing-Pointer Serial qPCR demonstrates different preservation of the nuclear and mitochondrial genome. Black-Right-Pointing-Pointer Serial qPCR provides a diagnostic tool to validate the integrity of bioptic material. Black-Right-Pointing-Pointer Serial qPCR excludes degradation-induced erroneous quantification. -- Abstract: Real-time PCR (qPCR) is the method of choice for quantification of mitochondrial DNA (mtDNA) by relative comparison of a nuclear to a mitochondrial locus. Quantitative abnormal mtDNA content is indicative of mitochondrial disorders and mostly confines in a tissue-specific manner. Thus handling of degradation-prone bioptic material is inevitable. We established a serial qPCR assay based on increasing amplicon size to measure degradation status of any DNA sample. Using this approach we can exclude erroneous mtDNA quantification due to degraded samples (e.g. long post-exicision time, autolytic processus, freeze-thaw cycles) and ensure abnormal DNA content measurements (e.g. depletion) in non-degraded patient material. By preparation of degraded DNA under controlled conditions using sonification and DNaseI digestion we show that erroneous quantification is due to the different preservation qualities of the nuclear and the mitochondrial genome. This disparate degradation of the two genomes results in over- or underestimation of mtDNA copy number in degraded samples. Moreover, as analysis of defined archival tissue would allow to precise the molecular pathomechanism of mitochondrial disorders presenting with abnormal mtDNA content, we compared fresh frozen (FF) with formalin-fixed paraffin-embedded (FFPE) skeletal muscle tissue of the same sample. By extrapolation of measured decay constants for nuclear DNA ({lambda}{sub nDNA}) and mtDNA ({lambda}{sub mtDNA}) we present an approach to possibly correct measurements in

  1. Statistical mechanics of base stacking and pairing in DNA melting

    OpenAIRE

    Ivanov, Vassili; Zeng, Yan; Zocchi, Giovanni

    2004-01-01

    We propose a statistical mechanics model for DNA melting in which base stacking and pairing are explicitly introduced as distinct degrees of freedom. Unlike previous approaches, this model describes thermal denaturation of DNA secondary structure in the whole experimentally accessible temperature range. Base pairing is described through a zipper model, base stacking through an Ising model. We present experimental data on the unstacking transition, obtained exploiting the observation that at m...

  2. Unique magnetic signatures of mismatched base pairs in DNA

    Science.gov (United States)

    Apalkov, Vadim; Berashevich, Julia; Chakraborty, Tapash

    2010-02-01

    Magnetic properties of DNA containing mispairs, such as different conformations of the GṡA mispair, or a GṡT mispair inserted into the DNA chain, have been theoretically investigated. The essential ingredients for these studies, the charge transfer integrals, were evaluated from the DNA sequences containing the mispair and optimized in the solvent. We find that the magnetic susceptibilities of the host DNA chain containing a large number of Watson-Crick base pairs are significantly altered in the presence of the mispairs, and the effects depend on the choice of mispairs. In particular, insertion of even a single GṡA mispair changes the nature of magnetization (sign of the susceptibility) of the host DNA. We propose that measurement of the magnetic properties of DNA might provide a direct route to detection and identification of those mispairs.

  3. DNA-based cryptographic methods for data hiding in DNA media.

    Science.gov (United States)

    Marwan, Samiha; Shawish, Ahmed; Nagaty, Khaled

    2016-12-01

    Information security can be achieved using cryptography, steganography or a combination of them, where data is firstly encrypted using any of the available cryptography techniques and then hid into any hiding medium. Recently, the famous genomic DNA has been introduced as a hiding medium, known as DNA steganography, due to its notable ability to hide huge data sets with a high level of randomness and hence security. Despite the numerous cryptography techniques, to our knowledge only the vigenere cipher and the DNA-based playfair cipher have been combined with the DNA steganography, which keeps space for investigation of other techniques and coming up with new improvements. This paper presents a comprehensive analysis between the DNA-based playfair, vigenere, RSA and the AES ciphers, each combined with a DNA hiding technique. The conducted analysis reports the performance diversity of each combined technique in terms of security, speed, hiding capacity in addition to both key size and data size. Moreover, this paper proposes a modification of the current combined DNA-based playfair cipher technique, which makes it not only simple and fast but also provides a significantly higher hiding capacity and security. The conducted extensive experimental studies confirm such outstanding performance in comparison with all the discussed combined techniques. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  4. DNA nanostructures based biosensor for the determination of aromatic compounds.

    Science.gov (United States)

    Gayathri, S Baby; Kamaraj, P; Arthanareeswari, M; Devikala, S

    2015-10-15

    Graphite electrode was modified using multi-walled carbon nanotubes (MWCNT), chitosan (CS), glutaraldehyde (GTA) and DNA nanostructures (nsDNA). DNA nanostructures of 50 nm in size were produced from single DNA template sequence using a simple two step procedure and were confirmed using TEM and AFM analysis. The modified electrode was applied to the electrochemical detection of aromatic compounds using EIS. The modified electrode was characterized using differential pulse voltammetry (DPV), electrochemical impedance spectroscopy (EIS) and cyclic voltammetry (CV). For comparison, electrochemical results derived from single stranded (50 bp length) and double stranded (50 bp length) DNA based biosensors were used. The results indicate that the modified electrode prior to nsDNA immobilization provides a viable platform that effectively promotes electron transfer between nsDNA and the electrode. The mode of binding between the nsDNA and aromatic compounds was investigated using EIS, indicating that the dominant interaction is non-covalent. nsDNA based biosensor was observed to act as an efficient biosensor in selective and sensitive identification of aromatic compounds.

  5. A novel DNA computing model based on RecA-mediated triple-stranded DNA structure

    Institute of Scientific and Technical Information of China (English)

    Fang Gang; Zhang Shemin; Dong Yafei; Xu Jin

    2007-01-01

    The field of DNA computing emerged in 1994 after Adleman's paper was published. Henceforth, a few scholars solved some noted NP-complete problems in this way. And all these methods of DNA computing are based on conventional Watson-Crick hydrogen bond of doublehelical DNA molecule. In this paper, we show that the triple-stranded DNA structure mediated by RecA protein can be used for solving computational problems. Sequence-specific recognition of double-stranded DNA by oligonucleotide-directed triple helix (triplex) formation is used to carry out the algorithm. We present procedure for the 3-vertex-colorability problems. In our proposed procedure, it is suggested that it is possible to solve more complicated problems with more variables by this model.

  6. DNA-based tunable THz oscillator

    NARCIS (Netherlands)

    Malyshev, A. V.; Malyshev, V. A.; Dominguez-Adame, F.

    2009-01-01

    The intrinsic helix conformation of the DNA strands is known to be the key ingredient of control of the electric current through the molecule by the perpendicular (gate) electric field. We show theoretically that Bloch oscillations in periodic systems with helical conformation are also strongly affe

  7. Taxonomy of pasteurella anatipestifer. 1. DNA base composition and DNA-DNA hybridization analysis.

    Science.gov (United States)

    Bangun, A; Johnson, J L; Tripathy, D N

    1987-01-01

    DNA was isolated from 15 strains of Pasteurella anatipestifer and from one strain each of Moraxella nonliquefaciens, M. bovis, Pasteurella multocida, P. haemolytica, P. gallinarum, P. pneumotropica, and P. ureae. The guanine-plus-cytosine contents of P. anatipestifer ranged from 32 to 35 mole %, whereas those of Moraxella and Pasteurella spp. were much higher, ranging from 40 to 45 mole %. DNA-DNA hybridization analysis revealed that homology of nine P. anatipestifer strains to strains ATCC 11845 and PA 15 was 52 to 100%, whereas homology of Moraxella and Pasteurella strains to these strains was only 3 to 17%. Similarly, homology of P. anatipestifer strains, Moraxella, and Pasteurella species other than P. multocida to P. multocida reference strain P-2192 was low. These results strongly suggest that P. anatipestifer is genetically unrelated to either Pasteurella or Moraxella.

  8. New Young Star Candidates in CG4 and Sa101

    CERN Document Server

    Rebull, L M; Hoette, V; Kim, J S; Laine, S; Foster, M; Laher, R; Legassie, M; Mallory, C R; McCarron, K; Sherry, W H

    2011-01-01

    The CG4 and Sa101 regions together cover a region of ~0.5 square degree in the vicinity of a "cometary globule" that is part of the Gum Nebula. There are seven previously identified young stars in this region; we have searched for new young stars using mid- and far-infrared data (3.6 to 70 microns) from the Spitzer Space Telescope, combined with ground-based optical data and near-infrared data from the Two-Micron All-Sky Survey (2MASS). We find infrared excesses in all 6 of the previously identified young stars in our maps, and we identify 16 more candidate young stars based on apparent infrared excesses. Most (73%) of the new young stars are Class II objects. There is a tighter grouping of young stars and young star candidates in the Sa101 region, in contrast to the CG4 region, where there are fewer young stars and young star candidates, and they are more dispersed. Few likely young objects are found in the "fingers" of the dust being disturbed by the ionization front from the heart of the Gum Nebula.

  9. hCG, the wonder of today's science

    Science.gov (United States)

    2012-01-01

    Background hCG is a wonder. Firstly, because hCG is such an extreme molecule. hCG is the most acidic glycoprotein containing the highest proportion of sugars. Secondly, hCG exists in 5 common forms. Finally, it has so many functions ranging from control of human pregnancy to human cancer. This review examines these molecules in detail. Content These 5 molecules, hCG, sulfated hCG, hyperglycosylated hCG, hCG free beta and hyperglycosylated free beta are produced by placental syncytiotrophoblast cells and pituitary gonadotrope cells (group 1), and by placental cytotrophoblast cells and human malignancies (group 2). Group 1 molecules are both hormones that act on the hCG/LH receptor. These molecules are central to human menstrual cycle and human pregnancy. Group 2 molecules are autocrines, that act by antagonizing a TGF beta receptor. These molecules are critical to all advanced malignancies. Conclusions The hCG groups are molecules critical to both the molecules of pregnancy or human life, and to the advancement of cancer, or human death. PMID:22455390

  10. A DNA based model for addition computation

    Institute of Scientific and Technical Information of China (English)

    GAO Lin; YANG Xiao; LIU Wenbin; XU Jin

    2004-01-01

    Much effort has been made to solve computing problems by using DNA-an organic simulating method, which in some cases is preferable to the current electronic computer. However, No one at present has proposed an effective and applicable method to solve addition problem with molecular algorithm due to the difficulty in solving the carry problem which can be easily solved by hardware of an electronic computer. In this article, we solved this problem by employing two kinds of DNA strings, one is called result and operation string while the other is named carrier. The result and operation string contains some carry information by its own and denotes the ultimate result while the carrier is just for carrying use. The significance of this algorithm is the original code, the fairly easy steps to follow and the feasibility under current molecular biological technology.

  11. A liquid-crystal-based DNA biosensor for pathogen detection

    Science.gov (United States)

    Khan, Mashooq; Khan, Abdur Rahim; Shin, Jae-Ho; Park, Soo-Young

    2016-03-01

    A liquid-crystal (LC)-filled transmission electron microscopy (TEM) grid cell coated with the cationic surfactant dodecyltrimethylammonium bromide (DTAB), to which a single-stranded deoxyribonucleic acid probe (ssDNAprobe) was adsorbed at the LC/aqueous interface (TEMDTAB/DNA), was applied for the highly specific detection of target DNA molecules. The DTAB-coated E7 (used LC mixture) in the TEM grid (TEMDTAB) exhibited a homeotropic orientation, and changed to a planar orientation upon adsorption of the ssDNAprobe. The TEMDTAB/DNA was then exposed to complementary (target) ssDNA, which resulted in a planar-to-homeotropic configurational change of E7 that could be observed through a polarized optical microscope under crossed polarizers. The optimum adsorption density (2 μM) of ssDNAprobe enabled the detection of ≥0.05 nM complementary ssDNA. This TEMDTAB/DNA biosensor could differentiate complementary ssDNA from mismatched ssDNA as well as double-stranded DNA. It also successfully detected the genomic DNAs of the bacterium Erwinia carotovora and the fungi Rhazictonia solani. Owe to the high specificity, sensitivity, and label-free detection, this biosensor may broaden the applications of LC-based biosensors to pathogen detection.

  12. DNA regulatory motif selection based on support vector machine ...

    African Journals Online (AJOL)

    DNA regulatory motif selection based on support vector machine (SVM) and its application in microarray ... African Journal of Biotechnology ... experiments to explore the underlying relationships between motif types and gene functions.

  13. Artifacts associated with the measurement of oxidized DNA bases.

    Science.gov (United States)

    Cadet, J; Douki, T; Ravanat, J L

    1997-10-01

    In this paper we review recent aspects of the measurement of oxidized DNA bases, currently a matter of debate. There has long been an interest in the determination of the level of oxidized bases in cellular DNA under both normal and oxidative stress conditions. In this respect, the situation is confusing because variations that may be as large as two orders of magnitude have been reported for the yield of the formation of 8-oxo-7,8-dihydroguanine (8-oxoGua) in similar DNA samples. However, recent findings clearly show that application of several assays like gas chromatography-mass spectrometry (GC-MS) and -32P--postlabeling may lead to a significant overestimation of the level of oxidized bases in cellular DNA. In particular, the silylation step, which is required to make the samples volatile for the GC-MS analysis, has been shown to induce oxidation of normal bases at the level of about one oxidized base per 10(4) normal bases. This has been found to be a general process that applies in particular to 8-oxoGua, 8-oxo-7, 8-dihydroadenine,5-hydroxycytosine, 5-(hydroxymethyl)uracil, and 5-formyluracil. Interestingly, prepurification of the oxidized bases from DNA hydrolysate prior to the derivatization reaction prevents artefactual oxidation. Under these conditions, the level of oxidized bases measured by GC-MS is similar to that obtained by HPLC associated with electrochemical detection (HPLC-EC). It should be added that the level of 8-oxo-7,8-dihydro-2;-deoxyguanosine in control cellular DNA has been found to be about fivefold lower than in earlier HPLC-EC measurements by using appropriate conditions of extraction and enzymatic digestion of DNA. Similar conclusions were reached by measuring formamidopyrimidine-DNA glycosylase sensitive sites as revealed by the single cell gel electrophoresis (comet) assay.

  14. Dynamic Simulation of Single DNA Molecule at the Base Level

    Institute of Scientific and Technical Information of China (English)

    LEI Xiao-Ling; WANG Xiao-Feng; HU Jun; FANG Hai-Ping

    2005-01-01

    @@ A mesoscopic discrete dsDNA model at the base level is proposed based on the statistical model (Phys. Rev. Lett.82 (1999) 4560). The numerical simulations reproduce the 65 pN plateau and those on the force vs extension for different supercoiling degrees are favourable with the experimental data. Our model has potential applications on the study of short DNA segments and provides a bridge between the statistical models and atomic modelling.

  15. How stable are the mutagenic tautomers of DNA bases?

    OpenAIRE

    Brovarets’ O. O.; Hovorun D. M.

    2010-01-01

    Aim. To determine the lifetime of the mutagenic tautomers of DNA base pairs through the investigation of the physicochemical mechanisms of their intramolecular proton transfer. Methods. Non-empirical quantum chemistry, the analysis of the electron density by means of Bader’s atom in molecules (AIM) theory and physicochemical kinetics were used. Results. Physicochemical character of the transition state of the intramolecular tautomerisation of DNA bases was investigated, the lifetime of mutage...

  16. Bisprimer--a program for the design of primers for bisulfite-based genomic sequencing of both plant and Mammalian DNA samples.

    Science.gov (United States)

    Kovacova, Viera; Janousek, Bohuslav

    2012-01-01

    Plants and animals differ in the sequence context of the methylated sites in DNA. Plants exhibit cytosine methylation in CG, CHG, and CHH sites, whereas CG methylation is the only form present in mammals (with an exception of the early embryonic development). This fact must be taken into account in the design of primers for bisulfite-based genomic sequencing because CHG and CHH sites can remain unmodified. Surprisingly, no user-friendly primer design program is publicly available that could be used to design primers in plants and to simultaneously check the properties of primers such as the potential for primer-dimer formation. For studies concentrating on particular DNA loci, the correct design of primers is crucial. The program, called BisPrimer, includes 2 different subprograms for the primer design, the first one for mammals and the second one for angiosperm plants. Each subprogram is divided into 2 variants. The first variant serves to design primers that preferentially bind to the bisulfite-modified primer-binding sites (C to U conversion). This type of primer preferentially amplifies the bisulfite-converted DNA strands. This feature can help to avoid problems connected with an incomplete bisulfite modification that can sometimes occur for technical reasons. The second variant is intended for the analysis of samples that are supposed to consist of a mixture of DNA molecules that have different levels of cytosine methylation (e.g., pollen DNA). In this case, the aim is to minimize the selection in favor of either less methylated or more methylated molecules.

  17. Variation, evolution, and correlation analysis of C+G content and genome or chromosome size in different kingdoms and phyla.

    Science.gov (United States)

    Li, Xiu-Qing; Du, Donglei

    2014-01-01

    C+G content (GC content or G+C content) is known to be correlated with genome/chromosome size in bacteria but the relationship for other kingdoms remains unclear. This study analyzed genome size, chromosome size, and base composition in most of the available sequenced genomes in various kingdoms. Genome size tends to increase during evolution in plants and animals, and the same is likely true for bacteria. The genomic C+G contents were found to vary greatly in microorganisms but were quite similar within each animal or plant subkingdom. In animals and plants, the C+G contents are ranked as follows: monocot plants>mammals>non-mammalian animals>dicot plants. The variation in C+G content between chromosomes within species is greater in animals than in plants. The correlation between average chromosome C+G content and chromosome length was found to be positive in Proteobacteria, Actinobacteria (but not in other analyzed bacterial phyla), Ascomycota fungi, and likely also in some plants; negative in some animals, insignificant in two protist phyla, and likely very weak in Archaea. Clearly, correlations between C+G content and chromosome size can be positive, negative, or not significant depending on the kingdoms/groups or species. Different phyla or species exhibit different patterns of correlation between chromosome-size and C+G content. Most chromosomes within a species have a similar pattern of variation in C+G content but outliers are common. The data presented in this study suggest that the C+G content is under genetic control by both trans- and cis- factors and that the correlation between C+G content and chromosome length can be positive, negative, or not significant in different phyla.

  18. The Risk of Preeclampsia According to High Thyroid Function in Pregnancy Differs by hCG Concentration.

    Science.gov (United States)

    Korevaar, Tim I M; Steegers, Eric A P; Chaker, Layal; Medici, Marco; Jaddoe, Vincent W V; Visser, Theo J; de Rijke, Yolanda B; Peeters, Robin P

    2016-12-01

    During pregnancy, there is an increased demand for thyroid hormone. The pregnancy hormone human chorionic gonadotropin (hCG) is an important physiological stimulator of thyroid function. Already high-normal maternal free T4 concentrations are associated with a higher risk of preeclampsia. The objective of the investigation was to study our hypothesis that hCG concentrations can distinguish a physiological form of high thyroid function from a more pathological form of high thyroid function and that the risk of preeclampsia would differ accordingly. TSH, free T4, hCG, or thyroperoxidase antibody concentrations were determined in pregnant women participating in a population-based prospective cohort study. The study was conducted in the general community. A nonselected sample of 5146 pregnant women participated in the study. There were no interventions. Preeclampsia was measured. Women with high hCG-associated high thyroid function did not have a higher risk of preeclampsia than women with normal thyroid function. In contrast, women with low hCG and high thyroid function had a 3.4- to 11.1-fold higher risk of preeclampsia. These risk estimates were amplified in women with a high body mass index. Women with a low hCG and suppressed TSH (hCG was not associated with preeclampsia, and results remained similar after exclusion of thyroperoxidase antibody-positive women. This study suggests that, in contrast to women with a high hCG associated high thyroid function, women with low hCG and high thyroid function during pregnancy are at a higher risk of developing preeclampsia. The additional measurement of hCG may therefore help to distinguish a more pathological form of high thyroid function and women at a high risk of preeclampsia.

  19. 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.

  20. NMR analysis of base-pair opening kinetics in DNA

    Science.gov (United States)

    Szulik, Marta W.; Voehler, Markus; Stone, Michael P.

    2014-01-01

    Base pairing in nucleic acids plays a crucial role in their structure and function. Differences in the base pair opening and closing kinetics of individual double stranded DNA sequences or between chemically modified base pairs provide insight into the recognition of these base pairs by DNA processing enzymes. This unit describes how to quantify the kinetics for localized base pairs by observing changes in the imino proton signals by nuclear magnetic resonance spectroscopy. The determination of all relevant parameters using state of the art techniques and NMR instrumentation, including cryoprobes, is discussed. PMID:25501592

  1. Elevated β-hCG associated with aggressive Osteoblastoma.

    Science.gov (United States)

    Morris, Carol D; Hameed, Meera R; Agaram, Narasimhan P; Hwang, Sinchun

    2017-09-01

    We present a unique case of an aggressive scapular osteoblastoma that produced β-hCG as a paraneoplastic manifestation in a 20-year-old woman. Serum β-hCG was found to be elevated during presurgical workup and consequently delayed surgical resection of the increasingly painful tumor because of suspected pregnancy. The paraneoplastic production of β-hCG was later proven by positive immunohistochemical stain of β-hCG in a curettage specimen and normalization of β-hCG levels after surgical resection of the aggressive osteoblastoma. Production of beta-human chorionic gonadotropin (β-hCG) has been reported in several carcinomas and sarcomas but, to our knowledge, it has not been reported in osteoblastoma in the English-language literature.

  2. How stable are the mutagenic tautomers of DNA bases?

    Directory of Open Access Journals (Sweden)

    Brovarets’ O. O.

    2010-02-01

    Full Text Available Aim. To determine the lifetime of the mutagenic tautomers of DNA base pairs through the investigation of the physicochemical mechanisms of their intramolecular proton transfer. Methods. Non-empirical quantum chemistry, the analysis of the electron density by means of Bader’s atom in molecules (AIM theory and physicochemical kinetics were used. Results. Physicochemical character of the transition state of the intramolecular tautomerisation of DNA bases was investigated, the lifetime of mutagenic tautomers was calculated. Conclusions. The lifetime of the DNA bases mutagenic tautomers by 3–10 orders exceeds typical time of DNA replication in the cell (~103 s. This fact confirms that the postulate, on which the Watson-Crick tautomeric hypothesis of spontaneous transitions grounds, is adequate. The absence of intramolecular H-bonds in the canonical and mutagenic tautomeric forms determine their high stability

  3. Charge Transport across DNA-Based Three-Way Junctions.

    Science.gov (United States)

    Young, Ryan M; Singh, Arunoday P N; Thazhathveetil, Arun K; Cho, Vincent Y; Zhang, Yuqi; Renaud, Nicolas; Grozema, Ferdinand C; Beratan, David N; Ratner, Mark A; Schatz, George C; Berlin, Yuri A; Lewis, Frederick D; Wasielewski, Michael R

    2015-04-22

    DNA-based molecular electronics will require charges to be transported from one site within a 2D or 3D architecture to another. While this has been shown previously in linear, π-stacked DNA sequences, the dynamics and efficiency of charge transport across DNA three-way junction (3WJ) have yet to be determined. Here, we present an investigation of hole transport and trapping across a DNA-based three-way junction systems by a combination of femtosecond transient absorption spectroscopy and molecular dynamics simulations. Hole transport across the junction is proposed to be gated by conformational fluctuations in the ground state which bring the transiently populated hole carrier nucleobases into better aligned geometries on the nanosecond time scale, thus modulating the π-π electronic coupling along the base pair sequence.

  4. Human nucleosomes: special role of CG dinucleotides and Alu-nucleosomes

    Directory of Open Access Journals (Sweden)

    Trifonov Edward N

    2011-05-01

    Full Text Available Abstract Background The periodical occurrence of dinucleotides with a period of 10.4 bases now is undeniably a hallmark of nucleosome positioning. Whereas many eukaryotic genomes contain visible and even strong signals for periodic distribution of dinucleotides, the human genome is rather featureless in this respect. The exact sequence features in the human genome that govern the nucleosome positioning remain largely unknown. Results When analyzing the human genome sequence with the positional autocorrelation method, we found that only the dinucleotide CG shows the 10.4 base periodicity, which is indicative of the presence of nucleosomes. There is a high occurrence of CG dinucleotides that are either 31 (10.4 × 3 or 62 (10.4 × 6 base pairs apart from one another - a sequence bias known to be characteristic of Alu-sequences. In a similar analysis with repetitive sequences removed, peaks of repeating CG motifs can be seen at positions 10, 21 and 31, the nearest integers of multiples of 10.4. Conclusions Although the CG dinucleotides are dominant, other elements of the standard nucleosome positioning pattern are present in the human genome as well. The positional autocorrelation analysis of the human genome demonstrates that the CG dinucleotide is, indeed, one visible element of the human nucleosome positioning pattern, which appears both in Alu sequences and in sequences without repeats. The dominant role that CG dinucleotides play in organizing human chromatin is to indicate the involvement of human nucleosomes in tuning the regulation of gene expression and chromatin structure, which is very likely due to cytosine-methylation/-demethylation in CG dinucleotides contained in the human nucleosomes. This is further confirmed by the positions of CG-periodical nucleosomes on Alu sequences. Alu repeats appear as monomers, dimers and trimers, harboring two to six nucleosomes in a run. Considering the exceptional role CG dinucleotides play in the

  5. 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.``

  6. Persistent low levels of serum hCG due to heterophilic mouse antibodies: an unrecognized pitfall in the diagnosis of trophoblastic disease.

    Science.gov (United States)

    González Aguilera, B; Syrios, P; Gadisseur, R; Luyckx, F; Cavalier, E; Beckers, A; Valdes-Socin, H

    2016-06-01

    Phantom hCG refers to persistent mild elevations of hCG, leading physicians to unnecessary treatments whereas neither a true hCG nor a trophoblastic disease is present. We report the case of a 23-year-old woman with persistent low levels of serum hCG detected one month after miscarriage. As choriocarcinoma was suspected, a chemotherapy trial of methotrexate was prescribed, without any hCG reduction. Subsequently, laparoscopy ruled out a trophoblastic residue and the patient was referred to the Endocrine Unit for further investigations. While low levels of hCG were still detected in serum, no hCG was detected in the urine. In addition, when serum was processed in a HBT tube for revealing heterophilic antibodies, hCG was no longer detected. Such finding indicated the presence of phantom hCG due to heterophilic mouse antibodies interaction. This case raises the need of clinico-biological discussion to avoid inappropriate therapeutic decisions. Based on this case experience and after review of the literature, we suggest that current gynecological protocols for the diagnosis and treatment of trophoblastic disease should consider the inclusion of urinary hCG and/or a test for serum heterophilic antibodies when appropriate.

  7. CG Methylation Covaries with Differential Gene Expression between Leaf and Floral Bud Tissues of Brachypodium distachyon.

    Directory of Open Access Journals (Sweden)

    Kyria Roessler

    Full Text Available DNA methylation has the potential to influence plant growth and development through its influence on gene expression. To date, however, the evidence from plant systems is mixed as to whether patterns of DNA methylation vary significantly among tissues and, if so, whether these differences affect tissue-specific gene expression. To address these questions, we analyzed both bisulfite sequence (BSseq and transcriptomic sequence data from three biological replicates of two tissues (leaf and floral bud from the model grass species Brachypodium distachyon. Our first goal was to determine whether tissues were more differentiated in DNA methylation than explained by variation among biological replicates. Tissues were more differentiated than biological replicates, but the analysis of replicated data revealed high (>50% false positive rates for the inference of differentially methylated sites (DMSs and differentially methylated regions (DMRs. Comparing methylation to gene expression, we found that differential CG methylation consistently covaried negatively with gene expression, regardless as to whether methylation was within genes, within their promoters or even within their closest transposable element. The relationship between gene expression and either CHG or CHH methylation was less consistent. In total, CG methylation in promoters explained 9% of the variation in tissue-specific expression across genes, suggesting that CG methylation is a minor but appreciable factor in tissue differentiation.

  8. Cooperativity-based modeling of heterotypic DNA nanostructure assembly.

    Science.gov (United States)

    Shapiro, Anastasia; Hozeh, Avital; Girshevitz, Olga; Abu-Horowitz, Almogit; Bachelet, Ido

    2015-07-27

    DNA origami is a robust method for the fabrication of nanoscale 2D and 3D objects with complex features and geometries. The process of DNA origami folding has been recently studied, however quantitative understanding of it is still elusive. Here, we describe a systematic quantification of the assembly process of DNA nanostructures, focusing on the heterotypic DNA junction-in which arms are unequal-as their basic building block. Using bulk fluorescence studies we tracked this process and identified multiple levels of cooperativity from the arms in a single junction to neighboring junctions in a large DNA origami object, demonstrating that cooperativity is a central underlying mechanism in the process of DNA nanostructure assembly. We show that the assembly of junctions in which the arms are consecutively ordered is more efficient than junctions with randomly-ordered components, with the latter showing assembly through several alternative trajectories as a potential mechanism explaining the lower efficiency. This highlights consecutiveness as a new design consideration that could be implemented in DNA nanotechnology CAD tools to produce more efficient and high-yield designs. Altogether, our experimental findings allowed us to devise a quantitative, cooperativity-based heuristic model for the assembly of DNA nanostructures, which is highly consistent with experimental observations.

  9. PCR-based typing of DNA extracted from cigarette butts.

    Science.gov (United States)

    Hochmeister, M N; Budowle, B; Jung, J; Borer, U V; Comey, C T; Dirnhofer, R

    1991-01-01

    Limited genetic marker information can be obtained from saliva by typing by conventional serological means. Thus, the application of PCR-based DNA typing methods was investigated as a potential approach for typing genetic markers in saliva. DNA was isolated from 200 cigarettes smoked by 10 different individuals (20 cigarettes per individual) and from 3 cigarette butts recovered from 2 crime scenes (adjudicated cases) using a Chelex 100 extraction procedure. The amount of recovered human DNA was quantified by slot-blot analysis and ranged from approximately less than 2-160 ng DNA per cigarette butt for the 200 samples, and 8 ng, 50 ng, and 100 ng for the cigarette butts from the adjudicated cases. The DNA was successfully amplified by the polymerase chain reaction (PCR) for the HLA-DQ alpha locus (99 out of 100 samples) as well as for the variable number of tandem repeat (VNTR) locus D1S80 (99 out of 100 samples). Amplification and typing of DNA was successful on all samples recovered from the crime scenes. The results suggest that PCR-based typing of DNA offers a potential method for genetically characterizing traces of saliva on cigarette butts.

  10. DNA fragments assembly based on nicking enzyme system.

    Directory of Open Access Journals (Sweden)

    Rui-Yan Wang

    Full Text Available A couple of DNA ligation-independent cloning (LIC methods have been reported to meet various requirements in metabolic engineering and synthetic biology. The principle of LIC is the assembly of multiple overlapping DNA fragments by single-stranded (ss DNA overlaps annealing. Here we present a method to generate single-stranded DNA overlaps based on Nicking Endonucleases (NEases for LIC, the method was termed NE-LIC. Factors related to cloning efficiency were optimized in this study. This NE-LIC allows generating 3'-end or 5'-end ss DNA overlaps of various lengths for fragments assembly. We demonstrated that the 10 bp/15 bp overlaps had the highest DNA fragments assembling efficiency, while 5 bp/10 bp overlaps showed the highest efficiency when T4 DNA ligase was added. Its advantage over Sequence and Ligation Independent Cloning (SLIC and Uracil-Specific Excision Reagent (USER was obvious. The mechanism can be applied to many other LIC strategies. Finally, the NEases based LIC (NE-LIC was successfully applied to assemble a pathway of six gene fragments responsible for synthesizing microbial poly-3-hydroxybutyrate (PHB.

  11. Direct DNA Analysis with Paper-Based Ion Concentration Polarization.

    Science.gov (United States)

    Gong, Max M; Nosrati, Reza; San Gabriel, Maria C; Zini, Armand; Sinton, David

    2015-11-01

    DNA analysis is essential for diagnosis and monitoring of many diseases. Conventional DNA testing is generally limited to the laboratory. Increasing access to relevant technologies can improve patient care and outcomes in both developed and developing regions. Here, we demonstrate direct DNA analysis in paper-based devices, uniquely enabled by ion concentration polarization at the interface of patterned nanoporous membranes in paper (paper-based ICP). Hepatitis B virus DNA targets in human serum are simultaneously preconcentrated, separated, and detected in a single 10 min operation. A limit of detection of 150 copies/mL is achieved without prior viral load amplification, sufficient for early diagnosis of hepatitis B. We clinically assess the DNA integrity of sperm cells in raw human semen samples. The percent DNA fragmentation results from the paper-based ICP devices strongly correlate (R(2) = 0.98) with the sperm chromatin structure assay. In all cases, agreement was 100% with respect to the clinical decision. Paper-based ICP can provide inexpensive and accessible advanced molecular diagnostics.

  12. A novel image encryption algorithm based on DNA subsequence operation.

    Science.gov (United States)

    Zhang, Qiang; Xue, Xianglian; Wei, Xiaopeng

    2012-01-01

    We present a novel image encryption algorithm based on DNA subsequence operation. Different from the traditional DNA encryption methods, our algorithm does not use complex biological operation but just uses the idea of DNA subsequence operations (such as elongation operation, truncation operation, deletion operation, etc.) combining with the logistic chaotic map to scramble the location and the value of pixel points from the image. The experimental results and security analysis show that the proposed algorithm is easy to be implemented, can get good encryption effect, has a wide secret key's space, strong sensitivity to secret key, and has the abilities of resisting exhaustive attack and statistic attack.

  13. An Optimal Seed Based Compression Algorithm for DNA Sequences

    Directory of Open Access Journals (Sweden)

    Pamela Vinitha Eric

    2016-01-01

    Full Text Available This paper proposes a seed based lossless compression algorithm to compress a DNA sequence which uses a substitution method that is similar to the LempelZiv compression scheme. The proposed method exploits the repetition structures that are inherent in DNA sequences by creating an offline dictionary which contains all such repeats along with the details of mismatches. By ensuring that only promising mismatches are allowed, the method achieves a compression ratio that is at par or better than the existing lossless DNA sequence compression algorithms.

  14. A Novel Image Encryption Algorithm Based on DNA Subsequence Operation

    Science.gov (United States)

    Zhang, Qiang; Xue, Xianglian; Wei, Xiaopeng

    2012-01-01

    We present a novel image encryption algorithm based on DNA subsequence operation. Different from the traditional DNA encryption methods, our algorithm does not use complex biological operation but just uses the idea of DNA subsequence operations (such as elongation operation, truncation operation, deletion operation, etc.) combining with the logistic chaotic map to scramble the location and the value of pixel points from the image. The experimental results and security analysis show that the proposed algorithm is easy to be implemented, can get good encryption effect, has a wide secret key's space, strong sensitivity to secret key, and has the abilities of resisting exhaustive attack and statistic attack. PMID:23093912

  15. A Novel Image Encryption Algorithm Based on DNA Subsequence Operation

    Directory of Open Access Journals (Sweden)

    Qiang Zhang

    2012-01-01

    Full Text Available We present a novel image encryption algorithm based on DNA subsequence operation. Different from the traditional DNA encryption methods, our algorithm does not use complex biological operation but just uses the idea of DNA subsequence operations (such as elongation operation, truncation operation, deletion operation, etc. combining with the logistic chaotic map to scramble the location and the value of pixel points from the image. The experimental results and security analysis show that the proposed algorithm is easy to be implemented, can get good encryption effect, has a wide secret key's space, strong sensitivity to secret key, and has the abilities of resisting exhaustive attack and statistic attack.

  16. Age dependency of base modification in rabbit liver DNA

    Science.gov (United States)

    Yamamoto, O.; Fuji, I.; Yoshida, T.; Cox, A. B.; Lett, J. T.

    1988-01-01

    Age-related modifications of DNA bases have been observed in the liver of the New Zealand white (NZW) rabbit (Oryctolagus cuniculus), a lagomorph with a median life span in captivity of 5-7 yr. The ages of the animals studied ranged from 6 wk to 9 yr. After the DNA had been extracted from the liver cell nuclei and hydrolyzed with acid, the bases were analyzed by column chromatography with Cellulofine gels (GC-15-m). Two peaks in the chromatogram, which eluted before the four DNA bases, contained modified bases. Those materials, which were obtained in relatively large amounts from old animals, were highly fluorescent, and were shown to be crosslinked base products by mass spectrometry. The yield of crosslinked products versus rabbit age (greater than 0.5 yr) can be fitted by an exponential function (correlation coefficient: 0.76 +/- 0.09).

  17. A universal, photocleavable DNA base: nitropiperonyl 2'-deoxyriboside.

    Science.gov (United States)

    Pirrung, M C; Zhao, X; Harris, S V

    2001-03-23

    A universal, photochemically cleavable DNA base analogue would add desirable versatility to a number of methods in molecular biology. A novel C-nucleoside, nitropiperonyl deoxyriboside (NPdR, P), has been investigated for this purpose. NPdR can be converted to its 5'-DMTr-3'-CE-phosphoramidite and was incorporated into pentacosanucleotides by conventional synthesis techniques. The destabilizing effect on hybrid formation with a complementary strand when this P base opposes A, T, and G was found to be 3-5 kcal/mol, but 9 kcal/mol when it opposes C. Brief irradiation (lambda > 360 nm, 20 min) of DNA containing the P base and piperidine treatment causes strand cleavage giving the 3'- and 5'-phosphates. Two significant recent interests, universal/non-hydrogen-bonding base analogues and photochemical backbone cleavage, have thus been combined in a single molecule that serves as a light-based DNA scissors.

  18. A Rewritable, Random-Access DNA-Based Storage System

    Science.gov (United States)

    Tabatabaei Yazdi, S. M. Hossein; Yuan, Yongbo; Ma, Jian; Zhao, Huimin; Milenkovic, Olgica

    2015-09-01

    We describe the first DNA-based storage architecture that enables random access to data blocks and rewriting of information stored at arbitrary locations within the blocks. The newly developed architecture overcomes drawbacks of existing read-only methods that require decoding the whole file in order to read one data fragment. Our system is based on new constrained coding techniques and accompanying DNA editing methods that ensure data reliability, specificity and sensitivity of access, and at the same time provide exceptionally high data storage capacity. As a proof of concept, we encoded parts of the Wikipedia pages of six universities in the USA, and selected and edited parts of the text written in DNA corresponding to three of these schools. The results suggest that DNA is a versatile media suitable for both ultrahigh density archival and rewritable storage applications.

  19. WRKY8 transcription factor functions in the TMV-cg defense response by mediating both abscisic acid and ethylene signaling in Arabidopsis.

    Science.gov (United States)

    Chen, Ligang; Zhang, Liping; Li, Daibo; Wang, Fang; Yu, Diqiu

    2013-05-21

    WRKY transcription factors are key players in the plant immune response, but less is known about their involvement in antiviral defense than about their roles in defense against bacterial or fungi pathogens. Here, we report that Arabidopsis thaliana WRKY DNA-binding protein 8 (WRKY8) has a role in mediating the long-distance movement of crucifer-infecting tobacco mosaic virus (TMV-cg). The expression of WRKY8 was inhibited by TMV-cg infection, and mutation of WRKY8 accelerated the accumulation of TMV-cg in systemically infected leaves. Quantitative RT-PCR analysis showed that the expression of ABA insensitive 4 (ABI4) was reduced and the expression of 1-aminocyclopropane-1-carboxylic acid synthase 6 (ACS6) and ethylene response factor 104 (ERF104) was enhanced in the systemically infected leaves of wrky8. Immunoprecipitation assays demonstrated that WRKY8 could bind selectively to putative W-boxes of the ABI4, ACS6, and ERF104 promoters. Furthermore, TMV-cg infection enhanced WRKY8 binding to the ABI4 promoter but reduced the binding of WRKY8 to the ACS6 and ERF104 promoters, indicating that regulation of ABI4, ACS6, and ERF104 by WRKY8 is at least partially dependent on TMV-cg. Exogenous applications of abscisic acid (ABA) reduced the systemic accumulation of TMV-cg. Mutations in ABA deficient 1, ABA deficient 2, ABA deficient 3, or abi4 accelerated systemic TMV-cg accumulation. In contrast, exogenous application of aminocyclopropane-1-carboxylic acid enhanced the systemic accumulation of TMV-cg, but mutations in acs6, erf104, or an octuple acs mutant inhibited systemic TMV-cg accumulation. Our results demonstrate that WRKY8 is involved in the defense response against TMV-cg through the direct regulation of the expression of ABI4, ACS6, and ERF104 and may mediate the crosstalk between ABA and ethylene signaling during the TMV-cg-Arabidopsis interaction.

  20. Measurement of oxidatively generated base damage in cellular DNA.

    Science.gov (United States)

    Cadet, Jean; Douki, Thierry; Ravanat, Jean-Luc

    2011-06-03

    This survey focuses on the critical evaluation of the main methods that are currently available for monitoring single and complex oxidatively generated damage to cellular DNA. Among chromatographic methods, HPLC-ESI-MS/MS and to a lesser extent HPLC-ECD which is restricted to a few electroactive nucleobases and nucleosides are appropriate for measuring the formation of single and clustered DNA lesions. Such methods that require optimized protocols for DNA extraction and digestion are sensitive enough for measuring base lesions formed under conditions of severe oxidative stress including exposure to ionizing radiation, UVA light and high intensity UVC laser pulses. In contrast application of GC-MS and HPLC-MS methods that are subject to major drawbacks have been shown to lead to overestimated values of DNA damage. Enzymatic methods that are based on the use of DNA repair glycosylases in order to convert oxidized bases into strand breaks are suitable, even if they are far less specific than HPLC methods, to deal with low levels of single modifications. Several other methods including immunoassays and (32)P-postlabeling methods that are still used suffer from drawbacks and therefore are not recommended. Another difficult topic is the measurement of oxidatively generated clustered DNA lesions that is currently achieved using enzymatic approaches and that would necessitate further investigations.

  1. The biological function of hyperglycosylated hCG

    Institute of Scientific and Technical Information of China (English)

    Laurence A Cole; Stephen A Butler

    2012-01-01

    Objective:Hyperglycosylated human chorionic gonadotropin(hCG) is a variant of hCG made by cytotrophoblast cell.Here we examine the role of hyperglycosylated hCG in placenta growth and invasion.Methods:JEG-3 choriocarcinoma cells and term cytotrophoblast monolayer culture were prepared.The effect of supplemental hyperglycosylated hCG and hCG was investigated. Growth of these cells was examined by increase incell number.Invasion was investigated using Matrigel basement membrane cells.The proportion of cell invadingMatrigel was determined. Results:Term cytotrophoblast cell andJEG-3 choriocarcinoma cells grew to5427±834 cells (109%) and7114±553 cells(142%).With the supplementation of hyperglycosylated hCG, they grew significantly wider to7633±177 cells(142%) and10315±1477 cells(206%).With the supplementation of hCG they diminished to4227±769 cells(78%) and5620±657 cells(79%).Term cytotrophoblast cell andJEG-3 choriocarcinoma cells penetratedMatigel membranes to(40.0±10.0)% and(46.0±9.8)%.Hyperglycosylated hCG significantly enhanced penetration to(76.0±13.0)% and(84.0±6.6)%. hCG diminished penetration to(32.0±9.1)% and(32.0±4.5)%.Conclusions:Hyperglycosylated hCG enhances both cytotrophoblast growth and cytotrophoblast cell invasion. hCG minimally suppresses growth and invasion.

  2. Microwave-induced inactivation of DNA-based hybrid catalyst in asymmetric catalysis.

    Science.gov (United States)

    Zhao, Hua; Shen, Kai

    2016-03-01

    DNA-based hybrid catalysts have gained strong interests in asymmetric reactions. However, to maintain the high enantioselectivity, these reactions are usually conducted at relatively low temperatures (e.g. DNA-based hybrid catalyst even at low temperatures (such as 5 °C). Circular dichroism (CD) spectra and gel electrophoresis of DNA suggest that microwave exposure degrades DNA molecules and disrupts DNA double-stranded structures, causing changes of DNA-metal ligand binding properties and thus poor DNA catalytic performance.

  3. A novel junctional adhesion molecule A (CgJAM-A-L) from oyster (Crassostrea gigas) functions as pattern recognition receptor and opsonin.

    Science.gov (United States)

    Liu, Conghui; Wang, Mengqiang; Jiang, Shuai; Wang, Lingling; Chen, Hao; Liu, Zhaoqun; Qiu, Limei; Song, Linsheng

    2016-02-01

    Junctional adhesion molecule (JAM), a subfamily of immunoglobulin superfamily (IgSF) with a couple of immunoglobulin domains, can act as regulator in homeostasis and inflammation of vertebrates. In the present study, a structural homolog of JAM-A (designated CgJAM-A-L) was screened out from oyster, Crassostrea gigas, through a search of JAM-A D1 domain (N-terminal Ig domain in JAM-A). The cDNA of CgJAM-A-L was of 1188 bp encoding a predicted polypeptide of 395 amino acids. The immunoreactive area of CgJAM-A-L mainly distributed over the plasma membrane of hemocytes. After Vibro splendidus or tumor necrosis factor (CgTNF-1) stimulation, the mRNA transcripts of CgJAM-A-L in hemocytes increased significantly by 4.46-fold and 9.00-fold (p oyster hemocytes towards Gram-negative bacteria V. anguillarum and yeast P. pastoris were significantly enhanced after the incubation of rCgJAM-A-L, and even increased more significantly after the pre-incubation of rCgJAM-A-L with microbes (p oyster. Moreover, as the most primitive specie with homolog of JAMs, the information of CgJAM-A-L in oyster would provide useful clues for the evolutionary study of JAMs and immunoglobulins.

  4. DNA Methylation Signatures of the Plant Chromomethyltransferases

    OpenAIRE

    Gouil, Quentin; Baulcombe, David C

    2016-01-01

    DNA methylation in plants is traditionally partitioned into CG, CHG and CHH contexts (with H any nucleotide but G). By investigating DNA methylation patterns in trinucleotide contexts in four angiosperm species, we show that such a representation hides spatial and functional partitioning of different methylation pathways and is incomplete. CG methylation (mCG) is largely context-independent whereas, at CHG motifs, there is under-representation of mCCG in pericentric regions of A. thaliana and...

  5. DNA based random key generation and management for OTP encryption.

    Science.gov (United States)

    Zhang, Yunpeng; Liu, Xin; Sun, Manhui

    2017-09-01

    One-time pad (OTP) is a principle of key generation applied to the stream ciphering method which offers total privacy. The OTP encryption scheme has proved to be unbreakable in theory, but difficult to realize in practical applications. Because OTP encryption specially requires the absolute randomness of the key, its development has suffered from dense constraints. DNA cryptography is a new and promising technology in the field of information security. DNA chromosomes storing capabilities can be used as one-time pad structures with pseudo-random number generation and indexing in order to encrypt the plaintext messages. In this paper, we present a feasible solution to the OTP symmetric key generation and transmission problem with DNA at the molecular level. Through recombinant DNA technology, by using only sender-receiver known restriction enzymes to combine the secure key represented by DNA sequence and the T vector, we generate the DNA bio-hiding secure key and then place the recombinant plasmid in implanted bacteria for secure key transmission. The designed bio experiments and simulation results show that the security of the transmission of the key is further improved and the environmental requirements of key transmission are reduced. Analysis has demonstrated that the proposed DNA-based random key generation and management solutions are marked by high security and usability. Published by Elsevier B.V.

  6. On the regularity of trust region-cg algorithm: With application to deconvolution problem

    Institute of Scientific and Technical Information of China (English)

    WANG; Yanfei(王彦飞)

    2003-01-01

    Deconvolution problem is a main topic in signal processing. Many practical applications are re-quired to solve deconvolution problems. An important example is image reconstruction. Usually, researcherslike to use regularization method to deal with this problem. But the cost of computation is high due to thefact that direct methods are used. This paper develops a trust region-cg method, a kind of iterative methodsto solve this kind of problem. The regularity of the method is proved. Based on the special structure of thediscrete matrix, FFT can be used for calculation. Hence combining trust region-cg method with FFT is suitablefor solving large scale problems in signal processing.

  7. DNA nanotechnology based on i-motif structures.

    Science.gov (United States)

    Dong, Yuanchen; Yang, Zhongqiang; Liu, Dongsheng

    2014-06-17

    CONSPECTUS: Most biological processes happen at the nanometer scale, and understanding the energy transformations and material transportation mechanisms within living organisms has proved challenging. To better understand the secrets of life, researchers have investigated artificial molecular motors and devices over the past decade because such systems can mimic certain biological processes. DNA nanotechnology based on i-motif structures is one system that has played an important role in these investigations. In this Account, we summarize recent advances in functional DNA nanotechnology based on i-motif structures. The i-motif is a DNA quadruplex that occurs as four stretches of cytosine repeat sequences form C·CH(+) base pairs, and their stabilization requires slightly acidic conditions. This unique property has produced the first DNA molecular motor driven by pH changes. The motor is reliable, and studies show that it is capable of millisecond running speeds, comparable to the speed of natural protein motors. With careful design, the output of these types of motors was combined to drive micrometer-sized cantilevers bend. Using established DNA nanostructure assembly and functionalization methods, researchers can easily integrate the motor within other DNA assembled structures and functional units, producing DNA molecular devices with new functions such as suprahydrophobic/suprahydrophilic smart surfaces that switch, intelligent nanopores triggered by pH changes, molecular logic gates, and DNA nanosprings. Recently, researchers have produced motors driven by light and electricity, which have allowed DNA motors to be integrated within silicon-based nanodevices. Moreover, some devices based on i-motif structures have proven useful for investigating processes within living cells. The pH-responsiveness of the i-motif structure also provides a way to control the stepwise assembly of DNA nanostructures. In addition, because of the stability of the i-motif, this

  8. Ultrasensitive electrochemical cocaine biosensor based on reversible DNA nanostructure.

    Science.gov (United States)

    Sheng, Qinglin; Liu, Ruixiao; Zhang, Sai; Zheng, Jianbin

    2014-01-15

    We proposed an ultrasensitive electrochemical cocaine biosensor based on the three-dimensional (3D) DNA structure conversion of nanostructure from Triangular Pyramid Frustum (TPFDNA) to Equilateral Triangle (ETDNA). The presence of cocaine triggered the aptamer-composed DNA nanostructure change from "Close" to "Open", leading to obvious faradaic impedance changes. The unique properties with excellent stability and specific rigid structure of the 3D DNA nanostructure made the biosensing functions stable, sensitive, and regenerable. The Faradaic impedance responses were linearly related to cocaine concentration between 1.0 nM and 2.0 μM with a correlation coefficient of 0.993. The limit of detection was calculated to be 0.21 nM following IUPAC recommendations (3Sb/b). It is expected that the distinctive features of DNA nanostructure would make it potentially advantageous for a broad range of biosensing, bionanoelectronics, and therapeutic applications.

  9. Application of DNA-based methods in forensic entomology.

    Science.gov (United States)

    Wells, Jeffrey D; Stevens, Jamie R

    2008-01-01

    A forensic entomological investigation can benefit from a variety of widely practiced molecular genotyping methods. The most commonly used is DNA-based specimen identification. Other applications include the identification of insect gut contents and the characterization of the population genetic structure of a forensically important insect species. The proper application of these procedures demands that the analyst be technically expert. However, one must also be aware of the extensive list of standards and expectations that many legal systems have developed for forensic DNA analysis. We summarize the DNA techniques that are currently used in, or have been proposed for, forensic entomology and review established genetic analyses from other scientific fields that address questions similar to those in forensic entomology. We describe how accepted standards for forensic DNA practice and method validation are likely to apply to insect evidence used in a death or other forensic entomological investigation.

  10. Magnetic Propulsion of Microswimmers with DNA-Based Flagellar Bundles.

    Science.gov (United States)

    Maier, Alexander M; Weig, Cornelius; Oswald, Peter; Frey, Erwin; Fischer, Peer; Liedl, Tim

    2016-02-10

    We show that DNA-based self-assembly can serve as a general and flexible tool to construct artificial flagella of several micrometers in length and only tens of nanometers in diameter. By attaching the DNA flagella to biocompatible magnetic microparticles, we provide a proof of concept demonstration of hybrid structures that, when rotated in an external magnetic field, propel by means of a flagellar bundle, similar to self-propelling peritrichous bacteria. Our theoretical analysis predicts that flagellar bundles that possess a length-dependent bending stiffness should exhibit a superior swimming speed compared to swimmers with a single appendage. The DNA self-assembly method permits the realization of these improved flagellar bundles in good agreement with our quantitative model. DNA flagella with well-controlled shape could fundamentally increase the functionality of fully biocompatible nanorobots and extend the scope and complexity of active materials.

  11. 基于EBE的Bi-CG迭代法求解Navier-Stokes方程的并行计算%The Parallel Computation of Steady Navier-Stokes Equations with Bi-CG Iterative Method Based on EBE Technique

    Institute of Scientific and Technical Information of China (English)

    杨忠超

    2002-01-01

    阐述了用有限元求解流场不可压Navier-Stokes方程时,基于单元接单元(Element-By-Element,EBE)技术的并行双共轭梯度法(Bi-CG).在国家高性能计算中心(成都)的曙光2000并行系统上,采用MPI消息传递实现了此种算法,计算定常三维空穴水域流场,取了较好的加速比.由于不需存储系数矩阵,在很大程度上节省了内存,大大提高了求解流场问题的规模.

  12. A NEW METHOD OF ENCRYPTION ON THE GPU PLATFORM BASED ON CG LANGUAGE%一种基于Cg语言在图形处理器GPU上实现加密的方法

    Institute of Scientific and Technical Information of China (English)

    徐少平; 文喜; 肖建; 曾文

    2008-01-01

    由于图形处理器GPU(Graphics Processing Unit)最近几年迅速发展,国内外学者已经将基于GPU的通用计算作为一个新的研究领域[1,2].在研究国外最新文献的基础上,分析了美国NVIDIA公司推出的Cg(C for Graphics)开发语言本身的特性,阐述了在GPU平台上利用Cg语言编写的分组加密程序需要特殊处理的地方,最后以DES算法为实例详细描述了编程的方法和实现过程.

  13. Antiequine chorionic gonadotropin (eCG) antibodies generated in goats treated with eCG for the induction of ovulation modulate the luteinizing hormone and follicle-stimulating hormone bioactivities of eCG differently.

    Science.gov (United States)

    Hervé, Virginie; Roy, François; Bertin, Jean; Guillou, Florian; Maurel, Marie-Christine

    2004-01-01

    In dairy goats, treatments associating a progestogen and the equine chorionic gonadotropin (eCG) are the easiest way to induce and synchronize estrus and ovulation and to permit artificial insemination (AI) and/or out of season breeding. From the first treatment, the injection of eCG induces, in some females, the production of anti-eCG antibodies (Abs) that will interfere with the effectiveness of subsequent treatments. These anti-eCG Abs delay the preovulatory LH surge and the ovulation time, leading to poor fertility of the treated females. In this study, by in vitro bioassays, we show that anti-eCG Abs can positively or negatively modulate the LH and/or FSH bioactivities of eCG. Moreover, the modulation level of eCG bioactivity does not depend on the anti-eCG Ab affinity for eCG, as shown by surface plasmon resonance technology. The specificity of anti-eCG Abs tested by competitive ELISA highlighted the importance of a glycan environment in the recognition mechanism, especially the sialic acids specific to eCG. The different effects of anti-eCG Abs on eCG bioactivities could be explained by two hypotheses. First, steric hindrance preventing the interaction of eCG with its receptors would explain the inhibitory effect of some anti-eCG Abs; second, a conformational change in eCG by anti-eCG Abs could induce inhibition or potentiation of eCG bioactivities. It is significant that these modulations of eCG bioactivities by anti-eCG Abs impact mainly on the FSH bioactivity of eCG, which is essential for ovarian stimulation and subsequent fertility after treatment and AI, and to a lesser extent on LH bioactivity.

  14. Base composition at mtDNA boundaries suggests a DNA triple helix model for human mitochondrial DNA large-scale rearrangements.

    Science.gov (United States)

    Rocher, Christophe; Letellier, Thierry; Copeland, William C; Lestienne, Patrick

    2002-06-01

    Different mechanisms have been proposed to account for mitochondrial DNA (mtDNA) instability based on the presence of short homologous sequences (direct repeats, DR) at the potential boundaries of mtDNA rearrangements. Among them, slippage-mispairing of the replication complex during the asymmetric replication cycle of the mammalian mitochondrial DNA has been proposed to account for the preferential localization of deletions. This mechanism involves a transfer of the replication complex from the first neo-synthesized heavy (H) strand of the DR1, to the DR2, thus bypassing the intervening sequence and producing a deleted molecule. Nevertheless, the nature of the bonds between the DNA strands remains unknown as the forward sequence of DR2, beyond the replication complex, stays double-stranded. Here, we have analyzed the base composition of the DR at the boundaries of mtDNA deletions and duplications and found a skewed pyrimidine content of about 75% in the light-strand DNA template. This suggests the possible building of a DNA triple helix between the G-rich neo-synthesized DR1 and the base-paired homologous G.C-rich DR2. In vitro experiments with the purified human DNA polymerase gamma subunits enabled us to show that the third DNA strand may be used as a primer for DNA replication, using a template with the direct repeat forming a hairpin, with which the primer could initiate DNA replication. These data suggest a novel molecular basis for mitochondrial DNA rearrangements through the distributive nature of the DNA polymerase gamma, at the level of the direct repeats. A general model accounting for large-scale mitochondrial DNA deletion and duplication is proposed. These experiments extend to a DNA polymerase from an eucaryote source the use of a DNA triple helix strand as a primer, like other DNA polymerases from phage and bacterial origins.

  15. Magnetophoretic-based microfluidic device for DNA Concentration.

    Science.gov (United States)

    Shim, Sangjo; Shim, Jiwook; Taylor, William R; Kosari, Farhad; Vasmatzis, George; Ahlquist, David A; Bashir, Rashid

    2016-04-01

    Nucleic acids serve as biomarkers of disease and it is highly desirable to develop approaches to extract small number of such genomic extracts from human bodily fluids. Magnetic particles-based nucleic acid extraction is widely used for concentration of small amount of samples and is followed by DNA amplification in specific assays. However, approaches to integrate such magnetic particles based capture with micro and nanofluidic based assays are still lacking. In this report, we demonstrate a magnetophoretic-based approach for target-specific DNA extraction and concentration within a microfluidic device. This device features a large chamber for reducing flow velocity and an array of μ-magnets for enhancing magnetic flux density. With this strategy, the device is able to collect up to 95 % of the magnetic particles from the fluidic flow and to concentrate these magnetic particles in a collection region. Then an enzymatic reaction is used to detach the DNA from the magnetic particles within the microfluidic device, making the DNA available for subsequent analysis. Concentrations of over 1000-fold for 90 bp dsDNA molecules is demonstrated. This strategy can bridge the gap between detection of low concentration analytes from clinical samples and a range of micro and nanofluidic sensors and devices including nanopores, nano-cantilevers, and nanowires.

  16. 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.

  17. Declarative Programming with Temporal Constraints, in the Language CG

    Directory of Open Access Journals (Sweden)

    Lorina Negreanu

    2015-01-01

    Full Text Available Specifying and interpreting temporal constraints are key elements of knowledge representation and reasoning, with applications in temporal databases, agent programming, and ambient intelligence. We present and formally characterize the language CG, which tackles this issue. In CG, users are able to develop time-dependent programs, in a flexible and straightforward manner. Such programs can, in turn, be coupled with evolving environments, thus empowering users to control the environment’s evolution. CG relies on a structure for storing temporal information, together with a dedicated query mechanism. Hence, we explore the computational complexity of our query satisfaction problem. We discuss previous implementation attempts of CG and introduce a novel prototype which relies on logic programming. Finally, we address the issue of consistency and correctness of CG program execution, using the Event-B modeling approach.

  18. Ab initio Study of Naptho-Homologated DNA Bases

    Energy Technology Data Exchange (ETDEWEB)

    Sumpter, Bobby G [ORNL; Vazquez-Mayagoitia, Alvaro [ORNL; Huertas, Oscar [Universitat de Barcelona; Fuentes-Cabrera, Miguel A [ORNL; Orozco, Modesto [Institut de Recerca Biomedica, Parc Cientific de Barcelona, Barcelona, Spain; Luque, Javier [Universitat de Barcelona

    2008-01-01

    Naptho-homologated DNA bases have been recently used to build a new type of size expanded DNA known as yyDNA. We have used theoretical techniques to investigate the structure, tautomeric preferences, base-pairing ability, stacking interactions, and HOMO-LUMO gaps of the naptho-bases. The structure of these bases is found to be similar to that of the benzo-fused predecessors (y-bases) with respect to the planarity of the aromatic rings and amino groups. Tautomeric studies reveal that the canonical-like form of naptho-thymine (yyT) and naptho-adenine (yyA) are the most stable tautomers, leading to hydrogen-bonded dimers with the corresponding natural nucleobases that mimic the Watson-Crick pairing. However, the canonical-like species of naptho-guanine (yyG) and naptho-cytosine (yyC) are not the most stable tautomers, and the most favorable hydrogen-bonded dimers involve wobble-like pairings. The expanded size of the naphto-bases leads to stacking interactions notably larger than those found for the natural bases, and they should presumably play a dominant contribution in modulating the structure of yyDNA duplexes. Finally, the HOMO-LUMO gap of the naptho-bases is smaller than that of their benzo-base counterparts, indicating that size-expansion of DNA bases is an efficient way of reducing their HOMO-LUMO gap. These results are examined in light of the available experimental evidence reported for yyT and yyC.

  19. Carbohydrate composition of the alpha-subunit of human choriogonadotropin (hCG alpha) and the free alpha molecules produced in pregnancy: most free alpha and some combined hCG alpha molecules are fucosylated.

    Science.gov (United States)

    Blithe, D L

    1990-06-01

    The carbohydrate compositions of pregnancy-derived hCG alpha (dissociated from intact hCG) and free alpha-subunit were analyzed using a combination of chemical analysis, lectin affinity chromatography, and glycosidase sensitivity. For direct compositional analysis, parallel samples were hydrolyzed in trifluoroacetic acid and analyzed for sialic acid and neutral sugars without prior derivatization. Separation of the monosaccharides was achieved by HPLC on a Dionex CarboPac column eluted at high pH, and the resolved monosaccharides were quantified by pulsed amperometric detection. The amounts of sugar that were found relative to peptide indicated the presence of two N-linked oligosaccharides per molecule on both hCG alpha and free alpha. Free alpha contained 2.5-fold higher amounts of sialic acid and galactose as well as a higher amount of N-acetylglucosamine than did hCG alpha. Free alpha also contained a 6-fold higher amount of fucose than did hCG alpha (1.2 vs. 0.2 residues of fucose/molecule). Serial fractionation of intact hCG alpha and free alpha molecules by lectin affinity chromatography indicated that virtually all of the hCG alpha-subunits contained at least one Concanavalin-A (Con-A)-binding site, whereas as many as 32% of the free alpha molecules could not bind to Con-A. Chromatography on Lens culinaris (Lch) resulted in 12% binding of hCG alpha and approximately 72% binding of free alpha (80-85% of the Con-A-bound free alpha and 47-48% of the Con-A-nonbound free alpha bound to Lch). Endoglycosidase-H (endo-H) treatment of hCG alpha released a portion of the oligosaccharides. The endo-H-released material appeared to be a monoantennary hybrid based on DEAE-binding properties and carbohydrate composition. In contrast to hCG alpha, free alpha was completely resistant to endo-H treatment. Incubation of endo-H-resistant hCG alpha with glycopeptidase-A resulted in the release of two components, which could be separated into monoantennary and biantennary

  20. Electrochemical DNA Hybridization Sensors Based on Conducting Polymers

    Directory of Open Access Journals (Sweden)

    Md. Mahbubur Rahman

    2015-02-01

    Full Text Available Conducting polymers (CPs are a group of polymeric materials that have attracted considerable attention because of their unique electronic, chemical, and biochemical properties. This is reflected in their use in a wide range of potential applications, including light-emitting diodes, anti-static coating, electrochromic materials, solar cells, chemical sensors, biosensors, and drug-release systems. Electrochemical DNA sensors based on CPs can be used in numerous areas related to human health. This review summarizes the recent progress made in the development and use of CP-based electrochemical DNA hybridization sensors. We discuss the distinct properties of CPs with respect to their use in the immobilization of probe DNA on electrode surfaces, and we describe the immobilization techniques used for developing DNA hybridization sensors together with the various transduction methods employed. In the concluding part of this review, we present some of the challenges faced in the use of CP-based DNA hybridization sensors, as well as a future perspective.

  1. Human chorionic gonadotropin (hCG) concentrations during the late first trimester are associated with fetal growth in a fetal sex-specific manner.

    Science.gov (United States)

    Barjaktarovic, Mirjana; Korevaar, Tim I M; Jaddoe, Vincent W V; de Rijke, Yolanda B; Visser, Theo J; Peeters, Robin P; Steegers, Eric A P

    2017-02-01

    Human chorionic gonadotropin (hCG) is a pregnancy-specific hormone that regulates placental development. hCG concentrations vary widely throughout gestation and differ based on fetal sex. Abnormal hCG concentrations are associated with adverse pregnancy outcomes including fetal growth restriction. We studied the association of hCG concentrations with fetal growth and birth weight. In addition, we investigated effect modification by gestational age of hCG measurement and fetal sex. Total serum hCG (median 14.4 weeks, 95 % range 10.1-26.2), estimated fetal weight (measured by ultrasound during 18-25th weeks and >25th weeks) and birth weight were measured in 7987 mother-child pairs from the Generation R cohort and used to establish fetal growth. Small for gestational age (SGA) was defined as a standardized birth weight lower than the 10th percentile of the study population. There was a non-linear association of hCG with birth weight (P = 0.009). However, only low hCG concentrations measured during the late first trimester (11th and 12th week) were associated with birth weight and SGA. Low hCG concentrations measured in the late first trimester were also associated with decreased fetal growth (P = 0.0002). This was the case for both male and female fetuses. In contrast, high hCG concentrations during the late first trimester were associated with increased fetal growth amongst female, but not male fetuses. Low hCG in the late first trimester is associated with lower birth weight due to a decrease in fetal growth. Fetal sex differences exist in the association of hCG concentrations with fetal growth.

  2. Establishing reference intervals for hCG in postmenopausal women.

    Science.gov (United States)

    Patel, Khushbu K; Qavi, Abraham J; Hock, Karl G; Gronowski, Ann M

    2017-03-01

    Plasma concentrations of human chorionic gonadotropin (hCG) have been shown to increase with age due to pituitary secretion. We previously recommended that an hCG cutoff of 14.0IU/L be used for women ≥55years of age. However, it remains unknown whether concentrations >14.0IU/L can be expected in women with advanced age. Our objectives were to establish plasma hCG reference intervals and correlate follicle stimulating hormone (FSH) and hCG concentrations in postmenopausal females ≥55years. Residual plasma samples from 798 women ≥55years were utilized with 303, 269, and 226 samples belonging to the age groups 55-69, 70-84, and ≥85years, respectively. FSH and hCG were measured using the Abbott ARCHITECT. All positive hCG samples (hCG ≥5IU/L) were analyzed for potential heterophile antibody interference and 3 were excluded. Electronic medical records were reviewed and patients with malignancy were excluded. 8% (56/666) of women age≥55years had plasma hCG ≥5IU/L. There were 19, 16, and 21 patients with hCG ≥5IU/L in the age groups 55-69, 70-84, and ≥85years, respectively. The highest hCG concentrations observed in each age group were: 55-69years maximum=11.7IU/L and 97.5th percentile=9.6IU/L; 70-84years maximum=18.09IU/L, 97.5th percentile=6.2IU/L; ≥85years maximum=11.1IU/L and 97.5th percentile=10.0IU/L, and the overall 97.5th percentile=8.5IU/L for all women ≥55years of age. Neither hCG nor FSH concentrations continued to increase with age in women ≥55years. The prevalence of positive hCG in women ≥55years is 8%. This study confirms our previously recommended cutoff of 14IU/L for women ≥55years of age. In women ≥55years of age, FSH concentrations do not predict hCG concentrations. Copyright © 2016 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

  3. DNA methylation based biomarkers: Practical considerations and applications

    DEFF Research Database (Denmark)

    Nielsen, Helene Myrtue; How Kit, Alexandre; Tost, Jorg

    2012-01-01

    of biomarker, DNA methylation, which is of great potential for many applications. This stable and heritable covalent modification mostly affects cytosines in the context of a CpG dinucleotide in humans. It can be detected and quantified by a number of technologies including genome-wide screening methods...... of biochemical molecules such as proteins, DNA, RNA or lipids, whereby protein biomarkers have been the most extensively studied and used, notably in blood-based protein quantification tests or immunohistochemistry. The rise of interest in epigenetic mechanisms has allowed the identification of a new type...... as well as locus- or gene-specific high-resolution analysis in different types of samples such as frozen tissues and FFPE samples, but also in body fluids such as urine, plasma, and serum obtained through non-invasive procedures. In some cases, DNA methylation based biomarkers have proven to be more...

  4. Finding human promoter groups based on DNA physical properties

    Science.gov (United States)

    Zeng, Jia; Cao, Xiao-Qin; Zhao, Hongya; Yan, Hong

    2009-10-01

    DNA rigidity is an important physical property originating from the DNA three-dimensional structure. Although the general DNA rigidity patterns in human promoters have been investigated, their distinct roles in transcription are largely unknown. In this paper, we discover four highly distinct human promoter groups based on similarity of their rigidity profiles. First, we find that all promoter groups conserve relatively rigid DNAs at the canonical TATA box [a consensus TATA(A/T)A(A/T) sequence] position, which are important physical signals in binding transcription factors. Second, we find that the genes activated by each group of promoters share significant biological functions based on their gene ontology annotations. Finally, we find that these human promoter groups correlate with the tissue-specific gene expression.

  5. Antibody activation using DNA-based logic gates.

    Science.gov (United States)

    Janssen, Brian M G; van Rosmalen, Martijn; van Beek, Lotte; Merkx, Maarten

    2015-02-16

    Oligonucleotide-based molecular circuits offer the exciting possibility to introduce autonomous signal processing in biomedicine, synthetic biology, and molecular diagnostics. Here we introduce bivalent peptide-DNA conjugates as generic, noncovalent, and easily applicable molecular locks that allow the control of antibody activity using toehold-mediated strand displacement reactions. Employing yeast as a cellular model system, reversible control of antibody targeting is demonstrated with low nM concentrations of peptide-DNA locks and oligonucleotide displacer strands. Introduction of two different toehold strands on the peptide-DNA lock allowed signal integration of two different inputs, yielding logic OR- and AND-gates. The range of molecular inputs could be further extended to protein-based triggers by using protein-binding aptamers. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Finding human promoter groups based on DNA physical properties.

    Science.gov (United States)

    Zeng, Jia; Cao, Xiao-Qin; Zhao, Hongya; Yan, Hong

    2009-10-01

    DNA rigidity is an important physical property originating from the DNA three-dimensional structure. Although the general DNA rigidity patterns in human promoters have been investigated, their distinct roles in transcription are largely unknown. In this paper, we discover four highly distinct human promoter groups based on similarity of their rigidity profiles. First, we find that all promoter groups conserve relatively rigid DNAs at the canonical TATA box [a consensus TATA(A/T)A(A/T) sequence] position, which are important physical signals in binding transcription factors. Second, we find that the genes activated by each group of promoters share significant biological functions based on their gene ontology annotations. Finally, we find that these human promoter groups correlate with the tissue-specific gene expression.

  7. Flow cytometry-based DNA hybridization and polymorphism analysis

    Energy Technology Data Exchange (ETDEWEB)

    Cai, H.; Kommander, K.; White, P.S.; Nolan, J.P.

    1998-07-01

    Functional analysis of the humane genome, including the quantification of differential gene expression and the identification of polymorphic sites and disease genes, is an important element of the Human Genome Project. Current methods of analysis are mainly gel-based assays that are not well-suited to rapid genome-scale analyses. To analyze DNA sequence on a large scale, robust and high throughput assays are needed. The authors are developing a suite of microsphere-based approaches employing fluorescence detection to screen and analyze genomic sequence. The approaches include competitive DNA hybridization to measure DNA or RNA targets in unknown samples, and oligo ligation or extension assays to analyze single-nucleotide polymorphisms. Apart from the advances of sensitivity, simplicity, and low sample consumption, these flow cytometric approaches have the potential for high throughput multiplexed analysis using multicolored microspheres and automated sample handling.

  8. Poly(dimethylsiloxane) based microchip for DNA electrophoresis

    Institute of Scientific and Technical Information of China (English)

    LIU Changchun; CUI Dafu; WANG Li

    2004-01-01

    A novel poly(dimethylsiloxane)(PDMS) -based microchip for DNA separation through electrophoresis has been developed using a micro-electro-mechanical-system(MEMS) technology. Unlike previous hybrid PDMS microchip, one PDMS film is first created on glass support by pressing method in our microchip. Thus, increased band-broadening phenomena, arising from the material nonuniformity at the walls of microchannel, can be avoided in electrophoresis process. A low-viscosity hydroxypropylmethylcellulose-100 (HPMC-100) is used as the separation medium for fluorescent intercalator-labeled double-stranded DNA (dsDNA) fragments. Mannitol is introduced to PDMS-based microchip as a separation medium additive to enhance separation efficiency. At applied electric field strength of 150 V/cm, excellent separations of the PCR marker could be achieved with an effective separation distance of 25mm .

  9. Molecular genotyping of Colletotrichum species based on arbitrarily primed PCR, A + T-Rich DNA, and nuclear DNA analyses

    Science.gov (United States)

    Freeman, S.; Pham, M.; Rodriguez, R.J.

    1993-01-01

    Molecular genotyping of Colletotrichum species based on arbitrarily primed PCR, A + T-rich DNA, and nuclear DNA analyses. Experimental Mycology 17, 309-322. Isolates of Colletotrichum were grouped into 10 separate species based on arbitrarily primed PCR (ap-PCR), A + T-rich DNA (AT-DNA) and nuclear DNA banding patterns. In general, the grouping of Colletotrichum isolates by these molecular approaches corresponded to that done by classical taxonomic identification, however, some exceptions were observed. PCR amplification of genomic DNA using four different primers allowed for reliable differentiation between isolates of the 10 species. HaeIII digestion patterns of AT-DNA also distinguished between species of Colletotrichum by generating species-specific band patterns. In addition, hybridization of the repetitive DNA element (GcpR1) to genomic DNA identified a unique set of Pst 1-digested nuclear DNA fragments in each of the 10 species of Colletotrichum tested. Multiple isolates of C. acutatum, C. coccodes, C. fragariae, C. lindemuthianum, C. magna, C. orbiculare, C. graminicola from maize, and C. graminicola from sorghum showed 86-100% intraspecies similarity based on ap-PCR and AT-DNA analyses. Interspecies similarity determined by ap-PCR and AT-DNA analyses varied between 0 and 33%. Three distinct banding patterns were detected in isolates of C. gloeosporioides from strawberry. Similarly, three different banding patterns were observed among isolates of C. musae from diseased banana.

  10. DNA methylation detection based on difference of base content

    Science.gov (United States)

    Sato, Shinobu; Ohtsuka, Keiichi; Honda, Satoshi; Sato, Yusuke; Takenaka, Shigeori

    2016-04-01

    Methylation frequently occurs in cytosines of CpG sites to regulate gene expression. The identification of aberrant methylation of certain genes is important for cancer marker analysis. The aim of this study was to determine the methylation frequency in DNA samples of unknown length and/or concentration. Unmethylated cytosine is known to be converted to thymine following bisulfite treatment and subsequent PCR. For this reason, the AT content in DNA increases with an increasing number of methylation sites. In this study, the fluorescein-carrying bis-acridinyl peptide (FKA) molecule was used for the detection of methylation frequency. FKA contains fluorescein and two acridine moieties, which together allow for the determination of the AT content of double-stranded DNA fragments. Methylated and unmethylated human genomes were subjected to bisulfide treatment and subsequent PCR using primers specific for the CFTR, CDH4, DBC1, and NPY genes. The AT content in the resulting PCR products was estimated by FKA, and AT content estimations were found to be in good agreement with those determined by DNA sequencing. This newly developed method may be useful for determining methylation frequencies of many PCR products by measuring the fluorescence in samples excited at two different wavelengths.

  11. Statistical mechanics of base stacking and pairing in DNA melting.

    Science.gov (United States)

    Ivanov, Vassili; Zeng, Yan; Zocchi, Giovanni

    2004-11-01

    We propose a statistical mechanics model for DNA melting in which base stacking and pairing are explicitly introduced as distinct degrees of freedom. Unlike previous approaches, this model describes thermal denaturation of DNA secondary structure in the whole experimentally accessible temperature range. Base pairing is described through a zipper model, base stacking through an Ising model. We present experimental data on the unstacking transition, obtained exploiting the observation that at moderately low pH this transition is moved down to experimentally accessible temperatures. These measurements confirm that the Ising model approach is indeed a good description of base stacking. On the other hand, comparison with the experiments points to the limitations of the simple zipper model description of base pairing.

  12. Ultrasensitive electrochemical DNA assay based on counting of single magnetic nanobeads by a combination of DNA amplification and enzyme amplification.

    Science.gov (United States)

    Zhang, Xiaoli; Li, Linlin; Li, Lu; Chen, Jia; Zou, Guizheng; Si, Zhikun; Jin, Wenrui

    2009-03-01

    An ultrasensitive electrochemical method for determination of DNA is developed based on counting of single magnetic nanobeads (MNBs) corresponding to single DNA sequences combined with a double amplification (DNA amplification and enzyme amplification). In this method, target DNA (t-DNA) is captured on a streptavidin-coated substrate via biotinylated capture DNA. Then, MNBs functionalized with first-probe DNAs (p1-DNA-MNBs) are conjugated to t-DNA sequences with a ratio of 1:1. Subsequently, the p1-DNA-MNBs are released from the substrate via dehybridization. The released p1-DNA-MNBs are labeled with alkaline phosphatase (AP) using biotinylated second-probe DNAs (p2-DNAs) and streptavidin-AP conjugates. The resultant AP-p2-DNA-p1-DNA-MNBs with enzyme substrate disodium phenyl phosphate (DPP) are continuously introduced through a capillary as the microsampler and microreactor at 40 degrees C. AP on the AP-p2-DNA-p1-DNA-MNBs converts a huge number of DPP into its product phenol, and phenol zones are produced around each moving AP-p2-DNA-p1-DNA-MNB. The phenol zones are continuously delivered to the capillary outlet and detected by a carbon fiber disk bundle electrode at 1.05 V. An elution curve with peaks is obtained. Each peak is corresponding to a phenol zone relative to single t-DNA sequence. The peaks on the elution curve are counted for quantification. The number of the peaks is proportional to the concentration of t-DNA in a range of 5.0 x 10(-16) to 1.0 x 10(-13) mol/L.

  13. A DNA-Based Encryption Method Based on Two Biological Axioms of DNA Chip and Polymerase Chain Reaction (PCR) Amplification Techniques.

    Science.gov (United States)

    Zhang, Yunpeng; Wang, Zhiwen; Wang, Zhenzhen; Liu, Xin; Yuan, Xiaojing

    2017-09-27

    Researchers have gained a deeper understanding of DNA-based encryption and its effectiveness in enhancing information security in recent years. However, there are many theoretical and technical issues about DNA-based encryption that need to be addressed before it can be effectively used in the field of security. Currently, the most popular DNA-based encryption schemes are based on traditional cryptography and the integration of existing DNA technology. These schemes are not completely based on DNA computing and biotechnology. Herein, as inspired by nature, encryption based on DNA has been developed, which is, in turn, based on two fundamental biological axioms about DNA sequencing: 1) DNA sequencing is difficult under the conditions of not knowing the correct sequencing primers and probes, and 2) without knowing the correct probe, it is difficult to decipher precisely and sequence the information of unknown and mixed DNA/peptide nucleic acid (PNA) probes, which only differ in nucleotide sequence, arranged on DNA chips (microarrays). In essence, when creating DNA-based encryption by means of biological technologies, such as DNA chips and polymerase chain reaction (PCR) amplification, the encryption method discussed herein cannot be decrypted, unless the DNA/PNA probe or PCR amplification is known. The biological analysis, mathematical analysis, and simulation results demonstrate the feasibility of the method, which provides much stronger security and reliability than that of traditional encryption methods. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. Base excision repair deficient mice lacking the Aag alkyladenine DNA glycosylase.

    NARCIS (Netherlands)

    B.P. Engelward (Bevin); G. Weeda (Geert); M.D. Wyatt; J.L.M. Broekhof (Jose'); J. de Wit (Jan); I. Donker (Ingrid); J.M. Allan (James); B. Gold (Bert); J.H.J. Hoeijmakers (Jan); L.D. Samson (Leona)

    1997-01-01

    textabstract3-methyladenine (3MeA) DNA glycosylases remove 3MeAs from alkylated DNA to initiate the base excision repair pathway. Here we report the generation of mice deficient in the 3MeA DNA glycosylase encoded by the Aag (Mpg) gene. Alkyladenine DNA glycosylase turns out to be the major DNA glyc

  15. Base excision repair deficient mice lacking the Aag alkyladenine DNA glycosylase.

    NARCIS (Netherlands)

    B.P. Engelward (Bevin); G. Weeda (Geert); M.D. Wyatt; J.L.M. Broekhof (Jose'); J. de Wit (Jan); I. Donker (Ingrid); J.M. Allan (James); B. Gold (Bert); J.H.J. Hoeijmakers (Jan); L.D. Samson (Leona)

    1997-01-01

    textabstract3-methyladenine (3MeA) DNA glycosylases remove 3MeAs from alkylated DNA to initiate the base excision repair pathway. Here we report the generation of mice deficient in the 3MeA DNA glycosylase encoded by the Aag (Mpg) gene. Alkyladenine DNA glycosylase turns out to be the major DNA glyc

  16. Indicator Based and Indicator - Free Electrochemical DNA Biosensors

    Science.gov (United States)

    2007-11-02

    of genomic material from infectious organisms. Methylene blue (MB) is an aromatic heterocycle that binds strongly to DNA via intercalation. MB...detection of disease- related point mutation in the guanine bases of the cyanobacteria . The resulting biosensors offer great promise for mismatch

  17. Mitochondrial and chloroplast DNA based phylogeny of Pelargonium (Geraniaceae)

    NARCIS (Netherlands)

    Bakker, F.T.; Culham, A.; Pankhurst, C.E.; Gibby, M.

    2000-01-01

    Overall phylogenetic relationships within the genus Pelargonium (Geraniaceae) were inferred based on DNA sequences from mitochondrial(mt)-encoded nad1 b/c exons and from chloroplast(cp)-encoded trnL (UAA) 5' exon-trnF (GAA) exon regions using two species of Geranium and Sarcocaulon vanderetiae as ou

  18. Endonuclease-based Method for Detecting the Sequence Specific DNA Binding Protein on Double-stranded DNA Microarray

    Institute of Scientific and Technical Information of China (English)

    Yun Fei BAI; Qin Yu GE; Tong Xiang LI; Jin Ke WANG; Quan Jun LIU; Zu Hong LU

    2005-01-01

    The double-stranded DNA (dsDNA) probe contains two different protein binding sites.One is for DNA- binding proteins to be detected and the other is for a DNA restriction enzyme.The two sites were arranged together with no base interval. The working principle of the capturing dsDNA probe is described as follows: the capturing probe can be cut with the DNA restriction enzyme (such as EcoR I) to cause a sticky terminal, if the probe is not bound with a target protein, and the sticky terminal can be extended and labeled with Cy3-dUTP by DNA polymerase. When the probe is bound with a target protein, the probe is not capable to be cut by the restriction enzyme because of space obstruction. The amount of the target DNA binding proteins can be measured according to the variations of fluorescent signals of the corresponding probes.

  19. Karyotyping of Brassica oleracea L.based on rDNA and Cot-1 DNA fluorescence in situ hybridization

    Institute of Scientific and Technical Information of China (English)

    WANG Taixia; WU Chunhong; HUANG Jinyong; WEI Wenhui

    2007-01-01

    To explore an effective and reliable karyotyping method in Brassica crop plants,Cot-1 DNA was isolated from Brassica oleracea genome,labeled as probe with Biotin-Nick Translation Mix kit,in situ hybridized to mitotic spreads,and where specific fluorescent bands showed on each chromosome pair.25S and 5S rDNA were labeled as probes with DIG-Nick Translation Mix kit and Biotin-Nick Translation Mix kit,respectively,in situ hybridized to mitotic preparations,where 25S rDNA could be detected on two chromosome pairs and 5S rDNA on only one.Cot-1 DNA contains rDNA and chromosome sites identity between Cot-1 DNA and 25S rDNA was determined by dual-colour fluorescence in situ hybridization.All these showed that the karyotyping technique based on a combination of rDNA and Cot-1 DNA chromosome landmarks is superior to all but one.A more exact karyotype ofB.oleracea has been analyzed based on a combination of rDNA sites,Cot-1 DNA fluorescent bands,chromosome lengths and arm ratios.

  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-Based Self-Assembly of Fluorescent Nanodiamonds.

    Science.gov (United States)

    Zhang, Tao; Neumann, Andre; Lindlau, Jessica; Wu, Yuzhou; Pramanik, Goutam; Naydenov, Boris; Jelezko, Fedor; Schüder, Florian; Huber, Sebastian; Huber, Marinus; Stehr, Florian; Högele, Alexander; Weil, Tanja; Liedl, Tim

    2015-08-12

    As a step toward deterministic and scalable assembly of ordered spin arrays we here demonstrate a bottom-up approach to position fluorescent nanodiamonds (NDs) with nanometer precision on DNA origami structures. We have realized a reliable and broadly applicable surface modification strategy that results in DNA-functionalized and perfectly dispersed NDs that were then self-assembled in predefined geometries. With optical studies we show that the fluorescence properties of the nitrogen-vacancy color centers in NDs are preserved during surface modification and DNA assembly. As this method allows the nanoscale arrangement of fluorescent NDs together with other optically active components in complex geometries, applications based on self-assembled spin lattices or plasmon-enhanced spin sensors as well as improved fluorescent labeling for bioimaging could be envisioned.

  2. Fluorescence of size-expanded DNA bases: reporting on DNA sequence and structure with an unnatural genetic set.

    Science.gov (United States)

    Krueger, Andrew T; Kool, Eric T

    2008-03-26

    We recently described the synthesis and helix assembly properties of expanded DNA (xDNA), which contains base pairs 2.4 A larger than natural DNA pairs. This designed genetic set is under study with the goals of mimicking the functions of the natural DNA-based genetic system and of developing useful research tools. Here, we study the fluorescence properties of the four expanded bases of xDNA (xA, xC, xG, xT) and evaluate how their emission varies with changes in oligomer length, composition, and hybridization. Experiments were carried out with short oligomers of xDNA nucleosides conjugated to a DNA oligonucleotide, and we investigated the effects of hybridizing these fluorescent oligomers to short complementary DNAs with varied bases opposite the xDNA bases. As monomer nucleosides, the xDNA bases absorb light in two bands: one at approximately 260 nm (similar to DNA) and one at longer wavelength ( approximately 330 nm). All are efficient violet-blue fluorophores with emission maxima at approximately 380-410 nm and quantum yields (Phifl) of 0.30-0.52. Short homo-oligomers of the xDNA bases (length 1-4 monomers) showed moderate self-quenching except xC, which showed enhancement of Phifl with increasing length. Interestingly, multimers of xA emitted at longer wavelengths (520 nm) as an apparent excimer. Hybridization of an oligonucleotide to the DNA adjacent to the xDNA bases (with the xDNA portion overhanging) resulted in no change in fluorescence. However, addition of one, two, or more DNA bases in these duplexes opposite the xDNA portion resulted in a number of significant fluorescence responses, including wavelength shifts, enhancements, or quenching. The strongest responses were the enhancement of (xG)n emission by hybridization of one or more adenines opposite them, and the quenching of (xT)n and (xC)n emission by guanines opposite. The data suggest multiple ways in which the xDNA bases, both alone and in oligomers, may be useful as tools in biophysical analysis

  3. Micromechanics of base pair unzipping in the DNA duplex.

    Science.gov (United States)

    Volkov, Sergey N; Paramonova, Ekaterina V; Yakubovich, Alexander V; Solov'yov, Andrey V

    2012-01-25

    All-atom molecular dynamics (MD) simulations of DNA duplex unzipping in a water environment were performed. The investigated DNA double helix consists of a Drew-Dickerson dodecamer sequence and a hairpin (AAG) attached to the end of the double-helix chain. The considered system is used to examine the process of DNA strand separation under the action of an external force. This process occurs in vivo and now is being intensively investigated in experiments with single molecules. The DNA dodecamer duplex is consequently unzipped pair by pair by means of the steered MD. The unzipping trajectories turn out to be similar for the duplex parts with G·C content and rather distinct for the parts with A·T content. It is shown that during the unzipping each pair experiences two types of motion: relatively quick rotation together with all the duplex and slower motion in the frame of the unzipping fork. In the course of opening, the complementary pair passes through several distinct states: (i) the closed state in the double helix, (ii) the metastable preopened state in the unzipping fork and (iii) the unbound state. The performed simulations show that water molecules participate in the stabilization of the metastable states of the preopened base pairs in the DNA unzipping fork.

  4. High-throughput engineering of a mammalian genome reveals building principles of methylation states at CG rich regions.

    Science.gov (United States)

    Krebs, Arnaud R; Dessus-Babus, Sophie; Burger, Lukas; Schübeler, Dirk

    2014-09-26

    The majority of mammalian promoters are CpG islands; regions of high CG density that require protection from DNA methylation to be functional. Importantly, how sequence architecture mediates this unmethylated state remains unclear. To address this question in a comprehensive manner, we developed a method to interrogate methylation states of hundreds of sequence variants inserted at the same genomic site in mouse embryonic stem cells. Using this assay, we were able to quantify the contribution of various sequence motifs towards the resulting DNA methylation state. Modeling of this comprehensive dataset revealed that CG density alone is a minor determinant of their unmethylated state. Instead, these data argue for a principal role for transcription factor binding sites, a prediction confirmed by testing synthetic mutant libraries. Taken together, these findings establish the hierarchy between the two cis-encoded mechanisms that define the DNA methylation state and thus the transcriptional competence of CpG islands.

  5. Persistence of DNA of Gaeumannomyces graminis var. tritici in soil as measured by a DNA-based assay.

    Science.gov (United States)

    Herdina; Neate, Stephen; Jabaji-Hare, Suha; Ophel-Keller, Kathy

    2004-02-01

    There are an increasing number of assays available for fungal plant pathogens based on DNA technology. We have developed such an assay for Gaeumannomyces graminis var. tritici (Ggt) in soil, using slot-blot hybridisation. To ensure the validity of DNA-based soil assays for the fungus, it is important to determine the stability of Ggt DNA in soil. This study was undertaken to quantify the DNA degradation of dead Ggt in soil using a DNA-based assay. Mycelia were killed using various treatments, then DNA was extracted and estimated by a slot-blot hybridisation technique using the specific Ggt DNA probe, pG158. Mycelia were also killed using a fungicide (triadimefon) at a concentration of 150-250 microg ml(-1). The amount of detectable DNA of Ggt, killed using triadimefon, declined by 82-93%. Inoculum in the form of diseased wheat roots, artificially inoculated ryegrass seed, particulate soil organic matter and whole soil was killed using heat-treatment. The amount of detectable DNA of Ggt declined markedly (90%) in both heat-treated roots and inoculated ryegrass seeds, and declined by 50% in both treated soil and soil organic matter. The rate of DNA degradation of Ggt in soil varied with the type of inoculum. The amount of detectable DNA of Ggt in dead mycelia declined by 99.8% after 4 days of incubation in soil. No DNA was detected after 8 days of incubation. In contrast, Ggt DNA in live mycelia declined by 70% after 8 days of incubation and declined to 10% of original DNA level after 32 days. In ground ryegrass seed inoculum, DNA in both killed and live Ggt declined by 50% after 8 days. In diseased roots, DNA from both live and killed Ggt did not appear to decline over 16 days. Estimates of the amount of Ggt in the soil using a DNA-based assay reflect both live and dead populations of the fungus. The rate of breakdown of DNA of the dead fungus is very high and the presence of dead fungi in roots probably a rare event so the DNA from dead fungus probably contributes

  6. Downregulation of LH and FSH receptors after hCG and eCG treatments in the porcine oviduct.

    Science.gov (United States)

    Małysz-Cymborska, I; Andronowska, A

    2016-10-01

    The influence of induction of ovulation and superovulation with eCG and hCG on LH and FSH receptor levels in porcine oviducts on day 3 postcoitum was studied. In experiment I, gilts were assigned into cyclic (control; n = 5) and inseminated (n = 5) groups. In experiment II, there were 3 groups of animals: inseminated (n = 5), induced ovulation/inseminated (750 IU eCG, 500 IU hCG; n = 5) and superovulated/inseminated (1500 IU eCG, 1000 IU hCG; n = 5) gilts. Oviduct tissues were collected 3 d after insemination or PBS infusion. The messenger RNA (mRNA) expression of FSH receptor (FSHR) and luteinizing hormone/chorionic gonadotropin receptor (LH/CGR) was measured by real-time reverse transcription PCR and protein levels using Western blots. Localization of LH/CGR and FSHR-positive cells was studied by immunohistochemical staining. Insemination by itself did not influence mRNA and protein levels of LH/CGR. However, FSHR mRNA expression in the isthmus and ampulla of the oviduct was affected by insemination (P hCG and eCG did not affect LH/CGR and FSHR mRNA expression, either in the isthmus or in the ampulla. Nevertheless, superovulation decreased LH/CGR protein level in the oviductal ampulla (P hCG, especially in high doses, can change LH/CGR and FSHR levels in porcine oviducts. This may in turn alter many signaling pathways, eg, PGs or vascular endothelial growth factor synthesis, and consequently disturb the oviductal environment, with possible detrimental effects on fertilization and/or embryonic development. Copyright © 2016 Elsevier Inc. All rights reserved.

  7. Bisulfite-based epityping on pooled genomic DNA provides an accurate estimate of average group DNA methylation

    Directory of Open Access Journals (Sweden)

    Docherty Sophia J

    2009-03-01

    Full Text Available Abstract Background DNA methylation plays a vital role in normal cellular function, with aberrant methylation signatures being implicated in a growing number of human pathologies and complex human traits. Methods based on the modification of genomic DNA with sodium bisulfite are considered the 'gold-standard' for DNA methylation profiling on genomic DNA; however, they require relatively large amounts of DNA and may be prohibitively expensive when used on the large sample sizes necessary to detect small effects. We propose that a high-throughput DNA pooling approach will facilitate the use of emerging methylomic profiling techniques in large samples. Results Compared with data generated from 89 individual samples, our analysis of 205 CpG sites spanning nine independent regions of the genome demonstrates that DNA pools can be used to provide an accurate and reliable quantitative estimate of average group DNA methylation. Comparison of data generated from the pooled DNA samples with results averaged across the individual samples comprising each pool revealed highly significant correlations for individual CpG sites across all nine regions, with an average overall correlation across all regions and pools of 0.95 (95% bootstrapped confidence intervals: 0.94 to 0.96. Conclusion In this study we demonstrate the validity of using pooled DNA samples to accurately assess group DNA methylation averages. Such an approach can be readily applied to the assessment of disease phenotypes reducing the time, cost and amount of DNA starting material required for large-scale epigenetic analyses.

  8. Rapid sequencing of DNA based on single-molecule detection

    Science.gov (United States)

    Soper, Steven A.; Davis, Lloyd M.; Fairfield, Frederick R.; Hammond, Mark L.; Harger, Carol A.; Jett, James H.; Keller, Richard A.; Marrone, Babetta L.; Martin, John C.; Nutter, Harvey L.; Shera, E. Brooks; Simpson, Daniel J.

    1991-07-01

    Sequencing the human genome is a major undertaking considering the large number of nucleotides present in the genome and the slow methods currently available to perform the task. The authors have recently reported on a scheme to sequence DNA rapidly using a non-gel based technique. The concept is based upon the incorporation of fluorescently labeled nucleotides into a strand of DNA, isolation and manipulation of a labeled DNA fragment and the detection of single nucleotides using ultra-sensitive laser-induced fluorescence detection following their cleavage from the fragment. Detection of individual fluorophores in the liquid phase was accomplished with time-gated detection following pulsed-laser excitation. The photon bursts from individual rhodamine 6G (R6G) molecules travelling through a laser beam have been observed, as have bursts from single fluorescently modified nucleotides. Using two different biotinylated nucleotides as a model system for fluorescently labeled nucleotides, the authors have observed synthesis of the complementary copy of M13 bacteriophage. Work with fluorescently labeled nucleotides is underway. Individual molecules of DNA attached to a microbead have been observed and manipulated with an epifluorescence microscope.

  9. Immunogenicity of a DNA-launched replicon-based canine parvovirus DNA vaccine expressing VP2 antigen in dogs.

    Science.gov (United States)

    Dahiya, Shyam S; Saini, Mohini; Kumar, Pankaj; Gupta, Praveen K

    2012-10-01

    A replicon-based DNA vaccine encoding VP2 gene of canine parvovirus (CPV) was developed by cloning CPV-VP2 gene into a replicon-based DNA vaccine vector (pAlpha). The characteristics of a replicon-based DNA vaccine like, self-amplification of transcripts and induction of apoptosis were analyzed in transfected mammalian cells. When the pAlpha-CPV-VP2 was injected intradermal as DNA-launched replicon-based DNA vaccine in dogs, it induced CPV-specific humoral and cell mediated immune responses. The virus neutralization antibody and lymphocyte proliferative responses were higher than conventional CPV DNA vaccine and commercial CPV vaccine. These results indicated that DNA-launched replicon-based CPV DNA vaccine was effective in inducing both CPV-specific humoral and cellular immune responses and can be considered as effective alternative to conventional CPV DNA vaccine and commercial CPV vaccine. Crown Copyright © 2012. Published by Elsevier India Pvt Ltd. All rights reserved.

  10. Hairpin DNA probe based surface plasmon resonance biosensor used for the activity assay of E. coli DNA ligase.

    Science.gov (United States)

    Luan, Qingfen; Xue, Ying; Yao, Xin; Lu, Wu

    2010-02-01

    Using hairpin DNA probe self-structure change during DNA ligation process, a sensitive, label-free and simple method of E. coli DNA ligase assay via a home-built high-resolution surface plasmon resonance (SPR) instrument was developed. The DNA ligation process was monitored in real-time and the effects of single-base mutation on the DNA ligation process were investigated. Then an assay of E. coli DNA ligase was completed with a lower detection limit (0.6 nM), wider concentration range and better reproducibility. Moreover, the influence of Quinacrine on the activity of E. coli DNA ligase was also studied, which demonstrated that our method was useful for drug screening.

  11. Detection Tuna and Processed Products Based Protein and DNA Barcoding

    Directory of Open Access Journals (Sweden)

    Nuring Wulansari

    2015-11-01

    Full Text Available Tuna is the second largest fishery commodity in Indonesia after the shrimp. Since the high demand and the limited stock of tuna resulted in fraudulent chance. Authentication is required to meassure consumers regarding the accuracy of its labeling and food safety. In this study, the authentication was based on protein and DNA barcoding using cytochrome-b gene (cyt-b of the mitochondrial DNA as the target of gene. Primer of cyt b gene was designed based on the tuna species. This study aimed to identify the authenticity of tuna fresh and its processed products through protein using SDS-PAGE and DNA barcoding techniques. The phases of this research were protein electrophoresis by SDS-PAGE, DNA extraction, PCR amplification, electrophoresis and sequencing. Samples of fresh fish (Tu1, Tu2, Tu3, Tu4, and Tu5 and processed tuna (canned and steak were successfully extracted. Result showed that SDS-PAGE proved the damage of proteins in the processed tuna, so this method was not appropriate if it is used to identify the authenticity of tuna. PCR electrophoresis results showed that the samples of tuna, tuna steak, sushi, meat ball, abon, and caned tuna were successfully amplified in the range of 500-750 bp except Ka3, which was in line with the target of DNA (620 bp. Resulted sequences of Tu2, Tu3, Tu4 and Tu5 were identified according the results of morphometric namely T. albacares, while Tu1 was identified as T. obesus with homology level of 99%. Processed tunas (steak and canned tuna were identified as T. albacares, as stated on the labels.

  12. Cryptanalysis of an image encryption algorithm based on DNA encoding

    Science.gov (United States)

    Akhavan, A.; Samsudin, A.; Akhshani, A.

    2017-10-01

    Recently an image encryption algorithm based on DNA encoding and the Elliptic Curve Cryptography (ECC) is proposed. This paper aims to investigate the security the DNA-based image encryption algorithm and its resistance against chosen plaintext attack. The results of the analysis demonstrate that security of the algorithm mainly relies on one static shuffling step, with a simple confusion operation. In this study, a practical plain image recovery method is proposed, and it is shown that the images encrypted with the same key could easily be recovered using the suggested cryptanalysis method with as low as two chosen plain images. Also, a strategy to improve the security of the algorithm is presented in this paper.

  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. Hairpin DNA Switch for Ultrasensitive Spectrophotometric Detection of DNA Hybridization Based on Gold Nanoparticles and Enzyme Signal Amplification

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Youyu; Tang, Zhiwen; Wang, Jun; Wu, Hong; Maham, Aihui; Lin, Yuehe

    2010-08-01

    A novel DNA detection platform based on a hairpin-DNA switch, nanoparticles, and enzyme signal amplification for ultrasensitive detection of DNA hybridization has been developed in this work. In this DNA assay, a “stem-loop” DNA probe dually labeled with a thiol at its 5’ end and a biotin at its 3’ end, respectively, was used. This probe was immobilized on the gold nanoparticles (AuNPs) anchored by a protein, globulin, on a 96-well microplate. In the absence of target DNA, the immobilized probe with the stem-loop structure shields the biotin from being approached by a bulky horseradish peroxidase linked-avidin (avidin-HRP) conjugate due to the steric hindrance. However, in the presence of target DNA, the hybridization between the hairpin DNA probe and the target DNA causes significant conformational change of the probe, which forces biotin away from the surface of AuNPs. As a result, the biotin becomes accessible by the avidin-HRP, and the target hybridization event can be sensitively detected via the HRP catalyzed substrate 3, 3', 5, 5'-tetramethylbenzidine using spectrophometric method. Some experimental parameters governing the performance of the assay have been optimized. At optimal conditions, this DNA assay can detect DNA at the concentration of femtomolar level by means of a signal amplification strategy based on the combination of enzymes and nanoparticles. This approach also has shown excellent specificity to distinguish single-base mismatches of DNA targets because of the intrinsic high selectivity of the hairpin DNA probe.

  15. Progress of DNA-based Methods for Species Identification

    Institute of Scientific and Technical Information of China (English)

    HU Zhen; ZHANG Su-hua; WANG Zheng; BIAN Ying-nan; LI Cheng-tao

    2015-01-01

    Species identification of biological samples is widely used in such fields as forensic science and food industry. A variety of accurate and reliable methods have been developed in recent years. The cur-rent reviewshows common target genes and screening criteria suitable for species identification, and de-scribed various DNA-based molecular biology methods about species identification. Additionally, it dis-cusses the future development of species identification combined with real-time PCR and sequencing technologies.

  16. Arduino-based automation of a DNA extraction system.

    Science.gov (United States)

    Kim, Kyung-Won; Lee, Mi-So; Ryu, Mun-Ho; Kim, Jong-Won

    2015-01-01

    There have been many studies to detect infectious diseases with the molecular genetic method. This study presents an automation process for a DNA extraction system based on microfluidics and magnetic bead, which is part of a portable molecular genetic test system. This DNA extraction system consists of a cartridge with chambers, syringes, four linear stepper actuators, and a rotary stepper actuator. The actuators provide a sequence of steps in the DNA extraction process, such as transporting, mixing, and washing for the gene specimen, magnetic bead, and reagent solutions. The proposed automation system consists of a PC-based host application and an Arduino-based controller. The host application compiles a G code sequence file and interfaces with the controller to execute the compiled sequence. The controller executes stepper motor axis motion, time delay, and input-output manipulation. It drives the stepper motor with an open library, which provides a smooth linear acceleration profile. The controller also provides a homing sequence to establish the motor's reference position, and hard limit checking to prevent any over-travelling. The proposed system was implemented and its functionality was investigated, especially regarding positioning accuracy and velocity profile.

  17. Proportion hyperglycosylated hCG: a new test for discriminating gestational trophoblastic diseases.

    Science.gov (United States)

    Cole, Laurence A

    2014-11-01

    Hyperglycosylated human chorionic gonadotropin (hCG) is a variant of hCG with large oligosaccharide side chains. Although hCG is produced by syncytiotrophoblast cells, hyperglycosylated hCG marks cytotrophoblast cell. Hyperglycosylated hCG signals placental implantation. Total hCG in serum and urine is measured by the Siemens Immulite hCG pregnancy test; the result is in milli-international unit per milliliter. Hyperglycosylated hCG is determined by the B152 microtiter plate assay; the result is in nanogram per milliliter. Hyperglycosylated hCG results can be converted to milli-international unit per milliliter equivalents by multiplying by 11. The test measures proportion hyperglycosylated hCG, hyperglycosylated hCG / total hCG. Proportion hyperglycosylated hCG marks cases intent on developing persistent hydatidiform mole (68% detection at 17% false detection). Proportion hyperglycosylated hCG also marks persistent hydatidiform mole (100% detection at 5.1% false detection). Proportion hyperglycosylated hCG distinguishes choriocarcinoma and gestational trophoblastic neoplasm cases, absolutely discriminating aggressive cases and minimally aggressive cases. Proportion hyperglycosylated hCG identifies quiescent gestational trophoblastic disease cases. It recognizes quiescent cases that become persistent disease (100% detection at 0% false positive). Proportion hyperglycosylated hCG is an invaluable test for discriminating gestational trophoblastic diseases.

  18. Direct Electrical Detection of DNA Hybridization Based on Electrolyte-Gated Graphene Field-Effect Transistor

    Science.gov (United States)

    Ohno, Yasuhide; Okamoto, Shogo; Maehashi, Kenzo; Matsumoto, Kazuhiko

    2013-11-01

    DNA hybridization was electrically detected by graphene field-effect transistors. Probe DNA was modified on the graphene channel by a pyrene-based linker material. The transfer characteristic was shifted by the negative charges on the probe DNA, and the drain current was changed by the full-complementary DNA while no current change was observed after adding noncomplementary DNA, indicating that the graphene field-effect transistor detected the DNA hybridization. In addition, the number of DNAs was estimated by the simple plate capacitor model. As a result, one probe DNA was attached on the graphene channel per 10×10 nm2, indicating their high density functionalization. We estimated that 30% of probe DNA on the graphene channel was hybridized with 200 nM full-complementary DNA while only 5% of probe DNA was bound to the noncomplementary DNA. These results will help to pave the way for future biosensing applications based on graphene FETs.

  19. A Graphene-Based Biosensing Platform Based on Regulated Release of an Aptameric DNA Biosensor.

    Science.gov (United States)

    Mao, Yu; Chen, Yongli; Li, Song; Lin, Shuo; Jiang, Yuyang

    2015-11-09

    A novel biosensing platform was developed by integrating an aptamer-based DNA biosensor with graphene oxide (GO) for rapid and facile detection of adenosine triphosphate (ATP, as a model target). The DNA biosensor, which is locked by GO, is designed to contain two sensing modules that include recognition site for ATP and self-replication track that yields the nicking domain for Nt.BbvCI. By taking advantage of the different binding affinity of single-stranded DNA, double-stranded DNA and aptamer-target complex toward GO, the DNA biosensor could be efficiently released from GO in the presence of target with the help of a complementary DNA strand (CPDNA) that partially hybridizes to the DNA biosensor. Then, the polymerization/nicking enzyme synergetic isothermal amplification could be triggered, leading to the synthesis of massive DNA amplicons, thus achieving an enhanced sensitivity with a wide linear dynamic response range of four orders of magnitude and good selectivity. This biosensing strategy expands the applications of GO-DNA nanobiointerfaces in biological sensing, showing great potential in fundamental research and biomedical diagnosis.

  20. Measurement of oxidative DNA damage by gas chromatography-mass spectrometry: ethanethiol prevents artifactual generation of oxidized DNA bases.

    Science.gov (United States)

    Jenner, A; England, T G; Aruoma, O I; Halliwell, B

    1998-04-15

    Analysis of oxidative damage to DNA bases by GC-MS enables identification of a range of base oxidation products, but requires a derivatization procedure. However, derivatization at high temperature in the presence of air can cause 'artifactual' oxidation of some undamaged bases, leading to an overestimation of their oxidation products, including 8-hydroxyguanine. Therefore derivatization conditions that could minimize this problem were investigated. Decreasing derivatization temperature to 23 degrees C lowered levels of 8-hydroxyguanine, 8-hydroxyadenine, 5-hydroxycytosine and 5-(hydroxymethyl)uracil measured by GC-MS in hydrolysed calf thymus DNA. Addition of the reducing agent ethanethiol (5%, v/v) to DNA samples during trimethylsilylation at 90 degrees C also decreased levels of these four oxidized DNA bases as well as 5-hydroxyuracil. Removal of guanine from hydrolysed DNA samples by treatment with guanase, prior to derivatization, resulted in 8-hydroxyguanine levels (54-59 pmol/mg of DNA) that were significantly lower than samples not pretreated with guanase, independent of the derivatization conditions used. Only hydrolysed DNA samples that were derivatized at 23 degrees C in the presence of ethanethiol produced 8-hydroxyguanine levels (56+/-8 pmol/mg of DNA) that were as low as those of guanase-pretreated samples. Levels of other oxidized bases were similar to samples derivatized at 23 degrees C without ethanethiol, except for 5-hydroxycytosine and 5-hydroxyuracil, which were further decreased by ethanethiol. Levels of 8-hydroxyguanine, 8-hydroxyadenine and 5-hydroxycytosine measured in hydrolysed calf thymus DNA by the improved procedures described here were comparable with those reported previously by HPLC with electrochemical detection and by GC-MS with prepurification to remove undamaged base. We conclude that artifactual oxidation of DNA bases during derivatization can be prevented by decreasing the temperature to 23 degrees C, removing air from the

  1. DNA-based approaches to identify forest fungi in Pacific Islands: A pilot study

    Science.gov (United States)

    Anna E. Case; Sara M. Ashiglar; Phil G. Cannon; Ernesto P. Militante; Edwin R. Tadiosa; Mutya Quintos-Manalo; Nelson M. Pampolina; John W. Hanna; Fred E. Brooks; Amy L. Ross-Davis; Mee-Sook Kim; Ned B. Klopfenstein

    2013-01-01

    DNA-based diagnostics have been successfully used to characterize diverse forest fungi (e.g., Hoff et al. 2004, Kim et al. 2006, Glaeser & Lindner 2011). DNA sequencing of the internal transcribed spacer (ITS) and large subunit (LSU) regions of nuclear ribosomal DNA (rDNA) has proved especially useful (Sonnenberg et al. 2007, Seifert 2009, Schoch et al. 2012) for...

  2. Validation of 125I-hCG as a marker for elimination of hCG and stability of 125I-hCG after in vivo injection in humans

    DEFF Research Database (Denmark)

    Christensen, T B; Marqversen, J; Engbaek, F;

    1999-01-01

    We have recently introduced 125I-hCG as an elimination marker in patients with human chorionic gonadotrophin (hCG) producing testicular cancer. 125I-hCG is a well-known reagent in clinical biochemistry and is used extensively in hCG assays. Previous studies have shown that the iodination process...... leaves the hCG molecule mainly intact. The iodination, purification and stability of 125I-hCG tracer are described. The aim of the present study was to determine whether or not 125I is associated with hCG after the injection of 125I-hCG intravenously (i.v.) in humans. Three different methods were used....... Following injection of 125I-hCG, the plasma disappearance of radioactivity and hCG were followed for a period of 28 days in 13 normal subjects. Serum from a normal healthy male following injection of 125I-hCG was analysed using a double antibody direct binding radioimmunoassay specific for holo-hCG and high...

  3. Main features of DNA-based immunization vectors

    Directory of Open Access Journals (Sweden)

    V. Azevedo

    1999-02-01

    Full Text Available DNA-based immunization has initiated a new era of vaccine research. One of the main goals of gene vaccine development is the control of the levels of expression in vivo for efficient immunization. Modifying the vector to modulate expression or immunogenicity is of critical importance for the improvement of DNA vaccines. The most frequently used vectors for genetic immunization are plasmids. In this article, we review some of the main elements relevant to their design such as strong promoter/enhancer region, introns, genes encoding antigens of interest from the pathogen (how to choose and modify them, polyadenylation termination sequence, origin of replication for plasmid production in Escherichia coli, antibiotic resistance gene as selectable marker, convenient cloning sites, and the presence of immunostimulatory sequences (ISS that can be added to the plasmid to enhance adjuvanticity and to activate the immune system. In this review, the specific modifications that can increase overall expression as well as the potential of DNA-based vaccination are also discussed.

  4. DNA-based influenza vaccines as immunoprophylactic agents toward universality.

    Science.gov (United States)

    Zhang, Han; El Zowalaty, Mohamed E

    2016-01-01

    Influenza is an illness of global public health concern. Influenza viruses have been responsible for several pandemics affecting humans. Current influenza vaccines have proved satisfactory safety; however, they have limitations and do not provide protection against unexpected emerging influenza virus strains. Therefore, there is an urgent need for alternative approaches to conventional influenza vaccines. The development of universal influenza vaccines will help alleviate the severity of influenza pandemics. Influenza DNA vaccines have been the subject of many studies over the past decades due to their ability to induce broad-based protective immune responses in various animal models. The present review highlights the recent advances in influenza DNA vaccine research and its potential as an affordable universal influenza vaccine.

  5. Pulse radiolysis studies of electron migration in DNA from DNA base-radical anions to nitroacridine intercalators in aqueous solution

    Energy Technology Data Exchange (ETDEWEB)

    Anderson, R.F.; Patel, K.B. (Mount Vernon Hospital, Northwood (United Kingdom). Gray Lab.); Wilson, W.R. (Univ. of Auckland School of Medicine (New Zealand))

    1991-12-07

    The reactions of the aquated electron (e{sub aq}{sup -}) with intercalators of high reduction potential (nitracrine and related basic nitroacridines) has been investigated by pulse radiolysis in the presence of DNA in aqueous solution. Under conditions where the majority of the e{sub aq}{sup -} species react initially with DNA bases (high DNA:drug ratios) a slower subsequent electron transfer to the intercalator was observed. The rate of this intra-complex transfer, expressed as DNA base pairs traversed per second, was in the range (1.2-3.1) x 10{sup 5} base pairs s{sup -1} and increased in order of the one-electron reduction potentials of the DNA-bound intercalators. No transfer was seen to the much less electron affinic des-nitro analogue of the nitroacridines. Only a small proportion of the initial DNA base radicals ({<=}50%) underwent this intra-complex electron transfer. Even for the most efficient electron trap, nitracrine, the apparent mean electron migration distance was only three base pairs. A slow secondary reduction of nitroacridines ((0.08-5.0) x 10{sup 4} base pairs s{sup -1}) was also observed with a proportion of the essentially immobile {sup .}OH-induced DNA radicals. This secondary reaction may well serve as a measure of the mobility of the DNa-bound intercalators. This study therefore implies a lack of extensive migration of DNA-associated electrons in aqueous solution, although it does not exclude the possibility that more mobile electrons produced by direct ionization of DNA might migrate over large distances. (author).

  6. Direct visual detection of DNA based on the light scattering of silica nanoparticles on a human papillomavirus DNA chip.

    Science.gov (United States)

    Piao, Jing Yu; Park, Eun Hee; Choi, Kihwan; Quan, Bo; Kang, Dong Ho; Park, Pan Yun; Kim, Dai Sik; Chung, Doo Soo

    2009-12-15

    A detection system for a human papillomavirus (HPV) DNA chip based on the light scattering of aggregated silica nanoparticle probes is presented. In the assay, a target HPV DNA is sandwiched between the capture DNA immobilized on the chip and the probe DNA immobilized on the plain silica nanoparticle. The spot where the sandwich reaction occurs appears bright white and is readily distinguishable to the naked eye. Scanning electron microscopy images clearly show the aggregation of the silica nanoparticle probes. When three different sized (55 nm, 137 nm, 286 nm) plain silica nanoparticles were compared, probes of the larger silica nanoparticles showed a higher scattering intensity. Using 286-nm silica nanoparticles, the spots obtained with 200 pM of target DNA were visually detectable. The demonstrated capability to detect a disease related target DNA with direct visualization without using a complex detection instrument provides the prerequisite for the development of portable testing kits for genotyping.

  7. Effect of additional human chorionic gonadotrophin (hCG) on follicular growth and ovulation in gonadotrophin-treated gilts.

    Science.gov (United States)

    Manjarín, Rodrigo; Cassar, Glen; Friendship, Robert M; Garcia, José C; Dominguez, J Carlos; Kirkwood, Roy N

    2015-07-01

    The objective of this study was to determine the effect of additional human chorionic gonadotrophin (hCG) on the ovarian response of gilts previously treated with 200 IU hCG combined with 400 IU equine chorionic gonadotrophin (eCG) (eCG/hCG). Seventy-one prepuberal gilts (105 ± 7.5 kg) were assigned to groups: i) eCG/hCG (hCG-0; n = 25); ii) eCG/hCG followed by 100 IU of hCG at 24 h (hCG-100; n = 24); iii) eCG/hCG followed by 200 IU hCG at 24 h (hCG-200; n = 10); and iv) controls (CON; n = 12). Ovulation response was assessed by ovarian dissection or real-time ultrasonography. Additional hCG did not significantly improve numbers of gilts ovulating. Numbers of corpora lutea increased with hCG, and was higher in hCG-200 (P hCG-0, the frequency of cysts in gilts was higher in hCG-100 (P hCG-200 (P hCG. We conclude that supplemental hCG will increase the number of corpora lutea but will be associated with follicular cyst development in a dose dependent manner.

  8. Urinary hyperglycosylated hCG in first trimester screening for chromosomal abnormalities

    NARCIS (Netherlands)

    Butler, SA; Mantingh, A; Cole, LA

    2000-01-01

    Hyperglycosylated human chorionic gonadotrophin (H-hCG), also known as Invasive Trophoblast Antigen or ITA, is a unique metabolic variant of hCG with more complex oligosaccharide side chains. Concentrations are independent of regular hCG. Urine H-hCG has recently proved to be a highly sensitive mark

  9. Urinary hyperglycosylated hCG in first trimester screening for chromosomal abnormalities

    NARCIS (Netherlands)

    Butler, SA; Mantingh, A; Cole, LA

    2000-01-01

    Hyperglycosylated human chorionic gonadotrophin (H-hCG), also known as Invasive Trophoblast Antigen or ITA, is a unique metabolic variant of hCG with more complex oligosaccharide side chains. Concentrations are independent of regular hCG. Urine H-hCG has recently proved to be a highly sensitive mark

  10. Complete sequence analysis of 18S rDNA based on genomic DNA extraction from individual Demodex mites (Acari: Demodicidae).

    Science.gov (United States)

    Zhao, Ya-E; Xu, Ji-Ru; Hu, Li; Wu, Li-Ping; Wang, Zheng-Hang

    2012-05-01

    The study for the first time attempted to accomplish 18S ribosomal DNA (rDNA) complete sequence amplification and analysis for three Demodex species (Demodex folliculorum, Demodex brevis and Demodex canis) based on gDNA extraction from individual mites. The mites were treated by DNA Release Additive and Hot Start II DNA Polymerase so as to promote mite disruption and increase PCR specificity. Determination of D. folliculorum gDNA showed that the gDNA yield reached the highest at 1 mite, tending to descend with the increase of mite number. The individual mite gDNA was successfully used for 18S rDNA fragment (about 900 bp) amplification examination. The alignments of 18S rDNA complete sequences of individual mite samples and those of pooled mite samples ( ≥ 1000mites/sample) showed over 97% identities for each species, indicating that the gDNA extracted from a single individual mite was as satisfactory as that from pooled mites for PCR amplification. Further pairwise sequence analyses showed that average divergence, genetic distance, transition/transversion or phylogenetic tree could not effectively identify the three Demodex species, largely due to the differentiation in the D. canis isolates. It can be concluded that the individual Demodex mite gDNA can satisfy the molecular study of Demodex. 18S rDNA complete sequence is suitable for interfamily identification in Cheyletoidea, but whether it is suitable for intrafamily identification cannot be confirmed until the ascertainment of the types of Demodex mites parasitizing in dogs.

  11. Physics of base-pairing dynamics in DNA

    Science.gov (United States)

    Manghi, Manoel; Destainville, Nicolas

    2016-05-01

    As a key molecule of life, Deoxyribo-Nucleic Acid (DNA) is the focus of numbers of investigations with the help of biological, chemical and physical techniques. From a physical point of view, both experimental and theoretical works have brought quantitative insights into DNA base-pairing dynamics that we review in this Report, putting emphasis on theoretical developments. We discuss the dynamics at the base-pair scale and its pivotal coupling with the polymer one, with a polymerization index running from a few nucleotides to tens of kilo-bases. This includes opening and closure of short hairpins and oligomers as well as zipping and unwinding of long macromolecules. We review how different physical mechanisms are either used by Nature or utilized in biotechnological processes to separate the two intertwined DNA strands, by insisting on quantitative results. They go from thermally-assisted denaturation bubble nucleation to force- or torque-driven mechanisms. We show that the helical character of the molecule, possibly supercoiled, can play a key role in many denaturation and renaturation processes. We categorize the mechanisms according to the relative timescales associated with base-pairing and chain orientational degrees of freedom such as bending and torsional elastic ones. In some specific situations, these chain orientational degrees of freedom can be integrated out, and the quasi-static approximation is valid. The complex dynamics then reduces to the diffusion in a low-dimensional free-energy landscape. In contrast, some important cases of experimental interest necessarily appeal to far-from-equilibrium statistical mechanics and hydrodynamics.

  12. Applications of nanoparticles for DNA based rabies vaccine.

    Science.gov (United States)

    Shah, Muhammad Ali A; Khan, Sajid Umar; Ali, Zeeshan; Yang, Haowen; Liu, Keke; Mao, Lanlan

    2014-01-01

    Rabies is a fatal encephalomyelitis. Most cases occur in developing countries and are transmitted by dogs. The cell culture vaccines as associated with high cost; therefore, have not replaced the unsafe brain-derived vaccines. In the developing countries these brain-derived rabies vaccines still can be seen in action. Moreover, there will be a need for vaccines against rabies-related viruses against which classical vaccines are not always effective. The worldwide incidence of rabies and the inability of currently used vaccination strategies to provide highly potent and cost-effective therapy indicate the need for alternate control strategies. DNA vaccines have emerged as the safest vaccines and best remedy for complicated diseases like hepatitis, HIV, and rabies. A number of recombinant DNA vaccines are now being developed against several diseases such as AIDS and malaria. Therefore, it can be a valuable alternative for the production of cheaper rabies vaccines against its larger spectrum of viruses. In this review we report published data on DNA-based immunization with sequences encoding rabies with special reference to nanotechnology.

  13. Ultrathin oligonucleotide layers for fluorescence-based DNA sensors

    Science.gov (United States)

    Furch, M.; Ueberfeld, J.; Hartmann, Andreas; Bock, Daniel; Seeger, Stefan

    1996-11-01

    Preliminary investigations into the design of an affinity sensor using evanescent wave technology concentrate upon the means of immobilization of the receptor molecules. In this work DNA served as the selective recognition element. The molecular principle of a sequence-selective biosensor for DNA is based on a sandwich-hybridization assay wherein the analyte, a single-stranded (ss)DNA, bound specifically to both an immobilized capture probe and a dye-labeled oligonucleotide in free solution. The efficiency of the capture array depends on the density of highly organized oligonucleotides on the waveguide surface and correlates therefore directly with the specificity and the sensitivity of the sensor. In the present approach using the Langmuir- Blodgett technique cinnamoylbutylether-cellulose monolayers were transferred onto optical fibers or planar waveguides. These films served as matrices for the immobilization of biotinylated oligonucleotides via streptavidin. For the first time streptavidin was immobilized by that manner. The specificity of the streptavidin layer or the following bounded nucleic acid molecules were controlled by an enzyme- linked immunosorbent assay (ELISA). Finally, this application has also shown to be suitable for the detection of Salmonella, which is an important pathogen associated with acute gastroenteritidis and food borne diseases.

  14. Electrochemical DNA biosensor based on the BDD nanograss array electrode.

    Science.gov (United States)

    Jin, Huali; Wei, Min; Wang, Jinshui

    2013-04-10

    The development of DNA biosensor has attracted considerable attention due to their potential applications, including gene analysis, clinical diagnostics, forensic study and more medical applications. Using electroactive daunomycin as an indicator, the hybridization detection was measured by differential pulse voltammetry in this study. Electrochemical DNA biosensor was developed based on the BDD film electrode (fBDD) and BDD nanograss array electrode (nBDD). In comparison with fBDD and AuNPs/CA/fBDD electrode, the lower semicircle diameter of electrochemical impedance spectroscopy obtained on nBDD and AuNPs/CA/nBDD electrode indicated that the presence of nanograss array improved the reactive site, reduced the interfacial resistance, and made the electron transfer easier. Using electroactive daunomycin as an indicator, the hybridization detection was measured by differential pulse voltammetry. The experimental results demonstrated that the prepared AuNPs/CA/nBDD electrode was suitable for DNA hybridization with favorable performance of faster response, higher sensitivity, lower detection limit and satisfactory selectivity, reproducibility and stability.

  15. Extending the QUDA Library with the eigCG Solver

    Energy Technology Data Exchange (ETDEWEB)

    Strelchenko, Alexei [Fermilab; Stathopoulos, Andreas [William-Mary Coll.

    2014-12-12

    While the incremental eigCG algorithm [ 1 ] is included in many LQCD software packages, its realization on GPU micro-architectures was still missing. In this session we report our experi- ence of the eigCG implementation in the QUDA library. In particular, we will focus on how to employ the mixed precision technique to accelerate solutions of large sparse linear systems with multiple right-hand sides on GPUs. Although application of mixed precision techniques is a well-known optimization approach for linear solvers, its utilization for the eigenvector com- puting within eigCG requires special consideration. We will discuss implementation aspects of the mixed precision deflation and illustrate its numerical behavior on the example of the Wilson twisted mass fermion matrix inversions

  16. A High Excision Potential of TALENs for Integrated DNA of HIV-Based Lentiviral Vector

    OpenAIRE

    Hirotaka Ebina; Yuka Kanemura; Naoko Misawa; Tetsushi Sakuma; Tomoko Kobayashi; Takashi Yamamoto; Yoshio Koyanagi

    2015-01-01

    DNA-editing technology has made it possible to rewrite genetic information in living cells. Human immunodeficiency virus (HIV) provirus, an integrated form of viral complementary DNA in host chromosomes, could be a potential target for this technology. We recently reported that HIV proviral DNA could be excised from the chromosomal DNA of HIV-based lentiviral DNA-transduced T cells after multiple introductions of a clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 endonuc...

  17. Recognizing a Single Base in an Individual DNA Strand: A Step Toward Nanopore DNA Sequencing**

    Science.gov (United States)

    Ashkenasy, N.; Sánchez-Quesada, J.; Ghadiri, M. R.; Bayley, H.

    2007-01-01

    Functional supramolecular chemistry at the single-molecule level. Single strands of DNA can be captured inside α-hemolysin transmembrane pore protein to form single-species α-HL·DNA pseudorotaxanes. This process can be used to identify a single adenine nucleotide at a specific location on a strand of DNA by the characteristic reductions in the α-HL ion conductance. This study suggests that α-HL-mediated single-molecule DNA sequencing might be fundamentally feasible. PMID:15666419

  18. A New DNA-based Logical Gate Comes into Being

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    @@ Across-disciplinary research team, headed by Prof. FAN Chunhai from the CAS Shanghai Institute of Applied Physics, Prof. HE Lin, a CAS Member, and Prof. ZHANG Zhizhou at the Bio-X Research Center under Shanghai Jiao Tong University (SJTU), succeeded in developing a new type of logical gates by applying the deoxyribozyme (DNAzyme), adding a new brick to the groundwork of a DNA-based computation. The related research results have been reported on the German journal Angew. Chem. Int.Ed., 2006, 45, 1759.

  19. Biomaterial-based Memory Device Development by Conducting Metallic DNA

    Science.gov (United States)

    2013-05-28

    basis of the redshift of UV absorption spectra, we think that the incorporation of metal ions may result in a reduction of the original DNA band gap ...memristor based on the changing of the boundary between the high-resistance and low-resistance layers of titanium dioxide TiO2 and TiO2 -x13. Their...microscope (FESEM, JEOL JSM-6500F ) was used to measure the morphology of patterned substrate. The gap width and length between electrodes are both

  20. DNA-energetics-based analyses suggest additional genes in prokaryotes

    Indian Academy of Sciences (India)

    Garima Khandelwal; Jalaj Gupta; B Jayaram

    2012-07-01

    We present here a novel methodology for predicting new genes in prokaryotic genomes on the basis of inherent energetics of DNA. Regions of higher thermodynamic stability were identified, which were filtered based on already known annotations to yield a set of potentially new genes. These were then processed for their compatibility with the stereo-chemical properties of proteins and tripeptide frequencies of proteins in Swissprot data, which results in a reliable set of new genes in a genome. Quite surprisingly, the methodology identifies new genes even in well-annotated genomes. Also, the methodology can handle genomes of any GC-content, size and number of annotated genes.

  1. Phylogeny of Korean Opuntia spp. based on multiple DNA regions

    OpenAIRE

    SRIKANTH, KRISHNAMOORTHY; WHANG, SUNG SOO

    2015-01-01

    Although Opuntia species are of high agronomic value in Korea, the taxonomic position of Korean Opuntia species has never been investigated. The taxonomic position of Korean Opuntia spp. Within the tribe Opuntieae was examined based on DNA sequence analysis of matK, trnL-F, atpB-rbcl, and ITS regions. The total amplified sequence length was 2977 bp; only 18 parsimonious informative sites were present, even though they belonged to different species. A phylogenetic tree using both the maximum l...

  2. Tetrahedron-structured DNA and functional oligonucleotide for construction of an electrochemical DNA-based biosensor.

    Science.gov (United States)

    Bu, Nan-Nan; Tang, Chun-Xia; He, Xi-Wen; Yin, Xue-Bo

    2011-07-21

    Tetrahedron-structured DNA (ts-DNA) in combination with a functionalized oligonucleotide was used to develop a "turn-on" biosensor for Hg(2+) ions. The ts-DNA provided an improved sensitivity and was used to block the active sites.

  3. Benchmarking DNA Metabarcoding for Biodiversity-Based Monitoring and Assessment

    KAUST Repository

    Aylagas, Eva

    2016-06-10

    Characterization of biodiversity has been extensively used to confidently monitor and assess environmental status. Yet, visual morphology, traditionally and widely used for species identification in coastal and marine ecosystem communities, is tedious and entails limitations. Metabarcoding coupled with high-throughput sequencing (HTS) represents an alternative to rapidly, accurately, and cost-effectively analyze thousands of environmental samples simultaneously, and this method is increasingly used to characterize the metazoan taxonomic composition of a wide variety of environments. However, a comprehensive study benchmarking visual and metabarcoding-based taxonomic inferences that validates this technique for environmental monitoring is still lacking. Here, we compare taxonomic inferences of benthic macroinvertebrate samples of known taxonomic composition obtained using alternative metabarcoding protocols based on a combination of different DNA sources, barcodes of the mitochondrial cytochrome oxidase I gene and amplification conditions. Our results highlight the influence of the metabarcoding protocol in the obtained taxonomic composition and suggest the better performance of an alternative 313 bp length barcode to the traditionally 658 bp length one used for metazoan metabarcoding. Additionally, we show that a biotic index inferred from the list of macroinvertebrate taxa obtained using DNA-based taxonomic assignments is comparable to that inferred using morphological identification. Thus, our analyses prove metabarcoding valid for environmental status assessment and will contribute to accelerating the implementation of this technique to regular monitoring programs.

  4. Solution-based targeted genomic enrichment for precious DNA samples

    Directory of Open Access Journals (Sweden)

    Shearer Aiden

    2012-05-01

    Full Text Available Abstract Background Solution-based targeted genomic enrichment (TGE protocols permit selective sequencing of genomic regions of interest on a massively parallel scale. These protocols could be improved by: 1 modifying or eliminating time consuming steps; 2 increasing yield to reduce input DNA and excessive PCR cycling; and 3 enhancing reproducible. Results We developed a solution-based TGE method for downstream Illumina sequencing in a non-automated workflow, adding standard Illumina barcode indexes during the post-hybridization amplification to allow for sample pooling prior to sequencing. The method utilizes Agilent SureSelect baits, primers and hybridization reagents for the capture, off-the-shelf reagents for the library preparation steps, and adaptor oligonucleotides for Illumina paired-end sequencing purchased directly from an oligonucleotide manufacturing company. Conclusions This solution-based TGE method for Illumina sequencing is optimized for small- or medium-sized laboratories and addresses the weaknesses of standard protocols by reducing the amount of input DNA required, increasing capture yield, optimizing efficiency, and improving reproducibility.

  5. ProteDNA: a sequence-based predictor of sequence-specific DNA-binding residues in transcription factors.

    Science.gov (United States)

    Chu, Wen-Yi; Huang, Yu-Feng; Huang, Chun-Chin; Cheng, Yi-Sheng; Huang, Chien-Kang; Oyang, Yen-Jen

    2009-07-01

    This article presents the design of a sequence-based predictor named ProteDNA for identifying the sequence-specific binding residues in a transcription factor (TF). Concerning protein-DNA interactions, there are two types of binding mechanisms involved, namely sequence-specific binding and nonspecific binding. Sequence-specific bindings occur between protein sidechains and nucleotide bases and correspond to sequence-specific recognition of genes. Therefore, sequence-specific bindings are essential for correct gene regulation. In this respect, ProteDNA is distinctive since it has been designed to identify sequence-specific binding residues. In order to accommodate users with different application needs, ProteDNA has been designed to operate under two modes, namely, the high-precision mode and the balanced mode. According to the experiments reported in this article, under the high-precision mode, ProteDNA has been able to deliver precision of 82.3%, specificity of 99.3%, sensitivity of 49.8% and accuracy of 96.5%. Meanwhile, under the balanced mode, ProteDNA has been able to deliver precision of 60.8%, specificity of 97.6%, sensitivity of 60.7% and accuracy of 95.4%. ProteDNA is available at the following websites: http://protedna.csbb.ntu.edu.tw/, http://protedna.csie.ntu.edu.tw/, http://bio222.esoe.ntu.edu.tw/ProteDNA/.

  6. ProteDNA: a sequence-based predictor of sequence-specific DNA-binding residues in transcription factors

    OpenAIRE

    2009-01-01

    This article presents the design of a sequence-based predictor named ProteDNA for identifying the sequence-specific binding residues in a transcription factor (TF). Concerning protein–DNA interactions, there are two types of binding mechanisms involved, namely sequence-specific binding and nonspecific binding. Sequence-specific bindings occur between protein sidechains and nucleotide bases and correspond to sequence-specific recognition of genes. Therefore, sequence-specific bindings are esse...

  7. A kinetic and structural investigation of DNA-Based asymmetric catalysis using first-generation ligands

    NARCIS (Netherlands)

    Rosati, Fiora; Boersma, Arnold J.; Klijn, Jaap E.; Meetsma, Auke; Feringa, Ben L.; Roelfes, Gerard

    2009-01-01

    The recently developed concept of DNA-based asymmetric catalysis involves the transfer of chirality from the DNA double helix in reactions using a noncovalently bound catalyst. To date, two generations of DNA-based catalysts have been reported that differ in the design of the ligand for the metal. H

  8. [Analysis of the structure and expression of the cluster of Drosophila melanogaster genes DIP1, CG32500, CG32819, and CG14476 in the flamenco gene region].

    Science.gov (United States)

    Potapova, M V; Nefedova, L N; Kim, A I

    2009-10-01

    The flamenco gene controlling transpositions of the gypsy retrovirus is localized in the 20A1-3 region, in which eight open reading frames organized in a cluster were discovered: DIP1, three repeats of CG32500 and CG32819, and CG14476. Analysis of the genes composing the cluster indicates that their transcription in Drosophila melanogaster is a stage-specific process. Comparison of the expression of these genes in the strains OreR, SS, and MS having the flamenco phenotype and in the strain 413 having the flamenco+ phenotype revealed differences only for the DIP1 gene, transcription of this gene being altered only in the OreR strain. Thus, mutant flamenco alleles are differently expressed in different strains. The structural organization of the flamenco gene region was studied in different Drosophila species: D. sechellia, D. simulans, D. mauritiana, D. yakuba, D. erecta, D. virilis, D. ananassae, D. grimshawi, and D. pseudoobscura. The genes of the cluster were found to be highly conserved in genomes of different species, but in none of them, except D. sechellia, the structural organization of the region repeats the structure of the D. melanogaster cluster.

  9. Induction of ovulation in quarter horse mares through the use of deslorelin acetate and human chorionic gonadotrophin (hCG

    Directory of Open Access Journals (Sweden)

    Tatiana Figueiredo

    2011-06-01

    Full Text Available The aim this study was to compare two protocols of induction for ovulation by desloreline acetate and hCG in Quarter Horse mares. The choice of the animals was based on the observations by the estrus, by rectal palpation of the ovaries and by ultrassonography of the follicular dynamics. After estrus detection and follicle control, the measurement of the follicles and the classification of uterus were carried out. The animals that had dominant follicle (diameter more than 35 mm and swollen uterus were used. In these conditions, the mares received hCG or desloreline acetate. Once ovulation occurred, the artificial insemination was carried. Two groups were performed: G1 (20 animals received 1.5 mg desloreline acetate and G2 (20 animals received 1700 IU of hCG. Following 6h intervals, the control follicular was performed by ultrasonography. The follicular average diameter was 42.6 cm for the groups and set up a score of 0 to 3 of uterine edema displayed by the device as well as the time of ovulation. In conclusion, the desloreline acetate showed better performance than hCG, because the ovulation was induced in less time (nine hours than hCG (p<0.05.The pregnancy rate was 80 and 75 %, respectively in G1 and G2.

  10. CG13250, a novel bromodomain inhibitor, suppresses proliferation of multiple myeloma cells in an orthotopic mouse model.

    Science.gov (United States)

    Imayoshi, Natsuki; Yoshioka, Makoto; Chauhan, Jay; Nakata, Susumu; Toda, Yuki; Fletcher, Steven; Strovel, Jeffrey W; Takata, Kazuyuki; Ashihara, Eishi

    2017-03-04

    Multiple myeloma (MM) is characterized by the clonal proliferation of neoplastic plasma cells. Despite a stream of new molecular targets based on better understanding of the disease, MM remains incurable. Epigenomic abnormalities contribute to the pathogenesis of MM. bromodomain 4 (BRD4), a member of the bromodomain and extraterminal (BET) family, binds to acetylated histones during M/G1 transition in the cell cycle promoting progression to S phase. In this study, we investigated the effects of a novel BET inhibitor CG13250 on MM cells. CG13250 inhibited ligand binding to BRD4 in a dose-dependent manner and with an IC50 value of 1.1 μM. It inhibited MM proliferation in a dose-dependent manner and arrested cells in G1, resulting in the induction of apoptosis through caspase activation. CG13250 inhibited the binding of BRD4 to c-MYC promoter regions suppressing the transcription of the c-MYC gene. Administered in vivo, CG13250 significantly prolonged survival of an orthotopic MM-bearing mice. In conclusion, CG13250 is a novel bromodomain inhibitor that is a promising molecular targeting agent against MM.

  11. Overexpression of DNA ligase III in mitochondria protects cells against oxidative stress and improves mitochondrial DNA base excision repair

    DEFF Research Database (Denmark)

    Akbari, Mansour; Keijzers, Guido; Maynard, Scott

    2014-01-01

    slower than the preceding mitochondrial BER steps. Overexpression of DNA ligase III in mitochondria improved the rate of overall BER, increased cell survival after menadione induced oxidative stress and reduced autophagy following the inhibition of the mitochondrial electron transport chain complex I...... by rotenone. Our results suggest that the amount of DNA ligase III in mitochondria may be critical for cell survival following prolonged oxidative stress, and demonstrate a functional link between mitochondrial DNA damage and repair, cell survival upon oxidative stress, and removal of dysfunctional......Base excision repair (BER) is the most prominent DNA repair pathway in human mitochondria. BER also results in a temporary generation of AP-sites, single-strand breaks and nucleotide gaps. Thus, incomplete BER can result in the generation of DNA repair intermediates that can disrupt mitochondrial...

  12. Intelligent DNA-based molecular diagnostics using linked genetic markers

    Energy Technology Data Exchange (ETDEWEB)

    Pathak, D.K.; Perlin, M.W.; Hoffman, E.P.

    1994-12-31

    This paper describes a knowledge-based system for molecular diagnostics, and its application to fully automated diagnosis of X-linked genetic disorders. Molecular diagnostic information is used in clinical practice for determining genetic risks, such as carrier determination and prenatal diagnosis. Initially, blood samples are obtained from related individuals, and PCR amplification is performed. Linkage-based molecular diagnosis then entails three data analysis steps. First, for every individual, the alleles (i.e., DNA composition) are determined at specified chromosomal locations. Second, the flow of genetic material among the individuals is established. Third, the probability that a given individual is either a carrier of the disease or affected by the disease is determined. The current practice is to perform each of these three steps manually, which is costly, time consuming, labor-intensive, and error-prone. As such, the knowledge-intensive data analysis and interpretation supersede the actual experimentation effort as the major bottleneck in molecular diagnostics. By examining the human problem solving for the task, we have designed and implemented a prototype knowledge-based system capable of fully automating linkage-based molecular diagnostics in X-linked genetic disorders, including Duchenne Muscular Dystrophy (DMD). Our system uses knowledge-based interpretation of gel electrophoresis images to determine individual DNA marker labels, a constraint satisfaction search for consistent genetic flow among individuals, and a blackboard-style problem solver for risk assessment. We describe the system`s successful diagnosis of DMD carrier and affected individuals from raw clinical data.

  13. DNA microarray-based mutation discovery and genotyping.

    Science.gov (United States)

    Gresham, David

    2011-01-01

    DNA microarrays provide an efficient means of identifying single-nucleotide polymorphisms (SNPs) in DNA samples and characterizing their frequencies in individual and mixed samples. We have studied the parameters that determine the sensitivity of DNA probes to SNPs and found that the melting temperature (T (m)) of the probe is the primary determinant of probe sensitivity. An isothermal-melting temperature DNA microarray design, in which the T (m) of all probes is tightly distributed, can be implemented by varying the length of DNA probes within a single DNA microarray. I describe guidelines for designing isothermal-melting temperature DNA microarrays and protocols for labeling and hybridizing DNA samples to DNA microarrays for SNP discovery, genotyping, and quantitative determination of allele frequencies in mixed samples.

  14. Comparison of triple-risk assessment of fetal trisomy 21 including total human choriogonadotropin (hCG) or its free beta-subunit (free beta hCG).

    Science.gov (United States)

    Sancken, U; Bahner, D

    2003-01-01

    Second trimester total hCG and free betahCG levels in maternal serum samples of 33 pregnancies affected by fetal trisomy 21 and of 188 matched controls were compared in a retrospective study. To find out differences of discriminating efficacy by using one of these markers a multivariate discriminant analysis was performed. Statistical evaluation was performed for hCG/free betahCG frequency distributions. Discriminant analysis was carried out using the status 'affected' or 'unaffected' as the group variable and the serum markers unconjugated estriol (uE3), alpha-fetoprotein (AFP), and alternatively, hCG or free betahCG, as discriminant variables. The median of free betahCG MoM values in affected pregnancies was slightly higher (1.90 MoM) than the median of total hCG MoM values (1.72 MoM) but a lower standard deviation was stated for the logarithmic hCG MoM values (SD = 0.49) compared with free betahCG MoM values (SD = 0.51). A two-tailed Student's t test revealed no significant differences of hCG and free betahCG MoM values in both the affected and unaffected pregnancies. By inclusion of free betahCG the discriminant analysis classified 26 out of 33 affected cases correctly and 45 out of 188 unaffected cases incorrectly. For the inclusion of hCG these ratios were 25/33 and 41/188, respectively. Taking in account the individual maternal age risks at a defined false-positive rate of 5% including free betahCG yielded a higher detection rate than including hCG. However, using 1:380 (age-related at-term risk of a 35-year-old woman) as a cut-off risk including hCG yielded a higher detection rate than including free betahCG. For the observed cases none of the markers, hCG or free betahCG, was superior in Down syndrome screening. Copyright 2003 S. Karger AG, Basel

  15. Overexpression of DNA ligase III in mitochondria protects cells against oxidative stress and improves mitochondrial DNA base excision repair.

    Science.gov (United States)

    Akbari, Mansour; Keijzers, Guido; Maynard, Scott; Scheibye-Knudsen, Morten; Desler, Claus; Hickson, Ian D; Bohr, Vilhelm A

    2014-04-01

    Base excision repair (BER) is the most prominent DNA repair pathway in human mitochondria. BER also results in a temporary generation of AP-sites, single-strand breaks and nucleotide gaps. Thus, incomplete BER can result in the generation of DNA repair intermediates that can disrupt mitochondrial DNA replication and transcription and generate mutations. We carried out BER analysis in highly purified mitochondrial extracts from human cell lines U2OS and HeLa, and mouse brain using a circular DNA substrate containing a lesion at a specific position. We found that DNA ligation is significantly slower than the preceding mitochondrial BER steps. Overexpression of DNA ligase III in mitochondria improved the rate of overall BER, increased cell survival after menadione induced oxidative stress and reduced autophagy following the inhibition of the mitochondrial electron transport chain complex I by rotenone. Our results suggest that the amount of DNA ligase III in mitochondria may be critical for cell survival following prolonged oxidative stress, and demonstrate a functional link between mitochondrial DNA damage and repair, cell survival upon oxidative stress, and removal of dysfunctional mitochondria by autophagy.

  16. Magnetic particle-based sandwich sensor with DNA-modified carbon nanotubes as recognition elements for detection of DNA hybridization.

    Science.gov (United States)

    Hu, Po; Huang, Cheng Zhi; Li, Yuan Fang; Ling, Jian; Liu, Yu Ling; Fei, Liang Run; Xie, Jian Ping

    2008-03-01

    In this contribution, we design a visual sensor for DNA hybridization with DNA probe-modified magnetic particles (MPs) and multiwalled carbon nanotubes (MWNTs) without involving a visual recognition element such as fluorescent/chemiluminescent reagents. It was found that DNA probe-modified MWNTs, which could be dispersed in aqueous medium and have strong light scattering signals under the excitation of a light beam in the UV-vis region, could connect with DNA probe-modified MPs together in the presence of perfectly complementary target DNA and form a sandwich structure. In a magnetic field, the formed MP-MWNT species can easily be removed from the solution, resulting in a decrease of light scattering signals. Thus, a magnetic particle-based sandwich sensor could be developed to detect DNA hybridization by measuring the light scattering signals with DNA-modified MWNTs as recognition elements. Experiments showed that the DNA-modified MPs sensor could be reused at least 17 times and was stable for more than 6 months.

  17. Serum hCG-β levels of postovulatory day 12 and 14 with the sequential application of hCG-β fold change significantly increased predictability of pregnancy outcome after IVF-ET cycle.

    Science.gov (United States)

    Sung, Nayoung; Kwak-Kim, Joanne; Koo, H S; Yang, K M

    2016-09-01

    To investigate hCG-β level on postovulatory day (POD) 12 and its fold increase as predictors for pregnancy outcome after in vitro fertilization (IVF) cycles. A retrospective cohort study was performed in total 1408 fresh and 598 frozen cycles between November 2008 and October 2011, which resulted in biochemical pregnancy, early pregnancy loss, or live birth of singleton pregnancy. The serum hCG-β levels of POD 12 and 14 were compared among biochemical pregnancy, early pregnancy loss, and live birth groups. The cutoff values of POD 12 and 14 hCG-β levels and the degree of hCG-β increase from POD 12 to 14 were determined for each pregnancy outcome. POD 12 and 14 hCG-β levels stratified based on pregnancy outcomes were significantly different among the biochemical pregnancy, early pregnancy loss, and live birth in both fresh and frozen cycles. Serum hCG-β levels of POD 12 and 14 and the fold increase of hCG-β levels from POD 12 to 14 significantly predict pregnancy outcomes after fresh and frozen cycles. Among these, the cutoff value of POD 14 hCG-β had the highest sensitivity and positive predictive value (PPV). In fresh cycles, the cutoff values of POD 12 and 14 serum hCG-β levels for clinical pregnancies were 30.2 mIU/mL (sensitivity 81.3 %, specificity 79.6 %, and PPV 92.3 %) and 70.5 mIU/mL (sensitivity 88.4 %, specificity 85.2 %, and PPV 94.7 %). In pregnancies with POD 12 serum hCG-β levels ≥30.2 mIU/mL, the cutoff level of increase of hCG-β for clinical pregnancy was 2.56 (sensitivity 73.6 %, specificity 72.4 %, and PPV 97.8 %). Sequential application of cutoff values such as POD 12 hCG-β and fold increase of hCG-β improved predictability of pregnancy outcome as compared with that of POD 12 hCG-β alone. The cutoff values of POD 12 and 14 serum hCG-β levels for live birth were 40.5 mIU/mL (sensitivity 75.2 %, specificity 72.6 %, PPV 78.9 %) and 104.5 mIU/mL (sensitivity 80.3 %, specificity 74.1 %, PPV 80.8 %). In the frozen

  18. Ultrafast dynamics in DNA base pairs following ultraviolet excitation.

    Science.gov (United States)

    Orr-Ewing, Andrew

    2015-03-01

    Photo-protective mechanisms in DNA are essential to maintain the integrity of the genetic code by preventing damage from absorption of solar ultraviolet (UV) radiation. We have used time-resolved infra-red (TRIR) spectroscopy to observe the dynamics of Watson-Crick nucleobase pairs following absorption of femtosecond UV laser pulses. The base pairs are prepared as nucleosides in solution, and photo-induced dynamics are probed in the carbonyl and N-H bond stretching regions using broadband IR pulses with picosecond time resolution. Results will be presented for the guanine-cytosine (G-C) base pair, contrasting the rapid recovery of ground-state products (the photo-protection pathway) with formation of other photoproducts which might represent photo-damage mechanisms. This work is a collaboration with the group of Prof F. Temps (Christian-Albrechts-Universitat zu Kiel). This research is supported by ERC Advanced Grant 290966 CAPRI.

  19. DNA-based programing of quantum dot properties.

    Science.gov (United States)

    Ma, Nan; Kelley, Shana O

    2013-01-01

    Nucleic acid molecules can serve as robust ligands for aqueous synthesis of semiconductor nanocrystals or quantum dots (QDs). QD properties including size, morphology, dispersity, emission maximum, and quantum yield are highly dependent on the sequences and structures of nucleic acids used for the synthesis. This synthetic strategy provides a novel facile means of constructing compact, stable, and biofunctionalized QDs in one step, which is of particular interest for a variety of applications such as biosensing, bioimaging, and self-assembly. This article summarizes recent advances in nucleic acid-templated QD synthesis with an emphasis on the nucleic acids-based programing of quantum dots properties. A variety of applications based on DNA-passivated QDs are also discussed. Copyright © 2012 Wiley Periodicals, Inc.

  20. DNA

    Science.gov (United States)

    Stent, Gunther S.

    1970-01-01

    This history for molecular genetics and its explanation of DNA begins with an analysis of the Golden Jubilee essay papers, 1955. The paper ends stating that the higher nervous system is the one major frontier of biological inquiry which still offers some romance of research. (Author/VW)

  1. Correlation between pre-miR-146a C/G polymorphism and gastric cancer risk in Chinese population

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    AIM:To investigate the association between pre-miR- 146a C/G polymorphism and gastric cancer risk. METHODS:We performed a hospital-based,case-control study using polymerase chain reaction-restriction fragment length polymorphism method in 608 individuals(304 gastric cancer patients and 304 age and sex matched cancer-free controls).RESULTS:The frequencies of pre-miR-146a C/G genotypes in the case group were significantly different from those in the control groups(P=0.037).Compared with CC genotype carriers,s...

  2. Recognizing a Single Base in an Individual DNA Strand: A Step Toward Nanopore DNA Sequencing**

    OpenAIRE

    Ashkenasy, N.; Sánchez-Quesada, J.; Ghadiri, M. R.; Bayley, H

    2005-01-01

    Functional supramolecular chemistry at the single-molecule level. Single strands of DNA can be captured inside α-hemolysin transmembrane pore protein to form single-species α-HL·DNA pseudorotaxanes. This process can be used to identify a single adenine nucleotide at a specific location on a strand of DNA by the characteristic reductions in the α-HL ion conductance. This study sug...

  3. DNA barcoding: error rates based on comprehensive sampling.

    Directory of Open Access Journals (Sweden)

    Christopher P Meyer

    2005-12-01

    Full Text Available DNA barcoding has attracted attention with promises to aid in species identification and discovery; however, few well-sampled datasets are available to test its performance. We provide the first examination of barcoding performance in a comprehensively sampled, diverse group (cypraeid marine gastropods, or cowries. We utilize previous methods for testing performance and employ a novel phylogenetic approach to calculate intraspecific variation and interspecific divergence. Error rates are estimated for (1 identifying samples against a well-characterized phylogeny, and (2 assisting in species discovery for partially known groups. We find that the lowest overall error for species identification is 4%. In contrast, barcoding performs poorly in incompletely sampled groups. Here, species delineation relies on the use of thresholds, set to differentiate between intraspecific variation and interspecific divergence. Whereas proponents envision a "barcoding gap" between the two, we find substantial overlap, leading to minimal error rates of approximately 17% in cowries. Moreover, error rates double if only traditionally recognized species are analyzed. Thus, DNA barcoding holds promise for identification in taxonomically well-understood and thoroughly sampled clades. However, the use of thresholds does not bode well for delineating closely related species in taxonomically understudied groups. The promise of barcoding will be realized only if based on solid taxonomic foundations.

  4. DNA surveillance: web-based molecular identification of whales, dolphins, and porpoises.

    Science.gov (United States)

    Ross, H A; Lento, G M; Dalebout, M L; Goode, M; Ewing, G; McLaren, P; Rodrigo, A G; Lavery, S; Baker, C S

    2003-01-01

    DNA Surveillance is a Web-based application that assists in the identification of the species and population of unknown specimens by aligning user-submitted DNA sequences with a validated and curated data set of reference sequences. Phylogenetic analyses are performed and results are returned in tree and table format summarizing the evolutionary distances between the query and reference sequences. DNA Surveillance is implemented with mitochondrial DNA (mtDNA) control region sequences representing the majority of recognized cetacean species. Extensions of the system to include other gene loci and taxa are planned. The service, including instructions and sample data, is available at http://www.dna-surveillance.auckland.ac.nz.

  5. Quality Control of Isothermal Amplified DNA Based on Short Tandem Repeat Analysis.

    Science.gov (United States)

    Kroneis, Thomas; El-Heliebi, Amin

    2015-01-01

    This protocol describes the use of a 16plex PCR for the purpose assessing DNA quality after isothermal whole genome amplification (WGA). In short, DNA products, generated by amplification multiple displacement amplification, are forwarded to PCR targeting 15 short tandem repeats (STR) as well as amelogenin generating up to 32 different PCR products. After amplification, the PCR products are separated via capillary electrophoresis and analyzed based on the obtained DNA profiles. Isothermal WGA products of good DNA quality will result in DNA profiles with efficiencies of >90 % of the full DNA profile.

  6. Roles of the Amino Group of Purine Bases in the Thermodynamic Stability of DNA Base Pairing

    Directory of Open Access Journals (Sweden)

    Shu-ichi Nakano

    2014-08-01

    Full Text Available The energetic aspects of hydrogen-bonded base-pair interactions are important for the design of functional nucleotide analogs and for practical applications of oligonucleotides. The present study investigated the contribution of the 2-amino group of DNA purine bases to the thermodynamic stability of oligonucleotide duplexes under different salt and solvent conditions, using 2'-deoxyriboinosine (I and 2'-deoxyribo-2,6-diaminopurine (D as non-canonical nucleotides. The stability of DNA duplexes was changed by substitution of a single base pair in the following order: G•C > D•T ≈ I•C > A•T > G•T > I•T. The apparent stabilization energy due to the presence of the 2-amino group of G and D varied depending on the salt concentration, and decreased in the water-ethanol mixed solvent. The effects of salt concentration on the thermodynamics of DNA duplexes were found to be partially sequence-dependent, and the 2-amino group of the purine bases might have an influence on the binding of ions to DNA through the formation of a stable base-paired structure. Our results also showed that physiological salt conditions were energetically favorable for complementary base recognition, and conversely, low salt concentration media and ethanol-containing solvents were effective for low stringency oligonucleotide hybridization, in the context of conditions employed in this study.

  7. Kathon CG y Dermatología Laboral: Actualización Kathon CG and Occupational Dermatology: An update

    Directory of Open Access Journals (Sweden)

    Ana Rita Rodrigues Barata

    2012-09-01

    Full Text Available El Kathon CG constituye el nombre comercial de una mezcla de isotiazolinas: Metilcloroisotiazolinona y Metilisotiazolinona. Es un conservante muy utilizado, sobre todo en la industria cosmética, aunque en los últimos años también se ha impuesto su presencia en productos de limpieza de uso doméstico y actualmente a concentraciones más altas en preparados de uso industrial como aceites de corte, emulsiones de látex, pinturas al temple, aceites para motores Diesel, etc. Por su alto poder sensibilizante y amplia utilización, constituye actualmente una de las causas más frecuentes de alergia de contacto por preservativos, tanto en nuestra vida privada, como en el ámbito profesional. Objetivos: Estudiar la capacidad sensibilizante del Kathon CG y su relación con el desarrollo de eczema de contacto alérgico de origen profesional. Métodos: Estudio observacional descriptivo, a través de la revisión de las historias clínicas de los pacientes vistos en el Servicio de Dermatología Laboral del Instituto Nacional de Medicina y Seguridad en el Trabajo durante los años 2008-2012; 1520 pacientes fueron evaluados y estudiados mediante pruebas epicutáneas para descartar una posible dermatosis profesional. Se registraron los casos de sensibilización al Kathon CG y se analizaron las siguientes variables: genero, edad, grupo profesional, localización de las lesiones cutáneas, relevancia y relación profesional. El análisis estadístico se realizó con el programa SPSS 15.0. Resultados: Se observó sensibilización al Kathon CG en 88 pacientes (5,8%, correspondiendo un 42% a sensibilizaciones de origen profesional. Conclusiones: La alergia de contacto profesional por Kathon CG constituye actualmente es un problema de alta prevalencia. Ante un paciente con positividad a este alérgeno hay que interrogar siempre por su profesión.Kathon CG is the tradename for a mixture of isothiazolines: methylchloroisothiazolinone and methylisothiazolinone. It

  8. Development of a lipase-based optical assay for detection of DNA

    DEFF Research Database (Denmark)

    Pinijsuwan, Suttiporn; Shipovskov, Stepan; Surareungchai, Werasak

    2011-01-01

    A lipase-based assay for detection of specific DNA sequences has been developed. Lipase from Candida antarctica was conjugated to DNA and captured on magnetic beads in a sandwich assay, in which the binding was dependent on the presence of a specific target DNA. For amplification and to generate...

  9. Pros and cons of methylation-based enrichment methods for ancient DNA

    DEFF Research Database (Denmark)

    Seguin-Orlando, Andaine; Gamba, Cristina; Der Sarkissian, Clio

    2015-01-01

    The recent discovery that DNA methylation survives in fossil material provides an opportunity for novel molecular approaches in palaeogenomics. Here, we apply to ancient DNA extracts the probe-independent Methylated Binding Domains (MBD)-based enrichment method, which targets DNA molecules contai...

  10. Phylogeny of Pelargonium (Geraniaceae) based on DNA sequences from three genomes

    NARCIS (Netherlands)

    Bakker, F.T.; Culham, A.; Hettiarachi, P.; Touloumendidou, T.; Gibby, M.

    2004-01-01

    Phylogenetic hypotheses for the largely South African genus Pelargonium L'Hér. (Geraniaceae) were derived based on DNA sequence data from nuclear, chloroplast and mitochondrial encoded regions. The datasets were unequally represented and comprised cpDNA trnL-F sequences for 152 taxa, nrDNA ITS seque

  11. PCR-based detection of a rare linear DNA in cell culture

    Directory of Open Access Journals (Sweden)

    Saveliev Sergei V.

    2002-01-01

    Full Text Available The described method allows for detection of rare linear DNA fragments generated during genomic deletions. The predicted limit of the detection is one DNA molecule per 107 or more cells. The method is based on anchor PCR and involves gel separation of the linear DNA fragment and chromosomal DNA before amplification. The detailed chemical structure of the ends of the linear DNA can be defined with the use of additional PCR-based protocols. The method was applied to study the short-lived linear DNA generated during programmed genomic deletions in a ciliate. It can be useful in studies of spontaneous DNA deletions in cell culture or for tracking intracellular modifications at the ends of transfected DNA during gene therapy trials.

  12. Conservation and divergence of DNA methylation in eukaryotes: new insights from single base-resolution DNA methylomes.

    Science.gov (United States)

    Su, Zhixi; Han, Leng; Zhao, Zhongming

    2011-02-01

    DNA methylation is one of the most important heritable epigenetic modifications of the genome and is involved in the regulation of many cellular processes. Aberrant DNA methylation has been frequently reported to influence gene expression and subsequently cause various human diseases, including cancer. Recent rapid advances in next-generation sequencing technologies have enabled investigators to profile genome methylation patterns at single-base resolution. Remarkably, more than 20 eukaryotic methylomes have been generated thus far, with a majority published since November 2009. Analysis of this vast amount of data has dramatically enriched our knowledge of biological function, conservation and divergence of DNA methylation in eukaryotes. Even so, many specific functions of DNA methylation and their underlying regulatory systems still remain unknown to us. Here, we briefly introduce current approaches for DNA methylation profiling and then systematically review the features of whole genome DNA methylation patterns in eight animals, six plants and five fungi. Our systematic comparison provides new insights into the conservation and divergence of DNA methylation in eukaryotes and their regulation of gene expression. This work aims to summarize the current state of available methylome data and features informatively.

  13. Characterisation and genetic polymorphism of metallothionein gene CgMT4 in experimental families of Pacific oyster Crassostrea gigas displaying summer mortality.

    Science.gov (United States)

    David, Elise; Tanguy, Arnaud; Moraga, Dario

    2012-02-01

    Summer mortality events have been observed in Pacific oyster Crassostrea gigas for several decades. This paper examines the selective pressure exerted by summer mortality on the polymorphism of a newly identified oyster metallothionein gene. CgMT4 cDNA and genomic sequences were obtained. CgMT4 was studied in two generations of oysters reared in three sites on the French Atlantic coast, using single strand conformation polymorphism analysis. Four alleles were detected. Individuals carrying genotype MT4-CD seem to have higher susceptibility to summer risk conditions. The MT4 gene could be a potential new genetic marker for susceptibility; further validation studies are recommended.

  14. The Role of Serum Beta hCG in Early Diagnosis and Management Strategy of Ectopic Pregnancy.

    Science.gov (United States)

    Surampudi, Kameswari; Gundabattula, Sirisha Rao

    2016-07-01

    The presentation of Ectopic Pregnancy (EP) can be highly variable and serum Beta hCG estimation plays an important role in early diagnosis. Aim of the study was to determine the trends of hCG levels in EP and to explore the role of hCG in decisions related to management and follow-up of EPs. A retrospective study of women who had EPs from January 2006 to December 2012 at an advanced tertiary care centre in southern India was carried out. These women had undergone treatment based on the hospital protocol. The study identified 337 women with EP. Thirty one surgically confirmed cases were diagnosed below the discriminatory zone of 1500 mIU/ml. Among women who had Beta hCG estimations 48 hours apart, plateauing was observed in 22.5% while decrease >15% was noted in 26.8%. Almost half (47.9%) of the cases had an increase >15% and a few (2.8%) demonstrated an initial fall followed by a rise in titres. In 23.9% of these women, there was a rise >53% similar to intrauterine pregnancy. The average pre-treatment Beta hCG was 429.8, 3866.2 and 12961.5 mIU/ml for those who received expectant, medical and direct surgical treatment respectively. 43 women with relative contraindications received medical management and 39 were lost to follow-up after medical and expectant management. Excluding them, the success rate of these two modalities was 76.6% and 85.0% respectively. No single level of Beta hCG is diagnostic of EP and serial levels can demonstrate atypical trends in some cases. Hence, interpretation of these results should be done in conjunction with clinical and sonographic findings to arrive at a correct diagnosis.

  15. Rhipicephalus (Boophilus microplus: expression and characterization of Bm86-CG in Pichia pastoris Rhipicephalus (Boophilus microplus: expressão e caracterização da Bm86-CG em Pichia pastoris

    Directory of Open Access Journals (Sweden)

    Rodrigo Casquero Cunha

    2011-06-01

    Full Text Available The cattle tick Rhipicephalus (Boophilus microplus is responsible for great economic losses. It is mainly controlled chemically, with limitations regarding development of resistance to the chemicals. Vaccines may help control this parasite, thereby reducing tick pesticide use. In this light, we performed subcloning of the gene of the protein Bm86-GC, the homologue protein that currently forms the basis of vaccines (GavacTM and TickGardPLUS that have been developed against cattle ticks. The subcloning was done in the pPIC9 expression vector, for transformation in the yeast Pichia pastoris. This protein was characterized by expression of the recombinant Mut+ strain, which expressed greater quantities of protein. The expressed protein (rBm86-CG was recognized in the Western-blot assay using anti-Gavac, anti-TickGard, anti-larval extract and anti-rBm86-CG polyclonal sera. The serum produced in cattle vaccinated with the antigen CG rBm86 presented high antibody titers and recognized the native protein. The rBm86-GC has potential relevance as an immunogen for vaccine formulation against cattle ticks.O carrapato-do-boi Rhipicephalus (Boophilus microplus é responsável por grandes perdas econômicas. Seu controle é principalmente químico e apresenta limitações quanto ao desenvolvimento de resistência aos princípios ativos. As vacinas podem auxiliar no controle deste parasita diminuindo as aplicações de carrapaticidas. Considerando isso, foi realizada a subclonagem do gene da proteína Bm86-CG, proteína homologa a que atualmente é a base das vacinas desenvolvidas (GavacTM e TickGardPLUS contra o carrapato-do-boi, no vetor de expressão pPIC9, para ser transformado em levedura, Pichia pastoris. Esta proteína foi caracterizada pela expressão da cepa recombinante Mut+ que expressou maior quantidade de proteína. A proteína expressa, rBm86-CG, foi reconhecida no ensaio de Western-blot pelos soros policlonais anti-Gavac, anti-TickGard, anti

  16. A base-excision DNA-repair protein finds intrahelical lesion bases by fast sliding in contact with DNA

    NARCIS (Netherlands)

    Blainey, Paul C.; Oijen, Antoine M. van; Banerjee, Anirban; Verdine, Gregory L.; Xie, X. Sunney; Hippel, Peter H. von

    2006-01-01

    A central mystery in the function of site-specific DNA-binding proteins is the detailed mechanism for rapid location and binding of target sites in DNA. Human oxoguanine DNA glycosylase 1 (hOgg1), for example, must search out rare 8-oxoguanine lesions to prevent transversion mutations arising from o

  17. Direct electrochemical detection of PCR product based on charge transfer through DNA

    Institute of Scientific and Technical Information of China (English)

    ZHAO Hongtao; ZHANG Zhijie; JU Huangxian

    2005-01-01

    @@ Human genome project and genetic identification for inherited diseases will definitely have a profound impact on the diagnosis of diseases[1], which calls for rapid and accurate assays of DNA. Among different types of sensors, electrochemical DNA biosensors offer a promising alternative means[2,3]. Recent efforts to elucidate the mechanism of charge transfer in DNA have demonstrated that the charge transfer is sensitive to the perturbation in base stack[4,5]. Long-range charge transfer in DNA therefore has been showing great potential application in the development of DNA-based biosensors, especially in the study of single nucleotide polymorphs[7―10].

  18. Bypass of a 5',8-cyclopurine-2'-deoxynucleoside by DNA polymerase β during DNA replication and base excision repair leads to nucleotide misinsertions and DNA strand breaks.

    Science.gov (United States)

    Jiang, Zhongliang; Xu, Meng; Lai, Yanhao; Laverde, Eduardo E; Terzidis, Michael A; Masi, Annalisa; Chatgilialoglu, Chryssostomos; Liu, Yuan

    2015-09-01

    5',8-Cyclopurine-2'-deoxynucleosides including 5',8-cyclo-dA (cdA) and 5',8-cyclo-dG (cdG) are induced by hydroxyl radicals resulting from oxidative stress such as ionizing radiation. 5',8-cyclopurine-2'-deoxynucleoside lesions are repaired by nucleotide excision repair with low efficiency, thereby leading to their accumulation in the human genome and lesion bypass by DNA polymerases during DNA replication and base excision repair (BER). In this study, for the first time, we discovered that DNA polymerase β (pol β) efficiently bypassed a 5'R-cdA, but inefficiently bypassed a 5'S-cdA during DNA replication and BER. We found that cell extracts from pol β wild-type mouse embryonic fibroblasts exhibited significant DNA synthesis activity in bypassing a cdA lesion located in replication and BER intermediates. However, pol β knock-out cell extracts exhibited little DNA synthesis to bypass the lesion. This indicates that pol β plays an important role in bypassing a cdA lesion during DNA replication and BER. Furthermore, we demonstrated that pol β inserted both a correct and incorrect nucleotide to bypass a cdA at a low concentration. Nucleotide misinsertion was significantly stimulated by a high concentration of pol β, indicating a mutagenic effect induced by pol β lesion bypass synthesis of a 5',8-cyclopurine-2'-deoxynucleoside. Moreover, we found that bypass of a 5'S-cdA by pol β generated an intermediate that failed to be extended by pol β, resulting in accumulation of single-strand DNA breaks. Our study provides the first evidence that pol β plays an important role in bypassing a 5',8-cyclo-dA during DNA replication and repair, as well as new insight into mutagenic effects and genome instability resulting from pol β bypassing of a cdA lesion.

  19. DNA-COMPACT: DNA COMpression based on a pattern-aware contextual modeling technique.

    Directory of Open Access Journals (Sweden)

    Pinghao Li

    Full Text Available Genome data are becoming increasingly important for modern medicine. As the rate of increase in DNA sequencing outstrips the rate of increase in disk storage capacity, the storage and data transferring of large genome data are becoming important concerns for biomedical researchers. We propose a two-pass lossless genome compression algorithm, which highlights the synthesis of complementary contextual models, to improve the compression performance. The proposed framework could handle genome compression with and without reference sequences, and demonstrated performance advantages over best existing algorithms. The method for reference-free compression led to bit rates of 1.720 and 1.838 bits per base for bacteria and yeast, which were approximately 3.7% and 2.6% better than the state-of-the-art algorithms. Regarding performance with reference, we tested on the first Korean personal genome sequence data set, and our proposed method demonstrated a 189-fold compression rate, reducing the raw file size from 2986.8 MB to 15.8 MB at a comparable decompression cost with existing algorithms. DNAcompact is freely available at https://sourceforge.net/projects/dnacompact/for research purpose.

  20. Sequential addition of short DNA oligos in DNA-polymerase-based synthesis reactions

    Science.gov (United States)

    Gardner, Shea N.; Mariella, Jr., Raymond P.; Christian, Allen T.; Young, Jennifer A.; Clague, David S.

    2011-01-18

    A method of fabricating a DNA molecule of user-defined sequence. The method comprises the steps of preselecting a multiplicity of DNA sequence segments that will comprise the DNA molecule of user-defined sequence, separating the DNA sequence segments temporally, and combining the multiplicity of DNA sequence segments with at least one polymerase enzyme wherein the multiplicity of DNA sequence segments join to produce the DNA molecule of user-defined sequence. Sequence segments may be of length n, where n is an even or odd integer. In one embodiment the length of desired hybridizing overlap is specified by the user and the sequences and the protocol for combining them are guided by computational (bioinformatics) predictions. In one embodiment sequence segments are combined from multiple reading frames to span the same region of a sequence, so that multiple desired hybridizations may occur with different overlap lengths. In one embodiment starting sequence fragments are of different lengths, n, n+1, n+2, etc.

  1. hCG in screening for aneuploidy: a possible role for its glycoforms?

    Science.gov (United States)

    Brun, S; Leguy, M C; Bruneel, A; Fournier, T; Anselem, O; Guibourdenche, J

    2014-06-01

    Fetal trisomy 21 is associated with elevated maternal serum hCG and its free beta-subunit (hCG-beta) in vivo, and abnormal placental hCG production and glycosylation in vitro. Other maternal serum markers may also be disrupted in major aneuploidies (T21, T18, T13). We evaluated our aneuploidy screening practices, focusing on hCG-beta and hCG glycoforms, and retrospectively analyzed 55 aneuploidy cases diagnosed over a 2 year period, determining maternal serum hCG glycoforms profiles using 2D-electrophoresis. Screening efficiency reached 96.7%. T21 was associated with elevated hCG-beta while T18 presented with diminished serum markers. hCG glycoforms tended to be basic in aneuploidy (mainly T13). Copyright © 2014 Elsevier Ltd. All rights reserved.

  2. Polymorphism of the DNA Base Excision Repair Genes in Keratoconus

    Directory of Open Access Journals (Sweden)

    Katarzyna A. Wojcik

    2014-10-01

    Full Text Available Keratoconus (KC is a degenerative corneal disorder for which the exact pathogenesis is not yet known. Oxidative stress is reported to be associated with this disease. The stress may damage corneal biomolecules, including DNA, and such damage is primarily removed by base excision repair (BER. Variation in genes encoding BER components may influence the effectiveness of corneal cells to cope with oxidative stress. In the present work we genotyped 5 polymorphisms of 4 BER genes in 284 patients and 353 controls. The A/A genotype of the c.–1370T>A polymorphism of the DNA polymerase γ (POLG gene was associated with increased occurrence of KC, while the A/T genotype was associated with decreased occurrence of KC. The A/G genotype and the A allele of the c.1196A>G polymorphism of the X-ray repair cross-complementing group 1 (XRCC1 were associated with increased, and the G/G genotype and the G allele, with decreased KC occurrence. Also, the C/T and T as well as C/C genotypes and alleles of the c.580C>T polymorphism of the same gene displayed relationship with KC occurrence. Neither the g.46438521G>C polymorphism of the Nei endonuclease VIII-like 1 (NEIL1 nor the c.2285T>C polymorphism of the poly(ADP-ribose polymerase-1 (PARP-1 was associated with KC. In conclusion, the variability of the XRCC1 and POLG genes may play a role in KC pathogenesis and determine the risk of this disease.

  3. Job shop scheduling problem based on DNA computing

    Institute of Scientific and Technical Information of China (English)

    Yin Zhixiang; Cui Jianzhong; Yang Yan; Ma Ying

    2006-01-01

    To solve job shop scheduling problem, a new approach-DNA computing is used in solving job shop scheduling problem. The approach using DNA computing to solve job shop scheduling is divided into three stands. Finally, optimum solutions are obtained by sequencing. A small job shop scheduling problem is solved in DNA computing, and the "operations" of the computation were performed with standard protocols, as ligation, synthesis, electrophoresis etc. This work represents further evidence for the ability of DNA computing to solve NP-complete search problems.

  4. DNA purification and gene typing:Based on multifunctional nanobeads

    Institute of Scientific and Technical Information of China (English)

    XIE Xin; ZHANG Xu; GAO Huafang; ZHANG Huan; CHEN Depu; CHENG Jing; FEI Weiyang

    2004-01-01

    In this report, a universal protocol for extracting genomic DNA from whole blood, saliva, and bacterial culture by using magnetic nanobeads as solid-phase absorbents was presented. The enrichment of target cells and adsorption of DNA have been functionally integrated onto the surfaces of the carboxyl-modified magnetic nano-beads, and the DNA segments bound on the surface of the beads can be directly used as PCR templates to amplify a target gene. The PCR products were applied to an oligonucleotide array to perform gene typing. The protocol proves to be simple, rapid, biologically and chemically nonhazardous, and promising for the microfabrication of DNA preparation chip.

  5. Detection of influenza A virus using carbon nanotubes field effect transistor based DNA sensor

    Science.gov (United States)

    Tran, Thi Luyen; Nguyen, Thi Thuy; Huyen Tran, Thi Thu; Chu, Van Tuan; Thinh Tran, Quang; Tuan Mai, Anh

    2017-09-01

    The carbon nanotubes field effect transistor (CNTFET) based DNA sensor was developed, in this paper, for detection of influenza A virus DNA. Number of factors that influence the output signal and analytical results were investigated. The initial probe DNA, decides the available DNA strands on CNTs, was 10 μM. The hybridization time for defined single helix was 120 min. The hybridization temperature was set at 30 °C to get a net change in drain current of the DNA sensor without altering properties of any biological compounds. The response time of the DNA sensor was less than one minute with a high reproducibility. In addition, the DNA sensor has a wide linear detection range from 1 pM to 10 nM, and a very low detection limit of 1 pM. Finally, after 7-month storage in 7.4 pH buffer, the output signal of DNA sensor recovered 97%.

  6. Effect of food processing on plant DNA degradation and PCR-based GMO analysis: a review.

    Science.gov (United States)

    Gryson, Nicolas

    2010-03-01

    The applicability of a DNA-based method for GMO detection and quantification depends on the quality and quantity of the DNA. Important food-processing conditions, for example temperature and pH, may lead to degradation of the DNA, rendering PCR analysis impossible or GMO quantification unreliable. This review discusses the effect of several food processes on DNA degradation and subsequent GMO detection and quantification. The data show that, although many of these processes do indeed lead to the fragmentation of DNA, amplification of the DNA may still be possible. Length and composition of the amplicon may, however, affect the result, as also may the method of extraction used. Also, many techniques are used to describe the behaviour of DNA in food processing, which occasionally makes it difficult to compare research results. Further research should be aimed at defining ingredients in terms of their DNA quality and PCR amplification ability, and elaboration of matrix-specific certified reference materials.

  7. Design and simulation of the CG1 beamline at HFIR

    Science.gov (United States)

    Nagler, S. E.; Lee, W.-T.; Moon, R. M.

    In the near future a super-critical hydrogen cold source will be installed in the HB4 beam tube of the High Flux Isotope Reactor (HFIR), Oak Ridge National Laboratory. The cold source will illuminate four neutron guides. Here we discuss the design and simulation of the guide CG1, dedicated to a new triple axis spectrometer. The conceptual design for the HFIR guides, including CG1, was aided by numerical calculations of neutron trajectories and acceptance diagrams. The CG1 guide consists of a partially trumpeting two-channel bender and a straight guide section. The design was subsequently modeled in detail from source to specimen, utilizing the McStas program. The lessons learned from the McStas simulations resulted in some minor but important changes in the design, and these were also verified using the original method of calculation. The resulting combination of guide and vertically focusing monochromator should deliver a beam with excellent spatial and angular distributions in and out of the scattering plane. The available intensity will enable the construction of a powerful spectrometer for incident energies as large as 20-25 meV.

  8. Design and simulation of the CG1 beamline at HFIR

    CERN Document Server

    Nagler, S E; Moon, R M

    2002-01-01

    In the near future a super-critical hydrogen cold source will be installed in the HB4 beam tube of the High Flux Isotope Reactor (HFIR), Oak Ridge National Laboratory. The cold source will illuminate four neutron guides. Here we discuss the design and simulation of the guide CG1, dedicated to a new triple axis spectrometer. The conceptual design for the HFIR guides, including CG1, was aided by numerical calculations of neutron trajectories and acceptance diagrams. The CG1 guide consists of a partially trumpeting two-channel bender and a straight guide section. The design was subsequently modeled in detail from source to specimen, utilizing the McStas program. The lessons learned from the McStas simulations resulted in some minor but important changes in the design, and these were also verified using the original method of calculation. The resulting combination of guide and vertically focusing monochromator should deliver a beam with excellent spatial and angular distributions in and out of the scattering plan...

  9. Electrochemiluminescence induced photoelectrochemistry for sensing of the DNA based on DNA-linked CdS NPs superstructure with intercalator molecules.

    Science.gov (United States)

    Guo, Yingshu; Sun, Yuanshun; Zhang, Shusheng

    2011-02-07

    A novel detection protocol of DNA was developed using electrochemiluminescence (ECL) induced photoelectrochemistry (PEC) synthesis based on DNA-linked CdS NPs superstructure with methylene blue as the intercalator molecule.

  10. Differential interactions of plasmid DNA, RNA and genomic DNA with amino acid-based affinity matrices.

    Science.gov (United States)

    Sousa, Angela; Sousa, Fani; Queiroz, João A

    2010-09-01

    The development of a strategy to plasmid DNA (pDNA) purification has become necessary for the development of gene therapy and DNA vaccine production processes in recent years, since this nucleic acid and most of contaminants, such as RNA, genomic DNA and endotoxins, are negatively charged. An ideal separation methodology may be achieved with the use of affinity interactions between immobilized amino acids and nucleic acids. In this study, the binding behaviour of nucleic acids under the influence of different environmental conditions, such as the composition and ionic strength of elution buffer, and the temperature, is compared with various amino acids immobilized on chromatography resins. Supercoiled (sc) plasmid isoform was isolated with all matrices used, but in some cases preferential interactions with other nucleic acids were found. Particularly, lysine chromatography showed to be an ideal technology mainly on RNA purification using low salt concentration. On the other hand, arginine ligands have shown a greater ability to retain the sc isoform comparatively to the other nucleic acids retention, becoming this support more adequate to sc pDNA purification. The temperature variation, competitive elution and oligonucleotides affinity studies also allowed to recognize the dominant interactions inherent to biorecognition of pDNA molecule and the affinity matrices.

  11. DBD-Hunter: a knowledge-based method for the prediction of DNA-protein interactions.

    Science.gov (United States)

    Gao, Mu; Skolnick, Jeffrey

    2008-07-01

    The structures of DNA-protein complexes have illuminated the diversity of DNA-protein binding mechanisms shown by different protein families. This lack of generality could pose a great challenge for predicting DNA-protein interactions. To address this issue, we have developed a knowledge-based method, DNA-binding Domain Hunter (DBD-Hunter), for identifying DNA-binding proteins and associated binding sites. The method combines structural comparison and the evaluation of a statistical potential, which we derive to describe interactions between DNA base pairs and protein residues. We demonstrate that DBD-Hunter is an accurate method for predicting DNA-binding function of proteins, and that DNA-binding protein residues can be reliably inferred from the corresponding templates if identified. In benchmark tests on approximately 4000 proteins, our method achieved an accuracy of 98% and a precision of 84%, which significantly outperforms three previous methods. We further validate the method on DNA-binding protein structures determined in DNA-free (apo) state. We show that the accuracy of our method is only slightly affected on apo-structures compared to the performance on holo-structures cocrystallized with DNA. Finally, we apply the method to approximately 1700 structural genomics targets and predict that 37 targets with previously unknown function are likely to be DNA-binding proteins. DBD-Hunter is freely available at http://cssb.biology.gatech.edu/skolnick/webservice/DBD-Hunter/.

  12. Stretched and overwound DNA forms a Pauling-like structure with exposed bases.

    Science.gov (United States)

    Allemand, J F; Bensimon, D; Lavery, R; Croquette, V

    1998-11-24

    We investigate structural transitions within a single stretched and supercoiled DNA molecule. With negative supercoiling, for a stretching force >0.3 pN, we observe the coexistence of B-DNA and denatured DNA from sigma approximately -0.015 down to sigma = -1. Surprisingly, for positively supercoiled DNA (sigma > +0.037) stretched by 3 pN, we observe a similar coexistence of B-DNA and a new, highly twisted structure. Experimental data and molecular modeling suggest that this structure has approximately 2.62 bases per turn and an extension 75% larger than B-DNA. This structure has tightly interwound phosphate backbones and exposed bases in common with Pauling's early DNA structure [Pauling, L. & Corey, R. B. (1953), Proc. Natl. Acad. Sci. USA 39, 84-97] and an unusual structure proposed for the Pf1 bacteriophage [Liu, D. J. & Day, L. A. (1994) Science 265, 671-674].

  13. Extracellular DNA affects NO content in human endothelial cells.

    Science.gov (United States)

    Efremova, L V; Alekseeva, A Yu; Konkova, M S; Kostyuk, S V; Ershova, E S; Smirnova, T D; Konorova, I L; Veiko, N N

    2010-08-01

    Fragments of extracellular DNA are permanently released into the blood flow due to cell apoptosis and possible de novo DNA synthesis. To find out whether extracellular DNA can affect the synthesis of nitric oxide (NO), one of key vascular tone regulators, we studied in vitro effects of three artificial DNA probes with different sequences and 10 samples of extracellular DNA (obtained from healthy people and patients with hypertension and atherosclerosis) on NO synthesis in endothelial cell culture (HUVEC). For detection of NO in live cells and culture medium, we used a NO-specific agent CuFL penetrating into the cells and forming a fluorescent product FL-NO upon interaction with NO. Human genome DNA fragments affected the content of NO in endothelial cells; this effect depended on both the base sequence and concentration of DNA fragments. Addition of artificial DNA and extracellular DNA from healthy people into the cell culture in a low concentration (5 ng/ml) increased the detected NO concentration by 4-fold at most. Cytosine-guanine (CG)-rich fragment of the transcribed sequence of ribosomal repeat was the most powerful NO-inductor. The effect of DNA fragments on NO synthesis was comparable with that of low doses of oxidizing agents, H(2)O(2) and 17β-estradiol. Extracellular DNA samples obtained from patients with hypertension and atherosclerosis decreased NO content in cells and medium by 1.3-28 times compared to the control; the effect correlated with the content of CG-rich sequences.

  14. Status of a Unique Vaccine against hCG for Contraception and Advanced Stage Cancers expressing ectopically hCG

    Directory of Open Access Journals (Sweden)

    Talwar GP

    2015-01-01

    Full Text Available Dear Egon!br God bless you on your 95th Birthday! May you complete 100 years.br Being submitted in your honor is a brief article on my continuing work to make available a unique vaccine preventing pregnancy in women without blocking ovulation, her normal production of sex steroid hormones and retaining her regular menstrual cycles and bleeding profiles.br The vaccine is directed at the Human chorionic gonadotropin (hCG, which emerges following fertilization of the egg [1]. Healthy, non-pregnant women do not make it, the basis on which its detection in serum or urine serves as a reliable test for diagnosis of pregnancy. It plays a critical role in implantation of the embryo & thereby to the onset of pregnancy. The purpose of the vaccine is to generate bioeffective antibodies neutralizing hCG & thereby prevent the onset of pregnancy.br As you can imagine, the making of a workable vaccine, competent to make antibodies against a tolerant molecule to the woman’s immune system (she literally bathes in hCG during pregnancy was not simple. What was also demanded was high immunogenicity of the vaccine to make fairly high titres of antibodies to counteract the large amount of hCG made in early pregnancy. At each stage, it required testing in humans and before that could be done, appropriate toxicology studies & approval of Regulatory and Ethics Committees was needed each taking its time. Eventually the vaccine has to be amenable to industrial production to reach the public, hence a recombinant vaccine had to be developed. Given below is a brief write-up on the evolution of the vaccine against the human chorionic gonadotropin.br Yours, Pran

  15. Development of a DNA Sensor Based on Alkanethiol Self- Assembled Monolayer-Modified Electrodes

    Directory of Open Access Journals (Sweden)

    José M. Pingarrón

    2005-11-01

    Full Text Available An electrochemical DNA biosensor based on recognition of double or singlestranded DNA (ds-DNA/ss-DNA immobilised on a self-assembled modified gold electrodeis presented for denaturalisation and hybridisation detection. DNA is covalently bond on aself assembled 3-mercaptopropionic acid monolayer by using water soluble N-3-(dimethylaminopropyl-N´ethylcarbodiimide hydrochloride (EDC and Nhydroxisulfosuccinimide(NHSS as linkers. The interaction between the immobilised DNAand methylene blue (MB is investigated using square wave voltammetry (SWV. Theincrease or diminution of peak currents of the MB upon the hybridisation or denaturalisationevent at the modified electrode surface is studied.

  16. High Interlaboratory Reprocucibility of DNA Sequence-based Typing of Bacteria in a Multicenter Study

    DEFF Research Database (Denmark)

    Sousa, MA de; Boye, Kit; Lencastre, H de

    2006-01-01

    Current DNA amplification-based typing methods for bacterial pathogens often lack interlaboratory reproducibility. In this international study, DNA sequence-based typing of the Staphylococcus aureus protein A gene (spa, 110 to 422 bp) showed 100% intra- and interlaboratory reproducibility without...... extensive harmonization of protocols for 30 blind-coded S. aureus DNA samples sent to 10 laboratories. Specialized software for automated sequence analysis ensured a common typing nomenclature....

  17. Molecular Design of Ionization-Induced Proton Switching Element Based on Fluorinated DNA Base Pair.

    Science.gov (United States)

    Tachikawa, Hiroto; Kawabata, Hiroshi

    2016-03-10

    To design theoretically the high-performance proton switching element based on DNA base pair, the effects of fluorine substitution on the rate of proton transfer (PT) in the DNA model base pair have been investigated by means of direct ab initio molecular dynamics (AIMD) method. The 2-aminopyridine dimer, (AP)2, was used as the model of the DNA base pair. One of the hydrogen atoms of the AP molecule in the dimer was substituted by a fluorine (F) atom, and the structures of the dimer, expressed by F-(AP)2, were fully optimized at the MP2/6-311++G(d,p) level. The direct AIMD calculations showed that the proton is transferred within the base pair after the vertical ionization. The rates of PT in F-(AP)2(+) were calculated and compared with that of (AP)2(+) without an F atom. It was found that PT rate is accelerated by the F-substitution. Also, the direction of PT between F-AP and AP molecules can be clearly controlled by the position of F-substitution (AP)2 in the dimer.

  18. Potential for DNA-based identification of Great Lakes fauna: Match and mismatch between taxa inventories and DNA barcode libraries

    Science.gov (United States)

    DNA-based identification of mixed-organism samples offers the potential to greatly reduce the need for resource-intensive morphological identification, which would be of value both to biotic condition assessment and non-native species early-detection monitoring. However, the abi...

  19. Direct electrochemical sensor for label-free DNA detection based on zero current potentiometry.

    Science.gov (United States)

    Wu, Nai-ying; Gao, Wei; He, Xu-lun; Chang, Zhu; Xu, Mao-tian

    2013-01-15

    A direct electrochemical DNA biosensor based on zero current potentiometry was fabricated by immobilization of ssDNA onto gold nanoparticles (AuNPs) coated pencil graphite electrode (PGE). One ssDNA/AuNPs/PGE was connected in series between clips of working and counter electrodes of a potentiostat, and then immersed into the solution together with a reference electrode, establishing a novel DNA biosensor for specific DNA detection. The variation of zero current potential difference (ΔE(zcp)) before and after hybridization of the self-assembled probe DNA with the target DNA was used as a signal to characterize and quantify the target DNA sequence. The whole DNA biosensor fabrication process was characterized by cyclic voltammetry and electrochemical impedance spectroscopy with the use of ferricyanide as an electrochemical redox indicator. Under the optimized conditions, ΔE(zcp) was linear with the concentrations of the complementary target DNA in the range from 10nM to 1μM, with a detection limit of 6.9nM. The DNA biosensor showed a good reproducibility and selectivity. Prepared DNA biosensor is facile and sensitive, and it eliminates the need of using exogenous reagents to monitor the oligonucleotides hybridization.

  20. New insights on the mechanism of quinoline-based DNA Methyltransferase inhibitors.

    Science.gov (United States)

    Gros, Christina; Fleury, Laurence; Nahoum, Virginie; Faux, Céline; Valente, Sergio; Labella, Donatella; Cantagrel, Frédéric; Rilova, Elodie; Bouhlel, Mohamed Amine; David-Cordonnier, Marie-Hélène; Dufau, Isabelle; Ausseil, Frédéric; Mai, Antonello; Mourey, Lionel; Lacroix, Laurent; Arimondo, Paola B

    2015-03-06

    Among the epigenetic marks, DNA methylation is one of the most studied. It is highly deregulated in numerous diseases, including cancer. Indeed, it has been shown that hypermethylation of tumor suppressor genes promoters is a common feature of cancer cells. Because DNA methylation is reversible, the DNA methyltransferases (DNMTs), responsible for this epigenetic mark, are considered promising therapeutic targets. Several molecules have been identified as DNMT inhibitors and, among the non-nucleoside inhibitors, 4-aminoquinoline-based inhibitors, such as SGI-1027 and its analogs, showed potent inhibitory activity. Here we characterized the in vitro mechanism of action of SGI-1027 and two analogs. Enzymatic competition studies with the DNA substrate and the methyl donor cofactor, S-adenosyl-l-methionine (AdoMet), displayed AdoMet non-competitive and DNA competitive behavior. In addition, deviations from the Michaelis-Menten model in DNA competition experiments suggested an interaction with DNA. Thus their ability to interact with DNA was established; although SGI-1027 was a weak DNA ligand, analog 5, the most potent inhibitor, strongly interacted with DNA. Finally, as 5 interacted with DNMT only when the DNA duplex was present, we hypothesize that this class of chemical compounds inhibit DNMTs by interacting with the DNA substrate.

  1. Assessment of serum β-hCG and lipid profile in early second trimester as predictors of hypertensive disorders of pregnancy.

    Science.gov (United States)

    Revankar, Vijaya M; Narmada, Lavu

    2017-09-01

    To assess and compare the ability of serum β-human chorionic gonadotropin (β-hCG) and serum lipid profile in early second trimester as predictors of hypertensive disorders of pregnancy. The present hospital-based prospective study was conducted between November 24, 2012, and April 30, 2014, at a tertiary hospital in Mangalore, India. Women of any parity with a pregnancy of 14-20 weeks were included. Venous blood (3 mL) was collected, and serum β-hCG and lipid profile were estimated by enzyme-linked immunosorbent assay and an enzymatic colorimetric test with lipid clearing factor, respectively. A cutoff value of β-hCG for predicting hypertensive disorders was obtained by receiver operating curve analysis. Serum β-hCG was significantly higher among women who subsequently developed hypertension (71 142 IU/L [n=27]) than among those who did not (20 541 IU/L [n=137]; PhCG to predict hypertension were 92.6% and 94.9% respectively. The positive and negative predictive values were 78.1% and 98.5%, respectively. Serum β-hCG might be used as a predictor of hypertensive disorders that complicate pregnancy. Dyslipidemia was not found to be a useful marker. © 2017 International Federation of Gynecology and Obstetrics.

  2. Visualizing the search for radiation-damaged DNA bases in real time

    Science.gov (United States)

    Lee, Andrea J.; Wallace, Susan S.

    2016-11-01

    The Base Excision Repair (BER) pathway removes the vast majority of damages produced by ionizing radiation, including the plethora of radiation-damaged purines and pyrimidines. The first enzymes in the BER pathway are DNA glycosylases, which are responsible for finding and removing the damaged base. Although much is known about the biochemistry of DNA glycosylases, how these enzymes locate their specific damage substrates among an excess of undamaged bases has long remained a mystery. Here we describe the use of single molecule fluorescence to observe the bacterial DNA glycosylases, Nth, Fpg and Nei, scanning along undamaged and damaged DNA. We show that all three enzymes randomly diffuse on the DNA molecule and employ a wedge residue to search for and locate damage. The search behavior of the Escherichia coli DNA glycosylases likely provides a paradigm for their homologous mammalian counterparts.

  3. Microcantilver-based DNA hybridization sensors for Salmonella identification

    Directory of Open Access Journals (Sweden)

    Carlo Ricciardi

    2012-02-01

    Full Text Available The detection of pathogenic microorganisms in foods remains a challenging since the safety of foodstuffs has to be ensured by the food producing companies. Conventional methods for the detection and identification of bacteria mainly rely on specific microbiological and biochemical identification. Biomolecular methods, are commonly used as a support for traditional techniques, thanks to their high sensitivity, specificity and not excessive costs. However, new methods like biosensors for example, can be an exciting alternative to the more traditional tecniques for the detection of pathogens in food. In this study we report Salmonella enterica serotype Enteritidis DNA detection through a novel class of label-free biosensors: microcantilevers (MCs. In general, MCs can operate as a microbalance and is used to detect the mass of the entities anchored to the cantilever surface using the decrease in the resonant frequency. We use DNA hybridization as model reaction system and for this reason, specific single stranded probe DNA of the pathogen and three different DNA targets (single-stranded complementary DNA, PCR product and serial dilutions of DNA extracted from S. Enteritidis strains were applied. Two protocols were reported in order to allow the probe immobilization on cantilever surface: i MC surface was functionalized with 3-aminopropyltriethoxysilane and glutaraldehyde and an amino-modified DNA probe was used; ii gold-coated sensors and thiolated DNA probes were used in order to generate a covalent bonding (Th-Au. For the first one, measures after hybridization with the PCR product showed related frequency shift 10 times higher than hybridization with complementary probe and detectable signals were obtained at the concentrations of 103 and 106 cfu/mL after hybridization with bacterial DNA. There are currently optimizations of the second protocol, where preliminary results have shown to be more uniform and therefore more precise within each of the

  4. High Interlaboratory Reprocucibility of DNA Sequence-based Typing of Bacteria in a Multicenter Study

    DEFF Research Database (Denmark)

    Sousa, MA de; Boye, Kit; Lencastre, H de;

    2006-01-01

    Current DNA amplification-based typing methods for bacterial pathogens often lack interlaboratory reproducibility. In this international study, DNA sequence-based typing of the Staphylococcus aureus protein A gene (spa, 110 to 422 bp) showed 100% intra- and interlaboratory reproducibility without...

  5. Ultratrace DNA Detection Based on the Condensing-Enrichment Effect of Superwettable Microchips.

    Science.gov (United States)

    Xu, Li-Ping; Chen, Yanxia; Yang, Gao; Shi, Wanxin; Dai, Bing; Li, Guannan; Cao, Yanhua; Wen, Yongqiang; Zhang, Xueji; Wang, Shutao

    2015-11-18

    A sensitive nucleic acid detection platform based on superhydrophilic microwells spotted on a superhydrophobic substrate is fabricated. Due to the wettability differences, ultratrace DNA molecules are enriched and the fluorescent signals are amplified to allow more sensitive detection. The biosensing interface based on superwettable materials provides a simple and cost-effective way for ultratrace DNA sensing.

  6. Instance-based concept learning from multiclass DNA microarray data

    Directory of Open Access Journals (Sweden)

    Dubitzky Werner

    2006-02-01

    Full Text Available Abstract Background Various statistical and machine learning methods have been successfully applied to the classification of DNA microarray data. Simple instance-based classifiers such as nearest neighbor (NN approaches perform remarkably well in comparison to more complex models, and are currently experiencing a renaissance in the analysis of data sets from biology and biotechnology. While binary classification of microarray data has been extensively investigated, studies involving multiclass data are rare. The question remains open whether there exists a significant difference in performance between NN approaches and more complex multiclass methods. Comparative studies in this field commonly assess different models based on their classification accuracy only; however, this approach lacks the rigor needed to draw reliable conclusions and is inadequate for testing the null hypothesis of equal performance. Comparing novel classification models to existing approaches requires focusing on the significance of differences in performance. Results We investigated the performance of instance-based classifiers, including a NN classifier able to assign a degree of class membership to each sample. This model alleviates a major problem of conventional instance-based learners, namely the lack of confidence values for predictions. The model translates the distances to the nearest neighbors into 'confidence scores'; the higher the confidence score, the closer is the considered instance to a pre-defined class. We applied the models to three real gene expression data sets and compared them with state-of-the-art methods for classifying microarray data of multiple classes, assessing performance using a statistical significance test that took into account the data resampling strategy. Simple NN classifiers performed as well as, or significantly better than, their more intricate competitors. Conclusion Given its highly intuitive underlying principles – simplicity

  7. Optical Characterization of Oligonucleotide DNA Influenced by Magnetic Fields

    Directory of Open Access Journals (Sweden)

    Seyedeh Maryam Banihashemian

    2013-09-01

    Full Text Available UV-VIS spectroscopic analysis of oligonucleotide DNA exposed to different magnetic fields was performed in order to investigate the relationship between DNA extinction coefficients and optical parameters according to magnetic-field strength. The results with the oligonucleotides adenine-thymine 100 mer (AT-100 DNA and cytosine-guanine 100 mer (CG-100 DNA indicate that the magnetic field influences DNA molar extinction coefficients and refractive indexes. The imaginary parts of the refractive index and molar extinction coefficients of the AT-100 and CG-100 DNA decreased after exposure to a magnetic field of 750 mT due to cleavage of the DNA oligonucleotides into smaller segments.

  8. DNA-based materials and their device applications (Conference Presentation)

    Science.gov (United States)

    Rau, Ileana; Kajzar, François; Grote, James G.

    2016-10-01

    In the last decade a lot of interest was paid to DNA materials in view of their practical applications in photonics and in electronics. This aspect is especially due to the fact that this polymer is eco-friendly, originating from renewable resources and can be obtained from any animal or vegetable waste. In this respect many studies have shown that DNA is an intriguing biopolymer which can find applications in many fields. In this paper we will review and discuss the functionalization of DNA and some practical applications.

  9. Solid phase based DNA solution of the coloring problem

    Institute of Scientific and Technical Information of China (English)

    PAN Linqiang; LIU Guangwu; XU Jin; LIU Yachun

    2004-01-01

    DNA computing has the potential to tackle computationally difficult problems that have real-world implications.The parallel search capabilities of DNA make it a valuable tool for approaching intractable computational problems,for which conventional computers have limited potentials.Up to now,many accomplishments have been achieved to improve its performance and increase its reliability.In this paper,the coloring problem has been solved by means of molecular biology techniques.The coloring problem is a well-known NP-complete problem.This work represents further evidence for the ability of DNA computing to solve NP-complete problems.

  10. DNA gridiron nanostructures based on four-arm junctions.

    Science.gov (United States)

    Han, Dongran; Pal, Suchetan; Yang, Yang; Jiang, Shuoxing; Nangreave, Jeanette; Liu, Yan; Yan, Hao

    2013-03-22

    Engineering wireframe architectures and scaffolds of increasing complexity is one of the important challenges in nanotechnology. We present a design strategy to create gridiron-like DNA structures. A series of four-arm junctions are used as vertices within a network of double-helical DNA fragments. Deliberate distortion of the junctions from their most relaxed conformations ensures that a scaffold strand can traverse through individual vertices in multiple directions. DNA gridirons were assembled, ranging from two-dimensional arrays with reconfigurability to multilayer and three-dimensional structures and curved objects.

  11. [Mechanism of regulation of synthesis and secretion of human chorionic gonadotropin (hCG) during pregnancy].

    Science.gov (United States)

    Barrera, David; Chirinos, Mayel; García-Becerra, Rocío

    2008-01-01

    Human chorionic gonadotropin (hCG) is an essential hormone for development and sustaining of gestation. Adequate hCG production is fundamental for pregnancy success since abnormal hCG serum concentrations have been correlated with pregnancy anomalies such as recurrent abortions and preeclampsia. Regulation of hCG production involves diverse molecules associated with different signaling pathways, which have complicated the establishment of the mechanisms involved in its production. The present study provides a critical review of the most relevant findings related to hCG production and functions during pregnancy, in order to help to understand some related pathologies and to treat them more adequately.

  12. Anodized aluminum oxide-based capacitance sensors for the direct detection of DNA hybridization.

    Science.gov (United States)

    Kang, Bongkeun; Yeo, Unjin; Yoo, Kyung-Hwa

    2010-03-15

    We fabricated a capacitance sensor based on an anodized aluminum oxide (AAO) nanoporous structure to detect DNA hybridization. We utilized Au film deposited on the surface of the AAO membrane and Au nanowires infiltrating the nanopores as the top and bottom electrodes, respectively. When completely complementary target DNA molecules were added to the sensor-immobilized DNA molecule probes, the capacitance was reduced; with a concentration of 1pM, the capacitance decreased by approximately 10%. We measured the capacitance change for different concentrations of the target DNA solution. A linear relationship was found between the capacitance change and DNA concentration on a semi-logarithmic scale. We also investigated the possibility of detecting DNA molecules with a single-base mismatch to the probe DNA molecule. In contrast to complementary target DNA molecules, the addition of one-base mismatch DNA molecules caused no significant change in capacitance, demonstrating that DNA hybridization was detected with single nucleotide polymorphism sensitivity. (c) 2009 Elsevier B.V. All rights reserved.

  13. An electrochemical DNA biosensor based on Oracet Blue as a label for detection of Helicobacter pylori.

    Science.gov (United States)

    Hajihosseini, Saeedeh; Nasirizadeh, Navid; Hejazi, Mohammad Saeid; Yaghmaei, Parichereh

    2016-10-01

    An innovative method of a DNA electrochemical biosensor based on Oracet Blue (OB) as an electroactive label and gold electrode (AuE) for detection of Helicobacter pylori, was offered. A single-stranded DNA probe with a thiol modification was covalently immobilized on the surface of the AuE by forming an Au-S bond. Differential pulse voltammetry (DPV) was used to monitor DNA hybridization by measuring the electrochemical signals of reduction of the OB binding to double-stranded DNA (ds-DNA). Our results showed that OB-based DNA biosensor has a decent potential for detection of single-base mismatch in target DNA. Selectivity of the proposed DNA biosensor was further confirmed in the presence of non-complementary and complementary DNA strands. Under optimum conditions, the electrochemical signal had a linear relationship with the concentration of the target DNA ranging from 0.3nmolL(-1) to 240.0nmolL(-1), and the detection limit was 0.17nmolL(-1), whit a promising reproducibility and repeatability.

  14. Ultrasensitive cDNA detection of dengue virus RNA using electrochemical nanoporous membrane-based biosensor.

    Directory of Open Access Journals (Sweden)

    Varun Rai

    Full Text Available A nanoporous alumina membrane-based ultrasensitive DNA biosensor is constructed using 5'-aminated DNA probes immobilized onto the alumina channel walls. Alumina nanoporous membrane-like structure is carved over platinum wire electrode of 76 µm diameter dimension by electrochemical anodization. The hybridization of complementary target DNA with probe DNA molecules attached inside the pores influences the pore size and ionic conductivity. The biosensor demonstrates linear range over 6 order of magnitude with ultrasensitive detection limit of 9.55×10(-12 M for the quantification of ss-31 mer DNA sequence. Its applicability is challenged against real time cDNA PCR sample of dengue virus serotype1 derived from asymmetric PCR. Excellent specificity down to one nucleotide mismatch in target DNA sample of DENV3 is also demonstrated.

  15. Silica-Based Solid Phase Extraction of DNA on a Microchip

    Institute of Scientific and Technical Information of China (English)

    陈晓芳; 沈科跃; 刘鹏; 郭旻; 程京; 周玉祥

    2004-01-01

    Micro total analysis systems for chemical and biological analysis have attracted much attention.However,microchips for sample preparation and especially DNA purification are still underdeveloped.This work describes a solid phase extraction chip for purifying DNA from biological samples based on the adsorption of DNA on bare silica beads prepacked in a microchannel.The chip was fabricated with poly-dimethylsiloxane.The silica beads were packed in the channel on the chip with a tapered microchannel to form the packed bed.Fluorescence detection was used to evaluate the DNA adsorbing efficiency of the solid phase.The polymerase chain reaction was used to evaluate the quality of the purified DNA for further use.The extraction efficiency for the DNA extraction chip is approximately 50% with a 150-nL extraction volume.Successful amplification of DNA extracted from human whole blood indicates that this method is compatible with the polymerase chain reaction.

  16. Absence of TGF-β Receptor Activation by Highly Purified hCG Preparations.

    Science.gov (United States)

    Koistinen, Hannu; Hautala, Laura; Koli, Katri; Stenman, Ulf-Håkan

    2015-12-01

    Recently, several LH/human chorionic gonadotropin (hCG) receptor-independent activities for hCG have been described, including activation of the TGF-β receptor (TGFβR) by hyperglycosylated hCG and stimulation of trophoblast invasion. Because the hCG concentrations used in these studies have been rather high, reflecting physiological hCG levels in pregnancy, even a minor contamination with growth factors, which act at very low concentrations, may be significant. Several commercial hCG preparations have been found to contain significant amounts of epidermal growth factor (EGF), which we also confirmed here. Furthermore, we found that some hCG preparations also contain significant amounts of TGF-β1. These hCG preparations were able to activate ERK1/2 in JEG-3 choriocarcinoma cells or TGFβR in mink lung epithelial cells transfected with a reporter gene for TGFβR activation. No such activation was found with highly purified hCG or its free β-subunit (hCGβ), irrespective of whether they were hyperglycosylated or not. Taken together, our results suggest that the growth factor contaminations in the hCG preparations can cause activation of TGFβR and, at least in JEG-3 cells, MAPK signaling. This highlights the importance to carefully control for potential contaminations and that highly purified hCG preparations have to be used for biological studies.

  17. Gold-based optical biosensor for single-mismatched DNA detection using salt-induced hybridization

    DEFF Research Database (Denmark)

    Zhan, Zongrui; Ma, Xingyi; Cao, Cuong

    2011-01-01

    In this study, a gold nanoparticle (Au-NP)-based detection method for sensitive and specific DNA-based diagnostic applications is described. A sandwich format consisting of Au-NPs/DNA/PMP (Streptavidin-coated MagnetSphere Para-Magnetic Particles) was fabricated. PMPs captured and separated target...... in the presence of different buffers was well investigated, and thus, the optimized salt concentration allowed for discrimination of single-mismatched DNA (MMT) from perfectly matched DNA (PMT). Therefore, quantitative information concerning the target analyte was translated into a colorimetric signal, which...

  18. Correlation of DNA methylation levels in blood and saliva DNA in young girls of the LEGACY Girls study.

    Science.gov (United States)

    Wu, Hui-Chen; Wang, Qiao; Chung, Wendy K; Andrulis, Irene L; Daly, Mary B; John, Esther M; Keegan, Theresa H M; Knight, Julia; Bradbury, Angela R; Kappil, Maya A; Gurvich, Irina; Santella, Regina M; Terry, Mary Beth

    2014-07-01

    Many epidemiologic studies of environmental exposures and disease susceptibility measure DNA methylation in white blood cells (WBC). Some studies are also starting to use saliva DNA as it is usually more readily available in large epidemiologic studies. However, little is known about the correlation of methylation between WBC and saliva DNA. We examined DNA methylation in three repetitive elements, Sat2, Alu, and LINE-1, and in four CpG sites, including AHRR (cg23576855, cg05575921), cg05951221 at 2q37.1, and cg11924019 at CYP1A1, in 57 girls aged 6-15 years with blood and saliva collected on the same day. We measured all DNA methylation markers by bisulfite-pyrosequencing, except for Sat2 and Alu, which were measured by the MethyLight assay. Methylation levels measured in saliva DNA were lower than those in WBC DNA, with differences ranging from 2.8% for Alu to 14.1% for cg05575921. Methylation levels for the three repetitive elements measured in saliva DNA were all positively correlated with those in WBC DNA. However, there was a wide range in the Spearman correlations, with the smallest correlation found for Alu (0.24) and the strongest correlation found for LINE-1 (0.73). Spearman correlations for cg05575921, cg05951221, and cg11924019 were 0.33, 0.42, and 0.79, respectively. If these findings are replicated in larger studies, they suggest that, for selected methylation markers (e.g., LINE-1), methylation levels may be highly correlated between blood and saliva, while for others methylation markers, the levels may be more tissue specific. Thus, in studies that differ by DNA source, each interrogated site should be separately examined in order to evaluate the correlation in DNA methylation levels across DNA sources.

  19. [Influence of hCG glycosylation on its functions in female reproduction].

    Science.gov (United States)

    Oborná, I; Fingerová, H

    2017-01-01

    To review contemporary knowledge of the hCG molecule, its isoforms and the importance of glycosylation. Biologic variants and glycoforms of hCG have different biological activities and functions related to the control of menstrual cycle, conception, gestation as well as gynaecologic and non-gynaecologic malignancies. A review. Department of Obstetrics and Gynaecology, University Hospital Olomouc. To present own experience and an overview of recent literature in molecular biology, clinical biochemistry and clinical practice. Recent knowledge of the role of hCG glycosylation in physiologic and pathologic events in female organism will provide a better understanding of regulation of processes like ovulation (co-operation of pituitary hCG with LH), implantation and hemochorial placentation (invasivity of hyperglycosylated hCG). Some biologic variants and isoforms of hCG are important for the prediction of certain pathologies of pregnancy, prenatal screening of inborn errors (free beta hCG) as well as in the treatment of infertility.

  20. DNA-Based Photonic Bandgap Structures and Devices

    Science.gov (United States)

    2009-11-29

    Genes to Machines: DNA Nanomechanical Devices, Trends in Biochemical Sciences 30, 119-125 (2005). 4. N.C. Seeman. Structural DNA Nanotechnology: An... kpc ≥ ω , k becomes purely real.. If the dispersion relation just given is written as =++ 22)( kpkak 1ε 2)( c ω , it resembles that for modes in a...waveguide. By analogy, the frequency region for which 1ε 22)( kpc < ω will be referred to as cutoff. IV. APPLICATIONS The presence of molecules

  1. A Novel DNA-Based Vaccine Methodology for Aids

    Science.gov (United States)

    1998-11-01

    delivery of DNA to the tongue suggests the tongue may be an inductive site for mucosal immunity . 18 To evaluate the immune effects of IL-6, we delivered DNA...indicate the enhanced protection seen with IL-6 and tongue delivery is not due to induction of localized mucosal immunity . These results further suggest...that the tongue is not an inductive site for mucosal immunity . However, these results do not account for potential differences between the mouse and

  2. Structure-based analysis of HU-DNA binding.

    Science.gov (United States)

    Swinger, Kerren K; Rice, Phoebe A

    2007-01-26

    HU and IHF are prokaryotic proteins that induce very large bends in DNA. They are present in high concentrations in the bacterial nucleoid and aid in chromosomal compaction. They also function as regulatory cofactors in many processes, such as site-specific recombination and the initiation of replication and transcription. HU and IHF have become paradigms for understanding DNA bending and indirect readout of sequence. While IHF shows significant sequence specificity, HU binds preferentially to certain damaged or distorted DNAs. However, none of the structurally diverse HU substrates previously studied in vitro is identical with the distorted substrates in the recently published Anabaena HU(AHU)-DNA cocrystal structures. Here, we report binding affinities for AHU and the DNA in the cocrystal structures. The binding free energies for formation of these AHU-DNA complexes range from approximately 10-14.5 kcal/mol, representing K(d) values in the nanomolar to low picomolar range, and a maximum stabilization of at least approximately 6.3 kcal/mol relative to complexes with undistorted, non-specific DNA. We investigated IHF binding and found that appropriate structural distortions can greatly enhance its affinity. On the basis of the coupling of structural and relevant binding data, we estimate the amount of conformational strain in an IHF-mediated DNA kink that is relieved by a nick (at least 0.76 kcal/mol) and pinpoint the location of the strain. We show that AHU has a sequence preference for an A+T-rich region in the center of its DNA-binding site, correlating with an unusually narrow minor groove. This is similar to sequence preferences shown by the eukaryotic nucleosome.

  3. Structure-based Analysis to Hu-DNA Binding

    Energy Technology Data Exchange (ETDEWEB)

    Swinger,K.; Rice, P.

    2007-01-01

    HU and IHF are prokaryotic proteins that induce very large bends in DNA. They are present in high concentrations in the bacterial nucleoid and aid in chromosomal compaction. They also function as regulatory cofactors in many processes, such as site-specific recombination and the initiation of replication and transcription. HU and IHF have become paradigms for understanding DNA bending and indirect readout of sequence. While IHF shows significant sequence specificity, HU binds preferentially to certain damaged or distorted DNAs. However, none of the structurally diverse HU substrates previously studied in vitro is identical with the distorted substrates in the recently published Anabaena HU(AHU)-DNA cocrystal structures. Here, we report binding affinities for AHU and the DNA in the cocrystal structures. The binding free energies for formation of these AHU-DNA complexes range from 10-14.5 kcal/mol, representing K{sub d} values in the nanomolar to low picomolar range, and a maximum stabilization of at least 6.3 kcal/mol relative to complexes with undistorted, non-specific DNA. We investigated IHF binding and found that appropriate structural distortions can greatly enhance its affinity. On the basis of the coupling of structural and relevant binding data, we estimate the amount of conformational strain in an IHF-mediated DNA kink that is relieved by a nick (at least 0.76 kcal/mol) and pinpoint the location of the strain. We show that AHU has a sequence preference for an A+T-rich region in the center of its DNA-binding site, correlating with an unusually narrow minor groove. This is similar to sequence preferences shown by the eukaryotic nucleosome.

  4. Nano-Bio Electronic Devices Based on DNA Bases and Proteins

    Science.gov (United States)

    Rinaldi, R.; Maruccio, G.; Bramanti, A.; Visconti, P.; Biasco, A.; Arima, V.; D'Amico, S.; Cingolani, R.

    A key challenge of the current research in nanoelectronics is the realization of biomolecular devices. The biomolecules have specific functionalies that can be exploited for the implementation of electronic and optoelectronic devices. Different nanotechnological strategies have been pursued to implement the biomolecular devices, following a bottom-up or a topdown approach depending on the used biomolecule and on its functionality. In this paper we present our results on the implementation of nano-biomolecular devices based on modified DNA nucleosides and metalloproteins.

  5. DNA origami-based standards for quantitative fluorescence microscopy.

    Science.gov (United States)

    Schmied, Jürgen J; Raab, Mario; Forthmann, Carsten; Pibiri, Enrico; Wünsch, Bettina; Dammeyer, Thorben; Tinnefeld, Philip

    2014-01-01

    Validating and testing a fluorescence microscope or a microscopy method requires defined samples that can be used as standards. DNA origami is a new tool that provides a framework to place defined numbers of small molecules such as fluorescent dyes or proteins in a programmed geometry with nanometer precision. The flexibility and versatility in the design of DNA origami microscopy standards makes them ideally suited for the broad variety of emerging super-resolution microscopy methods. As DNA origami structures are durable and portable, they can become a universally available specimen to check the everyday functionality of a microscope. The standards are immobilized on a glass slide, and they can be imaged without further preparation and can be stored for up to 6 months. We describe a detailed protocol for the design, production and use of DNA origami microscopy standards, and we introduce a DNA origami rectangle, bundles and a nanopillar as fluorescent nanoscopic rulers. The protocol provides procedures for the design and realization of fluorescent marks on DNA origami structures, their production and purification, quality control, handling, immobilization, measurement and data analysis. The procedure can be completed in 1-2 d.

  6. Association between Interleukin-12 Receptor B1 Gene Polymorphism (rs401502 C/G and Chronic Hepatitis B Virus Infection

    Directory of Open Access Journals (Sweden)

    M Salehi

    2016-06-01

    Full Text Available Introduction: Hepatitis B virus (HBV infection is a major health problem worldwide and may lead to serious clinical complications, including chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma. The host’s genetic background in immune system genes is a crucial etiologic factor in progression of HBV infection to chronic disease or clearance of the virus from the body. Interleukin 12 and its receptor (IL12 Receptor play an important role in the clearance of viral infections, especially HBV. The aim of this study is to investigate the association between interleukin 12 receptor B1 gene single nucleotide polymorphism (rs401502 C/G and chronic HBV infection. Methods: In this case control study, genomic DNA of 105 chronically HBV infected patients and 105 healthy controls was extracted. Genotype of (rs401502 C/G single nucleotide polymorphism was determined using polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP method. Results: The frequency of (rs401502 C/G SNP for GG, GC, CC genotypes and G, C alleles was %53.3, %41, %5.7 and %73.3, %26.7 in the chronic patients and %51.4, %41, %7.6 %71.9 , and %28.1 in the control group, respectively. Statistical analysis of the results showed that there was not any significant difference between the case and control groups (p=0.851. Conclusion: In this study, no association was found between (rs401502 C/G single nucleotide polymorphism within IL12RB1 gene and chronic hepatitis B virus infection. It seems that this SNP does not play a crucial role in susceptibility to HBV chronic infection

  7. Cellular models for mitochondrial DNA-based diseases: lymphoblastoid cell lines and transmitochondrial cybrids.

    Science.gov (United States)

    Jiji, Sun; Xiaoxu, Zhao; Lihua, Qiao; Shuang, Mei; Zhipeng, Nie; Qinghai, Zhang; Yanchun, Ji; Pingping, Jiang; Min-Xin, Guan

    2016-07-20

    Mitochondrial DNA (mtDNA) mutations cause a variety of mitochondrial DNA-based diseases which have been studied using Lymphoblastoid cell lines (LCLs) and transmitochondrial cybrids. Individual genetic information is preserved permanently in LCLs while the development of transmitochondrial cybrids provide ex-vivo cellular platform to study molecular mechanism of mitochondrial DNA-based diseases. The cytoplasmic donor cells for previous transmitochondrial cybrids come from patient's tissue or platelet directly. Here, we depicted in details the principle, methods and techniques to establish LCLs from frozen peripheral bloods harboring mitochondrial 4401G > A mutation by infection of Epstein Barr virus, and then to generate cybrids using ρ(0) 206 and LCLs. The process of establishing these two cellular models was summarized into four steps as follows: (1) Generation of LCLs; (2) Transformation; (3) Selection; (4) Verification. To faithfully represent the function of mtDNA mutation, we analyzed and identified the sites of mtDNA mutations and copy numbers of each cellular models as well as the karyotype of transmitochondrial cybrids. Those clones with consistent parameters were selected for preservation and future analysis of the function of point mutations of mtDNA. Although these two cellular models play important roles in understanding molecular mechanism of mitochondrial DNA-based diseases on the cellular level, their limitations should be considered when elucidating the character of tissue specificity of mitochondrial DNA-based diseases.

  8. Sequence-specific DNA interactions with calixarene-based langmuir monolayers.

    Science.gov (United States)

    Rullaud, Vanessa; Moridi, Negar; Shahgaldian, Patrick

    2014-07-29

    The interactions of an amphiphilic calixarene, namely p-guanidino-dodecyloxy-calix[4]arene, 1, self-assembled as Langmuir monolayers, with short double stranded DNA, were investigated by surface pressure-area (π-A) isotherms, surface ellipsometry and Brewster angle microscopy (BAM). Three DNA 30mers were used as models, poly(AT), poly(GC) and a random DNA sequence with 50% of G:C base pairs. The interactions of these model DNA duplexes with 1-based Langmuir monolayers were studied by measuring compression isotherms using increasing DNA concentrations (10(-6), 10(-5), 10(-4), and 5 × 10(-4) g L(-1)) in the aqueous subphase. The isotherms of 1 showed an expansion of the monolayer with, interestingly, significant differences depending on the duplex DNA sequence studied. Indeed, the interactions of 1-based monolayers with poly(AT) led to an expansion of the monolayer that was significantly more pronounced that for monolayers on subphases of poly(GC) and the random DNA sequence. The structure and thickness of 1-based Langmuir monolayers were investigated by BAM and surface ellipsometry that showed differences in thickness and structure between a monolayer formed on pure water or on a DNA subphase, with here again relevant dissimilarities depending on the DNA composition.

  9. Linearly programmed DNA-based molecular computer operated on magnetic particle surface in test-tube

    Institute of Scientific and Technical Information of China (English)

    ZHAO Jian; ZHANG Zhizhou; SHI Yongyong; Li Xiuxia; HE Lin

    2004-01-01

    The postgenomic era has seen an emergence of new applications of DNA manipulation technologies, including DNA-based molecular computing. Surface DNA computing has already been reported in a number of studies that, however, all employ different mechanisms other than automaton functions. Here we describe a programmable DNA surface-computing device as a Turing machine-like finite automaton. The laboratory automaton is primarily composed of DNA (inputs, output-detectors, transition molecules as software), DNA manipulating enzymes and buffer system that solve artificial computational problems autonomously. When fluoresceins were labeled in the 5′ end of (-) strand of the input molecule, direct observation of all reaction intermediates along the time scale was made so that the dynamic process of DNA computing could be conveniently visualized. The features of this study are: (i) achievement of finite automaton functions by linearly programmed DNA computer operated on magnetic particle surface and (ii) direct detection of all DNA computing intermediates by capillary electrophoresis. Since DNA computing has the massive parallelism and feasibility for automation, this achievement sets a basis for large-scale implications of DNA computing for functional genomics in the near future.

  10. A superstructure-based electrochemical assay for signal-amplified detection of DNA methyltransferase activity.

    Science.gov (United States)

    Zhang, Hui; Yang, Yin; Dong, Huilei; Cai, Chenxin

    2016-12-15

    DNA methyltransferase (MTase) activity is highly correlated with the occurrence and development of cancer. This work reports a superstructure-based electrochemical assay for signal-amplified detection of DNA MTase activity using M.SssI as an example. First, low-density coverage of DNA duplexes on the surface of the gold electrode was achieved by immobilized mercaptohexanol, followed by immobilization of DNA duplexes. The duplex can be cleaved by BstUI endonuclease in the absence of DNA superstructures. However, the cleavage is blocked after the DNA is methylated by M.SssI. The DNA superstructures are formed with the addition of helper DNA. By using an electroactive complex, RuHex, which can bind to DNA double strands, the activity of M.SssI can be quantitatively detected by differential pulse voltammetry. Due to the high site-specific cleavage by BstUI and signal amplification by the DNA superstructure, the biosensor can achieve ultrasensitive detection of DNA MTase activity down to 0.025U/mL. The method can be used for evaluation and screening of the inhibitors of MTase, and thus has potential in the discovery of methylation-related anticancer drugs.

  11. Label-free DNA biosensor based on resistance change of platinum nanoparticles assemblies.

    Science.gov (United States)

    Skotadis, Evangelos; Voutyras, Konstantinos; Chatzipetrou, Marianneza; Tsekenis, Georgios; Patsiouras, Lampros; Madianos, Leonidas; Chatzandroulis, Stavros; Zergioti, Ioanna; Tsoukalas, Dimitris

    2016-07-15

    A novel nanoparticle based biosensor for the fast and simple detection of DNA hybridization events is presented. The sensor utilizes hybridized DNA's charge transport properties, combining them with metallic nanoparticle networks that act as nano-gapped electrodes. The DNA hybridization events can be detected by a significant reduction in the sensor's resistance due to the conductive bridging offered by hybridized DNA. By modifying the nanoparticle surface coverage, which can be controlled experimentally being a function of deposition time, and the structural properties of the electrodes, an optimized biosensor for the in situ detection of DNA hybridization events is ultimately fabricated. The fabricated biosensor exhibits a wide response range, covering four orders of magnitude, a limit of detection of 1nM and can detect a single base pair mismatch between probe and complementary DNA.

  12. Dynamic GnRH- and hCG-testing

    DEFF Research Database (Denmark)

    Bang, A Kirstine; Nordkap, Loa; Almstrup, Kristian

    2017-01-01

    was illustrated by results from 45 patients suspected of disordered hypothalamic-pituitary-gonadal axis. 3. METHODS: Baseline, stimulated, relative and absolute changes in serum FSH and LH were determined by ultrasensitive TRIFMA, and testosterone was determined by LC-MS/MS. 4. RESULTS: For the reference group LH...... insufficiency, compared to the relative increase. 5. CONCLUSIONS: We provide novel reference ranges for GnRH and hCG test in healthy men, which allows future diagnostic evaluation of hypothalamic-pituitary-gonadal disorders in men....

  13. Fundamental Study about the Landscape Estimation and Analysis by CG

    Science.gov (United States)

    Nakashima, Yoshio; Miyagoshi, Takashi; Takamatsu, Mamoru; Sassa, Kazuhiro

    In recent years, the color of advertising signboards or vending machines on the streets should be harmonized with the surrounding landscape. In this study, we investigated how the colors (red and white) of the vending machines virtually installed by CG would affect the traditional landscape. 20 subjects estimated landscape samples in Hida-Furukawa by the SD technique. The result of our experiment shows that the vending machines have great influence on the surrounding landscape. On the other hand, we have confirmed that they can harmonize with the circumference landscape by the color to use.

  14. Synthesis, photochemical properties and DNA binding studies of dna cleaving agents based on chiral dipyridine dihydrodioxins salts

    Science.gov (United States)

    Shamaev, Alexei

    activated by UV-light. The mechanism of o-quinone release and intramolecular ET was studied in detail by methods of Ultrafast Transient Absortion Spectroscopy and supported by high-level quantum mechanical calculations. The binding properties of chiral intercalators based on PDHD to various DNA oligonucleotides were studied by various methods and DNA cleavage properties indicating strong binding and cleaving ability of the synthesized PDHDs. Also, a new method for synthesis of cyclohexa[e]pyrenes which possibly capable of intramolecular ET and electron transfer-oxidative stress (ET-OS) DNA cleavage was developed and partially accomplished.

  15. The new base excision repair pathway in mammals mediated by tyrosyl-DNA-phosphodiesterase 1

    Directory of Open Access Journals (Sweden)

    Lavrik O. I.

    2012-06-01

    Full Text Available Human tyrosyl-DNA phosphodiesterase 1 (Tdp1 hydrolyzes the phosphodiester bond at a DNA 3' end linked to a tyrosyl moiety and has been implicated in the repair of Topoisomerase I (TopI-DNA covalent complexes. Tdp1 can also hydrolyze other 3' end DNA alterations including 3' phosphoglycolate and 3' abasic (AP sites, and exhibits the 3' nucleosidase activity indicating that it may function as a general 3' end-processing DNA repair enzyme. Recently we have shown a new Tdp1 activity generating DNA strand break with the 3' phosphate termini from the AP site. AP sites are formed spontaneously and are inevitable intermediates during base excision repair of DNA base damages. AP sites are both mutagenic and cytotoxic, and key enzymes for their removal are AP endonucleases. However, AP endonuclease independent repair, initiated by DNA glycosylases performing beta, delta-elimination cleavage of the AP sites, has been described in mammalian cells. Here, we describe another AP endonuclease independent repair pathway for removal of AP sites that is initiated by tyrosyl phosphodiesterase Tdp1. We propose that repair is completed by the action of a polynucleotide kinase, a DNA polymerase and finally a DNA ligase to seal the gap.

  16. DNA-Based Synthesis and Assembly of Organized Iron Oxide Nanostructures

    Science.gov (United States)

    Khomutov, Gennady B.

    Organized bio-inorganic and hybrid bio-organic-inorganic nanostructures consisting of iron oxide nanoparticles and DNA complexes have been formed using methods based on biomineralization, interfacial and bulk phase assembly, ligand exchange and substitution, Langmuir-Blodgett technique, DNA templating and scaffolding. Interfacially formed planar DNA complexes with water-insoluble amphiphilic polycation or intercalator Langmuir monolayers were prepared and deposited on solid substrates to form immobilized DNA complexes. Those complexes were then used for the synthesis of organized DNA-based iron oxide nanostructures. Planar net-like and circular nanostructures of magnetic Fe3O4 nanoparticles were obtained via interaction of cationic colloid magnetite nanoparticles with preformed immobilized DNA/amphiphilic polycation complexes of net-like and toroidal morphologies. The processes of the generation of iron oxide nanoparticles in immobilized DNA complexes via redox synthesis with various iron sources of biological (ferritin) and artificial (FeCl3) nature have been studied. Bulk-phase complexes of magnetite nanoparticles with biomolecular ligands (DNA, spermine) were formed and studied. Novel nano-scale organized bio-inorganic nanostructures - free-floating sheet-like spermine/magnetite nanoparticle complexes and DNA/spermine/magnetite nanoparticle complexes were synthesized in bulk aqueous phase and the effect of DNA molecules on the structure of complexes was discovered.

  17. Luminescent Iridium(III) Complex Labeled DNA for Graphene Oxide-Based Biosensors.

    Science.gov (United States)

    Zhao, Qingcheng; Zhou, Yuyang; Li, Yingying; Gu, Wei; Zhang, Qi; Liu, Jian

    2016-02-02

    There has been growing interest in utilizing highly photostable iridium(III) complexes as new luminescent probes for biotechnology and life science. Herein, iridium(III) complex with carboxyl group was synthesized and activated with N-hydroxysuccinimide, followed by tagging to the amino terminate of single-stranded DNA (ssDNA). The Ir-ssDNA probe was further combined with graphene oxide (GO) nanosheets to develop a GO-based biosensor for target ssDNA detection. The quenching efficiency of GO, and the photostability of iridium(III) complex and GO-Ir-ssDNA biosensor, were also investigated. On the basis of the high luminescence quenching efficiency of GO toward iridium(III) complex, the GO-Ir-ssDNA biosensor exhibited minimal background signals, while strong emission was observed when Ir-ssDNA desorbed from GO nanosheets and formed a double helix with the specific target, leading to a high signal-to-background ratio. Moreover, it was found that luminescent intensities of iridium(III) complex and GO-Ir-ssDNA biosensor were around 15 and 3 times higher than those of the traditional carboxyl fluorescein (FAM) dye and the GO-FAM-ssDNA biosensor after UV irradiation, respectively. Our study suggested the sensitive and selective Ir-ssDNA probe was suitable for the development of highly photostable GO-based detection platforms, showing promise for application beyond the OLED (organic light emitting diode) area.

  18. CUPRAC colorimetric and electroanalytical methods determining antioxidant activity based on prevention of oxidative DNA damage.

    Science.gov (United States)

    Uzunboy, Seda; Çekiç, Sema Demirci; Eksin, Ece; Erdem, Arzum; Apak, Reşat

    2017-02-01

    An unbalanced excess of oxygen/nitrogen species (ROS/RNS) can give oxidative hazard to DNA and other biomacromolecules under oxidative stress conditions. While the 'comet' assay for measuring DNA damage is neither specific nor practical, monitoring oxidative changes on individual DNA bases and other oxidation products needs highly specialized equipment and operators. Thus, we developed a modified CUPRAC (cupric ion reducing antioxidant capacity) colorimetric method to determine the average total damage on DNA produced by Fenton oxidation, taking advantage of the fact that the degradation products of DNA but not the original macromolecule is CUPRAC-responsive. The DNA-protective effects of water-soluble antioxidants were used to devise a novel antioxidant activity assay, considered to be physiologically more realistic than those using artificial probes. Our method, based on the measurement of DNA oxidative products with CUPRAC colorimetry proved to be 2 orders-of-magnitude more sensitive than the widely used TBARS (thiobarbituric acid-reactive substances) colorimetric assay used as reference. Additionally, the DNA damage was electrochemically investigated using pencil graphite electrodes (PGEs) as DNA sensor platform in combination with differential pulse voltammetry (DPV). The interaction of the radical species with DNA in the absence/presence of antioxidants was detected according to the changes in guanine oxidation signal.

  19. DNA quantification based on FRET realized by combination with surfactant CPB.

    Science.gov (United States)

    Liu, Chunxia; Wang, Lei; Jiang, Wei

    2010-04-15

    In this work, we developed a novel DNA quantitative analysis based on fluorescence resonance energy transfer (FRET) realized by combination with a surfactant CPB. The approach was capable of detecting long-stranded DNA in a separation-free format. A sandwich-type FAM-c-DNA-t-DNA-r-DNA-TAMRA conjugate was first formed by the capture probe tagged with FAM, the reporter probe tagged with TAMRA and the target DNA through hybridization. The donor (FAM) and the acceptor (TAMRA) were bridged to afford a FRET system. Subsequently, an addition of the cationic surfactant CPB to the system resulted in a substantial change of the microenvironment and an effective condensation of DNA strands. Consequently, without altering the component of the double strands, an enhanced acceptor fluorescence signal from FRET was achieved and a quantification of the target DNA containing 30 bases was enabled. Under the optimal experimental conditions, an excellent linear relationship between the increase of acceptor fluorescent peak area and the target DNA concentration was obtained over the range from 1.0 x 10(-7) to 3.0 x 10(-9) mol L(-1). The proposed approach offered adequate sensitivity for the detection of the target DNA at 1.0 x 10(-9) mol L(-1).

  20. Predicting DNA-binding sites of proteins based on sequential and 3D structural information.

    Science.gov (United States)

    Li, Bi-Qing; Feng, Kai-Yan; Ding, Juan; Cai, Yu-Dong

    2014-06-01

    Protein-DNA interactions play important roles in many biological processes. To understand the molecular mechanisms of protein-DNA interaction, it is necessary to identify the DNA-binding sites in DNA-binding proteins. In the last decade, computational approaches have been developed to predict protein-DNA-binding sites based solely on protein sequences. In this study, we developed a novel predictor based on support vector machine algorithm coupled with the maximum relevance minimum redundancy method followed by incremental feature selection. We incorporated not only features of physicochemical/biochemical properties, sequence conservation, residual disorder, secondary structure, solvent accessibility, but also five three-dimensional (3D) structural features calculated from PDB data to predict the protein-DNA interaction sites. Feature analysis showed that 3D structural features indeed contributed to the prediction of DNA-binding site and it was demonstrated that the prediction performance was better with 3D structural features than without them. It was also shown via analysis of features from each site that the features of DNA-binding site itself contribute the most to the prediction. Our prediction method may become a useful tool for identifying the DNA-binding sites and the feature analysis described in this paper may provide useful insights for in-depth investigations into the mechanisms of protein-DNA interaction.

  1. Transgenerational inheritance: Models and mechanisms of non-DNA sequence-based inheritance.

    Science.gov (United States)

    Miska, Eric A; Ferguson-Smith, Anne C

    2016-10-07

    Heritability has traditionally been thought to be a characteristic feature of the genetic material of an organism-notably, its DNA. However, it is now clear that inheritance not based on DNA sequence exists in multiple organisms, with examples found in microbes, plants, and invertebrate and vertebrate animals. In mammals, the molecular mechanisms have been challenging to elucidate, in part due to difficulties in designing robust models and approaches. Here we review some of the evidence, concepts, and potential mechanisms of non-DNA sequence-based transgenerational inheritance. We highlight model systems and discuss whether phenotypes are replicated or reconstructed over successive generations, as well as whether mechanisms operate at transcriptional and/or posttranscriptional levels. Finally, we explore the short- and long-term implications of non-DNA sequence-based inheritance. Understanding the effects of non-DNA sequence-based mechanisms is key to a full appreciation of heritability in health and disease.

  2. Providing Source Code Level Portability Between CPU and GPU with MapCG

    Institute of Scientific and Technical Information of China (English)

    Chun-Tao Hong; De-Hao Chen; Yu-Bei Chen; Wen-Guang Chen; Wei-Min Zheng; Hai-Bo Lin

    2012-01-01

    Graphics processing units (GPU) have taken an important role in the general purpose computing market in recent years.At present,the common approach to programming GPU units is to write GPU specific code with low level GPU APIs such as CUDA.Although this approach can achieve good performance,it creates serious portability issues as programmers are required to write a specific version of the code for each potential target architecture.This results in high development and maintenance costs.We believe it is desirable to have a programming model which provides source code portability between CPUs and GPUs,as well as different GPUs.This would allow programmers to write one version of the code,which can be compiled and executed on either CPUs or GPUs efficiently without modification.In this paper,we propose MapCG,a MapReduce framework to provide source code level portability between CPUs and GPUs.In contrast to other approaches such as OpenCL,our framework,based on MapReduce,provides a high level programming model and makes programming much easier.We describe the design of MapCG,including the MapReduce-style high-level programming framework and the runtime system on the CPU and GPU.A prototype of the MapCG runtime,supporting multi-core CPUs and NVIDIA GPUs,was implemented. Our experimental results show that this implementation can execute the same source code efficiently on multi-core CPU platforms and GPUs,achieving an average speedup of 1.6~2.5x over previous implementations of MapReduce on eight commonly used applications.

  3. DNA methylation-based variation between human populations.

    Science.gov (United States)

    Kader, Farzeen; Ghai, Meenu

    2017-02-01

    Several studies have proved that DNA methylation affects regulation of gene expression and development. Epigenome-wide studies have reported variation in methylation patterns between populations, including Caucasians, non-Caucasians (Blacks), Hispanics, Arabs, and numerous populations of the African continent. Not only has DNA methylation differences shown to impact externally visible characteristics, but is also a potential biomarker for underlying racial health disparities between human populations. Ethnicity-related methylation differences set their mark during early embryonic development. Genetic variations, such as single-nucleotide polymorphisms and environmental factors, such as age, dietary folate, socioeconomic status, and smoking, impacts DNA methylation levels, which reciprocally impacts expression of phenotypes. Studies show that it is necessary to address these external influences when attempting to differentiate between populations since the relative impacts of these factors on the human methylome remain uncertain. The present review summarises several reported attempts to establish the contribution of differential DNA methylation to natural human variation, and shows that DNA methylation could represent new opportunities for risk stratification and prevention of several diseases amongst populations world-wide. Variation of methylation patterns between human populations is an exciting prospect which inspires further valuable research to apply the concept in routine medical and forensic casework. However, trans-generational inheritance needs to be quantified to decipher the proportion of variation contributed by DNA methylation. The future holds thorough evaluation of the epigenome to understand quantification, heritability, and the effect of DNA methylation on phenotypes. In addition, methylation profiling of the same ethnic groups across geographical locations will shed light on conserved methylation differences in populations.

  4. Sample processing for DNA chip array-based analysis of enterohemorrhagic Escherichia coli (EHEC)

    OpenAIRE

    Enfors Sven-Olof; Wegrzyn Grzegorz; Basselet Pascal; Gabig-Ciminska Magdalena

    2008-01-01

    Abstract Background Exploitation of DNA-based analyses of microbial pathogens, and especially simultaneous typing of several virulence-related genes in bacteria is becoming an important objective of public health these days. Results A procedure for sample processing for a confirmative analysis of enterohemorrhagic Escherichia coli (EHEC) on a single colony with DNA chip array was developed and is reported here. The protocol includes application of fragmented genomic DNA from ultrasonicated co...

  5. Phylogenetic relationships of the Gomphales based on nuc-25S-rDNA, mit-12S-rDNA, and mit-atp6-DNA combined sequences

    Science.gov (United States)

    Admir J. Giachini; Kentaro Hosaka; Eduardo Nouhra; Joseph Spatafora; James M. Trappe

    2010-01-01

    Phylogenetic relationships among Geastrales, Gomphales, Hysterangiales, and Phallales were estimated via combined sequences: nuclear large subunit ribosomal DNA (nuc-25S-rDNA), mitochondrial small subunit ribosomal DNA (mit-12S-rDNA), and mitochondrial atp6 DNA (mit-atp6-DNA). Eighty-one taxa comprising 19 genera and 58 species...

  6. In vitro measurement of DNA base excision repair in isolated mitochondria.

    Science.gov (United States)

    Page, Melissa M; Stuart, Jeffrey A

    2009-01-01

    Mitochondrial DNA (mtDNA) is in relatively close proximity to reactive oxygen species (ROS) arising from spontaneous superoxide formation during respiration. As a result, it sustains oxidative damage that may include base modifications, base loss, and strand breaks. mtDNA replication past sites of oxidative damage can result in the introduction of mutations. mtDNA mutations are associated with various human diseases and can manifest as loss of bioenergetic function. DNA repair processes exist in mitochondria from apparently all metazoans. A fully functional DNA base excision repair (BER) pathway is present in mitochondria of vertebrates. This pathway is catalyzed by a number of DNA glycosylases, an AP endonuclease, polymerase gamma, and a DNA ligase. This chapter outlines the step-by-step protocols for isolating mitochondrial fractions, from a number of different model organisms, of sufficient purity to allow mtDNA repair activities to be measured. It details in vitro assays for the measurement of BER enzyme activities in lysates prepared from isolated mitochondria.

  7. Advancing DNA-based Nanotechnology Capabilities and Applications

    Science.gov (United States)

    Marchi, Alexandria N.

    Biological systems have inspired interest in developing artificial molecular self-assembly techniques that imitate nature's ability to harness chemical forces to specifically position atoms within intricate assemblies. Of the biomolecules used to mimic nature's abilities, nucleic acids have gained special attention. Specifically, deoxyribonucleic acid is a stable molecule with a readily accessible code that exhibits predictable and programmable intermolecular interactions. These properties are exploited in the revolutionary structural DNA nanotechnology method known as scaffolded DNA origami. For DNA origami to establish itself as a widely used method for creating self-assembling, complex, functional materials, current limitations need to be overcome and new methods need to be established to move forward with developing structures for diverse applications in many fields. The limitations discussed in this dissertation include 1) pushing the scale of well-formed, fully-addressable origami to two and seven times the size of conventional origami, 2) testing cost-effective staple strand synthesis methods for producing pools of oligos for a specified origami, and 3) engineering mechanical properties using non-natural nucleotides in DNA assemblies. After accomplishing the above, we're able to design complex DNA origami structures that incorporate many of the current developments in the field into a useful material with applicability in wide-ranging fields, namely cell biology and photonics.

  8. Protein sequence for clustering DNA based on Artificial Neural Networks

    Directory of Open Access Journals (Sweden)

    Gamal. F. Elhadi

    2012-01-01

    Full Text Available DNA is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms and some viruses. Clustering is a process that groups a set of objects into clusters so that the similarity among objects in the same cluster is high, while that among the objects in different clusters is low. In this paper, we proposed an approach for clustering DNA sequences using Self-Organizing Map (SOM algorithm and Protein Sequence. The main objective is to analyze biological data and to bunch DNA to many clusters more easily and efficiently. We use the proposed approach to analyze both large and small amount of input DNA sequences. The results show that the similarity of the sequences does not depend on the amount of input sequences. Our approach depends on evaluating the degree of the DNA sequences similarity using the hierarchal representation Dendrogram. Representing large amount of data using hierarchal tree gives the ability to compare large sequences efficiently

  9. Statistical Moments Extracted from Eight Bins Formed by CG Partitioning of Histogram Modified using Linear Equations

    Directory of Open Access Journals (Sweden)

    H. B. Kekre

    2012-09-01

    Full Text Available This paper explores the novel idea for feature extraction based on bins approach for CBIR. This work has fulfilled all the criterion of efficient feature extraction method like dimensionality reduction, fast extraction and efficient retrieval. Main idea used in feature extraction is based on the histogram and the linear functions used to modify it. Each BMP image in database is separated in R, G and B planes. We have calculated the histogram for each of them which are modified using linear equations. These modified histograms are partitioned using CG so that mass of intensities of the image pixels will be distributed uniformly in two parts. This CG partitioning of three image planes leads to generate the eight bins. Information extracted from these bins is in the form of statistical first four absolute moments namely MEAN (MEAN, Standard deviation (STD, Skewness (SKEW, and Kurtosis (KURTO. Each of these moments are computed separately for R, G and B colors. This generates four types of feature vectors of dimension eight. Database of 2000 BMP images is used for the experimentation. Multiple feature vector databases are prepared as part of preprocessing work of this CBIR system. Comparison of query and database feature vector is carried out using three similarity measures namely Euclidean distance (ED, Absolute distance (AD and Cosine correlation distance (CD. To evaluate the retrieval efficiency of this system we have used three parameters, Precision Recall Cross over Point (PRCP, Longest String (LS and Length of String to Retrieve all Relevant (LSRR.

  10. DNA origami-based nanoribbons: assembly, length distribution, and twist

    Energy Technology Data Exchange (ETDEWEB)

    Jungmann, Ralf; Scheible, Max; Kuzyk, Anton; Pardatscher, Guenther; Simmel, Friedrich C [Lehrstuhl fuer Bioelektronik, Physik-Department and ZNN/WSI, Technische Universitaet Muenchen, Am Coulombwall 4a, 85748 Garching (Germany); Castro, Carlos E, E-mail: simmel@ph.tum.de [Labor fuer Biomolekulare Nanotechnologie, Physik-Department and ZNN/WSI, Technische Universitaet Muenchen, Am Coulombwall 4a, 85748 Garching (Germany)

    2011-07-08

    A variety of polymerization methods for the assembly of elongated nanoribbons from rectangular DNA origami structures are investigated. The most efficient method utilizes single-stranded DNA oligonucleotides to bridge an intermolecular scaffold seam between origami monomers. This approach allows the fabrication of origami ribbons with lengths of several micrometers, which can be used for long-range ordered arrangement of proteins. It is quantitatively shown that the length distribution of origami ribbons obtained with this technique follows the theoretical prediction for a simple linear polymerization reaction. The design of flat single layer origami structures with constant crossover spacing inevitably results in local underwinding of the DNA helix, which leads to a global twist of the origami structures that also translates to the nanoribbons.

  11. Anomalous extinction behaviour towards the Type Ia SN 2003cg

    CERN Document Server

    Elias-Rosa, N; Benetti, S; Cappellaro, E; Harutyunyan, A; Hillebrandt, W; Kotak, R; Mazzali, P A; Meikle, W P S; Navasardyan, H; Pastorello, A; Patat, F; Pignata, G; Qiu, Y; Salvo, M E; Stehle, M; Turatto, M

    2006-01-01

    We present optical and near-infrared photometry and spectroscopy of the Type Ia SN 2003cg, which exploded in the nearby galaxy NGC 3169. The observations cover a period between -8.5 and +414 days post-maximum. SN 2003cg is a normal but highly-reddened Type Ia event. Its B magnitude at maximum B_max = 15.94+/-0.04 and Delta m_15(B)_obs = 1.12+/-0.04 (Delta m_15(B)_intrinsic = 1.25+/-0.05). Allowing R_v to become a free parameter within the Cardelli et al. (1989) extinction law, simultaneous matches to a range of colour curves of normal SNe Ia yielded E(B-V) = 1.33+/-0.11, and R_v = 1.80+/-0.19. While the value obtained for R_v is small, such values have been invoked in the past, and may imply a grain size which is small compared with the average value for the local ISM.

  12. The interaction of taurine-salicylaldehyde Schiff base copper(II) complex with DNA and the determination of DNA using the complex as a fluorescence probe

    Science.gov (United States)

    Zhang, Xiaoyan; Wang, Yong; Zhang, Qianru; Yang, Zhousheng

    2010-09-01

    The interaction of taurine-salicylaldehyde Schiff base copper(II) (Cu(TSSB) 22+) complex with DNA was explored by using UV-vis, fluorescence spectrophotometry, and voltammetry. In pH 7.4 Tris-HCl buffer solution, the binding constant of the Cu(TSSB) 22+ complex interaction with DNA was 3.49 × 10 4 L mol -1. Moreover, due to the fluorescence enhancing of Cu(TSSB) 22+ complex in the presence of DNA, a method for determination of DNA with Cu(TSSB) 22+ complex as a fluorescence probe was developed. The fluorescence spectra indicated that the maximum excitation and emission wavelength were 389 nm and 512 nm, respectively. Under optimal conditions, the calibration graphs are linear over the range of 0.03-9.03 μg mL -1 for calf thymus DNA (CT-DNA), 0.10-36 μg mL -1 for yeast DNA and 0.01-10.01 μg mL -1 for salmon DNA (SM-DNA), respectively. The corresponding detection limits are 7 ng mL -1 for CT-DNA, 3 ng mL -1 for yeast DNA and 3 ng mL -1 for SM-DNA. Using this method, DNA in synthetic samples was determined with satisfactory results.

  13. Exponential quadruplex priming amplification for DNA-based isothermal diagnostics.

    Science.gov (United States)

    Partskhaladze, Tamar; Taylor, Adam; Lomidze, Levan; Gvarjaladze, David; Kankia, Besik

    2015-02-01

    Polymerase chain reaction (PCR) is a method of choice for molecular diagnostics. However, PCR relies on thermal cycling, which is not compatible with the goals of point-of-care diagnostics. A simple strategy to turn PCR into an isothermal method would be to use specific primers, which upon polymerase elongation can self-dissociate from the primer-binding sites. We recently demonstrated that a monomolecular DNA quadruplex, GGGTGGGTGGGTGGG, meets these requirements, which led to the development of the linear versions of quadruplex priming amplification (QPA). Here we demonstrate exponential version of isothermal QPA, which allows an unprecedented 10(10)-fold amplification of DNA signal in less than 40 min.

  14. Binding of copper(II) polypyridyl complexes to DNA and consequences for DNA-based asymmetric catalysis.

    Science.gov (United States)

    Draksharapu, Apparao; Boersma, Arnold J; Leising, Miriam; Meetsma, Auke; Browne, Wesley R; Roelfes, Gerard

    2015-02-28

    The interaction between salmon testes DNA (st-DNA) and a series of Cu(II) polypyridyl complexes, i.e. [Cu(dmbpy)(NO3)2] (1) (dmbpy = 4,4'-dimethyl-2,2'-bipyridine), [Cu(bpy)(NO3)2] (2) (bpy = 2,2'-bipyridine), [Cu(phen)(NO3)2] (3) (phen = phenanthroline), [Cu(terpy)(NO3)2]·H2O (4) (terpy = 2,2':6',2″-terpyridine), [Cu(dpq)(NO3)2] (5) (dpq = dipyrido-[3,2-d:2',3'-f]-quinoxaline) and [Cu(dppz)(NO3)2] (6) (dppz = dipyrido[3,2-a:2',3'-c]phenazine) was studied by UV/Vis absorption, Circular Dichroism, Linear Dichroism, EPR, Raman and (UV and vis) resonance Raman spectroscopies and viscometry. These complexes catalyse enantioselective C-C bond forming reactions in water with DNA as the source of chirality. Complex 1 crystallizes as an inorganic polymer with nitrate ligands bridging the copper ions, which adopt essentially a distorted square pyramidal structure with a fifth bridging nitrate ligand at the axial position. Raman spectroscopy indicates that in solution the nitrate ligands in 1, 2, 3 and 4 are displaced by solvent (H2O). For complex 1, multiple supramolecular species are observed in the presence of st-DNA in contrast to the other complexes, which appear to interact relatively uniformly as a single species predominantly, when st-DNA is present. Overall the data suggest that complexes 1 and 2 engage primarily through groove binding with st-DNA while 5 and 6 undergo intercalation. For complexes 3 and 4 the data indicates that both groove binding and intercalation takes place, albeit primarily intercalation. Although it is tempting to conclude that the groove binders give highest ee and rate acceleration, it is proposed that the flexibility and dynamics in binding of Cu(II) complexes to DNA are key parameters that determine the outcome of the reaction. These findings provide insight into the complex supramolecular structure of these DNA-based catalysts.

  15. A surface-based DNA algorithm for the minimal vertex cover problem

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    DNA computing was proposed for solving a class of intractable computational problems, of which the computing time will grow exponentially with the problem size. Up to now, many achievements have been made to improve its performance and increase its reliability. It has been shown many times that the surface-based DNA computing technique has very low error rate, but the technique has not been widely used in the DNA computing algorithms design. In this paper, a surface-based DNA computing algorithm for minimal vertex cover problem, a problem well-known for its exponential difficulty, is introduced. This work provides further evidence for the ability of surface-based DNA computing in solving NP-complete problems.

  16. Branched DNA-based Alu quantitative assay for cell-free plasma DNA levels in patients with sepsis or systemic inflammatory response syndrome.

    Science.gov (United States)

    Hou, Yan-Qiang; Liang, Dong-Yu; Lou, Xiao-Li; Zhang, Mei; Zhang, Zhen-huan; Zhang, Lu-rong

    2016-02-01

    Cell-free circulating DNA (cf-DNA) can be detected by various of laboratory techniques. We described a branched DNA-based Alu assay for measuring cf-DNA in septic patients. Compared to healthy controls and systemic inflammatory response syndrome (SIRS) patients, serum cf-DNA levels were significantly higher in septic patients (1426.54 ± 863.79 vs 692.02 ± 703.06 and 69.66 ± 24.66 ng/mL). The areas under the receiver operating characteristic curve of cf-DNA for normal vs sepsis and SIRS vs sepsis were 0.955 (0.884-1.025), and 0.856 (0.749-0.929), respectively. There was a positive correlation between cf-DNA and interleukin 6 or procalcitonin or Acute Physiology and Chronic Health Evaluation II. The cf-DNA concentration was higher in intensive care unit nonsurviving patients compared to surviving patients (2183.33 ± 615.26 vs 972.46 ± 648.36 ng/mL; P DNA-based Alu assays are feasible and useful to quantify serum cf-DNA levels. Increased cf-DNA levels in septic patients might complement C-reactive protein and procalcitonin in a multiple marker format. Cell-free circulating DNA might be a new marker in discrimination of sepsis and SIRS.

  17. hCG stimulates angiogenic signals in lymphatic endothelial and circulating angiogenic cells.

    Science.gov (United States)

    Schanz, Andrea; Lukosz, Margarete; Hess, Alexandra P; Baston-Büst, Dunja M; Krüssel, Jan S; Heiss, Christian

    2015-08-01

    Human chorionic gonadotropin (hCG) has long been associated with the initiation and maintenance of pregnancy, where angiogenesis plays an important role. However, the function of hCG in angiogenesis and the recruitment of vascular active cells are not fully understood. In this study, the role of hCG and its receptor in circulating angiogenic and human endothelial cells, including lymphatic, uterine microvascular, and umbilical vein endothelial cells, was examined. Immunohistochemistry and immunoblot analysis were used to detect LH/hCG receptor expression and the expression of hCG-induced angiogenic molecules. HIF-1α was determined via ELISA and downstream molecules, such as CXCL12 and CXCR4, via real-time PCR. Chemotaxis was analyzed using Boyden chambers. Our results show that the LH/hCG receptor was present in all tested cells. Furthermore, hCG was able to stimulate LH/hCG-receptor-specific migration in a dose-dependent fashion and induce key angiogenic molecules, including HIF-1α, CXCL12, and CXCR4. In conclusion, our findings underscore the importance of hCG as one of the first angiogenic molecules produced by the conceptus. hCG itself alters endothelial motility, recruitment, and expression of pro-angiogenic molecules and may therefore play an important role in vascular adaption during implantation and early placental formation. Copyright © 2015. Published by Elsevier Ireland Ltd.

  18. Single-strand DNA detection using a planar photonic-crystal-waveguide-based sensor.

    Science.gov (United States)

    Toccafondo, V; García-Rupérez, J; Bañuls, M J; Griol, A; Castelló, J G; Peransi-Llopis, S; Maquieira, A

    2010-11-01

    We report an experimental demonstration of single-strand DNA (ssDNA) detection at room temperature using a photonic-crystal-waveguide-based optical sensor. The sensor surface was previously biofunctionalized with ssDNA probes to be used as specific target receptors. Our experiments showed that it is possible to detect these hybridization events using planar photonic-crystal structures, reaching an estimated detection limit as low as 19.8 nM for the detection of the complementary DNA strand.

  19. A high-throughput fluorescence resonance energy transfer-based assay for DNA ligase.

    Science.gov (United States)

    Shapiro, Adam B; Eakin, Ann E; Walkup, Grant K; Rivin, Olga

    2011-06-01

    DNA ligase is the enzyme that catalyzes the formation of the backbone phosphodiester bond between the 5'-PO(4) and 3'-OH of adjacent DNA nucleotides at single-stranded nicks. These nicks occur between Okazaki fragments during replication of the lagging strand of the DNA as well as during DNA repair and recombination. As essential enzymes for DNA replication, the NAD(+)-dependent DNA ligases of pathogenic bacteria are potential targets for the development of antibacterial drugs. For the purposes of drug discovery, a high-throughput assay for DNA ligase activity is invaluable. This article describes a straightforward, fluorescence resonance energy transfer-based DNA ligase assay that is well suited for high-throughput screening for DNA ligase inhibitors as well as for use in enzyme kinetics studies. Its use is demonstrated for measurement of the steady-state kinetic constants of Haemophilus influenzae NAD(+)-dependent DNA ligase and for measurement of the potency of an inhibitor of this enzyme.

  20. Enhancing magnetic nanoparticle-based DNA transfection: Intracellular-active cassette features

    Science.gov (United States)

    Vernon, Matthew Martin

    Efficient plasmid DNA transfection of embryonic stem cells, mesenchymal stem cells, neural cell lines and the majority of primary cell lines is a current challenge in gene therapy research. Magnetic nanoparticle-based DNA transfection is a gene vectoring technique that is promising because it is capable of outperforming most other non-viral transfection methods in terms of both transfection efficiency and cell viability. The nature of the DNA vector implemented depends on the target cell phenotype, where the particle surface chemistry and DNA binding/unbinding kinetics of the DNA carrier molecule play a critical role in the many steps required for successful gene transfection. Accordingly, Neuromag, an iron oxide/polymer nanoparticle optimized for transfection of neural phenotypes, outperforms many other nanoparticles and lipidbased DNA carriers. Up to now, improvements to nanomagnetic transfection techniques have focused mostly on particle functionalization and transfection parameter optimization (cell confluence, growth media, serum starvation, magnet oscillation parameters, etc.). None of these parameters are capable of assisting the nuclear translocation of delivered plasmid DNA once the particle-DNA complex is released from the endosome and dissociates in the cell's cytoplasm. In this study, incorporation of a DNA targeting sequence (DTS) feature in the transfecting plasmid DNA confers improved nuclear translocation, demonstrating significant improvement in nanomagnetic transfection efficiency in differentiated SH-SY5Y neuroblastoma cells. Other parameters, such as days in vitro, are also found to play a role and represent potential targets for further optimization.

  1. Base-resolution DNA methylation landscape of zebrafish brain and liver

    Directory of Open Access Journals (Sweden)

    Aniruddha Chatterjee

    2014-12-01

    To our knowledge, these datasets are the only RRBS datasets and base-resolution DNA methylation data available at this time for zebrafish brain and liver. These datasets could serve as a resource for future studies to document the functional role of DNA methylation in zebrafish. In addition, these datasets could be used as controls while performing analysis on treated samples.

  2. Size-based molecular diagnostics using plasma DNA for noninvasive prenatal testing

    NARCIS (Netherlands)

    Yu, S.C.; Chan, K.C.; Zheng, Y.W.; Jiang, P.; Liao, G.J.; Sun, H; Akolekar, R.; Leung, T.Y.; Go, A.T.; Vugt, J.M.G. van; Minekawa, R.; Oudejans, C.B.; Nicolaides, K.H.; Chiu, R.W.; Lo, Y.M.

    2014-01-01

    Noninvasive prenatal testing using fetal DNA in maternal plasma is an actively researched area. The current generation of tests using massively parallel sequencing is based on counting plasma DNA sequences originating from different genomic regions. In this study, we explored a different approach th

  3. Investigation of the charge effect on the electrochemical transduction in a quinone-based DNA sensor

    DEFF Research Database (Denmark)

    Reisberg, S.; Piro, B.; Noel, V.

    2008-01-01

    To elucidate the mechanism involved in the electrochemical transduction process of a conducting polymer-based DNA sensor, peptide nucleic acids (PNA) were used. PNA are DNA analogues having similar hybridization properties but are neutral. This allows to discriminate the electrostatic effect of D...

  4. Quantum dot based DNA nanosensors for amplification-free detection of human topoisomerase I

    DEFF Research Database (Denmark)

    Jepsen, Morten Leth; Ottaviani, Alessio; Knudsen, Birgitta R.;

    2014-01-01

    We develop a quantum dot based DNA nanosensor specifically targeting the cleavage–religation activity of an essential DNA-modifying enzyme, human topoisomerase I. The assay has shown great promise in biological crude samples and thus is expected to contribute to clinical diagnostics and anti...

  5. Size-based molecular diagnostics using plasma DNA for noninvasive prenatal testing.

    Science.gov (United States)

    Yu, Stephanie C Y; Chan, K C Allen; Zheng, Yama W L; Jiang, Peiyong; Liao, Gary J W; Sun, Hao; Akolekar, Ranjit; Leung, Tak Y; Go, Attie T J I; van Vugt, John M G; Minekawa, Ryoko; Oudejans, Cees B M; Nicolaides, Kypros H; Chiu, Rossa W K; Lo, Y M Dennis

    2014-06-10

    Noninvasive prenatal testing using fetal DNA in maternal plasma is an actively researched area. The current generation of tests using massively parallel sequencing is based on counting plasma DNA sequences originating from different genomic regions. In this study, we explored a different approach that is based on the use of DNA fragment size as a diagnostic parameter. This approach is dependent on the fact that circulating fetal DNA molecules are generally shorter than the corresponding maternal DNA molecules. First, we performed plasma DNA size analysis using paired-end massively parallel sequencing and microchip-based capillary electrophoresis. We demonstrated that the fetal DNA fraction in maternal plasma could be deduced from the overall size distribution of maternal plasma DNA. The fetal DNA fraction is a critical parameter affecting the accuracy of noninvasive prenatal testing using maternal plasma DNA. Second, we showed that fetal chromosomal aneuploidy could be detected by observing an aberrant proportion of short fragments from an aneuploid chromosome in the paired-end sequencing data. Using this approach, we detected fetal trisomy 21 and trisomy 18 with 100% sensitivity (T21: 36/36; T18: 27/27) and 100% specificity (non-T21: 88/88; non-T18: 97/97). For trisomy 13, the sensitivity and specificity were 95.2% (20/21) and 99% (102/103), respectively. For monosomy X, the sensitivity and specificity were both 100% (10/10 and 8/8). Thus, this study establishes the principle of size-based molecular diagnostics using plasma DNA. This approach has potential applications beyond noninvasive prenatal testing to areas such as oncology and transplantation monitoring.

  6. [Under what conditions does G.C Watson-Crick DNA base pair acquire all four configurations characteristic for A.T Watson-Crick DNA base pair?].

    Science.gov (United States)

    Brovarets', O O

    2013-01-01

    At the MP2/6-311++G(2df,pd)//B3LYP/6-311++G(d,p) level of theory it was established for the first time, that the Löwdin's G*.C* DNA base pair formed by the mutagenic tautomers can acquire, as the A-T Watson-Crick DNA base pair, four biologically important configurations, namely: Watson-Crick, reverse Watson-Crick, Hoogsteen and reverse Hoogsteen. This fact demonstrates rather unexpected role of the tautomerisation of the one of the Watson-Crick DNA base pairs, in particular, via double proton transfer: exactly the G.C-->G*.C* tautomerisation allows to overcome steric hindrances for the implementation of the above mentioned configurations. Geometric, electron-topological and energetic properties of the H-bonds that stabilise the studied pairs, as well as the energetic characteristics of the latters are presented.

  7. Evaluation of DNA Extraction Methods Suitable for PCR-based Detection and Genotyping of Clostridium botulinum

    DEFF Research Database (Denmark)

    Auricchio, Bruna; Anniballi, Fabrizio; Fiore, Alfonsina

    2013-01-01

    Sufficient quality and quantity of extracted DNA is critical to detecting and performing genotyping of Clostridium botulinum by means of PCR-based methods. An ideal extraction method has to optimize DNA yield, minimize DNA degradation, allow multiple samples to be extracted, and be efficient...... in terms of cost, time, labor, and supplies. Eleven botulinum toxin–producing clostridia strains and 25 samples (10 food, 13 clinical, and 2 environmental samples) naturally contaminated with botulinum toxin–producing clostridia were used to compare 4 DNA extraction procedures: Chelex® 100 matrix, Phenol......-Cloroform-Isoamyl alcohol, NucliSENS® magnetic extraction kit, and DNeasy® Blood & Tissue kit. Integrity, purity, and amount of amplifiable DNA were evaluated. The results show that the DNeasy® Blood & Tissue kit is the best extraction method evaluated because it provided the most pure, intact, and amplifiable DNA. However...

  8. Feasibility of using DNA-immobilized nanocellulose-based immunoadsorbent for systemic lupus erythematosus plasmapheresis.

    Science.gov (United States)

    Xu, Changgang; Carlsson, Daniel O; Mihranyan, Albert

    2016-07-01

    The goal of this project was to study the feasibility of using a DNA-immobilized nanocellulose-based immunoadsorbent for possible application in medical apheresis such as systemic lupus erythematosus (SLE) treatment. Calf thymus DNA was bound to high surface area nanocellulose membrane at varying concentrations using UV-irradiation. The DNA-immobilized samples were characterized with scanning electron microscopy, atomic force microscopy, and phosphorus elemental analysis. The anti-ds-DNA IgG binding was tested in vitro using ELISA. The produced sample showed high affinity in vitro to bind anti-ds-DNA-antibodies from mice, as much as 80% of added IgG was bound by the membrane. Furthermore, the binding efficiency was quantitatively dependent on the amount of immobilized DNA onto nanocellulose membrane. The described nanocellulose membranes are interesting immunoadsorbents for continued clinical studies.

  9. 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.

  10. Adsorption of DNA on colloidal Ag nanoparticles: effects of nanoparticle surface charge, base content and length of DNA.

    Science.gov (United States)

    Abbasian, Sara; Moshaii, Ahmad; Nikkhah, Maryam; Farkhari, Nahid

    2014-04-01

    The adsorption of single and double stranded DNA on colloidal silver nanoparticles has been studied to investigate the effects of surface charge of the nanoparticles, the composition of the oligonucleotide and its length on the adsorption characteristics. The results explain that the nanoparticle surface charge is a key parameter determining the propensity of oligonucleotides to adsorb on nanoparticles. The adsorption also depends on the length and composition of oligonucleotide. The protective effects of both single and double stranded DNA against salt-induced aggregation dramatically increase as the DNA length increases. In contrast to other available reports, we observed that long oligonucleotides (single-stranded and double stranded) can well be adsorbed on the nanoparticles as the short ones leading to almost complete protection of nanoparticles against salt induced aggregation and hence are not suitable for the sensing applications. Finally, the light scattering from the Ag nanoparticles has been simulated and the results compared with the experiments. Our understanding should improve development of colorimetric assays for DNA detection based on aggregation of unmodified metallic nanoparticles.

  11. A chiroptical switch based on DNA/layered double hydroxide ultrathin films.

    Science.gov (United States)

    Shi, Wenying; Jia, Yankun; Xu, Simin; Li, Zhixiong; Fu, Yi; Wei, Min; Shi, Shuxian

    2014-11-04

    A highly oriented film was fabricated by layer-by-layer self-assembly of DNA and MgAl-layered double hydroxide nanosheets, and its application in chiroptical switch was demonstrated via intercalation and deintercalation of an achiral molecule into the DNA cavity. DNA molecules are prone to forming an ordered and dispersive state in the interlayer region of rigid layered double hydroxide (LDH) nanosheets as confirmed by scanning electron microscopy and atomic force microscopy. The induced chiroptical ultrathin film (UTF) is achieved via the intercalation of an achiral chromophore [5,10,15,20-tetrakis(4-N-methylpyridyl)porphine tetra(p-toluenesulfonate) (TMPyP)] into the spiral cavity of DNA stabilized in the LDH matrix [denoted as TMPyP-(DNA/LDH)20]. Fluorescence and circular dichroism spectroscopy are utilized to testify the intercalation of TMPyP into (DNA/LDH)20 UTF that involves two steps: the electrostatic binding of TMPyP onto the surface of (DNA/LDH)20 followed by intercalation into base pairs of DNA. In addition, the TMPyP-(DNA/LDH)20 UTF exhibits good reversibility and repeatability in induced optical chirality, based on the intercalation and deintercalation of TMPyP by alternate exposure to HCl and NH3/H2O vapor, which can be potentially used as a chiroptical switch in data storage.

  12. Species radiation by DNA replication that systematically exchanges nucleotides?

    Science.gov (United States)

    Seligmann, Hervé

    2014-12-21

    RNA and DNA syntheses share many properties. Therefore, the existence of 'swinger' RNAs, presumed 'orphan' transcripts matching genomic sequences only if transcription systematically exchanged nucleotides, suggests replication producing swinger DNA. Transcripts occur in many short-lived copies, the few cellular DNA molecules are long-lived. Hence pressures for functional swinger DNAs are greater than for swinger RNAs. Protein coding properties of swinger sequences differ from original sequences, suggesting rarity of corresponding swinger DNA. For genes producing structural RNAs, such as tRNAs and rRNAs, three exchanges (AT, CG and AT+CG) conserve self-hybridization properties. All nuclear eukaryote swinger DNA sequences detected in GenBank are for rRNA genes assuming AT+CG exchanges. In brachyuran crabs, 25 species had AT+CG swinger 18S rDNA, all matching the reverse-exchanged version of regular 18S rDNA of a related species. In this taxon, swinger replication of 18S rDNA apparently associated with, or even resulted in species radiation. AT+CG transformation doesn't invert sequence direction, differing from inverted repeats. Swinger repeats (detectable only assuming swinger transformations, AT+CG swinger repeats most frequent) within regular human rRNAs, independently confirm swinger polymerizations for most swinger types. Swinger replication might be an unsuspected molecular mechanism for ultrafast speciation.

  13. [DNA-based diagnosis of hereditary tumour predisposition

    NARCIS (Netherlands)

    Menko, F.H.; Ligtenberg, M.J.L.; Brouwer, T.; Hahn, D.E.; Ausems, M.G.E.M.

    2007-01-01

    Of all forms of cancer, approximately 5% are caused by factors leading to a strong genetic predisposition. DNA diagnosis is currently used in families with hereditary tumour syndromes, such as familial adenomatous polyposis, hereditary non-polyposis colorectal carcinoma (Lynch syndrome), and heredit

  14. Practical aspects of DNA-based forensic studies in dentistry.

    Science.gov (United States)

    Muruganandhan, J; Sivakumar, G

    2011-01-01

    Forensic dentistry as a science has evolved from simple methods of age estimation and bite-mark analysis, to a new era of genetic and serological investigations. DNA analysis in forensic science requires a sample or source from either an individual (living or dead) or a crime/incident site. The orofacial region is a good source of such material, due to the fact that certain oral tissues are relatively resistant to environmental degradation and destruction by thermal, electrical, and mechanical insult. Dentists may be called upon to provide samples and expert analysis in many such situations. Sources include soft and hard tissues of teeth and jaws, saliva, biopsy material, and mucosal swabs. Tissue samples should be handled with care, and correct protocol in collection and preparation has to be followed. This ensures a high yield of the required DNA. Hard tissues like teeth require specialized procedures to extract the genetic material. Research has shown that there is a wide variation in the quality and quantity of DNA extracted from different individuals from the same site even under similar conditions. This necessitates calibration of the various methods to achieve best results. DNA analysis can provide highly accurate identification if used correctly. Here a description of the various sources in the oral region has been provided from which samples could be forwarded to the forensic laboratory. Most commonly employed techniques of collection and handling for laboratory procedures have been outlined.

  15. Practical aspects of DNA-based forensic studies in dentistry

    Science.gov (United States)

    Muruganandhan, J; Sivakumar, G

    2011-01-01

    Forensic dentistry as a science has evolved from simple methods of age estimation and bite-mark analysis, to a new era of genetic and serological investigations. DNA analysis in forensic science requires a sample or source from either an individual (living or dead) or a crime/incident site. The orofacial region is a good source of such material, due to the fact that certain oral tissues are relatively resistant to environmental degradation and destruction by thermal, electrical, and mechanical insult. Dentists may be called upon to provide samples and expert analysis in many such situations. Sources include soft and hard tissues of teeth and jaws, saliva, biopsy material, and mucosal swabs. Tissue samples should be handled with care, and correct protocol in collection and preparation has to be followed. This ensures a high yield of the required DNA. Hard tissues like teeth require specialized procedures to extract the genetic material. Research has shown that there is a wide variation in the quality and quantity of DNA extracted from different individuals from the same site even under similar conditions. This necessitates calibration of the various methods to achieve best results. DNA analysis can provide highly accurate identification if used correctly. Here a description of the various sources in the oral region has been provided from which samples could be forwarded to the forensic laboratory. Most commonly employed techniques of collection and handling for laboratory procedures have been outlined. PMID:22022138

  16. An Electrochemical DNA Microbiosensor Based on Succinimide-Modified Acrylic Microspheres

    Directory of Open Access Journals (Sweden)

    Sharina Abu Hanifah

    2012-04-01

    Full Text Available An electrochemical microbiosensor for DNA has been fabricated based on new acrylic microspheres modified with reactive N-acryloxysuccinimide (NAS functional groups. Hydrophobic poly(n-butylacrylate-N-acryloxysuccinimide microspheres were synthesized in an emulsion form with a simple one-step photopolymerization technique. Aminated DNA probe was attached to the succinimde functional group of the acrylic microspheres via covalent bonding. The hybridization of the immobilized DNA probe with the complementary DNA was studied by differential pulse voltametry using anthraquninone-2-sulfonic acid monohydrate sodium salt (AQMS as the electroactive hybridization label. The influences of many factors such as duration of DNA probe immobilization and hybridization, pH, type of ions, buffer concentrations, ionic strength, operational temperature and non-complementary DNA on the biosensor performance were evaluated. Under optimized conditions, the DNA microbiosensor demonstrated a linear response range to target DNA over a wide concentration range of 1.0 × 10−16 and 1.0 ´ 10−8 M with a lower limit of detection (LOD of 9.46 ´ 10−17 M (R2 = 0.97. This DNA microbiosensor showed good reproducibility with 2.84% RSD (relative standard deviation (n = 3. Application of the NAS-modified acrylic microspheres in the construction of DNA microbiosensor had improved the overall analytical performance of the resultant DNA microbiosensor when compared with other reported DNA biosensors using other nano-materials for membranes and microspheres as DNA immobilization matrices.

  17. Reversibly locked thionucleobase pairs in DNA to study base flipping enzymes

    Directory of Open Access Journals (Sweden)

    Christine Beuck

    2014-10-01

    Full Text Available Covalently interstrand cross-linked DNA is an interesting tool to study DNA binding proteins that locally open up the DNA duplex by flipping single bases out of the DNA helix or melting whole stretches of base pairs to perform their function. The ideal DNA cross-link to study protein–DNA interactions should be specific and easy to synthesize, be stable during protein binding experiments, have a short covalent linker to avoid steric hindrance of protein binding, and should be available as a mimic for both A/T and G/C base pairs to cover all possible binding specificities. Several covalent interstrand cross-links have been described in the literature, but most of them fall short of at least one of the above criteria. We developed an efficient method to site-specifically and reversibly cross-link thionucleoside base pairs in synthetic duplex oligodeoxynucleotides by bisalkylation with 1,2-diiodoethane resulting in an ethylene-bridged base pair. Both linked A/T and G/C base pair analogs can conveniently be prepared which allows studying any base pair-opening enzyme regardless of its sequence specificity. The cross-link is stable in the absence of reducing agents but the linker can be quickly and tracelessly removed by the addition of thiol reagents like dithiothreitol. This property makes the cross-linking reaction fully reversible and allows for a switching of the linked base pair from locked to unlocked during biochemical experiments. Using the DNA methyltransferase from Thermus aquaticus (M.TaqI as example, we demonstrate that the presented cross-linked DNA with an ethylene-linked A/T base pair analog at the target position is a useful tool to determine the base-flipping equilibrium constant of a base-flipping enzyme which lies mostly on the extrahelical side for M.TaqI.

  18. HIVIS-DNA or HIVISopt-DNA priming followed by CMDR vaccinia-based boosts induce both humoral and cellular murine immune responses to HIV

    Directory of Open Access Journals (Sweden)

    J Hinkula

    2017-06-01

    Conclusions: HIVIS-DNA was modified to obtain HIVISopt-DNA that had fewer plasmids, and additional epitopes. Even with one DNA prime followed by two MVA-CMDR boosts, humoral and cell-mediated immune responses were readily induced by priming with either DNA construct composition. Priming by HIV-DNA augmented neutralizing antibody responses revealed by boosting with the vaccinia-based heterologous sequences. Cellular and antibody responses covered selected strains representing HIV-1 subtypes A, B, C and CRF01_AE. We assume this is related to the inclusion of heterologous full genes in the vaccine schedule.

  19. An Efficient Approach in Analysis of DNA Base Calling Using Neural Fuzzy Model

    Science.gov (United States)

    2017-01-01

    This paper presented the issues of true representation and a reliable measure for analyzing the DNA base calling is provided. The method implemented dealt with the data set quality in analyzing DNA sequencing, it is investigating solution of the problem of using Neurofuzzy techniques for predicting the confidence value for each base in DNA base calling regarding collecting the data for each base in DNA, and the simulation model of designing the ANFIS contains three subsystems and main system; obtain the three features from the subsystems and in the main system and use the three features to predict the confidence value for each base. This is achieving effective results with high performance in employment. PMID:28261268

  20. UV-Visible Spectroscopy-Based Quantification of Unlabeled DNA Bound to Gold Nanoparticles.

    Science.gov (United States)

    Baldock, Brandi L; Hutchison, James E

    2016-12-20

    DNA-functionalized gold nanoparticles have been increasingly applied as sensitive and selective analytical probes and biosensors. The DNA ligands bound to a nanoparticle dictate its reactivity, making it essential to know the type and number of DNA strands bound to the nanoparticle surface. Existing methods used to determine the number of DNA strands per gold nanoparticle (AuNP) require that the sequences be fluorophore-labeled, which may affect the DNA surface coverage and reactivity of the nanoparticle and/or require specialized equipment and other fluorophore-containing reagents. We report a UV-visible-based method to conveniently and inexpensively determine the number of DNA strands attached to AuNPs of different core sizes. When this method is used in tandem with a fluorescence dye assay, it is possible to determine the ratio of two unlabeled sequences of different lengths bound to AuNPs. Two sizes of citrate-stabilized AuNPs (5 and 12 nm) were functionalized with mixtures of short (5 base) and long (32 base) disulfide-terminated DNA sequences, and the ratios of sequences bound to the AuNPs were determined using the new method. The long DNA sequence was present as a lower proportion of the ligand shell than in the ligand exchange mixture, suggesting it had a lower propensity to bind the AuNPs than the short DNA sequence. The ratio of DNA sequences bound to the AuNPs was not the same for the large and small AuNPs, which suggests that the radius of curvature had a significant influence on the assembly of DNA strands onto the AuNPs.

  1. Fluorescent detection of copper(II) based on DNA-templated click chemistry and graphene oxide.

    Science.gov (United States)

    Zhou, Lifen; Shen, Qinpeng; Zhao, Peng; Xiang, Bingbing; Nie, Zhou; Huang, Yan; Yao, Shouzhuo

    2013-12-15

    A novel DNA-templated click chemistry strategy for homogenous fluorescent detection of Cu(2+) has been developed based on click ligation-dependent DNA structure switch and the selective quenching ability of graphene oxide (GO) nanosheet. The clickable duplex probe consists of two DNA strands with alkyne and azide group, respectively, and Cu(+)-catalyzed alkyne-azide cycloaddition (CuAAC) reaction can chemically ligate these two strands. Toehold sequence displacement was consequently exploited to achieve DNA structure transformation bearing fluorescent tag FAM. Cu(2+)-induced chemical ligation caused the probe transfer to hybrid structure with single stranded DNA (ssDNA) tail, while only duplex structure was obtained without Cu(2+). This structural difference can be probed by GO-based fluorescence detection due to the preferential binding of GO to ssDNA. Under the optimum conditions, this sensor can sensitively and specifically detect Cu(2+) with a low detection limit of 58 nM and a linear range of 0.1-10 μM. This new strategy is highly sensitive and selective for Cu(2+) detection because of the great specificity of click chemistry and super-quenching ability of GO. Moreover, with the aid of high efficient DNA templated synthesis, the detection process requires only about half an hour which is much quicker than previous click-chemistry-based Cu(2+) sensors.

  2. How Does Guanine-Cytosine Base Pair Affect Excess-Electron Transfer in DNA?

    Science.gov (United States)

    Lin, Shih-Hsun; Fujitsuka, Mamoru; Majima, Tetsuro

    2015-06-25

    Charge transfer and proton transfer in DNA have attracted wide attention due to their relevance in biological processes and so on. Especially, excess-electron transfer (EET) in DNA has strong relation to DNA repair. However, our understanding on EET in DNA still remains limited. Herein, by using a strongly electron-donating photosensitizer, trimer of 3,4-ethylenedioxythiophene (3E), and an electron acceptor, diphenylacetylene (DPA), two series of functionalized DNA oligomers were synthesized for investigation of EET dynamics in DNA. The transient absorption measurements during femtosecond laser flash photolysis showed that guanine:cytosine (G:C) base pair affects EET dynamics in DNA by two possible mechanisms: the excess-electron quenching by proton transfer with the complementary G after formation of C(•-) and the EET hindrance by inserting a G:C base pair as a potential barrier in consecutive thymines (T's). In the present paper, we provided useful information based on the direct kinetic measurements, which allowed us to discuss EET through oligonucleotides for the investigation of DNA damage/repair.

  3. Impact of Buserelin Acetate or hCG Administration on the Day of First Artificial Insemination on Subsequent Luteal Profile and Conception Rate in Murrah Buffalo (Bubalus bubalis).

    Science.gov (United States)

    Pandey, A K; Ghuman, Sps; Dhaliwal, G S; Agarwal, S K; Phogat, J B

    2016-08-01

    This study was designed to investigate the impact of buserelin acetate (BA) or human chorionic gonadotropin (hCG) administration on the day of first artificial insemination (AI) on subsequent luteal profile (diameter of corpus luteum (CL) and plasma progesterone) and conception rate in Murrah buffalo. The present experiment was carried out at two locations in 117 buffalo that were oestrus-synchronized using cloprostenol (500 μg) administered (i.m.) 11 days apart followed by AI during standing oestrus. Based on treatment (i.m.) at the time of AI, buffalo were randomly categorized (n = 39 in each group) into control (isotonic saline solution, 5 ml), dAI-BA (buserelin acetate, 20 μg) and dAI-hCG (hCG, 3000 IU) group. Out of these, 14 buffalo of each group were subjected to ovarian ultrasonography on the day of oestrus to monitor the preovulatory follicle and on days 5, 12, 16 and 21 post-ovulation to monitor CL diameter. On the day of each sonography, jugular vein blood samples were collected for the estimation of progesterone concentrations. All the buffalo (n = 117) were confirmed for pregnancy on day 40 post-ovulation. The conception rate was better (p hCG (66.7%) groups as compared to their control counterparts (30.8%). Furthermore, the buffalo of dAI-hCG group had improved (p  0.05) to exhibit stimulatory impact of treatment on luteal profile when compared to control group. In brief, buserelin acetate or hCG treatment on the day of first AI leads to an increase in conception rate; however, an appreciable impact on post-ovulation luteal profile was observed only in hCG-treated Murrah buffalo. © 2016 Blackwell Verlag GmbH.

  4. Human LH and hCG stimulate differently the early signalling pathways but result in equal testosterone synthesis in mouse Leydig cells in vitro.

    Science.gov (United States)

    Riccetti, Laura; De Pascali, Francesco; Gilioli, Lisa; Potì, Francesco; Giva, Lavinia Beatrice; Marino, Marco; Tagliavini, Simonetta; Trenti, Tommaso; Fanelli, Flaminia; Mezzullo, Marco; Pagotto, Uberto; Simoni, Manuela; Casarini, Livio

    2017-01-05

    Human luteinizing hormone (LH) and chorionic gonadotropin (hCG) are glycoprotein hormones regulating development and reproductive functions by acting on the same receptor (LHCGR). We compared the LH and hCG activity in gonadal cells from male mouse in vitro, i.e. primary Leydig cells, which is a common tool used for gonadotropin bioassay. Murine Leydig cells are naturally expressing the murine LH receptor (mLhr), which binds human LH/hCG. Cultured Leydig cells were treated by increasing doses of recombinant LH and hCG, and cell signaling, gene expression and steroid synthesis were evaluated. We found that hCG is about 10-fold more potent than LH in cAMP recruitment, and slightly but significantly more potent on cAMP-dependent Erk1/2 phosphorylation. However, no significant differences occur between LH and hCG treatments, measured as activation of downstream signals, such as Creb phosphorylation, Stard1 gene expression and testosterone synthesis. These data demonstrate that the responses to human LH/hCG are only quantitatively and not qualitatively different in murine cells, at least in terms of cAMP and Erk1/2 activation, and equal in activating downstream steroidogenic events. This is at odds with what we previously described in human primary granulosa cells, where LHCGR mediates a different pattern of signaling cascades, depending on the natural ligand. This finding is relevant for gonadotropin quantification used in the official pharmacopoeia, which are based on murine, in vivo bioassay and rely on the evaluation of long-term, testosterone-dependent effects mediated by rodent receptor.

  5. Discrepant serum and urine β-hCG results due to production of β-hCG by a cribriform-morular variant of thyroid papillary carcinoma.

    Science.gov (United States)

    Alikhan, Mir; Koshy, Anoopa; Hyjek, Elizabeth; Stenson, Kerstin; Cohen, Ronald N; Yeo, Kiang-Teck J

    2015-01-01

    Although patients with medullary thyroid cancer are known to present with paraneoplastic hormone production, this is much less common with papillary thyroid cancer. We present a patient with the cribriform morular variant of papillary thyroid cancer in association with familial adenomatous polyposis who developed a positive pregnancy test in the absence of known pregnancy. The patient had developed vaginal bleeding, and her laboratory testing was characterized by elevated serum human chorionic gonadotropin (β-hCG) concentrations, but negative qualitative urine results. After a thorough gynecological evaluation to exclude unexpected normal, ectopic, or molar pregnancy, we pursued an evaluation for other sources of β-hCG production. We showed that the elevated serum β-hCG concentrations were not the result of heterophile antibody interferences, and ultimately we proved that her recurrent tumor produced the ectopic β-hCG. This is the first report of β-hCG production by papillary thyroid cancer. Thus, the possibility of ectopic production of β-hCG by papillary thyroid cancer needs to be included in the differential diagnosis of elevated hCG concentration in the absence of pregnancy. This study of an unusual paraneoplastic syndrome highlights the importance of investigating discrepancies in the clinical laboratory. Copyright © 2014 Elsevier B.V. All rights reserved.

  6. Population-based study of DNA image cytometry as screening method for esophageal cancer

    Institute of Scientific and Technical Information of China (English)

    Lin Zhao; Guo-Qing Wang; Qi Shang; You-Lin Qiao; Wen-Qiang Wei; De-Li Zhao; Chang-Qing Hao; Dong-Mei Lin; Qin-Jing Pan; Xin-Qing Li; Fu-Hua Lei; Jin-Wu Wang

    2012-01-01

    AIM: To explore the DNA image cytometry (DNA-ICM) technique as a primary screening method for esophageal squamous precancerous lesions.METHODS: This study was designed as a populationbased screening study. A total of 582 local residents aged 40 years-69 years were recruited from Linzhou in Henan and Feicheng in Shandong. However, only 452 subjects had results of liquid-based cytology, DNA-ICM and pathology. The sensitivity and specificity of DNAICM were calculated and compared with liquid-based cytology in moderate dysplasia or worse. RESULTS: Sensitivities of DNA-ICM ranging from at least 1 to 4 aneuploid cells were 90.91%, 86.36%, 79.55% and 77.27%, respectively, which were better than that of liquid-based cytology (75%). Specificities of DNA-ICM were 70.83%, 84.07%, 92.65% and 96.81%, but the specificity of liquid-based cytology was 91.91%. The sensitivity and specificity of a combination of liquid-based cytology and DNA-ICM were 84.09% and 85.78%, respectively. CONCLUSION: It is possible to use DNA-ICM technique as a primary screening method for esophageal squamous precancerous lesions.

  7. Optical detection of PNA/DNA hybridization in resonant porous silicon-based devices

    Science.gov (United States)

    Rotiroti, Lucia; Arcari, Paolo; Lamberti, Annalisa; Sanges, Carmen; De Tommasi, Edoardo; Rea, Ilaria; Rendina, Ivo; De Stefano, Luca

    2008-04-01

    The development of label-free optical biosensors could have a great impact on life sciences as well as on screening techniques for medical and environmental applications. Peptide nucleic acid (PNA) is a nucleic acid analog in which the sugar phosphate backbone of natural nucleic acid has been replaced by a synthetic peptide backbone, resulting in an achiral and uncharged mimic. Due to the uncharged nature of PNA, PNA-DNA duplexes show a better thermal stability respect the DNA-DNA equivalents. In this work, we used an optical biosensor, based on the porous silicon (PSi) nanotechnology, to detect PNA-DNA interactions. PSi optical sensors are based on changes of reflectivity spectrum when they are exposed to the target analytes. The porous silicon surface was chemically modified to covalently link the PNA which acts as a very specific probe for its ligand (cDNA).

  8. An electrochemical DNA biosensor based on gold nanorods decorated graphene oxide sheets for sensing platform.

    Science.gov (United States)

    Han, Xiaowei; Fang, Xian; Shi, Anqi; Wang, Jiao; Zhang, Yuzhong

    2013-12-15

    A simple electrochemical sensor for sensitive and selective DNA detection was constructed based on gold nanorods (Au NRs) decorated graphene oxide (GO) sheets. The high-quality Au NRs-GO nanocomposite was synthesized via the electrostatic self-assembly technique, which is considered a potential sensing platform. Differential pulse voltammetry was used to monitor the DNA hybridization event using methylene blue as an electrochemical indicator. Under optimal conditions, the peak currents of methylene blue were linear with the logarithm of the concentrations of complementary DNA from 1.0 × 10(-9) to 1.0 × 10(-14)M with a detection limit of 3.5 × 10(-15)M (signal/noise=3). Moreover, the prepared electrochemical sensor can effectively distinguish complementary DNA sequences in the presence of a large amount of single-base mismatched DNA (1000:1), indicating that the biosensor has high selectivity.

  9. Timing of IUI Treatment after hCG Administration 1-48 h Affecting Pregnancy Rate

    Institute of Scientific and Technical Information of China (English)

    Fan YANG; Zu-mei SHI; Hui JIN; Li-ping ZHU; Kun-ming LI; Jian-zhi YANG; Zhi-qin CHEN; Xiao-ming TENG; Hui-fen CHEN; Yu WANG

    2008-01-01

    Objective To compare the different time of administration of hCG affecting pregnancy rate of IUI. Methods A total of 189 infertile couples underwent 331 cycles of IUI with husband’s sperm.They were separated into 3 groups according to the time of hCG administration in IUI:hCG 1-23 h(group A):hCG 24-36 h (group B);hCG 37—48 h(group C). Results There were no statistical differences among 3 groups.None of the other relative factors,such as the female age,the different methods of ovulation and the cause of infertility,showed differences in pregnancy rate among 3 groups. Conclusion IUI can be performed any time after administration of hCG(1—48 h).

  10. Effect of structure on sensing performance of a target induced signaling probe shifting DNA-based (TISPS-DNA) sensor.

    Science.gov (United States)

    Yu, Xiang; Yu, Zhigang; Li, Fengqin; Xu, Yanmei; He, Xunjun; Xu, Lan; Shi, Wenbing; Zhang, Guiling; Yan, Hong

    2017-05-15

    A type of "signal on" displacement-based sensors named target induced signaling probe shifting DNA-based (TISPS-DNA) sensor were developed for a designated DNA detection. The signaling mechanism of the signaling probe (SP) shifting different from the classical conformation/flexibility change mode endows the sensor with high sensitivity. Through using thiolated or no thiolated capturing probe (CP), two 3-probe sensing structures, sensor-1 and sensor-2, were designed and constructed. The systematical comparing research results show that both sensors exhibit some similarities or big differences in sensing performance. On the one hand, the similarity in structures determines the similarity in some aspects of signaling mechanism, background signal, signal changing form, anti-fouling ability and versatility; on the other hand, the slight difference in structures also results in two opposite hybridization modes of gradual increasing resistance and gradual decreasing resistance which can affect the hybridization efficiency between the assistant probe (AP) and the SP, further producing some big differences in sensing performance, for example, apparently different signal enhancement (SE) change, point mutation discrimination ability and response speed. Under the optimized fabrication and detection conditions, both sensors feature high sensitivity for target DNAs with the detection limits of ∼10 fM for sensor-1 and ∼7 fM for sensor-2, respectively. Among many acquired sensing virtues, the sensor-1 shows a peculiar specificity adjustability which is also a highlight in this work. Copyright © 2017 Elsevier B.V. All rights reserved.

  11. An Affinity Propagation-Based DNA Motif Discovery Algorithm

    Directory of Open Access Journals (Sweden)

    Chunxiao Sun

    2015-01-01

    Full Text Available The planted (l,d motif search (PMS is one of the fundamental problems in bioinformatics, which plays an important role in locating transcription factor binding sites (TFBSs in DNA sequences. Nowadays, identifying weak motifs and reducing the effect of local optimum are still important but challenging tasks for motif discovery. To solve the tasks, we propose a new algorithm, APMotif, which first applies the Affinity Propagation (AP clustering in DNA sequences to produce informative and good candidate motifs and then employs Expectation Maximization (EM refinement to obtain the optimal motifs from the candidate motifs. Experimental results both on simulated data sets and real biological data sets show that APMotif usually outperforms four other widely used algorithms in terms of high prediction accuracy.

  12. An Affinity Propagation-Based DNA Motif Discovery Algorithm.

    Science.gov (United States)

    Sun, Chunxiao; Huo, Hongwei; Yu, Qiang; Guo, Haitao; Sun, Zhigang

    2015-01-01

    The planted (l, d) motif search (PMS) is one of the fundamental problems in bioinformatics, which plays an important role in locating transcription factor binding sites (TFBSs) in DNA sequences. Nowadays, identifying weak motifs and reducing the effect of local optimum are still important but challenging tasks for motif discovery. To solve the tasks, we propose a new algorithm, APMotif, which first applies the Affinity Propagation (AP) clustering in DNA sequences to produce informative and good candidate motifs and then employs Expectation Maximization (EM) refinement to obtain the optimal motifs from the candidate motifs. Experimental results both on simulated data sets and real biological data sets show that APMotif usually outperforms four other widely used algorithms in terms of high prediction accuracy.

  13. TGF-β-induced hCG-β regulates redox homeostasis in glioma cells.

    Science.gov (United States)

    Ahmad, Fahim; Ghosh, Sadashib; Sinha, Sanchari; Joshi, Shanker Datt; Mehta, Veer Singh; Sen, Ellora

    2015-01-01

    Transforming growth factor (TGF-β) is associated with the progression of glioblastoma multiforme (GBM)-the most malignant of brain tumors. Since there is a structural homology between TGF-β and human chorionic gonadotropin (hCG) and as both TGF-β and hCG-β are known regulators of oxidative stress and survival responses in a variety of tumors, the role of TGF-β in the regulation of hCG-β and its consequences on redox modulation of glioblastoma cells was investigated. A heightened hCG-β level was observed in GBM tumors. TGF-β treatment increased hCG-β expression in glioma cell lines, and this heightened hCG-β was found to regulate redox homeostasis in TGF-β-treated glioma cells, as siRNA-mediated knockdown of hCG-β (i) elevated reactive oxygen species (ROS) generation, (ii) decreased thioredoxin Trx1 expression and thioredoxin reductase (TrxR) activity, and (iii) abrogated expression of TP53-induced glycolysis and apoptosis regulator (TIGAR). Silencing of hCG-β abrogated Smad2/3 levels, suggesting the existence of TGF-β-hCG-β cross-talk in glioma cells. siRNA-mediated inhibition of elevated TIGAR levels in TGF-β-treated glioma cells was accompanied by an increase in ROS levels. As a farnesyltransferase inhibitor, Manumycin is known to induce glioma cell apoptosis in a ROS-dependent manner, and we investigated whether Manumycin could induce apoptosis in TGF-β-treated cells with elevated hCG-β exhibiting ROS-scavenging property. Manumycin-induced apoptosis in TGF-β-treated cells was accompanied by elevated ROS levels and decreased expression of hCG-β, Trx1, Smad2/3, and TIGAR. These findings indicate the existence of a previously unknown TGF-β-hCG-β link that regulates redox homeostasis in glioma cells.

  14. Protocol Improvements for Low Concentration DNA-Based Bioaerosol Sampling and Analysis.

    Directory of Open Access Journals (Sweden)

    Irvan Luhung

    Full Text Available As bioaerosol research attracts increasing attention, there is a need for additional efforts that focus on method development to deal with different environmental samples. Bioaerosol environmental samples typically have very low biomass concentrations in the air, which often leaves researchers with limited options in choosing the downstream analysis steps, especially when culture-independent methods are intended.This study investigates the impacts of three important factors that can influence the performance of culture-independent DNA-based analysis in dealing with bioaerosol environmental samples engaged in this study. The factors are: 1 enhanced high temperature sonication during DNA extraction; 2 effect of sampling duration on DNA recoverability; and 3 an alternative method for concentrating composite samples. In this study, DNA extracted from samples was analysed using the Qubit fluorometer (for direct total DNA measurement and quantitative polymerase chain reaction (qPCR.The findings suggest that additional lysis from high temperature sonication is crucial: DNA yields from both high and low biomass samples increased up to 600% when the protocol included 30-min sonication at 65°C. Long air sampling duration on a filter media was shown to have a negative impact on DNA recoverability with up to 98% of DNA lost over a 20-h sampling period. Pooling DNA from separate samples during extraction was proven to be feasible with margins of error below 30%.

  15. Influence of amino acids Shiff bases on irradiated DNA stability in vivo.

    Science.gov (United States)

    Karapetyan, N H; Malakyan, M H; Bajinyan, S A; Torosyan, A L; Grigoryan, I E; Haroutiunian, S G

    2013-01-01

    To reveal protective role of the new Mn(II) complexes with Nicotinyl-L-Tyrosinate and Nicotinyl-L-Tryptophanate Schiff Bases against ionizing radiation. The DNA of the rats liver was isolated on 7, 14, and 30 days after X-ray irradiation. The differences between the DNA of irradiated rats and rats pre-treated with Mn(II) complexes were studied using the melting, microcalorimetry, and electrophoresis methods. The melting parameters and the melting enthalpy of rats livers DNA were changed after the X-ray irradiation: melting temperature and melting enthalpy were decreased and melting interval was increased. These results can be explained by destruction of DNA molecules. It was shown that pre-treatment of rats with Mn(II) complexes approximates the melting parameters to norm. Agarose gel electrophoresis data confirmed the results of melting studies. The separate DNA fragments were revealed in DNA samples isolated from irradiated animals. The DNA isolated from animals pre-treated with the Mn(II) chelates had better electrophoretic characteristics, which correspond to healthy DNA. Pre-treatment of the irradiated rats with Mn(II)(Nicotinil-L-Tyrosinate) and Mn(II)(Nicotinil-L-Tryptophanate)2 improves the DNA characteristics.

  16. Electronic transport through dsDNA based junction: a Fibonacci model

    Directory of Open Access Journals (Sweden)

    S A Ketabi

    2014-12-01

    Full Text Available A numerical study is presented to investigate the electronic transport properties through a synthetic DNA molecule based on a quasiperiodic arrangement of its constituent nucleotides. Using a generalized Green's function technique, the electronic conduction through the poly(GACT-poly(CTGA DNA molecule in a metal/DNA/metal model structure has been studied. Making use of a renormalization scheme we transform the Hamiltonian of double-stranded DNA (dsDNA molecule to an effective Hamiltonian corresponding to a one-dimensional chain in which the effective on-site energies are arranged as a quasiperiodic lattice according to Fibonacci sequence. The room temperature current-voltage characteristic of dsDNA has been investigated in this Fibonacci model and compared with those corresponding to poly(GACT-poly(CTGA DNA molecule. Our results indicate the main effect of the quasiperiodic arrangement of the nucleotides as the Fibonacci sequence on the electronic spectrum structure of the dsDNA is that the energy band gaps of the molecule have a tendency for suppression. The room temperature I-V characteristic of the DNA Fibonacci model shows a linear and ohmic-like behavior

  17. DNA Hybridization Sensors Based on Electrochemical Impedance Spectroscopy as a Detection Tool

    Directory of Open Access Journals (Sweden)

    Jin-Young Park

    2009-11-01

    Full Text Available Recent advances in label free DNA hybridization sensors employing electrochemical impedance spectroscopy (EIS as a detection tool are reviewed. These sensors are based on the modulation of the blocking ability of an electrode modified with a probe DNA by an analyte, i.e., target DNA. The probe DNA is immobilized on a self-assembled monolayer, a conducting polymer film, or a layer of nanostructures on the electrode such that desired probe DNA would selectively hybridize with target DNA. The rate of charge transfer from the electrode thus modified to a redox indicator, e.g., [Fe(CN6]3–/4–, which is measured by EIS in the form of charge transfer resistance (Rct, is modulated by whether or not, as well as how much, the intended target DNA is selectively hybridized. Efforts made to enhance the selectivity as well as the sensitivity of DNA sensors and to reduce the EIS measurement time are briefly described along with brief future perspectives in developing DNA sensors.

  18. DNA Hybridization Sensors Based on Electrochemical Impedance Spectroscopy as a Detection Tool

    Science.gov (United States)

    Park, Jin-Young; Park, Su-Moon

    2009-01-01

    Recent advances in label free DNA hybridization sensors employing electrochemical impedance spectroscopy (EIS) as a detection tool are reviewed. These sensors are based on the modulation of the blocking ability of an electrode modified with a probe DNA by an analyte, i.e., target DNA. The probe DNA is immobilized on a self-assembled monolayer, a conducting polymer film, or a layer of nanostructures on the electrode such that desired probe DNA would selectively hybridize with target DNA. The rate of charge transfer from the electrode thus modified to a redox indicator, e.g., [Fe(CN)6]3−/4−, which is measured by EIS in the form of charge transfer resistance (Rct), is modulated by whether or not, as well as how much, the intended target DNA is selectively hybridized. Efforts made to enhance the selectivity as well as the sensitivity of DNA sensors and to reduce the EIS measurement time are briefly described along with brief future perspectives in developing DNA sensors. PMID:22303136

  19. cDNA-AFLP-based genetical genomics in cotton fibers.

    Science.gov (United States)

    Claverie, Michel; Souquet, Marlène; Jean, Janine; Forestier-Chiron, Nelly; Lepitre, Vincent; Pré, Martial; Jacobs, John; Llewellyn, Danny; Lacape, Jean-Marc

    2012-03-01

    Genetical genomics, or genetic analysis applied to gene expression data, has not been widely used in plants. We used quantitative cDNA-AFLP to monitor the variation in the expression level of cotton fiber transcripts among a population of inter-specific Gossypium hirsutum × G. barbadense recombinant inbred lines (RILs). Two key fiber developmental stages, elongation (10 days post anthesis, dpa), and secondary cell wall thickening (22 dpa), were studied. Normalized intensity ratios of 3,263 and 1,201 transcript-derived fragments (TDFs) segregating over 88 RILs were analyzed for quantitative trait loci (QTL) mapping for the 10 and 22 dpa fibers, respectively. Two-thirds of all TDFs mapped between 1 and 6 eQTLs (LOD > 3.5). Chromosome 21 had a higher density of eQTLs than other chromosomes in both data sets and, within chromosomes, hotspots of presumably trans-acting eQTLs were identified. The eQTL hotspots were compared to the location of phenotypic QTLs for fiber characteristics among the RILs, and several cases of co-localization were detected. Quantitative RT-PCR for 15 sequenced TDFs showed that 3 TDFs had at least one eQTL at a similar location to those identified by cDNA-AFLP, while 3 other TDFs mapped an eQTL at a similar location but with opposite additive effect. In conclusion, cDNA-AFLP proved to be a cost-effective and highly transferable platform for genome-wide and population-wide gene expression profiling. Because TDFs are anonymous, further validation and interpretation (in silico analysis, qPCR gene profiling) of the eQTL and eQTL hotspots will be facilitated by the increasing availability of cDNA and genomic sequence resources in cotton.

  20. From molecules to management: adopting DNA-based methods for monitoring biological invasions in aquatic environments

    Science.gov (United States)

    Recent technological advances have driven rapid development of DNA-based methods designed to facilitate detection and monitoring of invasive species in aquatic environments. These tools promise to significantly alleviate difficulties associated with traditional monitoring approac...

  1. From molecules to management: adopting DNA-based methods for monitoring biological invasions in aquatic environments

    Science.gov (United States)

    Recent technological advances have driven rapid development of DNA-based methods designed to facilitate detection and monitoring of invasive species in aquatic environments. These tools promise to significantly alleviate difficulties associated with traditional monitoring approac...

  2. The essential component in DNA-based information storage system: robust error-tolerating module

    Directory of Open Access Journals (Sweden)

    Aldrin Kay-Yuen eYim

    2014-11-01

    Full Text Available The size of digital data is ever increasing and is expected to grow to 40,000EB by 2020, yet the estimated global information storage capacity in 2011 is less than 300EB, indicating that most of the data are transient. DNA, as a very stable nano-molecule, is an ideal massive storage device for long-term data archive. The two most notable illustrations are from Church et al. and Goldman et al., whose approaches are well-optimized for most sequencing platforms – short synthesized DNA fragments without homopolymer. Here we suggested improvements on error handling methodology that could enable the integration of DNA-based computational process, e.g. algorithms based on self-assembly of DNA. As a proof of concept, a picture of size 438 bytes was encoded to DNA with Low-Density Parity-Check error-correction code. We salvaged a significant portion of sequencing reads with mutations generated during DNA synthesis and sequencing and successfully reconstructed the entire picture. A modular-based programming framework - DNAcodec with a XML-based data format was also introduced. Our experiments demonstrated the practicability of long DNA message recovery with high error-tolerance, which opens the field to biocomputing and synthetic biology.

  3. Measurement of oxidized and methylated DNA bases by HPLC with electrochemical detection.

    Science.gov (United States)

    Kaur, H; Halliwell, B

    1996-08-15

    Oxidative DNA damage is thought to be an important contributor to cancer development and to be affected by dietary constituents, so its accurate measurement is important. DNA methylation is recognized as an important mechanism affecting gene expression. In the present paper we describe an HPLC-with-electrochemical-detection procedure that allows rapid and sensitive measurement of four oxidized (2,6-diamino-4-hydroxy-5-formamidopyrimidine, 5-hydroxyuracil, 8-hydroxyguanine, 8-hydroxyadenine) and three methylated (7-methylguanine, 1-methylguanine, O6-methylguanine) bases in acid hydrolysates of DNA. Guanine was also detected, but was clearly separated from the other bases.

  4. Fragment-based discovery of 6-azaindazoles as inhibitors of bacterial DNA ligase.

    Science.gov (United States)

    Howard, Steven; Amin, Nader; Benowitz, Andrew B; Chiarparin, Elisabetta; Cui, Haifeng; Deng, Xiaodong; Heightman, Tom D; Holmes, David J; Hopkins, Anna; Huang, Jianzhong; Jin, Qi; Kreatsoulas, Constantine; Martin, Agnes C L; Massey, Frances; McCloskey, Lynn; Mortenson, Paul N; Pathuri, Puja; Tisi, Dominic; Williams, Pamela A

    2013-12-12

    Herein we describe the application of fragment-based drug design to bacterial DNA ligase. X-ray crystallography was used to guide structure-based optimization of a fragment-screening hit to give novel, nanomolar, AMP-competitive inhibitors. The lead compound 13 showed antibacterial activity across a range of pathogens. Data to demonstrate mode of action was provided using a strain of S. aureus, engineered to overexpress DNA ligase.

  5. DNA Bases Thymine and Adenine in Bio-Organic Light Emitting Diodes

    Science.gov (United States)

    2014-11-24

    DNA Bases Thymine and Adenine in Bio-Organic Light Emitting Diodes Eliot F. Gomez1, Vishak Venkatraman1, James G. Grote2 & Andrew J. Steckl1...45433-7707 USA. We report on the use of nucleic acid bases (NBs) in organic light emitting diodes (OLEDs). NBs are small molecules that are the basic...polymer has been a frequent natural material integrated in electronic devices. DNA has been used in organic light - emitting diodes (OLEDs)4,5,7–14

  6. Expression of the Gene Encoding the Tetraploid of Carboxyl-terminal Peptide of β-hCG Containing Thirty-seven Amino Acid Residues in E. coli

    Institute of Scientific and Technical Information of China (English)

    王健; 沈卫英; 周清平; 申庆祥

    2000-01-01

    Objective This study was carried out to investigate the possible enhancement of immunogenicity of the carboxyl-terminal peptide of β-hCG which is made up of 37 amino acid residues (109~145) and contains the specific epitope (antigenic determinant) of hCG.Materials & Methods hCGβ-CTP37 tetraploid cDNA was constructed by linking four hCGβ-CTP37 cDNAs together. The product was then subcloned into the E. coli expression vector pQE60 to construct the expression vector pQE60/ (hCGβ-CTP37)4. Recombinant (hCGβ-CTP37 ) 4 was expressed in E. coil-X-blue.Results Western blot analysis showed that the tetraploid of hCGβ-CTP37 had an apparent molecular weight of 20 kD and had relatively stronger anti-hCG antibody-binding activity compared with the diploid from.Conclusion The tetraploid of hCGβ-CTP37 may be a more potent immunogen for raising anti-hCG vaccines for fertility regulation or suppression of tumor.

  7. Label-free detection of kanamycin based on a G-quadruplex DNA aptamer-based fluorescent intercalator displacement assay

    Science.gov (United States)

    Xing, Yun-Peng; Liu, Chun; Zhou, Xiao-Hong; Shi, Han-Chang

    2015-01-01

    This work was the first to report that the kanamycin-binding DNA aptamer (5'-TGG GGG TTG AGG CTA AGC CGA-3') can form stable parallel G-quadruplex DNA (G4-DNA) structures by themselves and that this phenomenon can be verified by nondenaturing polyacrylamide gel electrophoresis and circular dichroism spectroscopy. Based on these findings, we developed a novel label-free strategy for kanamycin detection based on the G4-DNA aptamer-based fluorescent intercalator displacement assay with thiazole orange (TO) as the fluorescence probe. In the proposed strategy, TO became strongly fluorescent upon binding to kanamycin-binding G4-DNA. However, the addition of kanamycin caused the displacement of TO from the G4-DNA-TO conjugate, thereby resulting in decreased fluorescent signal, which was inversely related to the kanamycin concentration. The detection limit of the proposed assay decreased to 59 nM with a linear working range of 0.1 μM to 20 μM for kanamycin. The cross-reactivity against six other antibiotics was negligible compared with the response to kanamycin. A satisfactory recovery of kanamycin in milk samples ranged from 80.1% to 98.0%, confirming the potential of this bioassay in the measurement of kanamycin in various applications. Our results also served as a good reference for developing similar fluorescent G4-DNA-based bioassays in the future.

  8. Two high-mobility group box domains act together to underwind and kink DNA

    Energy Technology Data Exchange (ETDEWEB)

    Sánchez-Giraldo, R.; Acosta-Reyes, F. J. [Universitat Politecnica de Catalunya, 08028 Barcelona (Spain); Malarkey, C. S. [University of Colorado School of Medicine, Aurora, CO 80045 (United States); Saperas, N. [Universitat Politecnica de Catalunya, 08028 Barcelona (Spain); Churchill, M. E. A., E-mail: mair.churchill@ucdenver.edu [University of Colorado School of Medicine, Aurora, CO 80045 (United States); Campos, J. L., E-mail: mair.churchill@ucdenver.edu [Universitat Politecnica de Catalunya, 08028 Barcelona (Spain)

    2015-06-30

    The crystal structure of HMGB1 box A bound to an unmodified AT-rich DNA fragment is reported at a resolution of 2 Å. A new mode of DNA recognition for HMG box proteins is found in which two box A domains bind in an unusual configuration generating a highly kinked DNA structure. High-mobility group protein 1 (HMGB1) is an essential and ubiquitous DNA architectural factor that influences a myriad of cellular processes. HMGB1 contains two DNA-binding domains, box A and box B, which have little sequence specificity but have remarkable abilities to underwind and bend DNA. Although HMGB1 box A is thought to be responsible for the majority of HMGB1–DNA interactions with pre-bent or kinked DNA, little is known about how it recognizes unmodified DNA. Here, the crystal structure of HMGB1 box A bound to an AT-rich DNA fragment is reported at a resolution of 2 Å. Two box A domains of HMGB1 collaborate in an unusual configuration in which the Phe37 residues of both domains stack together and intercalate the same CG base pair, generating highly kinked DNA. This represents a novel mode of DNA recognition for HMGB proteins and reveals a mechanism by which structure-specific HMG boxes kink linear DNA.

  9. Production of specific antisera for radioimmunoassay of human luteinizing hormone (LH) in the presence of human chorionic gonadotropin (hCG). [/sup 125/I

    Energy Technology Data Exchange (ETDEWEB)

    Thorell, J.I.; Jeppsson, S.; Holmstrom, B.

    1976-09-01

    A specific radioimmunoassay for LH, which measures plasma LH in the presence of human chorionic gonadotropin (hCG) is described. Rabbits were immunized with highly purified native LH. One of the antisera with a difference in its reactivity against LH and hCG was further purified by affinity chromatography on a column with hCG coupled to Sepharose 4B. The adsorbed antiserum and /sup 125/I-LH was used in a double antibody assay. The LH standard (MRC/68/40) efficiently inhibited the binding of /sup 125/I-LH, and the standard curve showed a sensitivity of 0.5 ng/ml in the sample. hCG up to 10,000 ng/ml did not inhibit the binding of /sup 125/I-LH. The plasma level of LH in pregnant women in the first trimester was low (1.3 +- 0.1 ng/ml). When LH was measured in fertile or menopausal women with or without stimulation with LH/FSH releasing hormone (LH-RH)/sup x/ the results agreed to those found with our conventional LH-assay based on antiserum against hCG.

  10. Dependence of maternal serum [AFP]/[hCG] median ratios on age of gestation: comparison of trisomy 21 to euploid pregnancies.

    Science.gov (United States)

    Marcus-Braun, N; Birk, O; Manor, E; Segal, D; Harari, G; Toma, I; Shalev, S; Borochowitz, Z U; Yaron, Y; Sharony, R; Itzhaky, D; Shtoyerman, R; Appelman, Z; Braun, G

    2009-12-01

    Current risk calculations for trisomy 21, which are based on multiples of median (MoM), do not take into account possible differences between euploid and trisomy 21 pregnancies that may develop with gestational age. In order to optimize the predictive value of screening tests, we calculated the ratio between maternal serum concentration of alpha-fetoprotein (AFP) and that of human chorionic gonadotropin (hCG) in euploid and in trisomy 21 pregnancies. The medians of the concentration ratios, [AFP]/[hCG] at 16-21 weeks of gestation, were plotted as a function of gestational age for 307 cases of trisomy 21 and were compared with the medians of 30 549 normal karyotype cases. [AFP]/[hCG] ratio medians were independent of body weight and maternal age. There was a significant difference in the [AFP]/[hCG] ratio when comparing trisomy 21 and euploid pregnancies at each week. This difference became greater with advancing gestational age (P hCG] between euploid and trisomy 21 pregnancies, which may be used to improve detection rates of Down syndrome screening.

  11. Construction of cDNA representational difference analysis based on two cDNA libraries and identification of garlic inducible expression genes in human gastric cancer cells

    Institute of Scientific and Technical Information of China (English)

    Yong Li; Lin Yang; Jian-Tao Cui; Wen-Mei Li; Rui-Fang Guo; You-Yong Lu

    2002-01-01

    AIM: To elucidate molecular mechanism of chemopreventiveefficacies of garlic against human gastric cancer (HGC):METHODS: HGC cell line BGC823 was treated with Allitridi (akind of garlic extract) and Allitridi-treated and parentalBGC823 cDNA librarles were constructed respectively byusing λZAP Ⅱ vector. cDNA Representatinal DifferenceAnalysis (cDNA RDA) was perfonmed using BamH Ⅰ cutting-site and abundant ~DNA messages provided by the Iibrarles.Northern blot analysls was applied to identifythe obtaineddifference prnducts.RESULTS: Two specific cDNA fragments were obtained andcharacterized to be derived from homo sapiens folatereceptorα (FRα) gene and calcyclin gene respectively.Northern blot results showed a 4-fold increase in FRα geneexpression level and 9-fold increase in calcyclin mRNA levelin BGC823 cells after Allilridi treatment for 72 h.CONCLUSION: The method of cDNA RDA based on cDNAlibraries combines the high specificity of cDNA RDA withabundant cDNA messages in cDNA library; this expands theapplication of cDNA library and increases the specificity ofcDNA RDA. Up-regulstion of FRα gene and calcyclin geneexpressions induced by Allitridi provide valuable molecularevidence for theefficacy of garlic in treating HGC as well asother diseases.

  12. Optimal Design of TS Fuzzy Control System Based on DNA Evolutionary Algorithm%采用DNA进化算法优化设计TS模糊控制器

    Institute of Scientific and Technical Information of China (English)

    翁妙凤

    2003-01-01

    The DNA evolutionary algorithm(DNA-EA)and the DNA genetic algorithm(DNA-GA)based on a new DNA encoding method are propsed based on the structure and the genetic mechanism of biological DNA. The DNA-EA and the DNA-GA are applied into the optimal design of TS fuzzy control system. The simulation results show the effectiveness of the two DNA algorithms, excellent self-learning capability. However, the DNA-EA is superior to the DNA-GA in the simulation performance.

  13. A pressure cooking-based DNA extraction from archival formalin fixed, paraffin embedded tissue

    Science.gov (United States)

    Chung, Joon-Yong; Yi, Joo Mi; Xie, Ran; Brown, Victoria; Lee, Olivia; Ahuja, Nita; Braunschweig, Till; Hewitt, Stephen M.

    2012-01-01

    As emerging novel DNA-based methodologies are adopted, nucleic acid-based assays depend critically on the quality and quantity of extracted DNA. Formalin fixed, paraffin embedded (FFPE) tissue samples provide an invaluable resource for subsequent molecular studies of clinical phenotypes, but high quality DNA extraction from archival FFPE tissue specimen remains complex and time consuming. To address this challenge, we have developed a reliable rapid DNA extraction method for FFPE tissue specimens. It is based on deparaffinization at high temperature coupled with relieving crosslink in a pressure cooker. The DNA yield by this rapid method resulted in an average 1.8-fold increase in comparison with the commercial kit; O.D 260/280 ratios between 1.87 and 1.95. The DNA obtained by the rapid method was suitable for methylation analyses in colon cancer patients. These data suggest that this new DNA extraction method coupled with MSP can be used for epigenetic studies with the advantages of rapidity and high quality, and may contribute to the development of biomarkers in clinical studies. PMID:22449494

  14. 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.

  15. Local compression properties of double-stranded DNA based on a dynamic simulation

    CERN Document Server

    Lei, Xiaoling; Fang, Haiping

    2013-01-01

    The local mechanical properties of DNA are believed to play an important role in their biological functions and DNA-based nanomechanical devices. Using a simple sphere-tip compression system, the local radial mechanical properties of DNA are systematically studied by changing the tip size. The compression simulation results for the 16 nm diameter sphere tip are well consistent with the experimental results. With the diameter of the tip decreasing, the radial compressive elastic properties under external loads become sensitive to the tip size and the local DNA conformation. There appears a suddenly force break in the compression-force curve when the sphere size is less than or equal to 12 nm diameter. The analysis of the hydrogen bonds and base stacking interaction shows there is a local unwinding process occurs. During the local unwinding process, first the hydrogen bonds between complement base pairs are broken. With the compression aggregating, the local backbones in the compression center are unwound from ...

  16. High-molecular-weight DNA and the sedimentation coefficient: a new perspective based on DNA from T7 bacteriophage and two novel forms of T4 bacteriophage.

    Science.gov (United States)

    Clark, R W; Wever, G H; Wiberg, J S

    1980-01-01

    The DNA molecules from T7 bacteriophage and a recently obtained mutant form of T4D were studied. The DNA of this T4 mutant contains cytosine in place of all of the glucosylated hydroxymethylcytosines normally present in T4. Molecular weights were measured with an electron microscope technique, and sedimentation coefficients were determined in isokinetic sucrose gradients. T7 DNA was found to have an Mr of 26.5 x 10(6). The T4 mutant, which we have termed T4c, produces two distinct phage head and DNA size clases. DNA from the standard heads (T4c DNA) has an Mr of 114.9 x 10(6), and DNA from the petite heads (T4cp DNA) has an Mr of 82.9 x 10(6). This enabled the derivation of an equation of sedimentation coefficient at zero concentration corrected to water at 20 degrees C versus Mr for the molecular weight range of 25 x 10(6) to 115 x 10(6) that is based solely on cytosine-containing DNA standards, thereby avoiding possible anomalies introduced by the glucosylation and hydroxymethylation of cytosine. The theory of Gray et al. provided the best description of the sedimentation coefficient versus Mr relationship, based on the sedimentation coefficients and the molecular weights of the three DNA standards and other evidence.

  17. DNA Isolation and GC Base Composition of Four Root-knot Nematode (Meloidogyne spp.) Genomes.

    Science.gov (United States)

    Pableo, E C; Triantaphyllou, A C; Kloos, W E

    1988-01-01

    Phenol extraction and cesium trifluoroacetate ultracentrifugation were compared for efficiency in the extraction of DNA from eggs and second-stage juveniles of four species of Meloidogyne. The second method proved to be more satisfactory in that it yielded larger amounts of DNA, shortened the extraction period, and reduced sample handling by eliminating phenol and ether extraction and RNAse treatment. It also made possible the extraction of DNA: from more than one sample at a time. The mean base compositions (% GC) of the total DNA of M. incognita, M. javanica, M. arenaria, and M. hapla, as determined by thermal denaturation tests, were quite similar, as they ranged only between 31 and 33%. Similarly, the thermal stability of the DNA of all four species covered a narrow range from 82.97 to 83.63 C.

  18. Novel cyclen-based linear polymer as a high-affinity binding material for DNA condensation

    Institute of Scientific and Technical Information of China (English)

    XIANG YongZhe; WANG Na; ZHANG Ji; LI Kun; ZHANG ZhongWei; LIN HongHui; YU XiaoQi

    2009-01-01

    A novel cyclen-based linear polyamine (POGEC) was designed and synthesized from the reaction be-tween 1,3-propanediol diglycidyl ether and 1,7-bis(diethoxyphosphory)-1,4,7,10-tetraazacyclod- odecane.High-affinity binding between POGEC and DNA was demonstrated by agarose gel electrophoresis and scanning electron microscopy (SEM). Moreover, the formed POGEC/DNA complex (termed polyplex) could be disassociated to release the free DNA through addition of the physiological concentration of NaCl solution. Fluorescence spectrum was used to measure the high-affinity binding and DNA con-densation capability of POGEC. Circular dichroism (CD) spectrum indicates that the DNA conformation did not change after binding to POEGC.

  19. Novel cyclen-based linear polymer as a high-affinity binding material for DNA condensation

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    A novel cyclen-based linear polyamine (POGEC) was designed and synthesized from the reaction between 1,3-propanediol diglycidyl ether and 1,7-bis(diethoxyphosphory)-1,4,7,10-tetraazacyclod-odecane. High-affinity binding between POGEC and DNA was demonstrated by agarose gel electrophoresis and scanning electron microscopy (SEM). Moreover,the formed POGEC/DNA complex (termed polyplex) could be disassociated to release the free DNA through addition of the physiological concentration of NaCl solution. Fluorescence spectrum was used to measure the high-affinity binding and DNA condensation capability of POGEC. Circular dichroism (CD) spectrum indicates that the DNA conformation did not change after binding to POEGC.

  20. A novel single-stranded DNA detection method based on organic semiconductor heterojunction

    Science.gov (United States)

    Gu, Wen; Liu, Hongbo; Zhang, Xia; Zhang, Hao; Chen, Xiong; Wang, Jun

    2016-12-01

    We demonstrate a novel DNA detection method with low-cost and disposable advantages by utilizing F16CuPc/CuPc planar organic heterojunction device. Single-stranded DNA (ssDNA) molecules have been well immobilized on the surface of CuPc film observed by atomic force microscopy, producing an obvious electrical response of the device. The conductivity of the organic heterojunction film was significantly increased by ssDNA immobilization because ssDNA molecules brought additional positive charges at heterojunction interface. Furthermore, the thickness dependence of CuPc upper layer on the electrical response was studied to optimize the sensitivity. This study will be helpful for the development of organic heterojunction based biosensors.

  1. Multiplex DNA assay based on nanoparticle probes by single particle inductively coupled plasma mass spectrometry.

    Science.gov (United States)

    Zhang, Shixi; Han, Guojun; Xing, Zhi; Zhang, Sichun; Zhang, Xinrong

    2014-04-01

    A multiplex DNA assay based on nanoparticle (NP) tags detection utilizing single particle mode inductively coupled plasma mass spectrometry (SP-ICP-MS) as ultrasensitive readout has been demonstrated in the article. Three DNA targets associated with clinical diseases (HIV, HAV, and HBV) down to 1 pM were detected by DNA probes labeled with AuNPs, AgNPs, and PtNPs via DNA sandwich assay. Single nucleotide polymorphisms in genes can also be effectively discriminated. Since our method is unaffected by the sample matrix, it is well-suited for diagnostic applications. Moreover, with the high sensitivity of SP-ICP-MS and the variety of NPs detectable by SP-ICP-MS, high-throughput DNA assay could be achieved without signal amplification or chain reaction amplification.

  2. Pros and cons of methylation-based enrichment methods for ancient DNA

    DEFF Research Database (Denmark)

    Seguin-Orlando, Andaine; Gamba, Cristina; Der Sarkissian, Clio;

    2015-01-01

    The recent discovery that DNA methylation survives in fossil material provides an opportunity for novel molecular approaches in palaeogenomics. Here, we apply to ancient DNA extracts the probe-independent Methylated Binding Domains (MBD)-based enrichment method, which targets DNA molecules...... containing methylated CpGs. Using remains of a Palaeo-Eskimo Saqqaq individual, woolly mammoths, polar bears and two equine species, we confirm that DNA methylation survives in a variety of tissues, environmental contexts and over a large temporal range (4,000 to over 45,000 years before present). MBD...... enrichment, however, appears principally biased towards the recovery of CpG-rich and long DNA templates and is limited by the fast post-mortem cytosine deamination rates of methylated epialleles. This method, thus, appears only appropriate for the analysis of ancient methylomes from very well preserved...

  3. Luteinizing Hormone Receptor Knockout (LuRKO) Mice and Transgenic Human Chorionic Gonadotropin (hCG)-Overexpressing Mice (hCG αβ+) Have Bone Phenotypes

    National Research Council Canada - National Science Library

    Yarram, S. J; Perry, M. J; Christopher, T. J; Westby, K; Brown, N. L; Lamminen, T; Rulli, S. B; Zhang, F.-P; Huhtaniemi, I; Sandy, J. R; Mansell, J. P

    2003-01-01

    Considerable attention has been paid to the role of sex steroids during periods of major skeletal turnover, but the interaction of the gonadotropic hormones, which include LH, FSH, and human chorionic gonadotropin (hCG...

  4. HIPS/CG-ATH纳米复合材料的性能%Properties of HIPS/CG-ATH Nanocomposite

    Institute of Scientific and Technical Information of China (English)

    崔文广; 高岩磊; 周二鹏; 梁惠霞; 牟微

    2011-01-01

    采用熔融共混法制备出了高抗冲聚苯乙烯(HIPS)/高性能纳米氢氧化铝(纳米CG-ATH)复合材料,研究了高性能纳米氢氧化铝的加入量对高抗冲聚苯乙烯阻燃性能、力学性能和热稳定性的影响.结果表明,高性能纳米氢氧化铝的加入有助于提高高抗冲聚苯乙烯的极限氧指数、拉伸强度、弯曲模量和热稳定性,但对高抗冲聚苯乙烯的冲击强度会产生不利影响.加入量过多时,高性能纳米氢氧化铝在高抗冲聚苯乙烯基体中的分散性变差.%High impact polystyrene (HIPS) /high performance nano-aluminium trihydroxide(ATH) (nano-CG-ATH) nanocomposites were prepared by melt blending high impact polystyrene with high performance nano-ATH. The effect of high performance nano-ATH amount on flame retardant, mechanical, and thermal properties of high impact polystyrene was studied. The results show that the addition of high performance nano-ATH is beneficial to improve limited oxygen index, tensile strength, flexural modulus, and thermal property of high impact polystyrene, but the addition of high performance nano-ATH reduces impact strength of high impact polystyrene. The dispersion of high performance nano-ATH in high impact polystyrene matrix becomes bad when its amount is too much.

  5. Quantitative and qualitative validations of a sonication-based DNA extraction approach for PCR-based molecular biological analyses.

    Science.gov (United States)

    Dai, Xiaohu; Chen, Sisi; Li, Ning; Yan, Han

    2016-05-15

    The aim of this study was to comprehensively validate the sonication-based DNA extraction method, in hope of the replacement of the so-called 'standard DNA extraction method' - the commercial kit method. Microbial cells in the digested sludge sample, containing relatively high amount of PCR-inhibitory substances, such as humic acid and protein, were applied as the experimental alternatives. The procedure involving solid/liquid separation of sludge sample and dilution of both DNA templates and inhibitors, the minimum templates for PCR-based analyses, and the in-depth understanding from the bias analysis by pyrosequencing technology were obtained and confirmed the availability of the sonication-based DNA extraction method. Copyright © 2016 Elsevier Inc. All rights reserved.

  6. Anhydrous crystals of DNA bases are wide gap semiconductors.

    Science.gov (United States)

    Maia, F F; Freire, V N; Caetano, E W S; Azevedo, D L; Sales, F A M; Albuquerque, E L

    2011-05-07

    We present the structural, electronic, and optical properties of anhydrous crystals of DNA nucleobases (guanine, adenine, cytosine, and thymine) found after DFT (Density Functional Theory) calculations within the local density approximation, as well as experimental measurements of optical absorption for powders of these crystals. Guanine and cytosine (adenine and thymine) anhydrous crystals are predicted from the DFT simulations to be direct (indirect) band gap semiconductors, with values 2.68 eV and 3.30 eV (2.83 eV and 3.22 eV), respectively, while the experimentally estimated band gaps we have measured are 3.83 eV and 3.84 eV (3.89 eV and 4.07 eV), in the same order. The electronic effective masses we have obtained at band extremes show that, at low temperatures, these crystals behave like wide gap semiconductors for electrons moving along the nucleobases stacking direction, while the hole transport are somewhat limited. Lastly, the calculated electronic dielectric functions of DNA nucleobases crystals in the parallel and perpendicular directions to the stacking planes exhibit a high degree of anisotropy (except cytosine), in agreement with published experimental results.

  7. Surface ligation-based resonance light scattering analysis of methylated genomic DNA on a microarray platform.

    Science.gov (United States)

    Ma, Lan; Lei, Zhen; Liu, Xia; Liu, Dianjun; Wang, Zhenxin

    2016-05-10

    DNA methylation is a crucial epigenetic modification and is closely related to tumorigenesis. Herein, a surface ligation-based high throughput method combined with bisulfite treatment is developed for analysis of methylated genomic DNA. In this method, a DNA microarray is employed as a reaction platform, and resonance light scattering (RLS) of nanoparticles is used as the detection principle. The specificity stems from allele-specific ligation of Taq DNA ligase, which is further enhanced by improving the fidelity of Taq DNA ligase in a heterogeneous reaction. Two amplification techniques, rolling circle amplification (RCA) and silver enhancement, are employed after the ligation reaction and a gold nanoparticle (GNP) labeling procedure is used to amplify the signal. As little as 0.01% methylated DNA (i.e. 2 pmol L(-1)) can be distinguished from the cocktail of methylated and unmethylated DNA by the proposed method. More importantly, this method shows good accuracy and sensitivity in profiling the methylation level of genomic DNA of three selected colonic cancer cell lines. This strategy provides a high throughput alternative with reasonable sensitivity and resolution for cancer study and diagnosis.

  8. [Optimization of genomic DNA extraction with magnetic bead- based semi-automatic system].

    Science.gov (United States)

    Ling, Jie; Wang, Hao; Zhang, Shuai; Zhang, Dan-dan; Lai, Mao-de; Zhu, Yi-min

    2012-05-01

    To develop a rapid and effective method for genomic DNA extraction with magnetic bead-based semi-automatic system. DNA was extracted from whole blood samples semi-automatically with nucleic acid automatic extraction system.The concentration and purity of samples was determined by UV-spectrophotometer. Orthogonal design was used to analyze the main effect of lysis time, blood volume, magnetic bead quantity and ethanol concentration on the DNA yield; also the 2-way interaction of these factors. Lysis time, blood volume, magnetic bead quantity and ethanol concentration were associated with DNA yield (PDNA yield was higher under the condition with 15 min of lysis time, 100 μl of blood volume, 80 μl of magnetic beads and 80 % of ethanol. A significant association was found between the magnetic bead quantity and DNA purity OD260/OD280 (P=0.008). Interaction of blood volume and lysis time also existed (P=0.013). DNA purity was better when the extracting condition was 40 μl of magnetic beads, 15 min of lysis time and 100 μl of blood volume. Magnetic beads and ethanol concentration were associated with DNA purity OD260/OD230 (P=0.017 and Pgenomic DNA from the whole blood samples.

  9. Triazene-Based Traceless Linkers for DNA-Directed Chemistry and Development of Methods for Linking Nanomaterials to DNA Origami

    DEFF Research Database (Denmark)

    Hejesen, Christian

    2013-01-01

    Denne ph.d.-afhandling indeholder fire kapitler, der hver beskriver forskellige områder indenfor det videnskabelig felt: DNA nanoteknologi. I kapitel 1 bliver der givet en generel introduktion til DNA og DNA-dirigeret kemi. Først bliver historien bag, og opdagelsen af DNA beskrevet, efterfulgt af...

  10. Analytical and Clinical Validation of the Immulite 1000 hCG Assay for Quantitative Analysis in Urine

    Science.gov (United States)

    Cate, Frances L.; Moffett, Courtney; Gronowski, Ann M.; Grenache, David G.; Hartmann, Katherine E.; Woodworth, Alison

    2013-01-01

    Background The Siemens Immulite hCG assay detects all major hCG variants in serum. Currently, this assay is only FDA approved for qualitative measurement of hCG in urine. Methods Complete validation of the hCG assay in urine was performed on the Siemens Immulite 1000 immunoassay platform. Reference intervals were established for females hCG assay was precise for measuring hCG in urine from pregnant patients with intra- and inter-assay imprecision of hCG and hCGβ respectively. The assay was non-linear for hCGβcf. No hook effect was observed at concentrations up to 1,200,000 pmol/l, for hCGβ or hCGβcf. The reference intervals were hCG assay can accurately quantify hCG in urine. PMID:23470427

  11. Early Steps in the DNA Base Excision Repair Pathway of a Fission Yeast Schizosaccharomyces pombe

    Directory of Open Access Journals (Sweden)

    Kyoichiro Kanamitsu

    2010-01-01

    Full Text Available DNA base excision repair (BER accounts for maintaining genomic integrity by removing damaged bases that are generated endogenously or induced by genotoxic agents. In this paper, we describe the roles of enzymes functioning in the early steps of BER in fission yeast. Although BER is an evolutionarily conserved process, some unique features of the yeast repair pathway were revealed by genetic and biochemical approaches. AP sites generated by monofunctional DNA glycosylases are incised mainly by AP lyase activity of Nth1p, a sole bifunctional glycosylase in yeast, to leave a blocked 3′ end. The major AP endonuclease Apn2p functions predominantly in removing the 3′ block. Finally, a DNA polymerase fills the gap, and a DNA ligase seals the nick (Nth1p-dependent or short patch BER. Apn1p backs up Apn2p. In long patch BER, Rad2p endonuclease removes flap DNA containing a lesion after DNA synthesis. A UV-specific endonuclease Uve1p engages in an alternative pathway by nicking DNA on the 5′ side of oxidative damage. Nucleotide excision repair and homologous recombination are involved in repair of BER intermediates including the AP site and single-strand break with the 3′ block. Other enzymes working in 3′ end processing are also discussed.

  12. An algorithm for the study of DNA sequence evolution based on the genetic code.

    Science.gov (United States)

    Sirakoulis, G Ch; Karafyllidis, I; Sandaltzopoulos, R; Tsalides, Ph; Thanailakis, A

    2004-11-01

    Recent studies of the quantum-mechanical processes in the DNA molecule have seriously challenged the principle that mutations occur randomly. The proton tunneling mechanism causes tautomeric transitions in base pairs resulting in mutations during DNA replication. The meticulous study of the quantum-mechanical phenomena in DNA may reveal that the process of mutagenesis is not completely random. We are still far away from a complete quantum-mechanical model of DNA sequence mutagenesis because of the complexity of the processes and the complex three-dimensional structure of the molecule. In this paper we have developed a quantum-mechanical description of DNA evolution and, following its outline, we have constructed a classical model for DNA evolution assuming that some aspects of the quantum-mechanical processes have influenced the determination of the genetic code. Conversely, our model assumes that the genetic code provides information about the quantum-mechanical mechanisms of mutagenesis, as the current code is the product of an evolutionary process that tries to minimize the spurious consequences of mutagenesis. Based on this model we develop an algorithm that can be used to study the accumulation of mutations in a DNA sequence. The algorithm has a user-friendly interface and the user can change key parameters in order to study relevant hypotheses.

  13. Image Encryption Algorithm Based on Dynamic DNA Coding and Chen’s Hyperchaotic System

    Directory of Open Access Journals (Sweden)

    Jian Zhang

    2016-01-01

    Full Text Available With the development of national information processes, specific image information from secret departments or individuals is often required to be confidentially transmitted. Numerous image encryption methods exist, especially since the initial value sensitivity and other characteristics of chaos theory and chaos theory-based encryption have become increasingly important in recent years. At present, DNA coding constitutes a new research direction of image encryption that uses the four base pairs of DNA code and image pixel values to establish a special correspondence, in order to achieve pixel diffusion. There are eight DNA encoding rules, and current methods of selecting the DNA encoding rules are largely fixed. Thus, the security of encoded data is not high. In this paper, we use the Lorenz chaotic system, Chen’s hyperchaotic system, and the DNA encoding combination and present a new image encryption algorithm that can dynamically select eight types of DNA encoding rules and eight types of DNA addition and subtraction rules, with significant improvements in security. Through simulation experiments and histograms, correlations, and NPCR analyses, we have determined that the algorithm possesses numerous desirable features, including good encryption effects and antishear and antinoise performances.

  14. Designing thermal diode and heat pump based on DNA nanowire: Multifractal approach

    Energy Technology Data Exchange (ETDEWEB)

    Behnia, S., E-mail: s.behnia@iaurmia.ac.ir; Panahinia, R.

    2017-07-12

    The management of heat flow in DNA nano wire was considered. Thermal diode effect in DNA and the domain of its appearance dependent to system parameters have been detected. The appearance of directed thermal flow in thermodynamic sizes proposes the possibility of designing the macroscopic thermal rectifier. By applying driven force, pumping effect has been also observed. The resonance frequency of DNA and threshold amplitudes of driving force for attaining permanent pumping effect have been detected. Forasmuch as detecting negative differential thermal resistance (NDTR) phenomenon, DNA can act as a thermal transistor. By using an analytical parallel investigation based on Rényi spectrum analysis, threshold values to transition to NDTR and pumping regimes have been detected. - Highlights: • The control and management of heat current in DNA have been investigated. • Directed thermal flow and NDTR in DNA have been identified. • By increasing the system size, the reversed thermal rectification appeared. So, it is proposed the possibility of designing the macroscopic thermal rectifier. • Pumping effect accompanied with detection of resonance frequency of DNA has been observed. • To verify the results, we did a parallel analysis based on multifractal concept to detect threshold values for transition to pumping state and NDTR regime.

  15. Label-Free Detection of Ag+ Based on Gold Nanoparticles and Ag+-Specific DNA.

    Science.gov (United States)

    Pu, Wendan; Zhao, Zhao; Wu, Liping; Liu, Yue; Zhao, Huawen

    2015-08-01

    A sensitive label-free method was presented for the determination of silver ion (Ag+) in this paper. Cytosine-rich DNA (C-DNA) was used as Ag+ specific DNA. Without Ag+ in the solution, fluorescence of fluorescein (FAM) is quenched by C-DNA stabilized gold nanoparticles (AuNPs) in high salt environment. When Ag+ is present in the solution, however, Ag+-mediated cytosine-Ag+-cytosine (C-Ag+-C) base pairs induced the C-DNA folding into a hairpin structure, which can not stabilize AuNPs in high salt environment, thus causing AuNPs aggregation. After centrifugation to remove the aggregated AuNPs, the quenching ability of the supernatant for FAM is decreased and the fluorescence intensity of solution increases with increasing the Ag+ concentration. Due to the highly specific interaction of the C-DNA towards Ag+ and the strong fluorescent quenching ability of AuNPs for FAM, the method has high selectivity and sensitivity for Ag+. Under the optimal conditions, the fluorescence intensity at 515 nm increased linearly with the concentration of Ag+ ranging from 15 nM to 700 nM, and the detection limit was determined as 6 nM based on 3 σ/slope. This method is simple, sensitive, and may be applied to other detection systems by selecting the appropriate DNA sequences.

  16. TAA Polyepitope DNA-Based Vaccines: A Potential Tool for Cancer Therapy

    Directory of Open Access Journals (Sweden)

    Roberto Bei

    2010-01-01

    Full Text Available DNA-based cancer vaccines represent an attractive strategy for inducing immunity to tumor associated antigens (TAAs in cancer patients. The demonstration that the delivery of a recombinant plasmid encoding epitopes can lead to epitope production, processing, and presentation to CD8+ T-lymphocytes, and the advantage of using a single DNA construct encoding multiple epitopes of one or more TAAs to elicit a broad spectrum of cytotoxic T-lymphocytes has encouraged the development of a variety of strategies aimed at increasing immunogenicity of TAA polyepitope DNA-based vaccines. The polyepitope DNA-based cancer vaccine approach can (a circumvent the variability of peptide presentation by tumor cells, (b allow the introduction in the plasmid construct of multiple immunogenic epitopes including heteroclitic epitope versions, and (c permit to enroll patients with different major histocompatibility complex (MHC haplotypes. This review will discuss the rationale for using the TAA polyepitope DNA-based vaccination strategy and recent results corroborating the usefulness of DNA encoding polyepitope vaccines as a potential tool for cancer therapy.

  17. A DNA methylation-based definition of biologically distinct breast cancer subtypes.

    Science.gov (United States)

    Stefansson, Olafur A; Moran, Sebastian; Gomez, Antonio; Sayols, Sergi; Arribas-Jorba, Carlos; Sandoval, Juan; Hilmarsdottir, Holmfridur; Olafsdottir, Elinborg; Tryggvadottir, Laufey; Jonasson, Jon G; Eyfjord, Jorunn; Esteller, Manel

    2015-03-01

    In cancer, epigenetic states are deregulated and thought to be of significance in cancer development and progression. We explored DNA methylation-based signatures in association with breast cancer subtypes to assess their impact on clinical presentation and patient prognosis. DNA methylation was analyzed using Infinium 450K arrays in 40 tumors and 17 normal breast samples, together with DNA copy number changes and subtype-specific markers by tissue microarrays. The identified methylation signatures were validated against a cohort of 212 tumors annotated for breast cancer subtypes by the PAM50 method (The Cancer Genome Atlas). Selected markers were pyrosequenced in an independent validation cohort of 310 tumors and analyzed with respect to survival, clinical stage and grade. The results demonstrate that DNA methylation patterns linked to the luminal-B subtype are characterized by CpG island promoter methylation events. In contrast, a large fraction of basal-like tumors are characterized by hypomethylation events occurring within the gene body. Based on these hallmark signatures, we defined two DNA methylation-based subtypes, Epi-LumB and Epi-Basal, and show that they are associated with unfavorable clinical parameters and reduced survival. Our data show that distinct mechanisms leading to changes in CpG methylation states are operative in different breast cancer subtypes. Importantly, we show that a few selected proxy markers can be used to detect the distinct DNA methylation-based subtypes thereby providing valuable information on disease prognosis.

  18. Tracking fungal community responses to maize plants by DNA- and RNA-based pyrosequencing.

    Directory of Open Access Journals (Sweden)

    Eiko E Kuramae

    Full Text Available We assessed soil fungal diversity and community structure at two sampling times (t1 = 47 days and t2 = 104 days of plant age in pots associated with four maize cultivars, including two genetically modified (GM cultivars by high-throughput pyrosequencing of the 18S rRNA gene using DNA and RNA templates. We detected no significant differences in soil fungal diversity and community structure associated with different plant cultivars. However, DNA-based analyses yielded lower fungal OTU richness as compared to RNA-based analyses. Clear differences in fungal community structure were also observed in relation to sampling time and the nucleic acid pool targeted (DNA versus RNA. The most abundant soil fungi, as recovered by DNA-based methods, did not necessary represent the most "active" fungi (as recovered via RNA. Interestingly, RNA-derived community compositions at t1 were highly similar to DNA-derived communities at t2, based on presence/absence measures of OTUs. We recovered large proportions of fungal sequences belonging to arbuscular mycorrhizal fungi and Basidiomycota, especially at the RNA level, suggesting that these important and potentially beneficial fungi are not affected by the plant cultivars nor by GM traits (Bt toxin production. Our results suggest that even though DNA- and RNA-derived soil fungal communities can be very different at a given time, RNA composition may have a predictive power of fungal community development through time.

  19. Highly sensitive detection of DNA methylation levels by using a quantum dot-based FRET method

    Science.gov (United States)

    Ma, Yunfei; Zhang, Honglian; Liu, Fangming; Wu, Zhenhua; Lu, Shaohua; Jin, Qinghui; Zhao, Jianlong; Zhong, Xinhua; Mao, Hongju

    2015-10-01

    DNA methylation is the most frequently studied epigenetic modification that is strongly involved in genomic stability and cellular plasticity. Aberrant changes in DNA methylation status are ubiquitous in human cancer and the detection of these changes can be informative for cancer diagnosis. Herein, we reported a facile quantum dot-based (QD-based) fluorescence resonance energy transfer (FRET) technique for the detection of DNA methylation. The method relies on methylation-sensitive restriction enzymes for the differential digestion of genomic DNA based on its methylation status. Digested DNA is then subjected to PCR amplification for the incorporation of Alexa Fluor-647 (A647) fluorophores. DNA methylation levels can be detected qualitatively through gel analysis and quantitatively by the signal amplification from QDs to A647 during FRET. Furthermore, the methylation levels of three tumor suppressor genes, PCDHGB6, HOXA9 and RASSF1A, in 20 lung adenocarcinoma and 20 corresponding adjacent nontumorous tissue (NT) samples were measured to verify the feasibility of the QD-based FRET method and a high sensitivity for cancer detection (up to 90%) was achieved. Our QD-based FRET method is a convenient, continuous and high-throughput method, and is expected to be an alternative for detecting DNA methylation as a biomarker for certain human cancers.DNA methylation is the most frequently studied epigenetic modification that is strongly involved in genomic stability and cellular plasticity. Aberrant changes in DNA methylation status are ubiquitous in human cancer and the detection of these changes can be informative for cancer diagnosis. Herein, we reported a facile quantum dot-based (QD-based) fluorescence resonance energy transfer (FRET) technique for the detection of DNA methylation. The method relies on methylation-sensitive restriction enzymes for the differential digestion of genomic DNA based on its methylation status. Digested DNA is then subjected to PCR

  20. Role of dissolved salts in thermophoresis of DNA: lattice-Boltzmann-based simulations.

    Science.gov (United States)

    Hammack, Audrey; Chen, Yeng-Long; Pearce, Jennifer Kreft

    2011-03-01

    We use a lattice Boltzmann based Brownian dynamics simulation to investigate the dependence of DNA thermophoresis on its interaction with dissolved salts. We find the thermal diffusion coefficient D{T} depends on the molecule size, in contrast with previous simulations without electrostatics. The measured S{T} also depends on the Debye length. This suggests thermophoresis of DNA is influenced by the electrostatic interactions between the polymer beads and the salt ions. However, when electrostatic forces are weak, DNA thermophoresis is not found, suggesting that other repulsive forces such as the excluded volume force prevent thermal migration.

  1. Rapid extraction of genomic DNA from saliva for HLA typing on microarray based on magnetic nanobeads

    Science.gov (United States)

    Xie, Xin; Zhang, Xu; Yu, Bingbin; Gao, Huafang; Zhang, Huan; Fei, Weiyang

    2004-09-01

    A series of simplified protocols are developed for extracting genomic DNA from saliva by using the magnetic nanobeads as absorbents. In these protocols, both the enrichment of the target cells and the adsorption of DNA can be achieved simultaneously by our functionally modified magnetic beads in one step, and the DNA-nanobeads complex can be used as PCR templates. HLA typing based on an oligonucleotide array was conducted by hybridization with the PCR products. The result shows that the protocols are robust and sensitive.

  2. [The application of mitochondrial genomics to forensic investigations based on human mitochondrial DNA testing].

    Science.gov (United States)

    Skonieczna, Katarzyna; Bednarek, Jarosław; Rogalla, Urszula; Woźniak, Marcin; Gorzkiewicz, Marta; Linkowska, Katarzyna; Duleba, Anna; Sliwka, Karol; Grzybowski, Tomasz

    2012-01-01

    In this study we present two forensic cases where mitochondrial DNA HVS I and HVS II haplotypes of evidentiary hairs match reference samples. Based on the information retrieved from mtDNA coding region of reference material, we selected single nucleotide polymorphisms (SNPs) located outside the HVS I and HVS II regions that could increase the informativeness of mtDNA analysis. The SNPs were typed via SNaPshot or dideoxy sequencing technology. In both cases the SNP results allowed for unambiguous exlusion of the evidence and for determining that reference samples originated from the same person.

  3. A unique perylene-based DNA intercalator: localization in cell nuclei and inhibition of cancer cells and tumors.

    Science.gov (United States)

    Xu, Zejun; Guo, Kunru; Yu, Jieshi; Sun, Haili; Tang, Jun; Shen, Jie; Müllen, Klaus; Yang, Wantai; Yin, Meizhen

    2014-10-29

    To date, perylene derivatives have not been explored as DNA intercalator to inhibit cancer cells by intercalating into the base pairs of DNA. Herein, a water-soluble perylene bisimide (PBDI) that efficiently intercalates into the base pairs of DNA is synthesized. Excitingly, PBDI is superior to the commercial DNA intercalator, amonafide, for specific nuclear accumulation and effective suppression of cancer cells and tumors. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. DNA bases assembled on the Au(110)/electrolyte interface: A combined experimental and theoretical study

    DEFF Research Database (Denmark)

    Salvatore, Princia; Nazmutdinov, Renat R.; Ulstrup, Jens

    2015-01-01

    of the adlayers of the four DNA bases by EC-STM disclosed lifting of the Au(110) reconstruction, specific molecular packing in dense monolayers, and pH dependence of the A and G adsorption. DFT computations based on a cluster model for the Au(110) surface were performed to investigate the adsorption energy...... and geometry of the DNA bases in different adsorbate orientations. The optimized geometry is further used to compute models for STM images which are compared with the recorded STM images. This has provided insight into the physical nature of the adsorption. The specific orientations of A, C, G, and T on Au(110......, accompanied by a pair of strong voltammetry peaks in the double-layer region in acid solutions. Adsorption of the DNA bases gives featureless voltammograms with lower double-layer capacitance, suggesting that all the bases are chemisorbed on the Au(110) surface. Further investigation of the surface structures...

  5. Direct Measurement of Single-Molecule DNA Hybridization Dynamics with Single-Base Resolution.

    Science.gov (United States)

    He, Gen; Li, Jie; Ci, Haina; Qi, Chuanmin; Guo, Xuefeng

    2016-07-25

    Herein, we report label-free detection of single-molecule DNA hybridization dynamics with single-base resolution. By using an electronic circuit based on point-decorated silicon nanowires as electrical probes, we directly record the folding/unfolding process of individual hairpin DNAs with sufficiently high signal-to-noise ratio and bandwidth. These measurements reveal two-level current oscillations with strong temperature dependence, enabling us to determine the thermodynamic and kinetic properties of hairpin DNA hybridization. More importantly, successive, stepwise increases and decreases in device conductance at low temperature on a microsecond timescale are successfully observed, indicating a base-by-base unfolding/folding process. The process demonstrates a kinetic zipper model for DNA hybridization/dehybridization at the single base-pair level. This measurement capability promises a label-free single-molecule approach to probe biomolecular interactions with fast dynamics.

  6. Stacking interaction in metal complexes with compositions of DNA and heteroaromatic N-bases

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The current development in the intramolecular aromatic-ring stacking i nteractions in the complexes with compositions of DNA and heteroaromatic N-bases has been reviewed to a great extent, especially the significant contributions i n several important systems about ternary mixed-ligand complexes, including nucl eotide-metal ion-po- lyaromatic amine, amino acid-metal ion-polyaromatic amine, nucleotide-metal ion-pyridine-like aromatic amine, nucleotide-metal ion-amino ac id, nucleotide-metal ion-nucleic acid base, nucleic acid base-metal ion, and the important factors affecting the intramolecular aromatic-ring stacking interacti ons in the complexes. Based on the study of stacking interaction in the complexe s, the mechanism of interaction between DNA molecules and complexes of heteroaro matic N-bases has been established, which is crucial for the design and synthesi s of the complexes acting as molecular devices of DNA.

  7. The role of DNA base excision repair in brain homeostasis and disease

    DEFF Research Database (Denmark)

    Akbari, Mansour; Morevati, Marya; Croteau, Deborah;

    2015-01-01

    Chemical modification and spontaneous loss of nucleotide bases from DNA are estimated to occur at the rate of thousands per human cell per day. DNA base excision repair (BER) is a critical mechanism for repairing such lesions in nuclear and mitochondrial DNA. Defective expression or function...... of proteins required for BER or proteins that regulate BER have been consistently associated with neurological dysfunction and disease in humans. Recent studies suggest that DNA lesions in the nuclear and mitochondrial compartments and the cellular response to those lesions have a profound effect on cellular...... energy homeostasis, mitochondrial function and cellular bioenergetics, with especially strong influence on neurological function. Further studies in this area could lead to novel approaches to prevent and treat human neurodegenerative disease....

  8. Molecular beacon-based enzyme-free strategy for amplified DNA detection.

    Science.gov (United States)

    Huang, Jiahao; Wu, Jueqi; Li, Zhigang

    2016-05-15

    We report an enzyme-free, sensitive strategy for DNA detections through fluorescence amplification. The sensing method employs molecular beacons (MBs) and two single-stranded helper DNA probes. In the presence of a DNA target, it binds and opens an MB. This triggers the hybridizations between the MB and helper probes, and consequently releases the DNA target, which becomes available to react with another MB and enhances the fluorescence emission of the MBs. The detection limit of the proposed strategy is 0.58 pM, which is about 3 orders of magnitude better than the conventional MB-based method. This method is also fast and exhibits good selectivity. It is superior to previous MB-based amplification approaches employing enzymes or nanomaterials.

  9. A Novel Image Encryption Algorithm Based on DNA Encoding and Spatiotemporal Chaos

    Directory of Open Access Journals (Sweden)

    Chunyan Song

    2015-10-01

    Full Text Available DNA computing based image encryption is a new, promising field. In this paper, we propose a novel image encryption scheme based on DNA encoding and spatiotemporal chaos. In particular, after the plain image is primarily diffused with the bitwise Exclusive-OR operation, the DNA mapping rule is introduced to encode the diffused image. In order to enhance the encryption, the spatiotemporal chaotic system is used to confuse the rows and columns of the DNA encoded image. The experiments demonstrate that the proposed encryption algorithm is of high key sensitivity and large key space, and it can resist brute-force attack, entropy attack, differential attack, chosen-plaintext attack, known-plaintext attack and statistical attack.

  10. Physically transient photonics: random versus distributed feedback lasing based on nanoimprinted DNA.

    Science.gov (United States)

    Camposeo, Andrea; Del Carro, Pompilio; Persano, Luana; Cyprych, Konrad; Szukalski, Adam; Sznitko, Lech; Mysliwiec, Jaroslaw; Pisignano, Dario

    2014-10-28

    Room-temperature nanoimprinted, DNA-based distributed feedback (DFB) laser operation at 605 nm is reported. The laser is made of a pure DNA host matrix doped with gain dyes. At high excitation densities, the emission of the untextured dye-doped DNA films is characterized by a broad emission peak with an overall line width of 12 nm and superimposed narrow peaks, characteristic of random lasing. Moreover, direct patterning of the DNA films is demonstrated with a resolution down to 100 nm, enabling the realization of both surface-emitting and edge-emitting DFB lasers with a typical line width of <0.3 nm. The resulting emission is polarized, with a ratio between the TE- and TM-polarized intensities exceeding 30. In addition, the nanopatterned devices dissolve in water within less than 2 min. These results demonstrate the possibility of realizing various physically transient nanophotonics and laser architectures, including random lasing and nanoimprinted devices, based on natural biopolymers.

  11. A NEW DNA BASED APPROACH OF GENERATING KEYDEPENDENTMIXCOLUMNS TRANSFORMATION

    Directory of Open Access Journals (Sweden)

    Auday H. Al-Wattar

    2015-03-01

    Full Text Available The use of key-dependent MixColumns can be regarded as one of the applied techniques for changing the quality of a cryptographic algorithm. This article explains one approach for altering the MixColumns transformation engaged in the AES algorithm. The approach employed methods inspired from DNA processes and structure, which relied on the key.The parameters of the proposedMixCloumns have characteristics identical to those of the original algorithm AES besides increasing its resistance against attack.The original transformation uses single static MDS matrix while the proposed methods used dynamic MDS. The security of the new MixColumns was analyzed, and the NIST Test Suite tests were used to test the randomness for the block cipher that used the new transformation.

  12. Association between the ADRA2A 1291 C/G polymorphism and the metabolic syndrome

    NARCIS (Netherlands)

    Risselada, Arne; Vehof, Jelle; Bruggeman, Richard; Wilffert, Bob; Cohen, Dan; Al Hadithy, Asmar F.; Arends, Johan; Mulder, Hans

    2010-01-01

    Background: Studies have found an association between the ADRA2A 1291 C/G polymorphism and antipsychoticinduced weight gain. A possible association with the metabolic syndrome has not been studied. Objectives: To investigate the association between the ADRA2A 1291 C/G polymorphism and the metabolic

  13. 33 CFR Appendix A to Part 105 - Facility Vulnerability and Security Measures Summary (Form CG-6025)

    Science.gov (United States)

    2010-07-01

    ... Security Measures Summary (Form CG-6025) A Appendix A to Part 105 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY MARITIME SECURITY MARITIME SECURITY: FACILITIES Pt. 105, App. A Appendix A to Part 105—Facility Vulnerability and Security Measures Summary (Form CG-6025)...

  14. Association between the ADRA2A 1291 C/G polymorphism and the metabolic syndrome

    NARCIS (Netherlands)

    Risselada, Arne; Vehof, Jelle; Bruggeman, Richard; Wilffert, Bob; Cohen, Dan; Al Hadithy, Asmar F.; Arends, Johan; Mulder, Hans

    2010-01-01

    Background: Studies have found an association between the ADRA2A 1291 C/G polymorphism and antipsychoticinduced weight gain. A possible association with the metabolic syndrome has not been studied. Objectives: To investigate the association between the ADRA2A 1291 C/G polymorphism and the metabolic

  15. Myth vs. Fact: The Human Chorionic Gonadotropin (hCG) Diet

    Science.gov (United States)

    ... exactly is hCG? Human chorionic gonadotropin is a hormone produced during pregnancy to help nourish the growing fetus. The U.S. Food and Drug Administration (FDA) approved hCG for a number of medical uses. ... understand that hormones are powerful and must be prescribed with caution. ...

  16. Predictive value of plasma hCG measured 14 days after Day-2 single embryo transfer

    DEFF Research Database (Denmark)

    Løssl, Kristine; Oldenburg, Anna; Toftager, Mette

    2017-01-01

    INTRODUCTION: Prediction of pregnancy outcome after IVF is important for patients and clinicians. Early plasma hCG (p-hCG) levels are the best known predictor of pregnancy outcome, but no studies has been restricted to single embryo transfer (SET) of Day-2 embryos. The aim of the present study...

  17. Reference ranges and determinants of total hCG levels during pregnancy: the Generation R Study

    NARCIS (Netherlands)

    T.I.M. Korevaar (Tim); E.A.P. Steegers (Eric); Y.B. de Rijke (Yolanda); S. Schalekamp-Timmermans (S.); W.E. Visser (Wil Edward); A. Hofman (Albert); V.W.V. Jaddoe (Vincent); H.W. Tiemeier (Henning); T.J. Visser (Theo); M. Medici (Marco); R.P. Peeters (Robin)

    2015-01-01

    textabstractHuman chorionic gonadotropin (hCG) is a pregnancy hormone secreted by the placental synctiotrophoblast cell layer that has been linked to fetal growth and various placental, uterine and fetal functions. In order to investigate the effects of hCG on clinical endpoints, knowledge on refere

  18. A novel HDAC inhibitor, CG200745, inhibits pancreatic cancer cell growth and overcomes gemcitabine resistance

    Science.gov (United States)

    Lee, Hee Seung; Park, Soo Been; Kim, Sun A; Kwon, Sool Ki; Cha, Hyunju; Lee, Do Young; Ro, Seonggu; Cho, Joong Myung; Song, Si Young

    2017-01-01

    Pancreatic cancer is predominantly lethal, and is primarily treated using gemcitabine, with increasing resistance. Therefore, novel agents that increase tumor sensitivity to gemcitabine are needed. Histone deacetylase (HDAC) inhibitors are emerging therapeutic agents, since HDAC plays an important role in cancer initiation and progression. We evaluated the antitumor effect of a novel HDAC inhibitor, CG200745, combined with gemcitabine/erlotinib on pancreatic cancer cells and gemcitabine-resistant pancreatic cancer cells. Three pancreatic cancer-cell lines were used to evaluate the antitumor effect of CG200745 combined with gemcitabine/erlotinib. CG200745 induced the expression of apoptotic proteins (PARP and caspase-3) and increased the levels of acetylated histone H3. CG200745 with gemcitabine/erlotinib showed significant growth inhibition and synergistic antitumor effects in vitro. In vivo, gemcitabine/erlotinib and CG200745 reduced tumor size up to 50%. CG200745 enhanced the sensitivity of gemcitabine-resistant pancreatic cancer cells to gemcitabine, and decreased the level of ATP-binding cassette-transporter genes, especially multidrug resistance protein 3 (MRP3) and MRP4. The novel HDAC inhibitor, CG200745, with gemcitabine/erlotinib had a synergistic anti-tumor effect on pancreatic cancer cells. CG200745 significantly improved pancreatic cancer sensitivity to gemcitabine, with a prominent antitumor effect on gemcitabine-resistant pancreatic cancer cells. Therefore, improved clinical outcome is expected in the future. PMID:28134290

  19. Role of CgHOG1 in Stress Responses and Glycerol Overproduction of Candida glycerinogenes.

    Science.gov (United States)

    Ji, Hao; Zhuge, Bin; Zong, Hong; Lu, Xinyao; Fang, Huiying; Zhuge, Jian

    2016-12-01

    Candida glycerinogenes, the glycerol producer with excellent multi-stress tolerances, is considered to be a potential biotechnological host used in the production of glycerol and its derivatives under extreme fermentation conditions. In this study, to evaluate the multiple roles of mitogen-activated protein kinase CgHOG1, we constructed a gene disruption system in the diploid C. glycerinogenes to obtain CgHOG1 null mutant. Pseudohyphae generation of the CgHOG1 mutant under non-inducing condition indicated a repressor role in morphological transitions. Disruption of CgHOG1 resulted in increased sensitivities to osmotic, acetic acid, and oxidative stress but not involved in thermotolerance. In the CgHOG1 mutant, NaCl shock failed to stimulate the accumulation of intracellular glycerol and was fatal. In addition, the CgHOG1 mutant displayed a significant prolonged growth lag phase in YPD medium with no decrease in glycerol production, whereas the mutant cannot grow under hyperosmotic condition with no detectable glycerol in broth. These results suggested that CgHOG1 plays important roles in morphogenesis and multi-stress tolerance. The growth and glycerol overproduction under osmotic stress are heavily dependent on CgHOG1 kinase.

  20. Reference ranges and determinants of total hCG levels during pregnancy: the Generation R Study

    NARCIS (Netherlands)

    T.I.M. Korevaar (Tim); E.A.P. Steegers (Eric); Y.B. de Rijke (Yolanda); S. Schalekamp-Timmermans (S.); W.E. Visser (Wil Edward); A. Hofman (Albert); V.W.V. Jaddoe (Vincent); H.W. Tiemeier (Henning); T.J. Visser (Theo); M. Medici (Marco); R.P. Peeters (Robin)

    2015-01-01

    textabstractHuman chorionic gonadotropin (hCG) is a pregnancy hormone secreted by the placental synctiotrophoblast cell layer that has been linked to fetal growth and various placental, uterine and fetal functions. In order to investigate the effects of hCG on clinical endpoints, knowledge on refere

  1. Association between the ADRA2A 1291 C/G polymorphism and the metabolic syndrome

    NARCIS (Netherlands)

    Risselada, Arne; Vehof, Jelle; Bruggeman, Richard; Wilffert, Bob; Cohen, Dan; Al Hadithy, Asmar F.; Arends, Johan; Mulder, Hans

    Background: Studies have found an association between the ADRA2A 1291 C/G polymorphism and antipsychoticinduced weight gain. A possible association with the metabolic syndrome has not been studied. Objectives: To investigate the association between the ADRA2A 1291 C/G polymorphism and the metabolic

  2. Exploration of cellular DNA lesion, DNA-binding and biocidal ordeal of novel curcumin based Knoevenagel Schiff base complexes incorporating tryptophan: Synthesis and structural validation

    Science.gov (United States)

    Chandrasekar, Thiravidamani; Raman, Natarajan

    2016-07-01

    A few novel Schiff base transition metal complexes of general formula [MLCl] (where, L = Schiff base, obtained by the condensation reaction of Knoevenagel condensate of curcumin, L-tryptophan and M = Cu(II), Ni(II), Co(II), and Zn(II)), were prepared by stencil synthesis. They were typified using UV-vis, IR, EPR spectral techniques, micro analytical techniques, magnetic susceptibility and molar conductivity. Geometry of the metal complexes was examined and recognized as square planar. DNA binding and viscosity studies revealed that the metal(II) complexes powerfully bound via an intercalation mechanism with the calf thymus DNA. Gel-electrophoresis technique was used to investigate the DNA cleavage competence of the complexes and they establish to approve the cleavage of pBR322 DNA in presence of oxidant H2O2. This outcome inferred that the synthesized complexes showed better nuclease activity. Moreover, the complexes were monitored for antimicrobial activities. The results exposed that the synthesized compounds were forceful against all the microbes under exploration.

  3. An enzyme-based DNA preparation method for application to forensic biological samples and degraded stains.

    Science.gov (United States)

    Lounsbury, Jenny A; Coult, Natalie; Miranian, Daniel C; Cronk, Stephen M; Haverstick, Doris M; Kinnon, Paul; Saul, David J; Landers, James P

    2012-09-01

    Extraction of DNA from forensic samples typically uses either an organic extraction protocol or solid phase extraction (SPE) and these methods generally involve numerous sample transfer, wash and centrifugation steps. Although SPE has been successfully adapted to the microdevice, it can be problematic because of lengthy load times and uneven packing of the solid phase. A closed-tube enzyme-based DNA preparation method has recently been developed which uses a neutral proteinase to lyse cells and degrade proteins and nucleases [14]. Following a 20 min incubation of the buccal or whole blood sample with this proteinase, DNA is polymerase chain reaction (PCR)-ready. This paper describes the optimization and quantitation of DNA yield using this method, and application to forensic biological samples, including UV- and heat-degraded whole blood samples on cotton or blue denim substrates. Results demonstrate that DNA yield can be increased from 1.42 (±0.21)ng/μL to 7.78 (±1.40)ng/μL by increasing the quantity of enzyme per reaction by 3-fold. Additionally, there is a linear relationship between the amount of starting cellular material added and the concentration of DNA in the solution, thereby allowing DNA yield estimations to be made. In addition, short tandem repeat (STR) profile results obtained using DNA prepared with the enzyme method were comparable to those obtained with a conventional SPE method, resulting in full STR profiles (16 of 16 loci) from liquid samples (buccal swab eluate and whole blood), dried buccal swabs and bloodstains and partial profiles from UV or heat-degraded bloodstains on cotton or blue denim substrates. Finally, the DNA preparation method is shown to be adaptable to glass or poly(methyl methacrylate) (PMMA) microdevices with little impact on STR peak height but providing a 20-fold reduction in incubation time (as little as 60 s), leading to a ≥1 h reduction in DNA preparation time.

  4. A CG Method for Multiple Right Hand Sides and Multiple Shifts in Lattice QCD Calculations

    CERN Document Server

    Birk, Sebastian

    2012-01-01

    We consider the task of computing solutions of linear systems that only differ by a shift with the identity matrix as well as linear systems with several different right hand sides. In the past Krylov subspace methods have been developed which exploit either the need for solutions to multiple right hand sides (e.g. deflation type methods and block methods) or multiple shifts (e.g. shifted CG) with some success. In this paper we present a block Krylov subspace method which, based on a block Lanczos process, exploits both features - shifts and multiple right hand sides - at once. Such situations arise, for example, in lattice QCD simulations within the Rational Hybrid Monte Carlo algorithm. We give numerical evidence that our method is superior to applying other iterative methods to each of the systems individually as well as, in some cases, to shifted or block Krylov subspace methods.

  5. 8-oxoG DNA Glycosylase-1 Inhibition Sensitizes Neuro-2a Cells to Oxidative DNA Base Damage Induced by 900 MHz Radiofrequency Electromagnetic Radiation

    Directory of Open Access Journals (Sweden)

    Xiaoya Wang

    2015-09-01

    Full Text Available Background/Aims: The purpose of this study was to explore the in vitro putative genotoxicity during exposure of Neuro-2a cells to radiofrequency electromagnetic fields (RF-EMFs with or without silencing of 8-oxoG DNA glycosylase-1 (OGG1. Methods: Neuro-2a cells treated with or without OGG1 siRNA were exposed to 900 MHz Global System for Mobile Communication (GSM Talk signals continuously at a specific absorption rate (SAR of 0, 0.5, 1 or 2 W/kg for 24 h. DNA strand breakage and DNA base damage were measured by the alkaline comet assay and a modified comet assay using formamidopyrimidine DNA glycosylase (FPG, respectively. Reactive oxygen species (ROS levels and cell viability were monitored using the non-fluorescent probe 2, 7-dichlorofluorescein diacetate (DCFH-DA and CCK-8 assay. Results: Exposure to 900 MHz RF-EMFs with insufficient energy could induce oxidative DNA base damage in Neuro-2a cells. These increases were concomitant with similar increases in the generation of reactive oxygen species (ROS. Without OGG1 siRNA, 2 W/kg RF-EMFs induced oxidative DNA base damage in Neuro-2a cells. Interestingly, with OGG1 siRNA, RF-EMFs could cause DNA base damage in Neuro-2a cells as low as 1 W/kg. However, neither DNA strand breakage nor altered cell viability was observed. Conclusion: Even if further studies remain conducted we support the hypothesis that OGG1 is involved in the process of DNA base repair and may play a pivotal role in protecting DNA bases from RF-EMF induced oxidative damage.

  6. DNA-based dye lasers: progress in this half a decade

    Science.gov (United States)

    Kawabe, Yutaka

    2016-09-01

    After the invention of DNA-surfactant films and the proposal of dye doping into them by Ogata, many applications were demonstrated. Among them tunable thin film laser is one of the most attractive functional devices. Development and progress in DNA based lasers after the first observation of amplified spontaneous emission (ASE) by us has been reviewed in a former paper published in 2011.1 In this proceeding, progresses in the subsequent half a decade are described.

  7. Technical note: improved DNA extraction from ancient bones using silica-based spin columns.

    Science.gov (United States)

    Yang, D Y; Eng, B; Waye, J S; Dudar, J C; Saunders, S R

    1998-04-01

    We describe a simple method for extracting polymerase chain reaction-amplifiable DNA from ancient bones without the use of organic solvents. Bone powders are digested with proteinase K, and the DNA is purified directly using silica-based spin columns (QIAquick3, QIAGEN). The efficiency of this protocol is demonstrated using human bone samples ranging in age from 15 to 5,000 years old.

  8. A DNA Microarray-Based Assay to Detect Dual Infection with Two Dengue Virus Serotypes

    OpenAIRE

    Alvaro Díaz-Badillo; María de Lourdes Muñoz; Gerardo Perez-Ramirez; Victor Altuzar; Juan Burgueño; Mendoza-Alvarez, Julio G.; Martínez-Muñoz, Jorge P.; Alejandro Cisneros; Joel Navarrete-Espinosa; Feliciano Sanchez-Sinencio

    2014-01-01

    Here; we have described and tested a microarray based-method for the screening of dengue virus (DENV) serotypes. This DNA microarray assay is specific and sensitive and can detect dual infections with two dengue virus serotypes and single-serotype infections. Other methodologies may underestimate samples containing more than one serotype. This technology can be used to discriminate between the four DENV serotypes. Single-stranded DNA targets were covalently attached to glass slides and hybrid...

  9. DNA barcoding: a genomic-based tool for authentication of phytomedicinals and its products

    OpenAIRE

    Balachandran KRS; Mohanasundaram S; Ramalingam S

    2015-01-01

    Karpaga Raja Sundari Balachandran, Saravanan Mohanasundaram, Sathishkumar Ramalingam Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu, India Abstract: DNA barcoding helps to identify the plant materials based on short, standardized gene sequences in a rapid, accurate, and cost-effective manner. Recent reports reveal that DNA barcoding can be used for the assignment of unknown specimens to a taxonomic group, authentic identificati...

  10. Swi5-Sfr1 protein stimulates Rad51-mediated DNA strand exchange reaction through organization of DNA bases in the presynaptic filament.

    KAUST Repository

    Fornander, Louise H

    2013-12-03

    The Swi5-Sfr1 heterodimer protein stimulates the Rad51-promoted DNA strand exchange reaction, a crucial step in homologous recombination. To clarify how this accessory protein acts on the strand exchange reaction, we have analyzed how the structure of the primary reaction intermediate, the Rad51/single-stranded DNA (ssDNA) complex filament formed in the presence of ATP, is affected by Swi5-Sfr1. Using flow linear dichroism spectroscopy, we observe that the nucleobases of the ssDNA are more perpendicularly aligned to the filament axis in the presence of Swi5-Sfr1, whereas the bases are more randomly oriented in the absence of Swi5-Sfr1. When using a modified version of the natural protein where the N-terminal part of Sfr1 is deleted, which has no affinity for DNA but maintained ability to stimulate the strand exchange reaction, we still observe the improved perpendicular DNA base orientation. This indicates that Swi5-Sfr1 exerts its activating effect through interaction with the Rad51 filament mainly and not with the DNA. We propose that the role of a coplanar alignment of nucleobases induced by Swi5-Sfr1 in the presynaptic Rad51/ssDNA complex is to facilitate the critical matching with an invading double-stranded DNA, hence stimulating the strand exchange reaction.

  11. Increased N-terminal CgA in circulation associated with cardiac reperfusin in pigs

    DEFF Research Database (Denmark)

    Frydland, Martin; Kousholt, Birgitte S.; Larsen, Jens Rolighed;

    2013-01-01

    Aim: Acute myocardial infarction causes neurohumoral activation characterized by increased sympathetic activity. CgA is a protein released during sympathoadrenal stress from neuroendocrine tissue. Recently, increased CgA concentrations in circulation have been reported and suggested...... to be an independent predictor of mortality after acute myocardial infarction. Materials & methods: Eighteen pigs underwent 1 h of regional myocardial ischemia followed by 3 h of reperfusion. Blood samples were collected every hour and plasma CgA was measured with two radioimmunoassays. Results: We found a 30......% increase in plasma N-terminal CgA 1 h after re-establishment of coronary blood supply. On the other hand, plasma pancreastatin did not change in response to ischemia or reperfusion but decreased during the entire experiment. Conclusion: Our results suggest a differentiated CgA response in myocardial...

  12. Feasibility study of molecular memory device based on DNA using methylation to store information

    Science.gov (United States)

    Jiang, Liming; Qiu, Wanzhi; Al-Dirini, Feras; Hossain, Faruque M.; Evans, Robin; Skafidas, Efstratios

    2016-07-01

    DNA, because of its robustness and dense information storage capability, has been proposed as a potential candidate for next-generation storage media. However, encoding information into the DNA sequence requires molecular synthesis technology, which to date is costly and prone to synthesis errors. Reading the DNA strand information is also complex. Ideally, DNA storage will provide methods for modifying stored information. Here, we conduct a feasibility study investigating the use of the DNA 5-methylcytosine (5mC) methylation state as a molecular memory to store information. We propose a new 1-bit memory device and study, based on the density functional theory and non-equilibrium Green's function method, the feasibility of electrically reading the information. Our results show that changes to methylation states lead to changes in the peak of negative differential resistance which can be used to interrogate memory state. Our work demonstrates a new memory concept based on methylation state which can be beneficial in the design of next generation DNA based molecular electronic memory devices.

  13. On-chip magnetic bead-based DNA melting curve analysis using a magnetoresistive sensor

    Energy Technology Data Exchange (ETDEWEB)

    Rizzi, Giovanni, E-mail: giori@nanotech.dtu.dk; Østerberg, Frederik W.; Henriksen, Anders D.; Dufva, Martin; Hansen, Mikkel F., E-mail: mikkel.hansen@nanotech.dtu.dk

    2015-04-15

    We present real-time measurements of DNA melting curves in a chip-based system that detects the amount of surface-bound magnetic beads using magnetoresistive magnetic field sensors. The sensors detect the difference between the amount of beads bound to the top and bottom sensor branches of the differential sensor geometry. The sensor surfaces are functionalized with wild type (WT) and mutant type (MT) capture probes, differing by a single base insertion (a single nucleotide polymorphism, SNP). Complementary biotinylated targets in suspension couple streptavidin magnetic beads to the sensor surface. The beads are magnetized by the field arising from the bias current passed through the sensors. We demonstrate the first on-chip measurements of the melting of DNA hybrids upon a ramping of the temperature. This overcomes the limitation of using a single washing condition at constant temperature. Moreover, we demonstrate that a single sensor bridge can be used to genotype a SNP. - Highlights: • We apply magnetoresistive sensors to study solid-surface hybridization kinetics of DNA. • We measure DNA melting profiles for perfectly matching DNA duplexes and for a single base mismatch. • We present a procedure to correct for temperature dependencies of the sensor output. • We reliably extract melting temperatures for the DNA hybrids. • We demonstrate direct measurement of differential binding signal for two probes on a single sensor.

  14. Sample processing for DNA chip array-based analysis of enterohemorrhagic Escherichia coli (EHEC

    Directory of Open Access Journals (Sweden)

    Enfors Sven-Olof

    2008-10-01

    Full Text Available Abstract Background Exploitation of DNA-based analyses of microbial pathogens, and especially simultaneous typing of several virulence-related genes in bacteria is becoming an important objective of public health these days. Results A procedure for sample processing for a confirmative analysis of enterohemorrhagic Escherichia coli (EHEC on a single colony with DNA chip array was developed and is reported here. The protocol includes application of fragmented genomic DNA from ultrasonicated colonies. The sample processing comprises first 2.5 min of ultrasonic treatment, DNA extraction (2×, and afterwards additional 5 min ultrasonication. Thus, the total sample preparation time for a confirmative analysis of EHEC is nearly 10 min. Additionally, bioinformatic revisions were performed in order to design PCR primers and array probes specific to most conservative regions of the EHEC-associated genes. Six strains with distinct pathogenic properties were selected for this study. At last, the EHEC chip array for a parallel and simultaneous detection of genes etpC-stx1-stx2-eae was designed and examined. This should permit to sense all currently accessible variants of the selected sequences in EHEC types and subtypes. Conclusion In order to implement the DNA chip array-based analysis for direct EHEC detection the sample processing was established in course of this work. However, this sample preparation mode may also be applied to other types of EHEC DNA-based sensing systems.

  15. Silencio/CG9754 connects the Piwi-piRNA complex to the cellular heterochromatin machinery.

    Science.gov (United States)

    Sienski, Grzegorz; Batki, Julia; Senti, Kirsten-André; Dönertas, Derya; Tirian, Laszlo; Meixner, Katharina; Brennecke, Julius

    2015-11-01

    The repression of transposable elements in eukaryotes often involves their transcriptional silencing via targeted chromatin modifications. In animal gonads, nuclear Argonaute proteins of the PIWI clade complexed with small guide RNAs (piRNAs) serve as sequence specificity determinants in this process. How binding of nuclear PIWI-piRNA complexes to nascent transcripts orchestrates heterochromatin formation and transcriptional silencing is unknown. Here, we characterize CG9754/Silencio as an essential piRNA pathway factor that is required for Piwi-mediated transcriptional silencing in Drosophila. Ectopic targeting of Silencio to RNA or DNA is sufficient to elicit silencing independently of Piwi and known piRNA pathway factors. Instead, Silencio requires the H3K9 methyltransferase Eggless/SetDB1 for its silencing ability. In agreement with this, SetDB1, but not Su(var)3-9, is required for Piwi-mediated transcriptional silencing genome-wide. Due to its interaction with the target-engaged Piwi-piRNA complex, we suggest that Silencio acts as linker between the sequence specificity factor Piwi and the cellular heterochromatin machinery. © 2015 Sienski et al.; Published by Cold Spring Harbor Laboratory Press.

  16. Silencio/CG9754 connects the Piwi–piRNA complex to the cellular heterochromatin machinery

    Science.gov (United States)

    Sienski, Grzegorz; Batki, Julia; Senti, Kirsten-André; Dönertas, Derya; Tirian, Laszlo; Meixner, Katharina; Brennecke, Julius

    2015-01-01

    The repression of transposable elements in eukaryotes often involves their transcriptional silencing via targeted chromatin modifications. In animal gonads, nuclear Argonaute proteins of the PIWI clade complexed with small guide RNAs (piRNAs) serve as sequence specificity determinants in this process. How binding of nuclear PIWI–piRNA complexes to nascent transcripts orchestrates heterochromatin formation and transcriptional silencing is unknown. Here, we characterize CG9754/Silencio as an essential piRNA pathway factor that is required for Piwi-mediated transcriptional silencing in Drosophila. Ectopic targeting of Silencio to RNA or DNA is sufficient to elicit silencing independently of Piwi and known piRNA pathway factors. Instead, Silencio requires the H3K9 methyltransferase Eggless/SetDB1 for its silencing ability. In agreement with this, SetDB1, but not Su(var)3-9, is required for Piwi-mediated transcriptional silencing genome-wide. Due to its interaction with the target-engaged Piwi–piRNA complex, we suggest that Silencio acts as linker between the sequence specificity factor Piwi and the cellular heterochromatin machinery. PMID:26494711

  17. AlkB recognition of a bulky DNA base adduct stabilized by chemical cross-linking

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    E.coli AlkB is a direct DNA/RNA repair protein that oxidatively reverses N1 alkylated purines and N3 alkylated pyrimidines to regular bases.Previous crystal structures have revealed N1-methyl adenine(1-meA) recognition by AlkB and a unique base flipping mechanism,but how the AlkB active site can accommodate bulky base adducts is largely unknown.Employing a previously developed chemical cross-linking technique,we crystallized AlkB with a duplex DNA containing a caged thymine base(cagedT).The structure revealed a flexible hairpin lid and a reorganized substrate recognition loop used by AlkB to accommodate cagedT.These observations demonstrate,at the molecular level,how bulky DNA adducts may be recognized and processed by AlkB.

  18. 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.

  19. Sequential Versus Continual Purified Urinary FSH/hCG in Men With Idiopathic Hypogonadotropic Hypogonadism.

    Science.gov (United States)

    Zhang, Manna; Tong, Guoyu; Liu, Yanling; Mu, Yiming; Weng, Jianping; Xue, Yaoming; Luo, Zuojie; Xue, Yuanming; Shi, Lixin; Wu, Xueyan; Sun, Shouyue; Zhu, Yanhua; Cao, Ying; Zhang, Jie; Huang, Hong; Niu, Ben; Li, Hong; Guo, Qinghua; Gao, Yan; Li, Zhibin; Ning, Guang; Zhu, Dalong; Li, Xiaoying

    2015-06-01

    Gonadotropin therapy using a human chorionic gonadotropin (hCG) and FSH preparation is an effective regimen in inducing masculinization and spermatogenesis in men with idiopathic hypogonadotropic hypogonadism (IHH). However, the high cost of medication and frequent injections affect compliance. The aim of this study was to determine the efficacy of sequential use of highly purified urinary FSH (uFSH)/hCG in men with IHH. A randomized, open-label, prospective, controlled noninferiority trial with an 18-month follow-up was conducted in 9 tertiary hospitals. A total of 67 Chinese men with IHH were randomly allocated into group A receiving continual uFSH (75 U, 3 times a week) and hCG (2000 U, twice a week) injection and group B receiving sequential uFSH (75 U, 3 times a week every other 3 months) and hCG (2000 U, twice a week) injection. The primary outcome was the proportion of subjects with a sperm concentration of ≥ 1.0 × 10(6)/mL during the 18 months. The efficacy between groups A and B was compared for noninferiority. Of the patients, 17/33 (51.5%) receiving continual uFSH/hCG and 19/34 (55.9%) receiving sequential uFSH/hCG achieved sperm concentrations of ≥ 1.0 × 10(6)/mL. The efficacy in the sequential uFSH/hCG group was not inferior to that in the continual uFSH/hCG group (noninferiority, P = .008) by intention-to-treat analysis. The efficacy of the sequential uFSH/hCG regimen is not inferior to that of the continual uFSH/hCG regimen in inducing spermatogenesis and masculinization of patients with IHH.

  20. Physical Characterization of Gemini Surfactant-Based Synthetic Vectors for the Delivery of Linear Covalently Closed (LCC DNA Ministrings.

    Directory of Open Access Journals (Sweden)

    Chi Hong Sum

    Full Text Available In combination with novel linear covalently closed (LCC DNA minivectors, referred to as DNA ministrings, a gemini surfactant-based synthetic vector for gene delivery has been shown to exhibit enhanced delivery and bioavailability while offering a heightened safety profile. Due to topological differences from conventional circular covalently closed (CCC plasmid DNA vectors, the linear topology of LCC DNA ministrings may present differences with regards to DNA interaction and the physicochemical properties influencing DNA-surfactant interactions in the formulation of lipoplexed particles. In this study, N,N-bis(dimethylhexadecyl-α,ω-propanediammonium(16-3-16gemini-based synthetic vectors, incorporating either CCC plasmid or LCC DNA ministrings, were characterized and compared with respect to particle size, zeta potential, DNA encapsulation, DNase sensitivity, and in vitro transgene delivery efficacy. Through comparative analysis, differences between CCC plasmid DNA and LCC DNA ministrings led to variations in the physical properties of the resulting lipoplexes after complexation with 16-3-16 gemini surfactants. Despite the size disparities between the plasmid DNA vectors (CCC and DNA ministrings (LCC, differences in DNA topology resulted in the generation of lipoplexes of comparable particle sizes. The capacity for ministring (LCC derived lipoplexes to undergo complete counterion release during lipoplex formation contributed to improved DNA encapsulation, protection from DNase degradation, and in vitro transgene delivery.

  1. "Off-on" electrochemical hairpin-DNA-based genosensor for cancer diagnostics.

    Science.gov (United States)

    Farjami, Elaheh; Clima, Lilia; Gothelf, Kurt; Ferapontova, Elena E

    2011-03-01

    A simple and robust "off-on" signaling genosensor platform with improved selectivity for single-nucleotide polymorphism (SNP) detection based on the electronic DNA hairpin molecular beacons has been developed. The DNA beacons were immobilized onto gold electrodes in their folded states through the alkanethiol linker at the 3'-end, while the 5'-end was labeled with a methylene blue (MB) redox probe. A typical "on-off" change of the electrochemical signal was observed upon hybridization of the 27-33 nucleotide (nt) long hairpin DNA to the target DNA, in agreement with all the hitherto published data. Truncation of the DNA hairpin beacons down to 20 nts provided improved genosensor selectivity for SNP and allowed switching of the electrochemical genosensor response from the on-off to the off-on mode. Switching was consistent with the variation in the mechanism of the electron transfer reaction between the electrode and the MB redox label, for the folded beacon being characteristic of the electrochemistry of adsorbed species, while for the "open" duplex structure being formally controlled by the diffusion of the redox label within the adsorbate layer. The relative current intensities of both processes were governed by the length of the formed DNA duplex, potential scan rate, and apparent diffusion coefficient of the redox species. The off-on genosensor design used for detection of a cancer biomarker TP53 gene sequence favored discrimination between the healthy and SNP-containing DNA sequences, which was particularly pronounced at short hybridization times.

  2. A high excision potential of TALENs for integrated DNA of HIV-based lentiviral vector.

    Science.gov (United States)

    Ebina, Hirotaka; Kanemura, Yuka; Misawa, Naoko; Sakuma, Tetsushi; Kobayashi, Tomoko; Yamamoto, Takashi; Koyanagi, Yoshio

    2015-01-01

    DNA-editing technology has made it possible to rewrite genetic information in living cells. Human immunodeficiency virus (HIV) provirus, an integrated form of viral complementary DNA in host chromosomes, could be a potential target for this technology. We recently reported that HIV proviral DNA could be excised from the chromosomal DNA of HIV-based lentiviral DNA-transduced T cells after multiple introductions of a clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 endonuclease system targeting HIV long terminal repeats (LTR). Here, we generated a more efficient strategy that enables the excision of HIV proviral DNA using customized transcription activator-like effector nucleases (TALENs) targeting the same HIV LTR site. A single transfection of TALEN-encoding mRNA, prepared from in vitro transcription, resulted in more than 80% of lentiviral vector DNA being successfully removed from the T cell lines. Furthermore, we developed a lentiviral vector system that takes advantage of the efficient proviral excision with TALENs and permits the simple selection of gene-transduced and excised cells in T cell lines.

  3. A high excision potential of TALENs for integrated DNA of HIV-based lentiviral vector.

    Directory of Open Access Journals (Sweden)

    Hirotaka Ebina

    Full Text Available DNA-editing technology has made it possible to rewrite genetic information in living cells. Human immunodeficiency virus (HIV provirus, an integrated form of viral complementary DNA in host chromosomes, could be a potential target for this technology. We recently reported that HIV proviral DNA could be excised from the chromosomal DNA of HIV-based lentiviral DNA-transduced T cells after multiple introductions of a clustered regularly interspaced short palindromic repeat (CRISPR/Cas9 endonuclease system targeting HIV long terminal repeats (LTR. Here, we generated a more efficient strategy that enables the excision of HIV proviral DNA using customized transcription activator-like effector nucleases (TALENs targeting the same HIV LTR site. A single transfection of TALEN-encoding mRNA, prepared from in vitro transcription, resulted in more than 80% of lentiviral vector DNA being successfully removed from the T cell lines. Furthermore, we developed a lentiviral vector system that takes advantage of the efficient proviral excision with TALENs and permits the simple selection of gene-transduced and excised cells in T cell lines.

  4. Highly Sensitive DNA Sensor Based on Upconversion Nanoparticles and Graphene Oxide.

    Science.gov (United States)

    Alonso-Cristobal, P; Vilela, P; El-Sagheer, A; Lopez-Cabarcos, E; Brown, T; Muskens, O L; Rubio-Retama, J; Kanaras, A G

    2015-06-17

    In this work we demonstrate a DNA biosensor based on fluorescence resonance energy transfer (FRET) between NaYF4:Yb,Er nanoparticles and graphene oxide (GO). Monodisperse NaYF4:Yb,Er nanoparticles with a mean diameter of 29.1 ± 2.2 nm were synthesized and coated with a SiO2 shell of 11 nm, which allowed the attachment of single strands of DNA. When these DNA-functionalized NaYF4:Yb,Er@SiO2 nanoparticles were in the proximity of the GO surface, the π-π stacking interaction between the nucleobases of the DNA and the sp(2) carbons of the GO induced a FRET fluorescence quenching due to the overlap of the fluorescence emission of the NaYF4:Yb,Er@SiO2 and the absorption spectrum of GO. By contrast, in the presence of the complementary DNA strands, the hybridization leads to double-stranded DNA that does not interact with the GO surface, and thus the NaYF4:Yb,Er@SiO2 nanoparticles remain unquenched and fluorescent. The high sensitivity and specificity of this sensor introduces a new method for the detection of DNA with a detection limit of 5 pM.

  5. Purification of Single-Stranded cDNA Based on RNA Degradation Treatment and Adsorption Chromatography.

    Science.gov (United States)

    Trujillo-Esquivel, Elías; Franco, Bernardo; Flores-Martínez, Alberto; Ponce-Noyola, Patricia; Mora-Montes, Héctor M

    2016-08-02

    Analysis of gene expression is a common research tool to study networks controlling gene expression, the role of genes with unknown function, and environmentally induced responses of organisms. Most of the analytical tools used to analyze gene expression rely on accurate cDNA synthesis and quantification to obtain reproducible and quantifiable results. Thus far, most commercial kits for isolation and purification of cDNA target double-stranded molecules, which do not accurately represent the abundance of transcripts. In the present report, we provide a simple and fast method to purify single-stranded cDNA, exhibiting high purity and yield. This method is based on the treatment with RNase H and RNase A after cDNA synthesis, followed by separation in silica spin-columns and ethanol precipitation. In addition, our method avoids the use of DNase I to eliminate genomic DNA from RNA preparations, which improves cDNA yield. As a case report, our method proved to be useful in the purification of single-stranded cDNA from the pathogenic fungus Sporothrix schenckii.

  6. A next generation semiconductor based sequencing approach for the identification of meat species in DNA mixtures.

    Science.gov (United States)

    Bertolini, Francesca; Ghionda, Marco Ciro; D'Alessandro, Enrico; Geraci, Claudia; Chiofalo, Vincenzo; Fontanesi, Luca

    2015-01-01

    The identification of the species of origin of meat and meat products is an important issue to prevent and detect frauds that might have economic, ethical and health implications. In this paper we evaluated the potential of the next generation semiconductor based sequencing technology (Ion Torrent Personal Genome Machine) for the identification of DNA from meat species (pig, horse, cattle, sheep, rabbit, chicken, turkey, pheasant, duck, goose and pigeon) as well as from human and rat in DNA mixtures through the sequencing of PCR products obtained from different couples of universal primers that amplify 12S and 16S rRNA mitochondrial DNA genes. Six libraries were produced including PCR products obtained separately from 13 species or from DNA mixtures containing DNA from all species or only avian or only mammalian species at equimolar concentration or at 1:10 or 1:50 ratios for pig and horse DNA. Sequencing obtained a total of 33,294,511 called nucleotides of which 29,109,688 with Q20 (87.43%) in a total of 215,944 reads. Different alignment algorithms were used to assign the species based on sequence data. Error rate calculated after confirmation of the obtained sequences by Sanger sequencing ranged from 0.0003 to 0.02 for the different species. Correlation about the number of reads per species between different libraries was high for mammalian species (0.97) and lower for avian species (0.70). PCR competition limited the efficiency of amplification and sequencing for avian species for some primer pairs. Detection of low level of pig and horse DNA was possible with reads obtained from different primer pairs. The sequencing of the products obtained from different universal PCR primers could be a useful strategy to overcome potential problems of amplification. Based on these results, the Ion Torrent technology can be applied for the identification of meat species in DNA mixtures.

  7. A next generation semiconductor based sequencing approach for the identification of meat species in DNA mixtures.

    Directory of Open Access Journals (Sweden)

    Francesca Bertolini

    Full Text Available The identification of the species of origin of meat and meat products is an important issue to prevent and detect frauds that might have economic, ethical and health implications. In this paper we evaluated the potential of the next generation semiconductor based sequencing technology (Ion Torrent Personal Genome Machine for the identification of DNA from meat species (pig, horse, cattle, sheep, rabbit, chicken, turkey, pheasant, duck, goose and pigeon as well as from human and rat in DNA mixtures through the sequencing of PCR products obtained from different couples of universal primers that amplify 12S and 16S rRNA mitochondrial DNA genes. Six libraries were produced including PCR products obtained separately from 13 species or from DNA mixtures containing DNA from all species or only avian or only mammalian species at equimolar concentration or at 1:10 or 1:50 ratios for pig and horse DNA. Sequencing obtained a total of 33,294,511 called nucleotides of which 29,109,688 with Q20 (87.43% in a total of 215,944 reads. Different alignment algorithms were used to assign the species based on sequence data. Error rate calculated after confirmation of the obtained sequences by Sanger sequencing ranged from 0.0003 to 0.02 for the different species. Correlation about the number of reads per species between different libraries was high for mammalian species (0.97 and lower for avian species (0.70. PCR competition limited the efficiency of amplification and sequencing for avian species for some primer pairs. Detection of low level of pig and horse DNA was possible with reads obtained from different primer pairs. The sequencing of the products obtained from different universal PCR primers could be a useful strategy to overcome potential problems of amplification. Based on these results, the Ion Torrent technology can be applied for the identification of meat species in DNA mixtures.

  8. A magnetic bead-based method for concentrating DNA from human urine for downstream detection.

    Science.gov (United States)

    Bordelon, Hali; Russ, Patricia K; Wright, David W; Haselton, Frederick R

    2013-01-01

    Due to the presence of PCR inhibitors, PCR cannot be used directly on most clinical samples, including human urine, without pre-treatment. A magnetic bead-based strategy is one potential method to collect biomarkers from urine samples and separate the biomarkers from PCR inhibitors. In this report, a 1 mL urine sample was mixed within the bulb of a transfer pipette containing lyophilized nucleic acid-silica adsorption buffer and silica-coated magnetic beads. After mixing, the sample was transferred from the pipette bulb to a small diameter tube, and captured biomarkers were concentrated using magnetic entrainment of beads through pre-arrayed wash solutions separated by small air gaps. Feasibility was tested using synthetic segments of the 140 bp tuberculosis IS6110 DNA sequence spiked into pooled human urine samples. DNA recovery was evaluated by qPCR. Despite the presence of spiked DNA, no DNA was detectable in unextracted urine samples, presumably due to the presence of PCR inhibitors. However, following extraction with the magnetic bead-based method, we found that ∼50% of spiked TB DNA was recovered from human urine containing roughly 5×10(3) to 5×10(8) copies of IS6110 DNA. In addition, the DNA was concentrated approximately ten-fold into water. The final concentration of DNA in the eluate was 5×10(6), 14×10(6), and 8×10(6) copies/µL for 1, 3, and 5 mL urine samples, respectively. Lyophilized and freshly prepared reagents within the transfer pipette produced similar results, suggesting that long-term storage without refrigeration is possible. DNA recovery increased with the length of the spiked DNA segments from 10±0.9% for a 75 bp DNA sequence to 42±4% for a 100 bp segment and 58±9% for a 140 bp segment. The estimated LOD was 77 copies of DNA/µL of urine. The strategy presented here provides a simple means to achieve high nucleic acid recovery from easily obtained urine samples, which does not contain inhibitors of PCR.

  9. A magnetic bead-based method for concentrating DNA from human urine for downstream detection.

    Directory of Open Access Journals (Sweden)

    Hali Bordelon

    Full Text Available Due to the presence of PCR inhibitors, PCR cannot be used directly on most clinical samples, including human urine, without pre-treatment. A magnetic bead-based strategy is one potential method to collect biomarkers from urine samples and separate the biomarkers from PCR inhibitors. In this report, a 1 mL urine sample was mixed within the bulb of a transfer pipette containing lyophilized nucleic acid-silica adsorption buffer and silica-coated magnetic beads. After mixing, the sample was transferred from the pipette bulb to a small diameter tube, and captured biomarkers were concentrated using magnetic entrainment of beads through pre-arrayed wash solutions separated by small air gaps. Feasibility was tested using synthetic segments of the 140 bp tuberculosis IS6110 DNA sequence spiked into pooled human urine samples. DNA recovery was evaluated by qPCR. Despite the presence of spiked DNA, no DNA was detectable in unextracted urine samples, presumably due to the presence of PCR inhibitors. However, following extraction with the magnetic bead-based method, we found that ∼50% of spiked TB DNA was recovered from human urine containing roughly 5×10(3 to 5×10(8 copies of IS6110 DNA. In addition, the DNA was concentrated approximately ten-fold into water. The final concentration of DNA in the eluate was 5×10(6, 14×10(6, and 8×10(6 copies/µL for 1, 3, and 5 mL urine samples, respectively. Lyophilized and freshly prepared reagents within the transfer pipette produced similar results, suggesting that long-term storage without refrigeration is possible. DNA recovery increased with the length of the spiked DNA segments from 10±0.9% for a 75 bp DNA sequence to 42±4% for a 100 bp segment and 58±9% for a 140 bp segment. The estimated LOD was 77 copies of DNA/µL of urine. The strategy presented here provides a simple means to achieve high nucleic acid recovery from easily obtained urine samples, which does not contain inhibitors of PCR.

  10. A randomized controlled dose-response pilot study of addition of hCG to recombinant FSH during controlled ovarian stimulation for in vitro fertilization.

    Science.gov (United States)

    Thuesen, L L; Loft, A; Egeberg, A N; Smitz, J; Petersen, J H; Andersen, A Nyboe

    2012-10-01

    Is it possible to define an optimal dose of hCG in combination with rFSH from the first day of stimulation in the GnRH agonist protocol applied to IVF? Supplementation with hCG from the first day of stimulation may increase the number of top-quality embryos per patient. Daily doses of hCG up to 150 IU are compatible with good live birth rates. A ceiling level of estradiol (E(2)) was reached with hCG doses above 100 IU/day. A positive dose-response was seen for pre-ovulatory progesterone, but concentrations remained below values for which an impairment of endometrial receptivity has been previously reported. We suggest a large clinical trial to be proceeded with a group given 100 IU hCG daily versus a control group. Prospective multicentre studies have indicated increased live birth rates and increased number of top-quality embryos when low doses of hCG were associated with FSH. We analysed the clinical, embryological and endocrine aspects of adding increasing doses of hCG to rFSH from the first day of stimulation for IVF. A prospective randomized, controlled, open-label dose-response pilot study was conducted between February 2009 and June 2010 at Copenhagen University Hospital, Rigshospitalet, Denmark. Adequate allocation concealment was assured from sequentially numbered, opaque, sealed envelopes prepared from a computer-generated list. Scoring of the embryos was done in an assessor-blinded way. Endocrinologically normal IVF patients aged 25-37 years, BMI 18-30 kg/m(2), regular cycles and FSH D100; n= 16) and Dose 150 (D150; n= 15). Two patients in D150 were withdrawn after randomization because of major (10- to 30-fold) hCG dosing errors, leaving 13 patients in this group. Thus, the results are based on the per protocol population. The mean numbers of top-quality embryos per patient were D0: 0.8 ± 1.2, D50: 0.5 ± 0.7, D100: 1.2 ± 1.7 and D150: 1.5 ± 1.7 (P= 0.04). All pregnancies were singleton gestations, and the live birth rates per started cycle were D0

  11. A novel chaos-based image encryption algorithm using DNA sequence operations

    Science.gov (United States)

    Chai, Xiuli; Chen, Yiran; Broyde, Lucie

    2017-01-01

    An image encryption algorithm based on chaotic system and deoxyribonucleic acid (DNA) sequence operations is proposed in this paper. First, the plain image is encoded into a DNA matrix, and then a new wave-based permutation scheme is performed on it. The chaotic sequences produced by 2D Logistic chaotic map are employed for row circular permutation (RCP) and column circular permutation (CCP). Initial values and parameters of the chaotic system are calculated by the SHA 256 hash of the plain image and the given values. Then, a row-by-row image diffusion method at DNA level is applied. A key matrix generated from the chaotic map is used to fuse the confused DNA matrix; also the initial values and system parameters of the chaotic system are renewed by the hamming distance of the plain image. Finally, after decoding the diffused DNA matrix, we obtain the cipher image. The DNA encoding/decoding rules of the plain image and the key matrix are determined by the plain image. Experimental results and security analyses both confirm that the proposed algorithm has not only an excellent encryption result but also resists various typical attacks.

  12. Oxidative DNA damage background estimated by a system model of base excision repair.

    Science.gov (United States)

    Sokhansanj, Bahrad A; Wilson, David M

    2004-08-01

    Human DNA can be damaged by natural metabolism through free radical production. It has been suggested that the equilibrium between innate damage and cellular DNA repair results in an oxidative DNA damage background that potentially contributes to disease and aging. Efforts to quantitatively characterize the human oxidative DNA damage background level, based on measuring 8-oxoguanine lesions as a biomarker, have led to estimates that vary over three to four orders of magnitude, depending on the method of measurement. We applied a previously developed and validated quantitative pathway model of human DNA base excision repair, integrating experimentally determined endogenous damage rates and model parameters from multiple sources. Our estimates of at most 100 8-oxoguanine lesions per cell are consistent with the low end of data from biochemical and cell biology experiments, a result robust to model limitations and parameter variation. Our findings show the power of quantitative system modeling to interpret composite experimental data and make biologically and physiologically relevant predictions for complex human DNA repair pathway mechanisms and capacity.

  13. DNA Hybridization Detection Based on Resonance Frequency Readout in Graphene on Au SPR Biosensor

    Directory of Open Access Journals (Sweden)

    Md. Biplob Hossain

    2016-01-01

    Full Text Available This paper demonstrates a numerical modeling of surface plasmon resonance (SPR biosensor for detecting DNA hybridization by recording the resonance frequency characteristics (RFC. The proposed sensor is designed based on graphene material as biomolecular recognition elements (BRE and the sharp SPR curve of gold (Au. Numerical analysis shows that the variation of RFC for mismatched DNA strands is quiet negligible whereas that for complementary DNA strands is considerably countable. Here, graphene is used to perform faster immobilization between target DNA and probe DNA. The usage of graphene also changes the RFC that ensure hybridization of DNA event by utilizing its optochemical property. In addition, proposed sensor successfully distinguishes between hybridization and single-nucleotide polymorphisms (SNP by observing the variation level of RFC and maximum transmittance. Therefore, the proposed frequency readout based SPR sensor could potentially open a new window of detection for biomolecular interactions. We also highlight the advantage of using graphene sublayer by performing the sensitivity analysis. Sandwiching of each graphene sublayer enhances 95% sensitivity comparing with conventional SPR sensor.

  14. A Dna And Amino-Acids Based Implementation Of Four-Square Cipher

    Directory of Open Access Journals (Sweden)

    Sonal Namdev

    2016-02-01

    Full Text Available The DNA cryptography is a new and very promising direction in cryptographic research. It is in the primitive stage. DNA cryptography is shown to be very effective. Currently, several DNA computing algorithms are proposed for many cryptography, cryptanalysis and steganography problems, and they are very powerful in these areas. This paper discusses a significant modification of the old approach of using DNA and Amino Acids based approach with Playfair Cipher to using the same approach with different encryption algorithm, i.e; foursquare cipher to the core of the ciphering process. In this study, a binary form of data, such as plaintext messages, or images are transformed into sequences of DNA nucleotides. Subsequently, these nucleotides pass through a Foursquare encryption process based on amino-acids structure. The fundamental idea behind using this type of encryption process is to enforce other conventional cryptographic algorithms which proved to be broken, and also to open the door for applying the DNA and Amino Acids concepts to more conventional cryptographic algorithms to enhance their security features.

  15. Ultrafast dynamics of solvation and charge transfer in a DNA-based biomaterial.

    Science.gov (United States)

    Choudhury, Susobhan; Batabyal, Subrata; Mondol, Tanumoy; Sao, Dilip; Lemmens, Peter; Pal, Samir Kumar

    2014-05-01

    Charge migration along DNA molecules is a key factor for DNA-based devices in optoelectronics and biotechnology. The association of a significant amount of water molecules in DNA-based materials for the intactness of the DNA structure and their dynamic role in the charge-transfer (CT) dynamics is less documented in contemporary literature. In the present study, we have used a genomic DNA-cetyltrimethyl ammonium chloride (CTMA) complex, a technological important biomaterial, and Hoechest 33258 (H258), a well-known DNA minor groove binder, as fluorogenic probe for the dynamic solvation studies. The CT dynamics of CdSe/ZnS quantum dots (QDs; 5.2 nm) embedded in the as-prepared and swollen biomaterial have also been studied and correlated with that of the timescale of solvation. We have extended our studies on the temperature-dependent CT dynamics of QDs in a nanoenvironment of an anionic, sodium bis(2-ethylhexyl)sulfosuccinate reverse micelle (AOT RMs), whereby the number of water molecules and their dynamics can be tuned in a controlled manner. A direct correlation of the dynamics of solvation and that of the CT in the nanoenvironments clearly suggests that the hydration barrier within the Arrhenius framework essentially dictates the charge-transfer dynamics.

  16. Construction of a fuzzy and Boolean logic gates based on DNA.

    Science.gov (United States)

    Zadegan, Reza M; Jepsen, Mette D E; Hildebrandt, Lasse L; Birkedal, Victoria; Kjems, Jørgen

    2015-04-17

    Logic gates are devices that can perform logical operations by transforming a set of inputs into a predictable single detectable output. The hybridization properties, structure, and function of nucleic acids can be used to make DNA-based logic gates. These devices are important modules in molecular computing and biosensing. The ideal logic gate system should provide a wide selection of logical operations, and be integrable in multiple copies into more complex structures. Here we show the successful construction of a small DNA-based logic gate complex that produces fluorescent outputs corresponding to the operation of the six Boolean logic gates AND, NAND, OR, NOR, XOR, and XNOR. The logic gate complex is shown to work also when implemented in a three-dimensional DNA origami box structure, where it controlled the position of the lid in a closed or open position. Implementation of multiple microRNA sensitive DNA locks on one DNA origami box structure enabled fuzzy logical operation that allows biosensing of complex molecular signals. Integrating logic gates with DNA origami systems opens a vast avenue to applications in the fields of nanomedicine for diagnostics and therapeutics.

  17. Quantifying the DNA binding characteristics of ruthenium based threading intercalator Λ Λ -P with optical tweezers

    Science.gov (United States)

    Bryden, Nicholas; McCauley, Micah; Westerlund, Fredrik; Lincoln, Per; Rouzina, Ioulia; Williams, Mark; Paramanathan, Thayaparan

    Utilizing optical tweezers, biophysics researchers have been able to study drug-DNA interactions on the single molecule level. Binuclear ruthenium complexes are a particular type of drug molecule that have been found to have potential cancer-fighting qualities, due to their high binding affinity and low dissociation rates. These complexes are threading intercalators, meaning that they must thread their bulky side chains through DNA base pairs to allow the central planar moiety to intercalate between the bases. In this study, we explored the binding properties of the binuclear ruthenium complex, ΛΛ -P (ΛΛ -[µ-bidppz(phen)4Ru2]4+) . A single DNA molecule is held at a constant force and the ΛΛ -P solution introduced to the system in varying concentrations until equilibrium is reached. DNA extension data at various concentrations of ΛΛ -P recorded as a function of time provide the DNA binding kinetics and equilibrium binding affinity. Preliminary data analysis suggests that ΛΛ -P exhibits fast binding kinetics compared to the very similar ΔΔ -P. These complexes have the same chemical structure and only differ in their chirality, which suggests that the left handed (ΛΛ) threading moieties require less DNA structural distortion for threading compared with the right handed (ΔΔ) threading moieties.

  18. Breathing dynamics based parameter sensitivity analysis of hetero-polymeric DNA

    Energy Technology Data Exchange (ETDEWEB)

    Talukder, Srijeeta; Sen, Shrabani; Chaudhury, Pinaki, E-mail: pinakc@rediffmail.com [Department of Chemistry, University of Calcutta, 92 A P C Road, Kolkata 700 009 (India); Chakraborti, Prantik; Banik, Suman K., E-mail: skbanik@jcbose.ac.in [Department of Chemistry, Bose Institute, 93/1 A P C Road, Kolkata 700 009 (India); Metzler, Ralf, E-mail: rmetzler@uni-potsdam.de [Institute for Physics and Astronomy, University of Potsdam, D-14476 Potsdam-Golm, Germany and Physics Department, Tampere University of Technology, FI-33101 Tampere (Finland)

    2014-03-28

    We study the parameter sensitivity of hetero-polymeric DNA within the purview of DNA breathing dynamics. The degree of correlation between the mean bubble size and the model parameters is estimated for this purpose for three different DNA sequences. The analysis leads us to a better understanding of the sequence dependent nature of the breathing dynamics of hetero-polymeric DNA. Out of the 14 model parameters for DNA stability in the statistical Poland-Scheraga approach, the hydrogen bond interaction ε{sub hb}(AT) for an AT base pair and the ring factor ξ turn out to be the most sensitive parameters. In addition, the stacking interaction ε{sub st}(TA-TA) for an TA-TA nearest neighbor pair of base-pairs is found to be the most sensitive one among all stacking interactions. Moreover, we also establish that the nature of stacking interaction has a deciding effect on the DNA breathing dynamics, not the number of times a particular stacking interaction appears in a sequence. We show that the sensitivity analysis can be used as an effective measure to guide a stochastic optimization technique to find the kinetic rate constants related to the dynamics as opposed to the case where the rate constants are measured using the conventional unbiased way of optimization.

  19. Oxidative DNA damage background estimated by a system model of base excision repair

    Energy Technology Data Exchange (ETDEWEB)

    Sokhansanj, B A; Wilson, III, D M

    2004-05-13

    Human DNA can be damaged by natural metabolism through free radical production. It has been suggested that the equilibrium between innate damage and cellular DNA repair results in an oxidative DNA damage background that potentially contributes to disease and aging. Efforts to quantitatively characterize the human oxidative DNA damage background level based on measuring 8-oxoguanine lesions as a biomarker have led to estimates varying over 3-4 orders of magnitude, depending on the method of measurement. We applied a previously developed and validated quantitative pathway model of human DNA base excision repair, integrating experimentally determined endogenous damage rates and model parameters from multiple sources. Our estimates of at most 100 8-oxoguanine lesions per cell are consistent with the low end of data from biochemical and cell biology experiments, a result robust to model limitations and parameter variation. Our results show the power of quantitative system modeling to interpret composite experimental data and make biologically and physiologically relevant predictions for complex human DNA repair pathway mechanisms and capacity.

  20. RAPID SCREENING OF AN ARRAYED cDNA LIBRARY BY IMPROVED PCR-BASED METHOD

    Institute of Scientific and Technical Information of China (English)

    杜光伟; 潘美辉; 袁建刚; 周彦; 强伯勤; 梁植权

    1998-01-01

    Tbe present study reports an improved PCR-based technique that allows quick and effecfive screening of eDNA libraries. First, the eDNA library was arrayed as follows: about 3×106 cDNA clones were multiplied as individual plsques on solid medium in 24-well culture dishes at 1 200 plaque forming units per well.The phage suspension of each well was transferred to an individual micrccentrifuge tube in 72-tube box. Then,box pool, row pools and column pools were set up that respectively represent a 72-tube box,rows and columns within the box. To screen a specific target cDNA,primers specific for novel ESTs obtained in our laboratory were eznployed to conduct PCR in a fiierarchy mode. PCR began with the box pools, resulting in the identification of some positive box pools. Then PCR went down to the row and column pools of the positive box. Tbe intersection of the positive row(s) and column(s) revealed the candidate positive tubes. The specificity of PCR products were meanwhile checked hy restriction enzyme digestion. Finally, hybridization was carried out to get single specific eDNA clones-from the positive tlabes. This PCR-hased technique features high specificity, high efficiency and Les-cost in large-scale cDNA library screening. Our initial implementation of the technique resulted in the isolation of three longer different cDNA clones from a hnman fetal brain eDNA library. Thus this improved technique can serve as an alternative to the time-consuming and laborious conventional hybridization-hased metfiod for screening cDNA library.