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Sample records for dna content based

  1. 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.

  2. Overcoming PCR Inhibition During DNA-Based Gut Content Analysis of Ants.

    Science.gov (United States)

    Penn, Hannah J; Chapman, Eric G; Harwood, James D

    2016-10-01

    Generalist predators play an important role in many terrestrial systems, especially within agricultural settings, and ants (Hymenoptera: Formicidae) often constitute important linkages of these food webs, as they are abundant and influential in these ecosystems. Molecular gut content analysis provides a means of delineating food web linkages of ants based on the presence of prey DNA within their guts. Although this method can provide insight, its use on ants has been limited, potentially due to inhibition when amplifying gut content DNA. We designed a series of experiments to determine those ant organs responsible for inhibition and identified variation in inhibition among three species (Tetramorium caespitum (L.), Solenopsis invicta Buren, and Camponotus floridanus (Buckley)). No body segment, other than the gaster, caused significant inhibition. Following dissection, we determined that within the gaster, the digestive tract and crop cause significant levels of inhibition. We found significant differences in the frequency of inhibition between the three species tested, with inhibition most evident in T. caespitum The most effective method to prevent inhibition before DNA extraction was to exude crop contents and crop structures onto UV-sterilized tissue. However, if extracted samples exhibit inhibition, addition of bovine serum albumin to PCR reagents will overcome this problem. These methods will circumvent gut content inhibition within selected species of ants, thereby allowing more detailed and reliable studies of ant food webs. As little is known about the prevalence of this inhibition in other species, it is recommended that the protocols in this study are used until otherwise shown to be unnecessary. © The Authors 2016. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  3. 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.

  4. Direct interrogation of DNA content distribution in nanoparticles by a novel microfluidics-based single-particle analysis.

    Science.gov (United States)

    Beh, Cyrus W; Pan, Deng; Lee, Jason; Jiang, Xuan; Liu, Kelvin J; Mao, Hai-Quan; Wang, Tza-Huei

    2014-08-13

    Nonviral gene delivery holds great promise not just as a safer alternative to viral vectors in traditional gene therapy applications, but also for regenerative medicine, induction of pluripotency in somatic cells, and RNA interference for gene silencing. Although it continues to be an active area of research, there remain many challenges to the rational design of vectors. Among these, the inability to characterize the composition of nanoparticles and its distribution has made it difficult to probe the mechanism of gene transfection process, since differences in the nanoparticle-mediated transfection exist even when the same vector is used. There is a lack of sensitive methods that allow for full characterization of DNA content in single nanoparticles and its distribution among particles in the same preparation. Here we report a novel spectroscopic approach that is capable of interrogating nanoparticles on a particle-by-particle basis. Using PEI/DNA and PEI-g-PEG/DNA nanoparticles as examples, we have shown that the distribution of DNA content among these nanoparticles was relatively narrow, with the average numbers of DNA of 4.8 and 6.7 per particle, respectively, in PEI/DNA and PEI-g-PEG/DNA nanoparticles. This analysis enables a more accurate description of DNA content in polycation/DNA nanoparticles. It paves the way toward comparative assessments of various types of gene carriers and provides insights into bridging the efficiency gap between viral and nonviral vehicles.

  5. A method for the determination of bacterial spore DNA content based on isotopic labelling, spore germination and diphenylamine assay; ploidy of spores of several Bacillus species.

    Science.gov (United States)

    Hauser, P M; Karamata, D

    1992-01-01

    A reliable method for measuring the spore DNA content, based on radioactive DNA labelling, spore germination in absence of DNA replication and diphenylamine assay, was developed. The accuracy of the method, within 10-15%, is adequate for determining the number of chromosomes per spore, provided that the genome size is known. B subtilis spores were shown to be invariably monogenomic, while those of larger bacilli Bacillus megaterium, Bacillus cereus and Bacillus thuringiensis, often, if not invariably, contain two genomes. Attempts to modify the spore DNA content of B subtilis by altering the richness of the sporulation medium, the sporulation conditions (liquid or solid medium), or by mutation, were apparently unsuccessful. An increase of spore size with medium richness, not accompanied by an increase in DNA content, was observed. The implication of the apparently species-specific spore ploidy and the influence of the sporulation conditions on spore size and shape are discussed.

  6. New sequence-based data on the relative DNA contents of chromosomes in the normal male and female human diploid genomes for radiation molecular cytogenetics

    Directory of Open Access Journals (Sweden)

    Repin Mikhail V

    2009-06-01

    Full Text Available Abstract Background The objective of this work is to obtain the correct relative DNA contents of chromosomes in the normal male and female human diploid genomes for the use at FISH analysis of radiation-induced chromosome aberrations. Results The relative DNA contents of chromosomes in the male and female human diploid genomes have been calculated from the publicly available international Human Genome Project data. New sequence-based data on the relative DNA contents of human chromosomes were compared with the data recommended by the International Atomic Energy Agency in 2001. The differences in the values of the relative DNA contents of chromosomes obtained by using different approaches for 15 human chromosomes, mainly for large chromosomes, were below 2%. For the chromosomes 13, 17, 20 and 22 the differences were above 5%. Conclusion New sequence-based data on the relative DNA contents of chromosomes in the normal male and female human diploid genomes were obtained. This approach, based on the genome sequence, can be recommended for the use in radiation molecular cytogenetics.

  7. Content-Based Instruction

    Science.gov (United States)

    DelliCarpini, M.; Alonso, O.

    2013-01-01

    DelliCarpini and Alonso's book "Content-Based Instruction" explores different approaches to teaching content-based instruction (CBI) in the English language classroom. They provide a comprehensive overview of how to teach CBI in an easy-to-follow guide that language teachers will find very practical for their own contexts. Topics…

  8. Content-Based Instruction

    Science.gov (United States)

    DelliCarpini, M.; Alonso, O.

    2013-01-01

    DelliCarpini and Alonso's book "Content-Based Instruction" explores different approaches to teaching content-based instruction (CBI) in the English language classroom. They provide a comprehensive overview of how to teach CBI in an easy-to-follow guide that language teachers will find very practical for their own contexts. Topics…

  9. Nuclear DNA Contents of Some Endemic Hedysarum L. Species

    OpenAIRE

    1999-01-01

    The nuclear DNA contents and nuclear areas of some endemic Hedysarum L. species were investigated. A significant variation in the DNA content of Hedysarum species was established. The 2C nuclear DNA amount in the Hedysarum species (x = 8) ranged from approximately 4 to 6 picograms. It was found that the variation in the 2C nuclear DNA content was not related to chromosome numbers. However, there was a very high positive linear relationship between nuclear DNA content and nuclear area.

  10. Intraguild Predation Among Three Common Coccinellids (Coleoptera: Coccinellidae) in China: Detection Using DNA-Based Gut-Content Analysis.

    Science.gov (United States)

    Yang, Fan; Wang, Qian; Wang, Dongmei; Xu, Bin; Xu, Jianxiang; Lu, Yanhui; Harwood, James D

    2017-02-01

    The ubiquity of intraguild predation (IGP) has been widely recognized for predatory coccinellids (Coleoptera: Coccinellidae). In Chinese agroecosystems, three species (Coccinella septempunctata L., Harmonia axyridis (Pallas), and Propylea japonica (Thunberg)) are particularly common, but there is little information of interactions occurring between them. In no-choice laboratory feeding trials, differential directional predation was observed between species: C. septempunctata preyed on eggs of P. japonica more than H. axyridis and H. axyridis consumed eggs of C. septempunctata and P. japonica equally, whereas P. japonica had a very low predation rate on eggs of the other two species. In choice trials, C. septempunctata and P. japonica larvae preyed less on H. axyridis eggs than those of P. japonica and C. septempunctata, respectively, contrasting with H. axyridis larvae, which showed similar preference for both species. Species-specific primers were developed for each coccinellid and used to determine the relative frequency of prey consumption in the field. Prior to field-based analysis, primer specificity was confirmed and consumption of prey elicited a positive reaction success, and detection time varied between different predator-prey combinations. Predators were then collected from cotton agroecosystems and, interestingly, no DNA of C. septempunctata was found in P. japonica, but all other predator-prey combinations yielded positive documentation of IGP in the field, with the greatest rate of 9% of C. septempunctata testing positive for H. axyridis DNA. This study confirmed the frequency of IGP among three common coccinellids in Chinese agroecosystems and the likelihood for interference to the biological control services provided by these important natural enemies. © The Authors 2016. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  11. 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.

  12. Repetitive DNA in three Gramineae species with low DNA content.

    Science.gov (United States)

    Deshpande, V G; Ranjekar, P K

    1980-08-01

    The genomes of three Gramineae species, namely finger millet (Eleusine coracana), pearl millet (Pennisetum americanum) and rice (Oryza sativa) are characterized by studying their DNA denaturation-reassociation properties. The reassociation kinetics measurement of the sonicated DNA (500--700 nucleotide pairs) indicate the presence of a heterogeneous, repetitive DNA fraction accounting for 49--54% of the total DNA in all three species. From the cot 1/2 value of the slow reassociating DNA, the genome size is estimated as 3.0 X 10(8) np in finger millet, 7.8 X 10(8) np in pearl millet and 9.0 X 10(8) np in rice. The melting patterns of the total DNAs reveal Tm value of 88.6 degrees C in the case of pearl millet and 85.0 degrees C in the case of finger millet and rice. Total repetitive and cot 1.0 DNA fractions in all the three species are isolated and their melting properties are compared with those of respective sonicated DNAs. In finger millet, the Tm values of cot 25 and cot 1 fractions are lower by 10.8 degrees C and 12.8 degrees C, respectively, than that of sonicated DNA and thus exhibit the presence of a base pair mismatch in the range of 10.8--12.8%. In rice, the Tm values of the fractions cot 50 and cot 1 are slightly lower than that of sonicated DNA and reveal a nucleotide mismatching of only 1.8--3.8%. In the case of pearl millet cot 10 DNA fraction a high-melting DNA component (Tm = 92 degrees C) representing 12% of the total cot 10 DNA and a low-melting component with a Tm of 78 degrees C are present. In cot 1 DNA fraction of pearl millet the proportion of the high-melting component is 35% and it has a Tm or 94.8 degrees C. Optical reassociation studies of cot 1.0 DNA fractions have revealed the presence of two kinetically distinct components, namely minor fast-reassociating and major slow-reassociating, having complexities in the range of 330--390 np and 1.28 X 10(5)--6.0 X 10(5) np, respectively in pearl millet and rice and only one DNA fraction with an

  13. Content Based Video Retrieval

    Directory of Open Access Journals (Sweden)

    B. V. Patel

    2012-10-01

    Full Text Available Content based video retrieval is an approach for facilitating the searching and browsing of large image collections over World Wide Web. In this approach, video analysis is conducted on low level visual properties extracted from video frame. We believed that in order to create an effective video retrieval system, visual perception must be taken into account. We conjectured that a technique which employs multiple features for indexing and retrieval would be more effective in the discrimination and search tasks of videos. In order to validate this claim, content based indexing and retrieval systems were implemented using color histogram, various texture features and other approaches. Videos were stored in Oracle 9i Database and a user study measured correctness of response.

  14. Two aspects of DNA base composition: G+C content and translation-coupled deviation from intra-strand rule of A = T and G = C.

    Science.gov (United States)

    Sueoka, N

    1999-07-01

    The relative contribution of mutation and selection to the G+C content of DNA was analyzed in bacterial species having widely different G+C contents. The analysis used two methods that were developed previously. The first method was to plot the average G+C content of a set of nucleotides against the G+C content of the third codon position for each gene. This method was used to present the G+C distribution of the third codon position and to assess the relative neutrality of a set of nucleotides to that of the G+C content of the third codon position. The second method was to plot the intrastrand bias of the third codon position from Parity Rule 2 (PR2), where A = T and G = C. It was found that whereas intragenomic distributions of the DNA G+C content of these bacteria are narrow in the majority of species, in some species the G+C content of the minor class of genes distributes over wider ranges than the major class of genes. On the other hand, ubiquitous PR2 biases are amino acid specific and independent of the G+C content of DNA, so that when averaged over the amino acids, the biases are small and not correlated with the DNA G+C content. Therefore, translation coupled PR2-biases are unlikely to explain the wide range of G+C contents among different species. Considering all data available, it was concluded that the amino acid-specific PR2 bias has only a minor effect, if any, on the average G+C content. In addition, PR2 bias patterns of different species show phylogenetic relationships, and the pattern can be as a taxal fingerprint.

  15. Karnyothrips flavipes, a previously unreported predatory thrips of the coffee berry borer: DNA-based gut content analysis

    Science.gov (United States)

    A new predator of the coffee berry borer, Hypothenemus hampei, was found in the coffee growing area of Kisii in Western Kenya. Field observations, laboratory trials and gut content analysis using molecular tools have confirmed the role of the predatory thrips Karnyothrips flavipes Jones (Phlaeothrip...

  16. Intra‐ and Interspecific Variation in DNA Content in Cistus (Cistaceae)

    Science.gov (United States)

    ELLUL, PHILIPPE; BOSCAIU, MONICA; VICENTE, OSCAR; MORENO, VICENTE; ROSSELLÓ, JOSEP A.

    2002-01-01

    Flow cytometry, using propidium iodide and 4′,6‐diamidano‐2-phenylindole staining, was used to estimate the nuclear DNA content (2C) and the proportion of A–T base pairs in 16 species of the Mediterranean genus Cistus. Genome sizes were shown to be constant within species, since no significant intraspecific variation in 2C DNA content was detected. At the genus level, up to about 1·5‐fold differences in absolute DNA amounts were observed, ranging from 3·92 pg in C. crispus to 5·88 pg in C. monspeliensis. The (AT) : (GC) ratio was close to 1, and was similar for all species examined, ranging from 47·87 % A–T content in C. clusii, to 50·67 % in C. populifolius. Pink‐flowered species (subgenus Cistus) had lower DNA amounts than white‐flowered species (subgenera Leucocistus and Halimioides). However, the distribution of DNA amounts in Cistus appeared to be continuous and did not permit a clear separation of infra‐generic ranks in the genus. PMID:12234146

  17. 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.

  18. Investigation Into the Effects of Nucleotide Content on the Electrical Characteristics of DNA Plasmid Molecular Wires.

    Science.gov (United States)

    Goshi, Noah; Narenji, Alaleh; Bui, Chris; Mokili, John L; Kassegne, Sam

    2016-09-01

    In this study, we investigate the effect of nucleotide content on the conductivity of plasmid length DNA molecular wires covalently bound to high aspect-ratio gold electrodes. The DNA wires were all between [Formula: see text] in length (>6000bp), and contained either 39%, 53%, or 64% GC base-pairs. We compared the current-voltage (I-V) and frequency-impedance characteristics of the DNA wires with varying GC content, and observed statistically significantly higher conductivity in DNA wires containing higher GC content in both AC and DC measurement methods. Additionally, we noted that the conductivity decreased as a function of time for all DNA wires, with the impedance at 100 Hz nearly doubling over a period of seven days. All readings were taken in humidity and temperature controlled environments on DNA wires suspended above an insulative substrate, thus minimizing the effect of experimental and environmental factors as well as potential for nonlinear alternate DNA confirmations. While other groups have studied the effect of GC content on the conductivity of nanoscale DNA molecules (DNA wires at scales that may be required during the fabrication of DNA-based electronics. Furthermore, our results provide further evidence that many of the charge transfer theories developed from experiments using nanoscale DNA molecules may still be applicable for DNA wires at the micro scale.

  19. Investigation of Effects of Nucleotide Content on Electrical Characteristics of DNA Plasmid Molecular Wires.

    Science.gov (United States)

    Goshi, Noah; Narenji, Alaleh; Bui, Chris; Mokili, John L; Kassegne, Sam

    2016-07-28

    In this study, we investigate the effect of nucleotide content on the conductivity of plasmid length DNA molecular wires covalently bound to high aspect-ratio gold electrodes. The DNA wires were all between 2.20-2.35μm in length (>6000bp), and contained either 39%, 53%, or 64% GC base-pairs. We compared the current-voltage (I-V) and frequency-impedance characteristics of the DNA wires with varying GC content, and observed statistically significantly higher conductivity in DNA wires containing higher GC content in both AC and DC measurement methods. Additionally, we noted that the conductivity decreased as a function of time for all DNA wires, with the impedance at 100Hz nearly doubling over a period of seven days. All readings were taken in humidity and temperature controlled environments on DNA wires suspended above an insulative substrate, thus minimizing the effect of experimental and environmental factors as well as potential for nonlinear alternate DNA confirmations. While other groups have studied the effect of GC content on the conductivity of nano-scale DNA molecules (DNA wires at scales that may be required during the fabrication of DNA-based electronics. Furthermore, our results provide further evidence that many of the charge transfer theories developed from experiments using nano-scale DNA molecules may still be applicable for DNA wires at the micro-scale.

  20. 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

  1. Influence of light on DNA content of Helianthus annuus Linnaeus.

    Science.gov (United States)

    Price, H J; Johnston, J S

    1996-10-01

    Mean nuclear 2C DNA content (C equaling haploid DNA per nucleus) of the first leaf of the sunflower, Helianthus annuus L., is influenced by the quality and the quantity of light. Seedlings of two inbred lines, RHA 299 and RHA 271 were germinated and grown in controlled environmental conditions. Lighting was adjusted to provide different combinations of photon flux densities and red to far red (R:FR) ratios. At R:FR = 5.8 and photon flux densities of 170 mumol.m-2.s-1, 200 mumol.m-2.s-1, and 230 mumol.m-2.s-1, DNA content remained high and relatively constant (x = 6.97 pg for RHA 271 and x = 7.32 pg for RHA 299). When the photon flux density range (R:FR = 5.8) was elevated to 350 mumol.m-2.s-1, 410 mumol.m-2.s-1, and 470 mumol.m-2.s-1, mean DNA content was reduced to 6.23 pg (RHA 271) and 6.46 pg (RHA 299). At R:FR = 1.5, mean DNA content was consistently high (7.2-7.9 pg) only at the lowest photon flux density of 170 mumol.m-2.s-1. Significant decreases in DNA content (densities of 200 mumol.m-2.s-1 and 230 mumol.m-2.s-1. At the higher photon flux densities (350 mumol.m-2.s-1, 410 mumol.m-2.s-1, and 470 mumol.m-2.s-1) and R:RF = 1.5, the plants had extremely low DNA contents (mean x = 3.36 pg for RHA 271 and 3.41 pg for RHA 299) and high between-plant variance. The instability of DNA content, particularly for plants grown under light that is far red rich, suggests that phytochromes may be involved in regulating DNA content of the sunflower.

  2. Blood cell mitochondrial DNA content and premature ovarian aging.

    Directory of Open Access Journals (Sweden)

    Marco Bonomi

    Full Text Available Primary ovarian insufficiency (POI is a critical fertility defect characterized by an anticipated and silent impairment of the follicular reserve, but its pathogenesis is largely unexplained. The frequent maternal inheritance of POI together with a remarkable dependence of ovarian folliculogenesis upon mitochondrial biogenesis and bioenergetics suggested the possible involvement of a generalized mitochondrial defect. Here, we verified the existence of a significant correlation between blood and ovarian mitochondrial DNA (mtDNA content in a group of women undergoing ovarian hyperstimulation (OH, and then aimed to verify whether mtDNA content was significantly altered in the blood cells of POI women. We recruited 101 women with an impaired ovarian reserve: 59 women with premature ovarian failure (POF and 42 poor responders (PR to OH. A Taqman copy number assay revealed a significant mtDNA depletion (P<0.001 in both POF and PR women in comparison with 43 women of similar age and intact ovarian reserve, or 53 very old women with a previous physiological menopause. No pathogenic variations in the mitochondrial DNA polymerase γ (POLG gene were detected in 57 POF or PR women with low blood mtDNA content. In conclusion, blood cell mtDNA depletion is a frequent finding among women with premature ovarian aging, suggesting that a still undetermined but generalized mitochondrial defect may frequently predispose to POI which could then be considered a form of anticipated aging in which the ovarian defect may represent the first manifestation. The determination of mtDNA content in blood may become an useful tool for the POI risk prediction.

  3. Blood Cell Mitochondrial DNA Content and Premature Ovarian Aging

    Science.gov (United States)

    Cacciatore, Chiara; Busnelli, Marta; Rossetti, Raffaella; Bonetti, Silvia; Paffoni, Alessio; Mari, Daniela; Ragni, Guido; Persani, Luca; Arosio, M.; Beck-Peccoz, P.; Biondi, M.; Bione, S.; Bruni, V.; Brigante, C.; Cannavo`, S.; Cavallo, L.; Cisternino, M.; Colombo, I.; Corbetta, S.; Crosignani, P.G.; D'Avanzo, M.G.; Dalpra, L.; Danesino, C.; Di Battista, E.; Di Prospero, F.; Donti, E.; Einaudi, S.; Falorni, A.; Foresta, C.; Fusi, F.; Garofalo, N.; Giotti, I.; Lanzi, R.; Larizza, D.; Locatelli, N.; Loli, P.; Madaschi, S.; Maghnie, M.; Maiore, S.; Mantero, F.; Marozzi, A.; Marzotti, S.; Migone, N.; Nappi, R.; Palli, D.; Patricelli, M.G.; Pisani, C.; Prontera, P.; Petraglia, F.; Radetti, G.; Renieri, A.; Ricca, I.; Ripamonti, A.; Rossetti, R.; Russo, G.; Russo, S.; Tonacchera, M.; Toniolo, D.; Torricelli, F.; Vegetti, W.; Villa, N.; Vineis, P.; Wasniewsk, M.; Zuffardi, O.

    2012-01-01

    Primary ovarian insufficiency (POI) is a critical fertility defect characterized by an anticipated and silent impairment of the follicular reserve, but its pathogenesis is largely unexplained. The frequent maternal inheritance of POI together with a remarkable dependence of ovarian folliculogenesis upon mitochondrial biogenesis and bioenergetics suggested the possible involvement of a generalized mitochondrial defect. Here, we verified the existence of a significant correlation between blood and ovarian mitochondrial DNA (mtDNA) content in a group of women undergoing ovarian hyperstimulation (OH), and then aimed to verify whether mtDNA content was significantly altered in the blood cells of POI women. We recruited 101 women with an impaired ovarian reserve: 59 women with premature ovarian failure (POF) and 42 poor responders (PR) to OH. A Taqman copy number assay revealed a significant mtDNA depletion (P<0.001) in both POF and PR women in comparison with 43 women of similar age and intact ovarian reserve, or 53 very old women with a previous physiological menopause. No pathogenic variations in the mitochondrial DNA polymerase γ (POLG) gene were detected in 57 POF or PR women with low blood mtDNA content. In conclusion, blood cell mtDNA depletion is a frequent finding among women with premature ovarian aging, suggesting that a still undetermined but generalized mitochondrial defect may frequently predispose to POI which could then be considered a form of anticipated aging in which the ovarian defect may represent the first manifestation. The determination of mtDNA content in blood may become an useful tool for the POI risk prediction. PMID:22879975

  4. Nuclear DNA content and chromosome number in Brachiaria spp. genotypes

    Directory of Open Access Journals (Sweden)

    Ana Luiza de Oliveira Timbó

    Full Text Available Breeding programs for Brachiaria spp. use both intraspecies and interspecies crosses between sexual and apomictic plants in order to obtain new cultivars with the desired characteristics. As there are different ploidy levels both within and between species of this genus, it becomes necessary to evaluate the genotypes used in breeding programs, as a guide to breeders when adopting crossing strategies. In this work, DNA content and chromosome number were determined in order to characterise ploidy levels in Brachiaria spp. genotypes. In the analysis of 15 genotypes, DNA content varied with the ploidy levels (2x, 3x and 4x, and between species and/or taxon. The average DNA content was 1.74 pg (2x in B. ruziziensis, 3.74 pg (4x in B. decumbens and 3.52 pg (4x for B. brizantha. For the genotype 86, 2.57 pg of DNA was obtained and 2n = 3x = 27, indicating a triploid accession, probably a natural hybrid. The variation in the total DNA content allowed the differentiation of Brachiaria ruziziensis (2n = 2x = 18 from the tetraploid species Brachiaria Brizantha and Brachiaria decumbens (2n = 4x = 36, as well as the probable hybrid triploid (2n = 3x = 18 of these species.

  5. Pleomorphic myofibrosarcoma of the tibia with aneuploid DNA content.

    Science.gov (United States)

    Gonzalez, Fernando A Candanedo; Vazquez, Arturo Cerbulo; Uscanga, Candelaria Cordova; Cortes, Ivan Jacinto; Malagon, Domínguez

    2007-10-01

    Myofibrosarcomas of the tibia are exceedingly rare, with only one case reported in the literature. We describe DNA ploidy of high-grade myofibrosarcoma of the tibia in correlation with clinicomorphologic and ultrastructural features in a 16-year-old adolescent girl. Radiological studies revealed an expanding osteolytic bone lesion in the metaphysis of proximal tibia. A biopsy was consistent with malignant fibrous histiocytoma. The final diagnosis of myofibrosarcoma was supported by light microscopy and corroborated by electron microscopy and immunohistochemistry findings. The DNA content analysis showed an aneuploid tumor. She developed local recurrence at 6 months after initial treatment with no evidence of lung metastases and 16 months later is alive with persistence of disease. This is the second case reported in the literature with this location. In this case, the high grade correlated with recurrence behavior and aneuploidy DNA content but not with metastases. By ultrastructural analyses, fibronexus and intracellular collagen persisted in high-grade myofibrosarcoma.

  6. Markovian language model of the DNA and its information content

    CERN Document Server

    Srivastava, Shambhavi

    2015-01-01

    This work proposes a markovian memoryless model for the DNA that simplifies enormously the complexity of it. We encode nucleotide sequences into symbolic sequences, called words, from which we establish meaningful length of words and group of words that share symbolic similarities. Interpreting a node to represent a group of similar words and edges to represent their functional connectivity allows us to construct a network of the grammatical rules governing the appearance of group of words in the DNA. Our model allows to predict the transition between group of words in the DNA with unprecedented accuracy, and to easily calculate many informational quantities to better characterize the DNA. In addition, we reduce the DNA of known bacteria to a network of only tens of nodes, show how our model can be used to detect similar (or dissimilar) genes in different organisms, and which sequences of symbols are responsible for the most of the information content of the DNA. Therefore, the DNA can indeed be treated as a ...

  7. Increased mitochondrial DNA content in peripheral blood lymphocytes from HIV-infected patients with lipodystrophy.

    Science.gov (United States)

    Cossarizza, Andrea; Riva, Agostino; Pinti, Marcello; Ammannato, Silvia; Fedeli, Paolo; Mussini, Cristina; Esposito, Roberto; Galli, Massimo

    2003-08-01

    We have evaluated mitochondrial (mt) DNA content in CD4 and CD8 peripheral blood lymphocytes (PBLs) from HIV-infected patients taking highly active antiretroviral therapy (HAART) who display different types of adipose tissue alterations. A cross-sectional study was performed in a total of 23 patients with lipodystrophy (LD): nine patients with fat accumulation, six patients with fat loss, eight patients with combined form, who were compared to 11 individuals infected by HIV without LD (HIV-positive) and 10 seronegative controls (CTRL). PBLs were obtained by standard methods, that is, gradient density centrifugation on Ficoll, and CD4 or CD8 cells were positively isolated by magnetic sorting to eliminate the contamination of platelets. mtDNA content was then measured by an original assay based upon real-time PCR. mtDNA content was significantly increased in CD4 T cells from patients with LD, while no differences were present between CD4 and CD8 cells from HIV-positive and CTRL individuals. Nor were any differences found when comparing LD or HIV-positive patients treated with stavudine or zidovudine, or taking D-drugs or non D-drugs. Patients with fat accumulation had significantly higher mtDNA content compared to HIV-positive and CTRL, this phenomenon regarding both CD4 and CD8 PBLs. Considering all HIV-positive patients (including LD), mtDNA content showed a significant, positive correlation with cholesterolaemia but not with triglyceridaemia and glycaemia. Relatively high mtDNA content in LD patients, as well as the correlation between mtDNA content and cholesterol in all HIV-positive subjects, suggest the involvement of mitochondria in such a pathology. However, further studies are needed to confirm these initial observations and ascertain whether the quantification of mtDNA in PBL is a useful and reliable marker to investigate and monitor HAART-related changes in fat distribution.

  8. Karyotype and nuclear DNA content of Trichomycterus areolatus (Siluriformes, Trichomycteridae

    Directory of Open Access Journals (Sweden)

    Nelson Colihueque

    2006-01-01

    Full Text Available Cytogenetic analysis of Trichomycterus areolatus, collected from the Tijeral and Huilma Rivers in southern Chile has shown a diploid chromosome number of 2n = 54, a fundamental number of FN = 106, and a karyotypic formula of 44m + 8sm + 2st. Intra-individual polymorphism of chromosome number (2n = 54, 55 and 56 in specimens from the Huilma River has also been documented, providing further evidence of the occurrence of this phenomenon in Trichomycterus. The karyotype exhibited large chromosome pairs: metacentric pairs 1 (relative length 7.54%, 2 (5.75% and 3 (5.09%, submetacentric pair 23 (5.25%, and subtelocentic pair 27 (5.28%. Nuclear DNA content analysis showed an average value of 5.04 ± 1.09 pg/nucleus. This DNA content is higher than the mean value described for other species in this genus.

  9. 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.

  10. Applying Content Analysis to Web-based Content

    OpenAIRE

    Kim, Inhwa; Kuljis, Jasna

    2010-01-01

    Using Content Analysis onWeb-based content, in particular the content available onWeb 2.0 sites, is investigated. The relative strengths and limitations of the method are described. To illustrate how content analysis may be used, we provide a brief overview of a case study that investigates cultural impacts on the use of design features with regard to self-disclosure on the blogs of South Korean and United Kingdom’s users. In this study we took a standard approach to conducting the content an...

  11. Mitochondrial DNA content in breast cancer: Impact on in vitro and in vivo phenotype and patient prognosis

    Science.gov (United States)

    Weerts, Marjolein J.A.; Sieuwerts, Anieta M.; Smid, Marcel; Look, Maxime P.; Foekens, John A.; Sleijfer, Stefan; Martens, John W.M.

    2016-01-01

    Reduced mitochondrial DNA (mtDNA) content in breast cancer cell lines has been associated with transition towards a mesenchymal phenotype, but its clinical consequences concerning breast cancer dissemination remain unidentified. Here, we aimed to clarify the link between mtDNA content and a mesenchymal phenotype and its relation to prognosis of breast cancer patients. We analyzed mtDNA content in 42 breast cancer cell lines and 207 primary breast tumor specimens using a combination of quantitative PCR and array-based copy number analysis. By associating mtDNA content with expression levels of genes involved in epithelial-to-mesenchymal transition (EMT) and with the intrinsic breast cancer subtypes, we could not identify a relation between low mtDNA content and mesenchymal properties in the breast cancer cell lines or in the primary breast tumors. In addition, we explored the relation between mtDNA content and prognosis in our cohort of primary breast tumor specimens that originated from patients with lymph node-negative disease who did not receive any (neo)adjuvant systemic therapy. When patients were divided based on the tumor quartile levels of mtDNA content, those in the lowest quarter (≤ 350 mtDNA molecules per cell) showed a poorer 10-year distant metastasis-free survival than patients with > 350 mtDNA molecules per cell (HR 0.50 [95% CI 0.29–0.87], P = 0.015). The poor prognosis was independent of established clinicopathological markers (HR 0.54 [95% CI 0.30–0.97], P = 0.038). We conclude that, despite a lack of evidence between mtDNA content and EMT, low mtDNA content might provide meaningful prognostic value for distant metastasis in breast cancer. PMID:27081694

  12. 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.

  13. High resolution DNA content measurements of mammalian sperm

    Energy Technology Data Exchange (ETDEWEB)

    Pinkel, D.; Lake, S.; Gledhill, B.L.; Van Dilla, M.A.; Stephenson, D.; Watchmaker, G.

    1982-01-01

    The high condensation and flat shape of the mammalian sperm nucleus present unique difficulties to flow cytometric measurement of DNA content. Chromatin compactness makes quantitative fluorescent staining for DNA difficult and causes a high index of refraction. The refractive index makes optical measurements sensitive to sperm head orientation. We demonstrate that the optical problems can be overcome using the commercial ICP22 epiillumination flow cytometer (Ortho Instruments, Westwood, MA) or a specially built cell orientating flow cytometer (OFCM). The design and operation of the OFCM are described. Measurements of the angular dependence of fluorescence from acriflavine stained rabbit sperm show that it is capable of orienting flat sperm with a tolerance of +-7/sup 0/. Differences in the angular dependence for the similarly shaped bull and rabbit sperm allow discrimination of these cells. We show that DNA staining with 4-6 diamidino-2-phenylindole (DAPI) or an ethidium bromide mithramycin combination allows resolution of the X and Y populations in mouse sperm. They have also been successful with sperm from the bull, ram, rabbit, and boar. Reliable results with human sperm are not obtained. The accuracy of the staining and measurement techniques are verified by the correct determination of the relative content of these two populations in sperm from normal mice and those with the Cattanach (7 to X) translocation. Among the potential uses of these techniques are measurement of DNA content errors induced in sperm due to mutagen exposure, and assessment of the fractions of X and Y sperm in semen that may have one population artifically enriched.

  14. Improved Lower Bounds for Constant GC-Content DNA Codes

    CERN Document Server

    Chee, Yeow Meng

    2008-01-01

    The design of large libraries of oligonucleotides having constant GC-content and satisfying Hamming distance constraints between oligonucleotides and their Watson-Crick complements is important in reducing hybridization errors in DNA computing, DNA microarray technologies, and molecular bar coding. Various techniques have been studied for the construction of such oligonucleotide libraries, ranging from algorithmic constructions via stochastic local search to theoretical constructions via coding theory. We introduce a new stochastic local search method which yields improvements up to more than one third of the benchmark lower bounds of Gaborit and King (2005) for n-mer oligonucleotide libraries when n <= 14. We also found several optimal libraries by computing maximum cliques on certain graphs.

  15. Changes in neuronal DNA content variation in the human brain during aging.

    Science.gov (United States)

    Fischer, Hans-Georg; Morawski, Markus; Brückner, Martina K; Mittag, Anja; Tarnok, Attila; Arendt, Thomas

    2012-08-01

    The human brain has been proposed to represent a genetic mosaic, containing a small but constant number of neurons with an amount of DNA exceeding the diploid level that appear to be generated through various chromosome segregation defects initially. While a portion of these cells apparently die during development, neurons with abnormal chromosomal copy number have been identified in the mature brain. This genomic alteration might to lead to chromosomal instability affecting neuronal viability and could thus contribute to age-related mental disorders. Changes in the frequency of neurons with such structural genomic variation in the adult and aging brain, however, are unknown. Here, we quantified the frequency of neurons with a more than diploid DNA content in the cerebral cortex of normal human brain and analyzed its changes between the fourth and ninth decades of life. We applied a protocol of slide-based cytometry optimized for DNA quantification of single identified neurons, which allowed to analyze the DNA content of about 500 000 neurons for each brain. On average, 11.5% of cortical neurons showed DNA content above the diploid level. The frequency of neurons with this genomic alteration was highest at younger age and declined with age. Our results indicate that the genomic variation associated with DNA content exceeding the diploid level might compromise viability of these neurons in the aging brain and might thus contribute to susceptibilities for age-related CNS disorders. Alternatively, a potential selection bias of "healthy aging brains" needs to be considered, assuming that DNA content variation above a certain threshold associates with Alzheimer's disease.

  16. Identifying sensitive windows for prenatal particulate air pollution exposure and mitochondrial DNA content in cord blood.

    Science.gov (United States)

    Rosa, Maria José; Just, Allan C; Guerra, Marco Sánchez; Kloog, Itai; Hsu, Hsiao-Hsien Leon; Brennan, Kasey J; García, Adriana Mercado; Coull, Brent; Wright, Rosalind J; Téllez Rojo, Martha María; Baccarelli, Andrea A; Wright, Robert O

    2017-01-01

    Changes in mitochondrial DNA (mtDNA) can serve as a marker of cumulative oxidative stress (OS) due to the mitochondria's unique genome and relative lack of repair systems. In utero particulate matter ≤2.5μm (PM2.5) exposure can enhance oxidative stress. Our objective was to identify sensitive windows to predict mtDNA damage experienced in the prenatal period due to PM2.5 exposure using mtDNA content measured in cord blood. Women affiliated with the Mexican social security system were recruited during pregnancy in the Programming Research in Obesity, Growth, Environment and Social Stressors (PROGRESS) study. Mothers with cord blood collected at delivery and complete covariate data were included (n=456). Mothers' prenatal daily exposure to PM2.5 was estimated using a satellite-based spatio-temporally resolved prediction model and place of residence during pregnancy. DNA was extracted from umbilical cord leukocytes. Quantitative real-time polymerase chain reaction (qPCR) was used to determine mtDNA content. A distributive lag regression model (DLM) incorporating weekly averages of daily PM2.5 predictions was constructed to plot the association between exposure and OS over the length of pregnancy. In models that included child's sex, mother's age at delivery, prenatal environmental tobacco smoke exposure, birth year, maternal education, and assay batch, we found significant associations between higher PM2.5 exposure during late pregnancy (35-40weeks) and lower mtDNA content in cord blood. Increased PM2.5 during a specific prenatal window in the third trimester was associated with decreased mtDNA content suggesting heightened sensitivity to PM-induced OS during this life stage. Copyright © 2016 Elsevier Ltd. All rights reserved.

  17. DNA content in embryo and endosperm of maize kernel (Zea mays L.): impact on GMO quantification.

    Science.gov (United States)

    Trifa, Youssef; Zhang, David

    2004-03-10

    PCR-based techniques are the most widely used methods for the quantification of genetically modified organisms (GMOs) through the determination of the ratio of transgenic DNA to total DNA. It is shown that the DNA content per mass unit is significantly different among 10 maize cultivars. The DNA contents of endosperms, embryos, and teguments of individual kernels from 10 maize cultivars were determined. According to our results, the tegument's DNA ratio reaches at maximum 3.5% of the total kernel's DNA, whereas the endosperm's and the embryo's DNA ratios are nearly equal to 50%. The embryo cells are diploid and made of one paternal and one maternal haploid genome, whereas the endosperm is constituted of triploid cells made of two maternal haploid genomes and one paternal haploid genome. Therefore, it is shown, in this study, that the accuracy of the GMO quantification depends on the reference material used as well as on the category of the transgenic kernels present in the mixture.

  18. CONTENT BASED BATIK IMAGE RETRIEVAL

    Directory of Open Access Journals (Sweden)

    A. Haris Rangkuti

    2014-01-01

    Full Text Available Content Based Batik Image Retrieval (CBBIR is an area of research that focuses on image processing based on characteristic motifs of batik. Basically the image has a unique batik motif compared with other images. Its uniqueness lies in the characteristics possessed texture and shape, which has a unique and distinct characteristics compared with other image characteristics. To study this batik image must start from a preprocessing stage, in which all its color images must be removed with a grayscale process. Proceed with the feature extraction process taking motifs characteristic of every kind of batik using the method of edge detection. After getting the characteristic motifs seen visually, it will be calculated by using 4 texture characteristic function is the mean, energy, entropy and stadard deviation. Characteristic function will be added as needed. The results of the calculation of characteristic functions will be made more specific using the method of wavelet transform Daubechies type 2 and invariant moment. The result will be the index value of every type of batik. Because each motif there are the same but have different sizes, so any kind of motive would be divided into three sizes: Small, medium and large. The perfomance of Batik Image similarity using this method about 90-92%.

  19. Relationship between DAPI-fluorescence fading and nuclear DNA content: An alternative method to DNA quantification?

    Science.gov (United States)

    Gallardo-Escárate, Cristian; Alvarez-Borrego, Josué; Von Brand, Elisabeth; Dupré, Enrique; Del Río-Portilla, Miguel Angel

    2007-01-01

    In observations by confocal or conventional fluorescence microscopy, important factors should be considered in order to obtain accurate images. One of them, such as the fluorescence bleaching from highest intensity to lowest signal of fluorescence is a common problem with several DNA fluorochromes and especially for DAPI stain. The fluorescence of DAPI fades rapidly when it is exposed to UV light, under optimal conditions of observation. Although the fading process can be retarded using a mounting medium with antifading reagents, the photochemical process underlying the fluorescence decay has not yet been fully explained. In addition, no relationship between fluorescence fading and nuclear DNA content has been tested. In order to test this relationship, we measured by means of image analysis the DAPI-fluorescence intensity in several cellular types (spermatozoa, erythrocytes and haemocytes) during their fluorescence bleaching. An algorithm specifically built in MATLAB software was used for this approach. The correlation coefficient between nuclear DNA content and DAPI-fluorescence fading was found equal to 99%. This study demonstrates the feasibility to measure nuclear DNA content by fluorescence fading quantification, as an alternative method concurrently with image analysis procedures.

  20. Cytometric analysis of shape and DNA content in mammalian sperm

    Energy Technology Data Exchange (ETDEWEB)

    Gledhill, B.L.

    1983-10-10

    Male germ cells respond dramatically to a variety of insults and are important reproductive dosimeters. Semen analyses are very useful in studies on the effects of drugs, chemicals, and environmental hazards on testicular function, male fertility and heritable germinal mutations. Sperm were analyzed by flow cytometry and slit-scan flow analysis for injury following the exposure of testes to mutagens. The utility of flow cytometry in genotoxin screening and monitoring of occupational exposure was evaluated. The technique proved valuable in separation of X- and Y-chromosome bearing sperm and the potential applicability of this technique in artificial insemination and a solution, of accurately assessing the DNA content of sperm were evaluated-with reference to determination of X- and Y-chromosome bearing sperm.

  1. Metadata for Content-Based Image Retrieval

    Directory of Open Access Journals (Sweden)

    Adrian Sterca

    2010-12-01

    Full Text Available This paper presents an image retrieval technique that combines content based image retrieval with pre-computed metadata-based image retrieval. The resulting system will have the advantages of both approaches: the speed/efficiency of metadata-based image retrieval and the accuracy/power of content-based image retrieval.

  2. DNA content alterations in Tetrahymena pyriformis macronucleus after exposure to food preservatives sodium nitrate and sodium benzoate.

    Science.gov (United States)

    Loutsidou, Ariadni C; Hatzi, Vasiliki I; Chasapis, C T; Terzoudi, Georgia I; Spiliopoulou, Chara A; Stefanidou, Maria E

    2012-12-01

    The toxicity, in terms of changes in the DNA content, of two food preservatives, sodium nitrate and sodium benzoate was studied on the protozoan Tetrahymena pyriformis using DNA image analysis technology. For this purpose, selected doses of both food additives were administered for 2 h to protozoa cultures and DNA image analysis of T. pyriformis nuclei was performed. The analysis was based on the measurement of the Mean Optical Density which represents the cellular DNA content. The results have shown that after exposure of the protozoan cultures to doses equivalent to ADI, a statistically significant increase in the macronuclear DNA content compared to the unexposed control samples was observed. The observed increase in the macronuclear DNA content is indicative of the stimulation of the mitotic process and the observed increase in MOD, accompanied by a stimulation of the protozoan proliferation activity is in consistence with this assumption. Since alterations at the DNA level such as DNA content and uncontrolled mitogenic stimulation have been linked with chemical carcinogenesis, the results of the present study add information on the toxicogenomic profile of the selected chemicals and may potentially lead to reconsideration of the excessive use of nitrates aiming to protect public health.

  3. 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.

  4. Nuclear DNA contents of Echinchloa crus-galli and its Gaussian relationships with environments

    Science.gov (United States)

    Li, Dan-Dan; Lu, Yong-Liang; Guo, Shui-Liang; Yin, Li-Ping; Zhou, Ping; Lou, Yu-Xia

    2017-02-01

    Previous studies on plant nuclear DNA content variation and its relationships with environmental gradients produced conflicting results. We speculated that the relationships between nuclear DNA content of a widely-distributed species and its environmental gradients might be non-linear if it was sampled in a large geographical gradient. Echinochloa crus-galli (L.) P. Beauv. is a worldwide species, but without documents on its intraspecific variation of nuclear DNA content. Our objectives are: 1) to detect intraspecific variation scope of E. crus-galli in its nuclear DNA content, and 2) to testify whether nuclear DNA content of the species changes with environmental gradients following Gaussian models if its populations were sampled in a large geographical gradient. We collected seeds of 36 Chinese populations of E. crus-galli across a wide geographical gradient, and sowed them in a homogeneous field to get their offspring to determine their nuclear DNA content. We analyzed the relationships of nuclear DNA content of these populations with latitude, longitude, and nineteen bioclimatic variables by using Gaussian and linear models. (1) Nuclear DNA content varied from 2.113 to 2.410 pg among 36 Chinese populations of E. crus-galli, with a mean value of 2.256 pg. (2) Gaussian correlations of nuclear DNA content (y) with geographical gradients were detected, with latitude (x) following y = 2.2923*e -(x - 24.9360)2/2*63.79452 (r = 0.546, P DNA content by using Gaussian models than by linear models. There exists intra-specific variation among 36 Chinese populations of E. crus-galli, Gaussian models could be applied to fit the correlations of its Nuclear DNA content with geographical and most bioclimatic gradients.

  5. DNA nuclear content in the cytotaxonomy of Galago senegalensis and Galago crassicaudatus

    NARCIS (Netherlands)

    Manfredi-Romanini, M.G.; Boer, L.E.M. de; Chiarelli, B.; Tinozzi Massari, S.

    The DNA nuclear content in lymphocytes of peripheral blood from Galago senegalensis (2 males and 2 females), Galago crassicaudatus (3 males and 2 females) and Perodicticus potto (2 males) was measured by means of the Deeley integrating microdensitometer. The mean of the DNA content does not

  6. DNA nuclear content in the cytotaxonomy of Galago senegalensis and Galago crassicaudatus

    NARCIS (Netherlands)

    Manfredi-Romanini, M.G.; Boer, L.E.M. de; Chiarelli, B.; Tinozzi Massari, S.

    1972-01-01

    The DNA nuclear content in lymphocytes of peripheral blood from Galago senegalensis (2 males and 2 females), Galago crassicaudatus (3 males and 2 females) and Perodicticus potto (2 males) was measured by means of the Deeley integrating microdensitometer. The mean of the DNA content does not differ

  7. 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.

  8. Flow microfluorometric DNA content measurements of tissue culture cells and peripheral lymphocytes

    Energy Technology Data Exchange (ETDEWEB)

    Cram, L.S. (Los Alamos Scientific Lab., NM); Lehman, J.M.

    1977-01-01

    The difference in DNA content of peripheral lymphocytes from normal males, normal females, and an individual with a 48 (xxxy) chromosome constitution was determined by rapid flow microfluorometric techniques. A similar comparison was performed using tissue culture fibroblasts derived from an individual with a 49 (xxxxy) chromosome constitution and WI-38 cells as a normal control. Less than 60 min were required to isolate the lymphocytes, to stain the cells fluorescently, and to measure the increased DNA content. The measured increase in DNA content is consistent with chromosome DNA analyses and chromosome length measurements.

  9. Content-based vessel image retrieval

    Science.gov (United States)

    Mukherjee, Satabdi; Cohen, Samuel; Gertner, Izidor

    2016-05-01

    This paper describes an approach to vessel classification from satellite images using content based image retrieval methodology. Content-based image retrieval is an important problem in both medical imaging and surveillance applications. In many cases the archived reference database is not fully structured, thus making content-based image retrieval a challenging problem. In addition, in surveillance applications, the query image may be affected by weather or/and geometric distortions. Our approach of content-based vessel image retrieval consists of two phases. First, we create a structured reference database, then for each new query image of a vessel we find the closest cluster of images in the structured reference database, thus identifying and classifying the vessel. Then we update the closest cluster with new query image.

  10. 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

  11. Determination of DNA Content of Aquatic Bacteria by Flow Cytometry

    OpenAIRE

    Button, D. K.; Robertson, Betsy R.

    2001-01-01

    The distribution of DNA among bacterioplankton and bacterial isolates was determined by flow cytometry of DAPI (4′,6′-diamidino-2-phenylindole)-stained organisms. Conditions were optimized to minimize error from nonspecific staining, AT bias, DNA packing, changes in ionic strength, and differences in cell permeability. The sensitivity was sufficient to characterize the small 1- to 2-Mb-genome organisms in freshwater and seawater, as well as low-DNA cells (“dims”). The dims could be formed fro...

  12. Determination and Difference Analysis of DNA Methylation Content Both in Blood and Muscle Tissue of Pigs

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    In this experiment, DNA samples from parental lines Large White, Landrace, and Meishan pigs, and their hybrids Large White×Landrace, Landrace×Large White, Large White×Meishan, and Meishan×Large White pigs were used for the determination of DNA methylation content in both blood and muscle tissue. The differences about DNA methylation content between parental lines and their hybrids were analyzed. These will offer theoretical support from molecular level for heterosis. High performance liquid chromatography (HPLC) was firstly used to detect DNA methylation content. The average DNA methylation content in 163 DNA samples of muscle tissue was 16.92%, whereas, the average DNA methylation content in 182 samples of blood was 6.49%, the difference between which was especially prominent (P 0.05); and the differences between reciprocal cross hybrids in both hybrid systems were not significant (P > 0.05), but between different hybrid systems, the hybrids had a significant difference (P<0.05). The average methylation content in muscle samples was higher than that in blood samples, and the methylation in different tissues was different.

  13. 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.

  14. Analysis of Cellular DNA Content by Flow and Laser Scanning Cytometry

    Science.gov (United States)

    Darzynkiewicz, Zbigniew; Halicka, H. Dorota; Zhao, Hong

    2010-01-01

    This chapter covers several aspects of methodology of DNA content analysis in individual cells that is most commonly used for assessment of DNA ploidy and for enumeration of cells in particular phases of the cell cycle. Briefly presented are general principles of instrumentation and cell analysis by flow- and laser scanning- cytometry. Described are major methods designed to stain DNA with fluorochromes in live cells, in detergent-permeabilized cells, in cells fixed prior to DNA staining as well as in nuclei of cells isolated from paraffin-embedded tissues. Briefly addressed are approaches to estimate cellular DNA content in conjunction with cellular immunophenotype. Discussed are factors that affect accuracy of DNA content measurement such as: (i) differences in chromatin structure of the analyzed cells that restrict DNA accessibility to fluorochromes, (ii) stoichiometry of interaction between fluorochromes and DNA in chromatin and (iii) chemical mass action law defining dependency of fluorochrome binding to DNA in relation to fluorochrome concentration and number of potential binding sites in a sample. Described also are controls used to ensure accuracy of DNA ploidy determination, the principles in ploidy assessment and possible pitfalls in analysis. PMID:20687474

  15. 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.

  16. Content-based retrieval of visual information

    NARCIS (Netherlands)

    Oerlemans, Adrianus Antonius Johannes

    2011-01-01

    In this dissertation, I investigate new approaches relevant to content-based image retrieval techniques. First, the MOD paradigm is proposed, a method for detecting salient points in images. These salient points are specifically designed to enhance image retrieval accuracy by maximizing distinctive

  17. Material Recognition for Content Based Image Retrieval

    NARCIS (Netherlands)

    Geusebroek, J.M.

    2002-01-01

    One of the open problems in content-based Image Retrieval is the recognition of material present in an image. Knowledge about the set of materials present gives important semantic information about the scene under consideration. For example, detecting sand, sky, and water certainly classifies the im

  18. Material Recognition for Content Based Image Retrieval

    NARCIS (Netherlands)

    Geusebroek, J.M.

    2002-01-01

    One of the open problems in content-based Image Retrieval is the recognition of material present in an image. Knowledge about the set of materials present gives important semantic information about the scene under consideration. For example, detecting sand, sky, and water certainly classifies the

  19. 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

  20. Decreased mitochondrial DNA content in blood samples of patients with stage I breast cancer

    Directory of Open Access Journals (Sweden)

    Fokas Emmanouil

    2009-12-01

    Full Text Available Abstract Background Alterations of mitochondrial DNA (mtDNA have been implicated in carcinogenesis. We developed an accurate multiplex quantitative real-time PCR for synchronized determination of mtDNA and nuclear DNA (nDNA. We sought to investigate whether mtDNA content in the peripheral blood of breast cancer patients is associated with clinical and pathological parameters. Methods Peripheral blood samples were collected from 60 patients with breast cancer and 51 age-matched healthy individuals as control. DNA was extracted from peripheral blood for the quantification of mtDNA and nDNA, using a one-step multiplex real-time PCR. A FAM labeled MGB probe and primers were used to amplify the mtDNA sequence of the ATP 8 gene, and a VIC labeled MGB probe and primers were employed to amplify the glyceraldehyde-3-phosphate-dehydrogenase gene. mtDNA content was correlated with tumor stage, menstruation status, and age of patients as well as lymph node status and the expression of estrogen receptor (ER, progesterone receptor (PR and Her-2/neu protein. Results The content of mtDNA in stage I breast cancer patients was significantly lower than in other stages (overall P = 0.023. Reduced mtDNA was found often in post menopausal cancer group (P = 0.024. No difference in mtDNA content, in regards to age (p = 0.564, lymph node involvement (p = 0.673, ER (p = 0.877, PR (p = 0.763, and Her-2/neu expression (p = 0.335, was observed. Conclusion Early detection of breast cancer has proved difficult and current detection methods are inadequate. In the present study, decreased mtDNA content in the peripheral blood of patients with breast cancer was strongly associated with stage I. The use of mtDNA may have diagnostic value and further studies are required to validate it as a potential biomarker for early detection of breast cancer.

  1. Chromosome numbers and DNA content in some species of Mecardonia (Gratiolae, Plantaginaceae)

    Science.gov (United States)

    Sosa, María M.; Angulo, María B.; Greppi, Julián A.; Bugallo, Verónica

    2016-01-01

    Abstract Cytogenetic characterization and determination of DNA content by flow cytometry of five species of Mecardonia Ruiz et Pavon, 1798 (Gratiolae, Plantaginaceae) was performed. This is the first study of nuclear DNA content carried out in the genus. Mitotic analysis revealed a base chromosome number x = 11 for all entities and different ploidy levels, ranging from diploid (2n = 2x = 22) to hexaploid (2n = 6x = 66). The results include the first report of the chromosome numbers for Mecardonia flagellaris (Chamisso & Schlechtendal, 1827) (2n = 22), Mecardonia grandiflora (Bentham) Pennell, 1946 (2n = 22), Mecardonia kamogawae Greppi & Hagiwara, 2011 (2n = 66), and Mecardonia sp. (2n = 44). The three ploidy levels here reported suggest that polyploidy is common in Mecardonia and appear to be an important factor in the evolution of this genus. The 2C- and 1Cx-values were also estimated in all the species. The 2C-values ranged from 1.91 to 5.29 pg. The 1Cx-values ranged from 0.88 to 1.03 pg. The general tendency indicated a decrease in the 1Cx-value with increasing ploidy level. The significance of the results is discussed in relation to taxonomy of the genus. PMID:28123693

  2. DNA and RNA content analysis by flow cytometry in the pathobiologic assessment of bone tumors

    Energy Technology Data Exchange (ETDEWEB)

    El-Naggar, A.K.; Hurr, K.; Tu, Z.N.; Teague, K.; Raymond, K.A.; Ayala, A.G.; Murray, J. [Univ. of Texas, Houston, TX (United States)

    1995-03-01

    Studies of simultaneous DNA and RNA contents by flow cytometry in hematologic and some solid neoplasms have been shown to provide information that may be useful in pathobiological evaluation of these neoplasms. We contend that similar analysis may be equally valuable in assessing bone tumors. Our data revealed significant statistical differences in DNA ploidy and proliferative fraction between benign and malignant bone neoplasms. Benign tumors manifested predominantly DNA diploidy and low proliferative activity, whereas the majority of malignant tumors were DNA aneuploid and showed high proliferation rate. No significant difference in the RNA content between different histopathologic categories was found. We observed, however, a distinct and consistently high RNA content pattern in giant cell tumors, aneurysmal bone cysts, and chondroblastomas that may be useful in their differential diagnosis. Analysis of different prognostic factors in malignant tumors indicated that histologic grade and DNA content are significant prognostic factors. Further analysis of malignant tumors showed that a correlation between the proliferative activity and the clinical outcome in the low grade category and between RNA content and patients` survival in osteosarcomas. Our study also showed that preoperative treatment significantly impacted on the extent of the proliferative fraction in malignant tumors. We conclude that DNA/RNA analysis of bone tumor may assist in: (1) the differential diagnosis of certain bone tumors, (2) evaluation of treatment response, and (3) the biological assessment of osteosarcomas. 38 refs., 4 figs., 5 tabs.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. Heterogeneity of DNA content and expression of cell cycle genes in axenically growing Entamoeba histolytica HM1:IMSS clone A.

    Science.gov (United States)

    Gangopadhyay, S S; Ray, S S; Kennady, K; Pande, G; Lohia, A

    1997-12-01

    The cell division cycle of Entamoeba histolytica was studied using multi-parametric flow cytometry in asynchronous and partially synchronised cells. Dynamic changes in the DNA synthesis and DNA content of axenically growing trophozoites were observed by using 5-bromo-2'-deoxyuridine (BrdU) uptake and DNA specific fluorochromes. It was observed that DNA synthesis in these cells continues beyond the typical S-phase stop point when DNA duplication is complete. Asynchronously growing E. histolytica cells could be synchronised by serum starvation followed by serum re-addition. BrdU incorporation in synchronised cells showed that cell synchrony is maintained for at least one generation time, in which the G1 phase lasts for 2-3 h and the S-phase lasts for 5-6 h. Analysis of our results revealed that E. histolytica trophozoites, growing in axenic medium, are made up of a heterogenous population of euploid and polyploid cells. The number of polyploid cells increases with age of the cells in culture. Expression of putative cell cycle and signal transduction markers was studied using specific antibodies and changes in their expression levels have been correlated with changes in the DNA content. Based upon our results we could identify G1, S and G2 phases of the cell cycle of E. histolytica and also predict the mechanism underlying the generation of polyploidy in these cells, which may have significant effects on its biology and pathogenesis.

  8. Nuclear DNA content in 20 species of Siluriformes (Teleostei: Ostariophysi from the Neotropical region

    Directory of Open Access Journals (Sweden)

    Paulo César Fenerich

    2004-01-01

    Full Text Available In the present study, 20 species of Siluriformes fish were analyzed in order to determine their nuclear DNA content and compare these data with their diploid number. In addition, the extension and importance of the changes that occurred during the process of diversification in the group of Neotropical freshwater catfish were investigated. The only species studied of the family Doradidae, Rhinodoras d'orbignyi (2n = 58, presented 3.46 ± 0.13 pg of DNA. Among the species of the family Heptapteridae, the values of nuclear DNA content and the diploid numbers ranged from 1.13 ± 0.09 pg of DNA in Pimelodella sp. (2n = 46 to 2.38 ± 0.07 pg of DNA in Imparfinis mirini (2n = 58. The family Loricariidae showed the widest variation in diploid number and nuclear DNA content values, ranging from 2n = 52 and 3.96 ± 0.22 pg of DNA in Liposarcus anisitsi to 2n = 76 and 4.90 ± 0.12 pg of DNA in Hypostomus sp. 4. In this group, two local samples of Pimelodus maculatus (Pimelodidae were analyzed, and both exhibited 2n = 56, but different nuclear DNA content values (2.68 ± 0.22 pg and 2.82 ± 0.20 pg, respectively. Among the Pseudopimelodidae species analyzed, Pseudopimelodus mangurus (2n = 54 showed 2.23 ± 0.15 pg and Microglanis cottoides (2n = 54 exhibited 2.50 ± 0.18 pg of DNA. Two species of Trichomycterus (Trichomycteridae also presented the same diploid number, 2n = 54 chromosomes, but, while the species from the Quinta stream presented a DNA content of 2.62 ± 0.19 pg, in the sample from the Capivara river this value was 2.30 ± 0.23 pg. In the analyzed species, the results showed that the changes in DNA content were frequently not followed by changes in the diploid number. This fact permits to suggest that, in addition to structural chromosome rearrangements, other mechanisms, including deletions, duplications and polyploidy, could be involved in the process of species differentiation in the representatives of the fish order Siluriformes.

  9. Information Audit Based on Image Content Filtering

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    At present, network information audit system is almost based on text information filtering, but badness information is embedded into image or image file directly by badness information provider, in order to avoid monitored by. The paper realizes an information audit system based on image content filtering. Taking the pornographic program identification for an example, the system can monitor the video including any abnormal human body information by matching the texture characters with those defined in advance, which consist of contrast, energy, correlation measure and entropy character measure and so on.

  10. 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.

  11. 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.

  12. COMBINED DETECTION OF CYCLIN D1, P27 AND DNA CONTENT IN ESOPHAGEAL CANCER

    Institute of Scientific and Technical Information of China (English)

    MA Ping; YIN Yuan-qin; WANG Xiao-hua

    2006-01-01

    Objective: To investigate the expressions of cyclin D1 and p27 and DNA content in esophageal cancer and adjacent normal tissues, and to discuss the relationship between them. Methods: The cyclinD1 and p27 were detected by immunohistochemical staining; DNA content was measured by flow cytometry. Results: The positive expression rates of cyclinD1 and p27 in cancer were 45.8% and 33.3% respectively, the DNA content in the positive group of cyclinD1 was higher than that in the negative group of cyclinD1(1.54(0.21 versus 1.08(0.43, P<0.05), while the DNA content and SPF (S-phase fraction) in the positive group of p27 were lower than those in the negative group (1.10(0.19 and 5.56%(5.18% versus 1.66(0.28 and 19.78%(6.12%, P<0.05). Conclusion: The data show that the expression of cyclinD1 and p27 are related to the ontogenesis and progression of esophageal cancer. The combined detection of cyclinD1, p27 and DNA content may be indicators of diagnosis and assessment of esophageal cancer.

  13. 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.

  14. Decreased Integrity, Content, and Increased Transcript Level of Mitochondrial DNA Are Associated with Keratoconus

    Science.gov (United States)

    Hao, Xiao-Dan; Chen, Zhao-Li; Qu, Ming-Li; Zhao, Xiao-Wen; Li, Su-Xia; Chen, Peng

    2016-01-01

    Oxidative stress may play an important role in the pathogenesis of keratoconus (KC). Mitochondrial DNA (mtDNA) is involved in mitochondrial function, and the mtDNA content, integrity, and transcript level may affect the generation of reactive oxygen species (ROS) and be involved in the pathogenesis of KC. We designed a case-control study to research the relationship between KC and mtDNA integrity, content and transcription. One-hundred ninety-eight KC corneas and 106 normal corneas from Chinese patients were studied. Quantitative real-time PCR was used to measure the relative mtDNA content, transcript levels of mtDNA and related genes. Long-extension PCR was used to detect mtDNA damage. ROS, mitochondrial membrane potential and ATP were measured by respective assay kit, and Mito-Tracker Green was used to label the mitochondria. The relative mtDNA content of KC corneas was significantly lower than that of normal corneas (P = 9.19×10−24), possibly due to decreased expression of the mitochondrial transcription factor A (TFAM) gene (P = 3.26×10−3). In contrast, the transcript levels of mtDNA genes were significantly increased in KC corneas compared with normal corneas (NADH dehydrogenase subunit 1 [ND1]: P = 1.79×10−3; cytochrome c oxidase subunit 1 [COX1]: P = 1.54×10−3; NADH dehydrogenase subunit 1, [ND6]: P = 4.62×10−3). The latter may be the result of increased expression levels of mtDNA transcription-related genes mitochondrial RNA polymerase (POLRMT) (P = 2.55×10−4) and transcription factor B2 mitochondrial (TFB2M) (P = 7.88×10−5). KC corneas also had increased mtDNA damage (P = 3.63×10−10), higher ROS levels, and lower mitochondrial membrane potential and ATP levels compared with normal corneas. Decreased integrity, content and increased transcript level of mtDNA are associated with KC. These changes may affect the generation of ROS and play a role in the pathogenesis of KC. PMID:27783701

  15. Nuclear DNA content of the pigeon orchid (Dendrobium crumenatum Sw. with the analysis of flow cytometry

    Directory of Open Access Journals (Sweden)

    Upatham Meesawat

    2008-05-01

    Full Text Available Nuclear DNA content for the adult plants grown in a greenhouse and in vitro young plantlets of the pigeon orchid (Dendrobium crumenatum Sw. was analyzed using flow cytometry. The resulting 2C DNA values ranged from 2.30±0.14 pgto 2.43±0.06 pg. However, nuclear DNA ploidy levels of long-term in vitro plantlets were found to be triploid and tetraploid.These ploidy levels were confirmed by chromosome counting. Tetraploid individuals (2n = 4x = 76 had approximately two times DNA content than diploid (2n = 2x = 38 individuals. This variation may be due to prolonged cultivation and thepresence of exogenous plant growth regulators.

  16. 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.

  17. Decreased mitochondrial DNA content in association with exposure to polycyclic aromatic hydrocarbons in house dust during wintertime: from a population enquiry to cell culture.

    Directory of Open Access Journals (Sweden)

    Nicky Pieters

    Full Text Available Polycyclic aromatic hydrocarbons (PAHs are widespread environmental pollutants that are formed in combustion processes. At the cellular level, exposure to PAHs causes oxidative stress and/or some of it congeners bind to DNA, which may interact with mitochondrial function. However, the influence of these pollutants on mitochondrial DNA (mtDNA content remains largely unknown. We determined whether indoor exposure to PAHs is associated with mitochondrial damage as represented by blood mtDNA content. Blood mtDNA content (ratio mitochondrial/nuclear DNA copy number was determined by real-time qPCR in 46 persons, both in winter and summer. Indoor PAH exposure was estimated by measuring PAHs in sedimented house dust, including 6 volatile PAHs and 8 non-volatile PAHs. Biomarkers of oxidative stress at the level of DNA and lipid peroxidation were measured. In addition to the epidemiologic enquiry, we exposed human TK6 cells during 24 h at various concentrations (range: 0 to 500 µM of benzo(apyrene and determined mtDNA content. Mean blood mtDNA content averaged (± SD 0.95 ± 0.185. The median PAH content amounted 554.1 ng/g dust (25(th-75(th percentile: 390.7-767.3 and 1385 ng/g dust (25(th-75(th percentile: 1000-1980 in winter for volatile and non-volatile PAHs respectively. Independent for gender, age, BMI and the consumption of grilled meat or fish, blood mtDNA content decreased by 9.85% (95% CI: -15.16 to -4.2; p = 0.002 for each doubling of non-volatile PAH content in the house dust in winter. The corresponding estimate for volatile PAHs was -7.3% (95% CI: -13.71 to -0.42; p = 0.04. Measurements of oxidative stress were not correlated with PAH exposure. During summer months no association was found between mtDNA content and PAH concentration. The ability of benzo(apyrene (range 0 µM to 500 µM to lower mtDNA content was confirmed in vitro in human TK6 cells. Based on these findings, mtDNA content can be a target of PAH toxicity in humans.

  18. Decreased mitochondrial DNA content in association with exposure to polycyclic aromatic hydrocarbons in house dust during wintertime: from a population enquiry to cell culture.

    Science.gov (United States)

    Pieters, Nicky; Koppen, Gudrun; Smeets, Karen; Napierska, Dorota; Plusquin, Michelle; De Prins, Sofie; Van De Weghe, Hendrik; Nelen, Vera; Cox, Bianca; Cuypers, Ann; Hoet, Peter; Schoeters, Greet; Nawrot, Tim S

    2013-01-01

    Polycyclic aromatic hydrocarbons (PAHs) are widespread environmental pollutants that are formed in combustion processes. At the cellular level, exposure to PAHs causes oxidative stress and/or some of it congeners bind to DNA, which may interact with mitochondrial function. However, the influence of these pollutants on mitochondrial DNA (mtDNA) content remains largely unknown. We determined whether indoor exposure to PAHs is associated with mitochondrial damage as represented by blood mtDNA content. Blood mtDNA content (ratio mitochondrial/nuclear DNA copy number) was determined by real-time qPCR in 46 persons, both in winter and summer. Indoor PAH exposure was estimated by measuring PAHs in sedimented house dust, including 6 volatile PAHs and 8 non-volatile PAHs. Biomarkers of oxidative stress at the level of DNA and lipid peroxidation were measured. In addition to the epidemiologic enquiry, we exposed human TK6 cells during 24 h at various concentrations (range: 0 to 500 µM) of benzo(a)pyrene and determined mtDNA content. Mean blood mtDNA content averaged (± SD) 0.95 ± 0.185. The median PAH content amounted 554.1 ng/g dust (25(th)-75(th) percentile: 390.7-767.3) and 1385 ng/g dust (25(th)-75(th) percentile: 1000-1980) in winter for volatile and non-volatile PAHs respectively. Independent for gender, age, BMI and the consumption of grilled meat or fish, blood mtDNA content decreased by 9.85% (95% CI: -15.16 to -4.2; p = 0.002) for each doubling of non-volatile PAH content in the house dust in winter. The corresponding estimate for volatile PAHs was -7.3% (95% CI: -13.71 to -0.42; p = 0.04). Measurements of oxidative stress were not correlated with PAH exposure. During summer months no association was found between mtDNA content and PAH concentration. The ability of benzo(a)pyrene (range 0 µM to 500 µM) to lower mtDNA content was confirmed in vitro in human TK6 cells. Based on these findings, mtDNA content can be a target of PAH toxicity in humans.

  19. Whole-Mount DAPI Staining and Measurement of DNA Content in Plant Cells.

    Science.gov (United States)

    Schnittger, Arp; Hülskamp, Martin

    2007-01-01

    INTRODUCTIONDuring development, many plant cells undergo endoreduplication, whereby ploidy increases to a multiple of the normal 2C content. For example, trichome development is accompanied by an increase in ploidy to 32C, indicating that trichome cells undergo four rounds of endoreduplication. In the protocol described here, DNA levels, and hence developmental progress in the corresponding cells, are measured by staining the DNA with a fluorescent marker and then quantifying the fluorescence of individual nuclei.

  20. Estimates of nuclear DNA content in 98 species of brown algae (Phaeophyta)

    OpenAIRE

    Phillips, Naomi; Kapraun, Donald F.; Gómez Garreta, Amelia; Ribera Siguan, M. Antonia; Rull, Jorde L.; Salvador Soler, Noemi; Lewis, Raymond; Kawai, Hiroshi

    2011-01-01

    Background and aims Brown algae are critical components of marine ecosystems around the world. However, the genome of only one species of the class has so far been sequenced. This contrasts with numerous sequences available for model organisms such as higher plants, flies or worms. The present communication expands our coverage of DNA content information to 98 species of brown algae with a view to facilitating further genomic investigations of the class. Methodology The DNA-localizing fluoroc...

  1. Nuclear DNA content in Miscanthus sp. and the geographical variation pattern in Miscanthus lutarioriparius

    Science.gov (United States)

    Sheng, Jiajing; Hu, Xiaohu; Zeng, Xiaofei; Li, Ye; Zhou, Fasong; Hu, Zhongli; Jin, Surong; Diao, Ying

    2016-10-01

    The genome sizes of five Miscanthus species, including 79 accessions of M. lutarioriparius, 8 of M. floridulus, 6 of M. sacchariflorus, 7 of M. sinensis, and 4 of M. × giganteus were examined using flow cytometry. The overall average nuclear DNA content were 4.256 ± 0.6 pg/2C in M. lutarioriparius, 5.175 ± 0.3 pg/2C in M. floridulus, 3.956 ± 0.2 pg/2C in M. sacchariflorus, 5.272 ± 0.2 pg/2C in M. sinensis, and 6.932 ± 0.1 pg/2C in M. × giganteus. Interspecific variation was found at the diploid level, suggesting that DNA content might be a parameter that can be used to differentiate the species. Tetraploid populations were found in M. lutarioriparius, M. sacchariflorus, and M. sinensis, and their DNA content were 8.34 ± 1.2, 8.52, and 8.355 pg, respectively. The association between the DNA content of M. lutarioriparius, collected from representative ranges across the Yangtze River, and its geographic distribution was statistically analyzed. A consistent pattern of DNA content variation in 79 M. lutarioriparius accessions across its entire geographic range was found in this study. Along the Yangtze River, the DNA content of M. lutarioriparius tended to increase from the upstream to the downstream areas, and almost all tetraploids gathered in the upstream area extended to coastal regions.

  2. Relationship between histologic grade and cytofluorometric cellular DNA and RNA content in primary bone tumors.

    Science.gov (United States)

    Takeshita, H; Kusuzaki, K; Kuzuhara, A; Tsuji, Y; Ashihara, T; Gebhardt, M C; Mankin, H J; Springfield, D S; Hirasawa, Y

    2001-01-01

    The diagnosis and grading of bone tumors remains a challenging problem. We studied the relationship between histologic grade and cytofluorometric cellular DNA and RNA content in 108 primary bone tumors. The data included DNA ploidy, mean DNA content (MDC), S-phase fraction (SPF), mean RNA content (MRC) and RNA/DNA ratio (RDR; MRC/MDC) which represents the RNA content normalized for the DNA content. Benign tumors had a diploid stem line with low MDC (mean; 1.04), low SPF (0.9), high MRC (2.41) and high RDR (2.31). Giant cell tumors of bone, which are locally aggressive benign tumors, showed diploidy with relatively higher MDC (1.07, p osteosarcomas revealed aneuploidy with remarkably higher MDC (1.70 in osteosarcomas, p < 0.01) and SPF (6.5, p < 0.01), but lower RDR (1.70, p < 0.01). In contrast, small cell sarcomas, such as Ewing's sarcomas, showed diploidy with low MDC (1.11 in Ewing's sarcomas, N.S.) and SPF (2.5, p < 0.01) and extremely low RDR (1.34, p < 0.01). The RDR value was higher in well-differentiated tumors than in primitive tumors, rendering it useful in grading bone tumors with a diploid stem line. By combining the RDR value with the MDC value, 96% of diploid sarcomas could be distinguished from benign tumors. These results indicate that cellular DNA and RNA content analysis may be of value in assessing the malignant potential of diploid as well as aneuploid bone sarcomas.

  3. Content Based Image Retrieval through Clustering

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    Sandhya

    2012-06-01

    Full Text Available Content-based image retrieval (CBIR is a technique usedfor extracting similar images from an image database.CBIR system is required to access images effectively andefficiently using information contained in image databases.Here, K-Means is to be used for Image retrieval. The Kmeansmethod can be applied only in those cases when themean of a cluster is defined. The K-means method is notsuitable for discovering clusters with non-convex shapes orclusters of very different size. In this paper, CBIR,clustering and K-Means are defined. With the help of these,the data consisting images can be grouped and retrieved.

  4. Client Device Based Content Adaptation Using Rule Base

    Directory of Open Access Journals (Sweden)

    Velammal

    2011-01-01

    Full Text Available Problem statement: Content adaptation have been playing an important role in mobile devices, wherein the content display differs from desktop computers in many aspects, such as display screens, processing power, network connection bandwidth. In order to display web contents appropriately on mobile devices and on other types of devices such as hand computers, PDAs, Smart phones, it is important to adapt or transcode them to fit the characteristics of these devices. Approach: Existing content adaptation systems deploy various techniques which have been developed for specific purposes and goals. By exploiting various possible combinations of available resources, appropriate adaptation process can be carried over on the actual data, so that the information can be assimilated in a different end system other than the intended system. In this study, we present a content adaptation system based on rules created for mobile devices. Rules are invoked based on the individual client device information. Results: The adaptation has been performed according to the delivery device which was formalized through the profiler system. A profile holds information about the hardware and software specifications of the device thereby enabling the adaption of web content based on their characteristics which enables the user to access the web easily on various devices. Conclusion/Recommendation: This study enhances the viability of the information being presented to user, which will be independent of the end system being used for accessing the information. With the help of configurable rules, effective content adaptation can be achieved to provide optimal result.

  5. Removing external DNA contamination from arthropod predators destined for molecular gut-content analysis.

    Science.gov (United States)

    Greenstone, Matthew H; Weber, Donald C; Coudron, Thomas A; Payton, Mark E; Hu, Jing S

    2012-05-01

    Ecological research requires large samples for statistical validity, typically hundreds or thousands of individuals, which are most efficiently gathered by mass-collecting techniques. For the study of interspecific interactions, molecular gut-content analysis enables detection of arthropod predation with minimal disruption of community interactions. Field experiments have demonstrated that standard mass-collection methods, such as sweep netting, vacuum sampling and foliage beating, sometimes lead to contamination of predators with nontarget DNA, thereby compromising resultant gut-content data. We deliberately contaminated immature Coleomegilla maculata and Podisus maculiventris that had been fed larvae of Leptinotarsa decemlineata by topically applying homogenate of the alternate prey Leptinotarsa juncta. We then attempted to remove contaminating DNA by washing in ethanol or bleach. A 40-min wash with end-over-end rotation in 80% EtOH did not reliably reduce external DNA contamination. Identical treatment with 2.5% commercial bleach removed most externally contaminating DNA without affecting the detectability of the target prey DNA in the gut. Use of this bleaching protocol, perhaps with minor modifications tailored to different predator-prey systems, should reliably eliminate external DNA contamination, thereby alleviating concerns about this possible source of cross-contamination for mass-collected arthropod predators destined for molecular gut-content analysis. Published 2012. This article is a US Government work and is in the public domain in the USA.

  6. Detecting DNA regulatory motifs by incorporating positional trendsin information content

    Energy Technology Data Exchange (ETDEWEB)

    Kechris, Katherina J.; van Zwet, Erik; Bickel, Peter J.; Eisen,Michael B.

    2004-05-04

    On the basis of the observation that conserved positions in transcription factor binding sites are often clustered together, we propose a simple extension to the model-based motif discovery methods. We assign position-specific prior distributions to the frequency parameters of the model, penalizing deviations from a specified conservation profile. Examples with both simulated and real data show that this extension helps discover motifs as the data become noisier or when there is a competing false motif.

  7. 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.

  8. Content-Based Image Retrial Based on Hadoop

    Directory of Open Access Journals (Sweden)

    DongSheng Yin

    2013-01-01

    Full Text Available Generally, time complexity of algorithms for content-based image retrial is extremely high. In order to retrieve images on large-scale databases efficiently, a new way for retrieving based on Hadoop distributed framework is proposed. Firstly, a database of images features is built by using Speeded Up Robust Features algorithm and Locality-Sensitive Hashing and then perform the search on Hadoop platform in a parallel way specially designed. Considerable experimental results show that it is able to retrieve images based on content on large-scale cluster and image sets effectively.

  9. 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.

  10. Significance of somatic mutations and content alteration of mitochondrial DNA in esophageal cancer

    Directory of Open Access Journals (Sweden)

    Wang Yu-Fen

    2006-04-01

    Full Text Available Abstract Background The roles of mitochondria in energy metabolism, the generation of ROS, aging, and the initiation of apoptosis have implicated their importance in tumorigenesis. In this study we aim to establish the mutation spectrum and to understand the role of somatic mtDNA mutations in esophageal cancer. Methods The entire mitochondrial genome was screened for somatic mutations in 20 pairs (18 esophageal squamous cell carcinomas, one adenosquamous carcinoma and one adenocarcinoma of tumor/surrounding normal tissue of esophageal cancers, using temporal temperature gradient gel electrophoresis (TTGE, followed by direct DNA sequencing to identify the mutations. Results Fourteen somatic mtDNA mutations were identified in 55% (11/20 of tumors analyzed, including 2 novel missense mutations and a frameshift mutation in ND4L, ATP6 subunit, and ND4 genes respectively. Nine mutations (64% were in the D-loop region. Numerous germline variations were found, at least 10 of them were novel and five were missense mutations, some of them occurred in evolutionarily conserved domains. Using real-time quantitative PCR analysis, the mtDNA content was found to increase in some tumors and decrease in others. Analysis of molecular and other clinicopathological findings does not reveal significant correlation between somatic mtDNA mutations and mtDNA content, or between mtDNA content and metastatic status. Conclusion Our results demonstrate that somatic mtDNA mutations in esophageal cancers are frequent. Some missense and frameshift mutations may play an important role in the tumorigenesis of esophageal carcinoma. More extensive biochemical and molecular studies will be necessary to determine the pathological significance of these somatic mutations.

  11. 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.

  12. Accurate measurement of circulating mitochondrial DNA content from human blood samples using real-time quantitative PCR.

    Science.gov (United States)

    Ajaz, Saima; Czajka, Anna; Malik, Afshan

    2015-01-01

    We describe a protocol to accurately measure the amount of human mitochondrial DNA (MtDNA) in peripheral blood samples which can be modified to quantify MtDNA from other body fluids, human cells, and tissues. This protocol is based on the use of real-time quantitative PCR (qPCR) to quantify the amount of MtDNA relative to nuclear DNA (designated the Mt/N ratio). In the last decade, there have been increasing numbers of studies describing altered MtDNA or Mt/N in circulation in common nongenetic diseases where mitochondrial dysfunction may play a role (for review see Malik and Czajka, Mitochondrion 13:481-492, 2013). These studies are distinct from those looking at genetic mitochondrial disease and are attempting to identify acquired changes in circulating MtDNA content as an indicator of mitochondrial function. However, the methodology being used is not always specific and reproducible. As more than 95 % of the human mitochondrial genome is duplicated in the human nuclear genome, it is important to avoid co-amplification of nuclear pseudogenes. Furthermore, template preparation protocols can also affect the results because of the size and structural differences between the mitochondrial and nuclear genomes. Here we describe how to (1) prepare DNA from blood samples; (2) pretreat the DNA to prevent dilution bias; (3) prepare dilution standards for absolute quantification using the unique primers human mitochondrial genome forward primer (hMitoF3) and human mitochondrial genome reverse primer(hMitoR3) for the mitochondrial genome, and human nuclear genome forward primer (hB2MF1) and human nuclear genome reverse primer (hB2MR1) primers for the human nuclear genome; (4) carry out qPCR for either relative or absolute quantification from test samples; (5) analyze qPCR data; and (6) calculate the sample size to adequately power studies. The protocol presented here is suitable for high-throughput use.

  13. 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.

  14. DNA content and methylation of p16, DAPK and RASSF1A gene in tumour and distant, normal mucosal tissue of head and neck squamous cell carcinoma patients.

    Science.gov (United States)

    Laytragoon-Lewin, Nongnit; Chen, Fu; Castro, Juan; Elmberger, Göran; Rutqvist, Lars Erik; Lewin, Freddi; Turesson, Ingela; Lundgren, Jan

    2010-11-01

    Long-term survival of head and neck squamous cell carcinoma (HNSCC) patients has not improved significantly during the last 20 years and recurrent disease is frequently observed. In this study, the potential presence of pre-malignant cells or rare malignant cells at the time of diagnosis in HNSCC was investigated. Fifty-nine biopsies obtained from 41 HNSCC patients were analysed. Eighteen of these biopsies were normal mucosal tissue, located at least 5 cm from the tumour margin. DNA content and DNA methylation of p16, DAPK and RASSF1A was examined. Thirty-nine out of 41 (95%) tumour biopsies showed p16 methylation and 21 (51%) of them displayed aneuploidy. Of 18 distant normal mucosal biopsies, 6 (33%) of these showed evidence of aneuploidy and 15(83%) of them showed methylated p16 genes. Among paired samples, the highest frequencies of DNA methylation were found in tumours with aneuploidy. Regardless of DNA content, methylation at DAPK, RASSF1A or p16 were found in the corresponding distant mucosal biopsies. The cells with abnormal DNA content or DNA methylation in mucosal tissue were not detected clinically or by pathological macroscopic and microscopic examination. Thus, distant mucosal tissue DNA content and DNA methylation analyses in combination with histopathology will provide a better prognostic base for the evaluation and treatment of HNSCC patients.

  15. Cytometric analysis of mammalian sperm for induced morphologic and DNA content errors

    Energy Technology Data Exchange (ETDEWEB)

    Pinkel, D.

    1983-06-27

    Some flow-cytometric and image analysis procedures under development for quantitative analysis of sperm morphology are reviewed. The results of flow-cytometric DNA-content measurements on sperm from radiation exposed mice are also summarized, the results related to the available cytological information, and their potential dosimetric sensitivity discussed. (ACR)

  16. CONTENT-BASED AUTOFOCUSING IN AUTOMATED MICROSCOPY

    Directory of Open Access Journals (Sweden)

    Peter Hamm

    2010-11-01

    Full Text Available Autofocusing is the fundamental step when it comes to image acquisition and analysis with automated microscopy devices. Despite all efforts that have been put into developing a reliable autofocus system, recent methods still lack robustness towards different microscope modes and distracting artefacts. This paper presents a novel automated focusing approach that is generally applicable to different microscope modes (bright-field, phase contrast, Differential Interference Contrast (DIC and fluorescence microscopy. The main innovation consists in a Content-based focus search that makes use of a priori knowledge about the observed objects by employing local object features and Boosted Learning. Hence, this method turns away from common autofocus approaches that apply solely whole image frequency measurements to obtain the focus plane. Thus, it is possible to exclude artefacts from being brought into focus calculation as well as locating the in-focus layer of specific microscopic objects.

  17. Changes in DNA, dry mass and protein content of leaf epidermis nuclei during aging of perennial monocotyledonous plants

    Directory of Open Access Journals (Sweden)

    Hanna Kuran

    2014-01-01

    Full Text Available DNA, NYS and DNFB protein contents were measured cytophotometrically using the Feulgen method in the nuclei of the epidermis from. the basal zone of young leaves and from the basal and apical zones of old leaves in two perennial monocotyledonous species, Clivia miniata and Rhoeo discolor. Dry mass was determined interferometrically. It was shown that nuclei with a 2C DNA content dominated in both zones of old leaves, and that a significant percentage of cells with a DNA content below 2C were present. The ratio between euchromatin DNA and heterochromatin DNA indicates a greater decrease in euchromatin during aging. Changes in DNA due to real DNA loss are accompanied by decreases in NYS and DNFB stained proteins and a decrease in dry mass content correlated mainly with the decrease in the amount of NYS proteins.

  18. DAPI-fluorescent fading: a problem in microscopy or a way to measure nuclear DNA content?

    Science.gov (United States)

    Gallardo-Escárate, Cristian; Álvarez-Borrego, Josué; Kober, V.; del Río-Portilla, Miguel Á.

    2006-01-01

    In observation by confocal or conventional fluorescence microscopy, the retardation of the lost in fluorescence, from highest signal of fluorescence to lowest intensity are important factors in order to obtain accurate images. This problem is very common in fluorochromes for nuclear DNA and especially for DAPI stain. The fluorescence of DAPI is rapidly lost when it is exposure to excitation by ultra violet (UV) light, and especially under optimal condition of observation. Although the fading process could be retardate by using of mounting medium with antifading solutions, the photochemical process underlying the fluorescence decay has not yet been fully explained. In addiction, neither relationship has been tested between the fluorescence fading and nuclear DNA content. However, the capacity of the DNA to absorb UV light is knows. In order to test this relationship we measured by means of image analysis the fluorescence intensity in several nuclei types during a fading period. The analysis was performed by an algorithm specifically built in MATLAB software. The relationship between nuclear DNA content and DAPI-fluorescence fading was found equal to 99%. This study demonstrates the feasibility for estimates genome size by quantification of fluorescence fading. In this context, the present method allows to measure nuclear DNA content in several medical applications (cancer, HIV, organ transplants, etc). Nowadays, for measuring DNA content, flow cytometry is widely used; however, with the flow cytometry method it is not possible to select a specific group of cells, such as from a specific region of a tumor. Moreover, the using of image analysis allows automatizing diagnostics procedures.

  19. 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.

  20. Content Based Image Retrieval Based on Color: A Survey

    Directory of Open Access Journals (Sweden)

    Mussarat Yasmin

    2015-11-01

    Full Text Available Information sharing, interpretation and meaningful expression have used digital images in the past couple of decades very usefully and extensively. This extensive use not only evolved the digital communication world with ease and usability but also produced unwanted difficulties around the use of digital images. Because of their extensive usage it sometimes becomes harder to filter images based on their visual contents. To overcome these problems, Content Based Image Retrieval (CBIR was introduced as one of the recent ways to find specific images in massive databases of digital images for efficiency or in other words for continuing the use of digital images in information sharing. In the past years, many systems of CBIR have been anticipated, developed and brought into usage as an outcome of huge research done in CBIR domain. Based on the contents of images, different approaches of CBIR have different implementations for searching images resulting in different measures of performance and accuracy. Some of them are in fact very effective approaches for fast and efficient content based image retrieval. This research highlights the hard work done by researchers to develop the image retrieval techniques based on the color of images. These techniques along with their pros and cons as well as their application in relevant fields are discussed in the survey paper. Moreover, the techniques are also categorized on the basis of common approach used.

  1. Effects of reduced mitochondrial DNA content on secondary mitochondrial toxicant exposure in Caenorhabditis elegans.

    Science.gov (United States)

    Luz, Anthony L; Meyer, Joel N

    2016-09-01

    The mitochondrial genome (mtDNA) is intimately linked to cellular and organismal health, as demonstrated by the fact that mutations in and depletion of mtDNA result in severe mitochondrial disease in humans. However, cells contain hundreds to thousands of copies of mtDNA, which provides genetic redundancy, and creates a threshold effect in which a large percentage of mtDNA must be lost prior to clinical pathogenesis. As certain pharmaceuticals and genetic mutations can result in depletion of mtDNA, and as many environmental toxicants target mitochondria, it is important to understand whether reduced mtDNA will sensitize an individual to toxicant exposure. Here, using ethidium bromide (EtBr), which preferentially inhibits mtDNA replication, we reduced mtDNA 35-55% in the in vivo model organism Caenorhabditis elegans. Chronic, lifelong, low-dose EtBr exposure did not disrupt nematode development or lifespan, and induced only mild alterations in mitochondrial respiration, while having no effect on steady-state ATP levels. Next, we exposed nematodes with reduced mtDNA to the known and suspected mitochondrial toxicants aflatoxin B1, arsenite, paraquat, rotenone or ultraviolet C radiation (UVC). EtBr pre-exposure resulted in mild sensitization of nematodes to UVC and arsenite, had no effect on AfB1 and paraquat, and provided some protection from rotenone toxicity. These mixed results provide a first line of evidence suggesting that reduced mtDNA content may sensitize an individual to certain environmental exposures.

  2. rDNA mapping, heterochromatin characterization and AT/GC content of Agapanthus africanus (L. Hoffmanns (Agapanthaceae

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    ARYANE C. REIS

    2016-01-01

    Full Text Available ABSTRACT Agapanthus (Agapanthaceae has 10 species described. However, most taxonomists differ respect to this number because the great phenotypic plasticity of the species. The cytogenetic has been an important tool to aid the plant taxon identification, and to date, all taxa of Agapanthus L'Héritier studied cytologically, presented 2n = 30. Although the species possess large chromosomes, the group is karyologically little explored. This work aimed to increase the cytogenetic knowledge of Agapanthus africanus (L. Hoffmanns by utilization of chromosome banding techniques with DAPI / CMA3 and Fluorescent in situ Hybridization (FISH. In addition, flow cytometry was used for determination of DNA content and the percentage of AT / GC nitrogenous bases. Plants studied showed 2n = 30 chromosomes, ranging from 4.34 - 8.55 µm, with the karyotype formulae (KF = 10m + 5sm. Through FISH, one 45S rDNA signal was observed proximally to centromere of the chromosome 7, while for 5S rDNA sites we observed one signal proximally to centromere of chromosome 9. The 2C DNA content estimated for the species was 2C = 24.4 with 59% of AT and 41% of GC. Our data allowed important upgrade for biology and cytotaxonomy of Agapanthus africanus (L. Hoffmanns.

  3. Analysis of Nuclear DNA Content in Capsicum (Solanaceae) by Flow Cytometry and Feulgen Densitometry

    OpenAIRE

    MOSCONE, EDUARDO A.; BARANYI, MONIKA; EBERT, IRMA; Greilhuber, Johann; Ehrendorfer, Friedrich; Hunziker, Armando T.

    2003-01-01

    Flow cytometric measurements of nuclear DNA content were performed using ethidium bromide as the DNA stain (internal standard, Hordeum vulgare ‘Ditta’, 1C = 5·063 pg) in 25 samples belonging to nine diploid species and four varieties of Capsicum: C. chacoense, C. parvifolium, C. frutescens, C. chinense, C. annuum var. annuum, C. baccatum var. baccatum, C. baccatum var. pendulum, C. baccatum var. umbilicatum, C. eximium and C. pubescens, all with 2n = 24, and C. campylopodium with 2n = 26. In ...

  4. Myonuclear transcription is responsive to mechanical load and DNA content but uncoupled from cell size during hypertrophy.

    Science.gov (United States)

    Kirby, Tyler J; Patel, Rooshil M; McClintock, Timothy S; Dupont-Versteegden, Esther E; Peterson, Charlotte A; McCarthy, John J

    2016-03-01

    Myofibers increase size and DNA content in response to a hypertrophic stimulus, thus providing a physiological model with which to study how these factors affect global transcription. Using 5-ethynyl uridine (EU) to metabolically label nascent RNA, we measured a sevenfold increase in myofiber transcription during early hypertrophy before a change in cell size and DNA content. The typical increase in myofiber DNA content observed at the later stage of hypertrophy was associated with a significant decrease in the percentage of EU-positive myonuclei; however, when DNA content was held constant by preventing myonuclear accretion via satellite cell depletion, both the number of transcriptionally active myonuclei and the amount of RNA generated by each myonucleus increased. During late hypertrophy, transcription did not scale with cell size, as smaller myofibers (hypertrophy and that myofiber transcription is responsive to DNA content but uncoupled from cell size during hypertrophy.

  5. Genetic stock assessment of spawning arctic cisco (Coregonus autumnalis) populations by flow cytometric determination of DNA content.

    Science.gov (United States)

    Lockwood, S F; Bickham, J W

    1991-01-01

    Intraspecific variation in cellular DNA content was measured in five Coregonus autumnalis spawning populations from the Mackenzie River drainage, Canada, using flow cytometry. The rivers assayed were the Peel, Arctic Red, Mountain, Carcajou, and Liard rivers. DNA content was determined from whole blood preparations of fish from all rivers except the Carcajou, for which kidney tissue was used. DNA content measurements of kidney and blood preparations of the same fish from the Mountain River revealed statistically indistinguishable results. Mosaicism was found in blood preparations from the Peel, Arctic Red, Mountain, and Liard rivers, but was not observed in kidney tissue preparations from the Mountain or Carcajou rivers. The Liard River sample had significantly elevated mean DNA content relative to the other four samples; all other samples were statistically indistinguishable. Significant differences in mean DNA content among spawning stocks of a single species reinforces the need for adequate sample sizes of both individuals and populations when reporting "C" values for a particular species.

  6. 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

  7. Metadata and API Based Environment Aware Content Delivery Architecture

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    One of the limitations of current content delivery networks is lack of support for environment aware content delivery. This paper first discusses the requirements of such support, and proposes a new metadata gateway based environment aware content delivery architecture. The paper discusses in some details key functions and technologies of environment aware content delivery architecture, including its APIs and control policies. Finally the paper presents an application to illustrate advantages of environment aware content delivery architecture in the context of next generation network.

  8. Construction and validation of two metagenomic DNA libraries from Cerrado soil with high clay content.

    Science.gov (United States)

    de Castro, Alinne Pereira; Quirino, Betania Ferraz; Allen, Heather; Williamson, Lynn L; Handelsman, Jo; Krüger, Ricardo Henrique

    2011-11-01

    A challenge of metagenomic studies is in the extraction and purification of DNA from environmental samples. The soils of the Cerrado region of Brazil present several technical difficulties to DNA extraction: high clay content (>55% w/w), low pH (4.7) and high iron levels (146 ppm). Here we describe for the first time the efficient recovery and purification of microbial DNA associated with these unusual soil characteristics and the construction and validation of two metagenomic libraries: a 150,000 clones library with insert size of approximately 8 kb and a 65,000 clones library with insert size of approximately 35 kb. The construction of these metagenomic libraries will allow the biotechnological exploitation of the microbial community present in the soil from this endangered biome.

  9. Prognostic Value of Telomere DNA Content in Ductal Carcinoma in Situ

    Science.gov (United States)

    2006-06-01

    associated with reduced survival in breast and prostate cancers. We hypothesized that TC could be a unique prognostic marker in DCIS. The goals of this...that reduced telomere DNA content (TC) was associated with decreased survival in prostate (6) and breast cancers (7). Remarkably, reduced TC was...were stained with H&E and used as a reference for microdissection. Serial sections were used for microdissesction or IHC for Cox2 protein as

  10. Barcoding, types and the Hirudo files: using information content to critically evaluate the identity of DNA barcodes.

    Science.gov (United States)

    Kvist, Sebastian; Oceguera-Figueroa, Alejandro; Siddall, Mark E; Erséus, Christer

    2010-12-01

    Species identifications based on DNA barcoding rely on the correct identity of previously barcoded specimens, but little attention has been given to whether deposited barcodes include correspondence to the species' name-bearing type. The information content associated with COX1 sequences in the two most commonly used repositories of barcodes, GenBank and the Barcode of Life Data System (BOLD), is often insufficient for subsequent evaluation of the robustness of the identification procedure. We argue that DNA barcoding and taxonomy alike will benefit from more information content in the annotations of barcoded specimens as this will allow for validation and re-evaluation of the initial specimen identification. The aim should be to closely connect specimens from which reference barcodes are generated with the holotype through straight-forward taxonomy, and geographical and genetic correlations. Annotated information should also include voucher specimens and collector/identifier information. We examine two case studies based on empirical data, in which barcoding and taxonomy benefit from increased information content. On the basis of data from the first case study, we designate a barcoded neotype of the European medicinal leech, Hirudo medicinalis, on morphological and geographical grounds.

  11. Dynamic Measurements of the Position, Orientation, and DNA Content of Individual Unlabeled Bacteriophages.

    Science.gov (United States)

    Goldfain, Aaron M; Garmann, Rees F; Jin, Yan; Lahini, Yoav; Manoharan, Vinothan N

    2016-07-01

    A complete understanding of the cellular pathways involved in viral infections will ultimately require a diverse arsenal of experimental techniques, including methods for tracking individual viruses and their interactions with the host. Here we demonstrate the use of holographic microscopy to track the position, orientation, and DNA content of unlabeled bacteriophages (phages) in solution near a planar, functionalized glass surface. We simultaneously track over 100 individual λ phages at a rate of 100 Hz across a 33 μm × 33 μm portion of the surface. The technique determines the in-plane motion of the phage to nanometer precision, and the height of the phage above the surface to 100 nm precision. Additionally, we track the DNA content of individual phages as they eject their genome following the addition of detergent-solubilized LamB receptor. The technique determines the fraction of DNA remaining in the phage to within 10% of the total 48.5 kilobase pairs. Analysis of the data reveals that under certain conditions, λ phages move along the surface with their heads down and intermittently stick to the surface by their tails, causing them to stand up. Furthermore, we find that in buffer containing high concentrations of both monovalent and divalent salts, λ phages eject their entire DNA in about 7 s. Taken together, these measurements highlight the potential of holographic microscopy to resolve the fast kinetics of the early stages of phage infection.

  12. Karyotype and nuclear DNA content of hexa-, octo-, and duodecaploid lines of Bromus subgen. Ceratochloa

    Directory of Open Access Journals (Sweden)

    Joanna Klos

    2009-01-01

    Full Text Available The subgenus Ceratochloa of the genus Bromus includes a number of closely related allopolyploid forms or species that present a difficult taxonomic problem. The present work combines data concerning chromosome length, heterochromatin distribution and nuclear genome size of different 6x, 8x and 12x accessions in this subgenus. Special attention is paid to the karyotype structure and genomic constitution of duodecaploid plants recently found in South America. Hexaploid lineages possess six almost indistinguishable genomes and a nuclear DNA content between 12.72 pg and 15.10 pg (mean 1Cx value = 2.32 pg, whereas octoploid lineages contain the same six genomes (AABBCC plus two that are characterized by longer chromosomes and a greater DNA content (1Cx = 4.47 pg. Two duodecaploid accessions found in South America resemble each other and apparently differ from the North American duodecaploid B. arizonicus as regards chromosome size and nuclear DNA content (40.00 and 40.50 pg vs. 27.59 pg. These observations suggest that the South American duodecaploids represent a separate evolutionary lineage of the B. subgenus Ceratochloa, unrecognized heretofore.

  13. 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.

  14. Graph Based Segmentation in Content Based Image Retrieval

    Directory of Open Access Journals (Sweden)

    P. S. Suhasini

    2008-01-01

    Full Text Available Problem statement: Traditional image retrieval systems are content based image retrieval systems which rely on low-level features for indexing and retrieval of images. CBIR systems fail to meet user expectations because of the gap between the low level features used by such systems and the high level perception of images by humans. To meet the requirement as a preprocessing step Graph based segmentation is used in Content Based Image Retrieval (CBIR. Approach: Graph based segmentation is has the ability to preserve detail in low-variability image regions while ignoring detail in high-variability regions. After segmentation the features are extracted for the segmented images, texture features using wavelet transform and color features using histogram model and the segmented query image features are compared with the features of segmented data base images. The similarity measure used for texture features is Euclidean distance measure and for color features Quadratic distance approach. Results: The experimental results demonstrate about 12% improvement in the performance for color feature with segmentation. Conclusions/Recommendations: Along with this improvement Neural network learning can be embedded in this system to reduce the semantic gap.

  15. Speech Transduction Based on Linguistic Content

    DEFF Research Database (Denmark)

    Juel Henrichsen, Peter; Christiansen, Thomas Ulrich

    material six times the duration of previous investigations. Our results show that the correlation of spectral tilt with information content is relatively constant across time, even if averaged across talkers. This indicates that it is possible to devise a robust method for estimating information density...

  16. COMPENSATORY LUNG GROWTH: LUNG PROTEIN,DNA AND RNA CONTENTS IN TRILOBECTOMIZED RATS

    Directory of Open Access Journals (Sweden)

    Raul Lopes Ruiz Junior

    1998-01-01

    Full Text Available Aiming at assessing compensatory lung growth after trilobectomy in rats, 3 groups of animals (control, thoracotomy and trilobectomy were studied over 3 time intervals (7, 30 and 180 days post-operation. Protein, DNA and RNA contents in each lung were evaluated. The study of the left lung protein content reveals that compensatory growth ceased by day 30, whereas it continued to occur in the cranial lobe as long as 180 days post-operation. The lung DNA content in trilobectomized animals remained smaller than in the animals of the other groups demonstrating that compensatory growth was not brought about by hyperplasia. The lung RNA content in trilobectomized animals increased similarly to the lung protein content, demonstrating that the cells of the lung tissue must have had an increase in volume as no significant increase in their number occurred, as shown by the analysis of the lung DNA content. Therefore, it may be concluded that, in our experiment with adult animals, compensatory lung growth after trilobectomy in rats occurred due to an increase in the lung protein content and RNA content, suggesting a cellular volume increase (hypertrophy and a probable increase in the intralveolar septs rather than an important cell multiplicationObjetivando analisar o tipo de crescimento compensatório dos pulmões após trilobectomia no rato, foram analisados três momentos ( sete, trinta e cento e oitenta dias após o tratamento em três grupos de animais (controle, toracotomia e trilobectomia. Foram estudados os seguintes atributos: conteúdo protéico, conteúdo de DNA e conteúdo de RNA em cada um dos pulmões. O crescimento compensatório no pulmão esquerdo, quando analisamos o seu conteúdo protéico, cessou aos trinta dias, enquanto que, no lobo cranial, continuou ocorrendo até os cento e oitenta dias. O conteúdo pulmonar de DNA nos animais trilobectomizados manteve-se sempre abaixo dos outros grupos estudados, mostrando que o crescimento

  17. 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.

  18. 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.

  19. Changes in DNA, dry mass and protein content of leaf epidermis nuclei during aging of perennial monocotyledonous plants

    OpenAIRE

    Hanna Kuran

    2014-01-01

    DNA, NYS and DNFB protein contents were measured cytophotometrically using the Feulgen method in the nuclei of the epidermis from. the basal zone of young leaves and from the basal and apical zones of old leaves in two perennial monocotyledonous species, Clivia miniata and Rhoeo discolor. Dry mass was determined interferometrically. It was shown that nuclei with a 2C DNA content dominated in both zones of old leaves, and that a significant percentage of cells with a DNA content below 2C were ...

  20. The relationships among IGF-1, DNA content, and protein accumulation during skeletal muscle hypertrophy

    Science.gov (United States)

    Adams, G. R.; Haddad, F.

    1996-01-01

    Insulin-like growth factor-1 (IGF-1) is known to have anabolic effects on skeletal muscle cells. This study examined the time course of muscle hypertrophy and associated IGF-1 peptide and mRNA expression. Data were collected at 3, 7, 14, and 28 days after surgical removal of synergistic muscles of both normal and hypophysectomized (HX) animals. Overloading increased the plantaris (Plant) mass, myofiber size, and protein-to-body weight ratio in both groups (normal and HX; P Muscle IGF-1 peptide levels peaked at 3 (normal) and 7 (HX) days of overloading with maximum 4.1-fold (normal) and 6.2-fold (HX) increases. Increases in muscle IGF-1 preceded the hypertrophic response. Total DNA content of the overloaded Plant increased in both groups. There was a strong positive relationship between IGF-1 peptide and DNA content in the overloaded Plant from both groups. These results indicate that 1) the muscles from rats with both normal and severely depressed systemic levels of IGF-1 respond to functional overload with an increase in local IGF-1 expression and 2) this elevated IGF-1 may be contributing to the hypertrophy response, possibly via the mobilization of satellite cells to provide increases in muscle DNA.

  1. The relationships among IGF-1, DNA content, and protein accumulation during skeletal muscle hypertrophy

    Science.gov (United States)

    Adams, G. R.; Haddad, F.

    1996-01-01

    Insulin-like growth factor-1 (IGF-1) is known to have anabolic effects on skeletal muscle cells. This study examined the time course of muscle hypertrophy and associated IGF-1 peptide and mRNA expression. Data were collected at 3, 7, 14, and 28 days after surgical removal of synergistic muscles of both normal and hypophysectomized (HX) animals. Overloading increased the plantaris (Plant) mass, myofiber size, and protein-to-body weight ratio in both groups (normal and HX; P peptide levels peaked at 3 (normal) and 7 (HX) days of overloading with maximum 4.1-fold (normal) and 6.2-fold (HX) increases. Increases in muscle IGF-1 preceded the hypertrophic response. Total DNA content of the overloaded Plant increased in both groups. There was a strong positive relationship between IGF-1 peptide and DNA content in the overloaded Plant from both groups. These results indicate that 1) the muscles from rats with both normal and severely depressed systemic levels of IGF-1 respond to functional overload with an increase in local IGF-1 expression and 2) this elevated IGF-1 may be contributing to the hypertrophy response, possibly via the mobilization of satellite cells to provide increases in muscle DNA.

  2. The relationships among IGF-1, DNA content, and protein accumulation during skeletal muscle hypertrophy

    Science.gov (United States)

    Adams, G. R.; Haddad, F.

    1996-01-01

    Insulin-like growth factor-1 (IGF-1) is known to have anabolic effects on skeletal muscle cells. This study examined the time course of muscle hypertrophy and associated IGF-1 peptide and mRNA expression. Data were collected at 3, 7, 14, and 28 days after surgical removal of synergistic muscles of both normal and hypophysectomized (HX) animals. Overloading increased the plantaris (Plant) mass, myofiber size, and protein-to-body weight ratio in both groups (normal and HX; P Muscle IGF-1 peptide levels peaked at 3 (normal) and 7 (HX) days of overloading with maximum 4.1-fold (normal) and 6.2-fold (HX) increases. Increases in muscle IGF-1 preceded the hypertrophic response. Total DNA content of the overloaded Plant increased in both groups. There was a strong positive relationship between IGF-1 peptide and DNA content in the overloaded Plant from both groups. These results indicate that 1) the muscles from rats with both normal and severely depressed systemic levels of IGF-1 respond to functional overload with an increase in local IGF-1 expression and 2) this elevated IGF-1 may be contributing to the hypertrophy response, possibly via the mobilization of satellite cells to provide increases in muscle DNA.

  3. 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 ...

  4. 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 ...

  5. Content-Based Instruction and Content and Language Integrated Learning: The Same or Different?

    Science.gov (United States)

    Cenoz, Jasone

    2015-01-01

    This article looks at the characteristics of Content-Based Instruction (CBI) and Content and Language Integrated Learning (CLIL) in order to examine their similarities and differences. The analysis shows that CBI/CLIL programmes share the same essential properties and are not pedagogically different from each other. In fact, the use of an L2 as…

  6. Putrescine, DNA, RNA and protein contents in human uterine, breast and rectal cancer.

    Directory of Open Access Journals (Sweden)

    Bandopadhyay M

    2000-07-01

    Full Text Available AIMS: To find out the status of DNA, RNA and protein in human uterine, ovarian, breast and rectal carcinoma. MATERIAL AND METHODS: In this prospective study, patients of age group between late thirties and late fifties suffering from uterine, ovarian, breast and rectal cancer were taken as subjects of the present study. The total number of cases studied for each cases was ten. Pieces of human carcinomatous tissues of above mentioned cases were taken along with surrounding normal tissues. From the tissue samples, putrescine is separated by the method of Herbst et al, DNA analysed by Diphenylamine method, RNA by Orcinol method and protein by Biuret method. RESULTS: Tissue content of putrescine rises simultaneously with that of DNA, RNA and protein in carcinomatous growths as above in comparison to their respective adjacent normal tissue, the differences being statistically highly significant. CONCLUSIONS: Increase in DNA, RNA and protein concentration may be a pre-requisite for increased synthesis of putrescine in carcinomatous tissue and thereby the concentration of other di- and poly-amines.

  7. DNA G+C content of the third codon position and codon usage biases of human genes.

    Science.gov (United States)

    Sueoka, N; Kawanishi, Y

    2000-12-30

    The human genome, as in other eukaryotes, has a wide heterogeneity in the DNA base composition. The evolutionary basis for this heterogeneity has been unknown. A previous study of the human genome (846 genes analyzed) has shown that, in the major range of the G+C content in the third codon position (0.25-0.75), biases from the Parity Rule 2 (PR2) among the synonymous codons of the four-codon amino acids are similar except in the highest G+C range (Sueoka, N., 1999. Translation-coupled violation of Parity Rule 2 in human genes is not the cause of heterogeneity of the DNA G+C content of third codon position. Gene 238, 53-58.). PR2 is an intra-strand rule where A=T and G=C are expected when there are no biases between the two complementary strands of DNA in mutation and selection rates (substitution rates). In this study, 14,026 human genes were analyzed. In addition, the third codon positions of two-codon amino acids were analyzed. New results show the following: (a) The G+C contents of the third codon position of human genes are scattered in the G+C range of 0.22-0.96 in the third codon position. (b) The PR2 biases are similar in the range of 0.25-0.75, whereas, in the high G+C range (0.75-0.96; 13% of the genes), the PR2-bias fingerprints are different from those of the major range. (c) Unlike the PR2 biases, the G+C contents of the third codon position for both four-codon and two-codon amino acids are all correlated almost perfectly with the G+C content of the third codon position over the total G+C ranges. These results support the notion that the directional mutation pressure, rather than the directional selection pressure, is mainly responsible for the heterogeneity of the G+C content of the third codon position.

  8. Development of a traceable molecular hygiene control method (TMHCM) for human DNA content in foods.

    Science.gov (United States)

    Şakalar, Ergün; Ergün, Şeyma Özçirak; Pala, Çiğdem; Akar, Emine; Ataşoğlu, Cengiz

    2017-06-15

    The aim of this study was to develop a molecular technique to determine the level of human originated DNA contamination in unhygienic food products. In the study, four model foods were prepared under both hygienic (H) and non-hygienic (NH) conditions and the human originated microbial loads of these products were determined. DNA was extracted from the model foods and human buccal samples by GIDAGEN Multi-fast DNA isolation kit. A primer specific region of human mitochondrial D-Loop was designed. The level of human DNA contamination in the model foods was determined by real-time PCR. The sensitivity of the technique developed here was 0.00001ng DNA/PCR. In addition, the applicability of the traceable molecular hygiene control method (TMHCM) was tested in 60 food samples from the market. The results of this study demonstrate that DNA based TMHCM can be used to predict to what extent foods meet the human oriented hygienic conditions. Copyright © 2016. Published by Elsevier Ltd.

  9. 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.

  10. Identification of resting cells by dual-parameter flow cytometry of statin expression and DNA content

    Energy Technology Data Exchange (ETDEWEB)

    Pellicciari, C.; Mangiarotti, R.; Bottone, M.G.; Danova, M. [Univ. of Pavia (Italy); Wang, E. [Jewish General Hospital, Montreal, Quebec (Canada)

    1995-12-01

    Statin, a 57-kDa nuclear protein, has been recognized as a unique marker of quiescent (G{sub 0}) cells; specific monoclonal antibodies (MoAb) against statin have been produced and used to label resting cells in tissue sections and in cultured cells. We present an improved method for the identification of G{sub 0} cells by dual-parameter flow cytometry of statin expression and DNA content. The appropriate technical conditions were set up by using resting and cycling human fibroblasts as a model cell system. Several fixatives proved to be suitable for the immunocytochemical detection of statin; among them, 70% ethanol was selected because this fixation procedure is suitable for DNA staining with intercalating dyes and is routinely used for the immunolabeling of proliferation markers (such as proliferating cell nuclear antigen [PCNA] and Ki-67) and of bromodeoxyuridine (BrdUrd) incorporation. Following cell permeabilization with detergent, exposure to the antistatin antibody (S-44), and indirect fluorescein isothiocyanate immunolabeling, cells were counterstained for DNA with propidium iodide and analyzed by dual-parameter flow cytometry. In cells from several animal sources (rat thymocytes and C6 glioma cells, mouse 3T3 cells, and human MCF-7 cells), under different experimental conditions, the expression of statin was found to correlate inversely with that of PCNA and Ki-67, and with the BrdUrd labeling index. In dual-parameter flow scattergrams, G{sub 0} (statin positive) cells can be discriminated from the potentially cycling (statin negative) G{sub 1} cells, i.e., within a cell fraction having the same DNA content. This approach can be envisaged as a powerful tool both for monitoring changes in the resting cell fraction and for investigating the process of G{sub 0}-G{sub 1} transition in unperturbed and drug-treated cell populations. 48 refs., 5 figs., 1 tab.

  11. Translation-coupled violation of Parity Rule 2 in human genes is not the cause of heterogeneity of the DNA G+C content of third codon position.

    Science.gov (United States)

    Sueoka, N

    1999-09-30

    The genome of higher eukaryotes consists of genes having a widely heterogeneous base composition at the third codon position. Ubiquitous variability of the DNA base composition has the following two aspects: intragenomic heterogeneity of the G+C content and the amino-acid-specific translation-coupled biases from the Parity Rule 2 (PR2). PR2 is an intrastrand rule where A = T and G = C are expected if there is no bias in mutation and selection between the two complementary strands of DNA. To examine whether or not the biases from PR2 are responsible for the wide heterogeneity of the DNA G+C content in human, the third codon position of 846 human genes was analyzed. Genes were separated into six groups according to their G+C content of the third codon position, and each group was examined for the translation-coupled PR2 biases in the nucleotide composition of the third codon position for two- and four-codon amino acids. The results show that genes in the different G+C content groups have similar PR2 biases, indicating that the intragenomic heterogeneity of the G+C content is not correlated with translation-coupled biases from the PR2. Therefore, the heterogeneity of the G+C content is likely to be determined by some other mechanism (e.g. locally variable directional mutation pressures) than amino-acid-specific selections for the codon preference.

  12. DNA content in reactive hyperplasia, precancerosis, and carcinomas of the oral cavity. A cytophotometric study.

    Science.gov (United States)

    Doseva, D; Christov, K; Kristeva, K

    1984-01-01

    Cytophotometry has been used to study DNA content in oral epithelial cells of Feulgen-stained specimens from a total of 43 patients: 3 with erythema exudativum multiforme (EEM), 5 with pemphigus, 3 with stomatitis aphtosa, 5 with lichen ruber planus, 8 with leukoplakia, and 19 with carcinomas. In contrast to reactive hyperplasia (EEM, pemphigus, stomatitis aphthosa) leukoplakia has histograms closest to those of carcinoma, with a high percentage of cells in the polyploid regions. This emphasizes the significance of cytophotometry for diagnosis of preneoplastic and neoplastic lesions of the oral cavity.

  13. Cobra: A Content-Based Video Retrieval System

    NARCIS (Netherlands)

    Petkovic, M.; Jonker, W.

    2002-01-01

    An increasing number of large publicly available video libraries results in a demand for techniques that can manipulate the video data based on content. In this paper, we present a content-based video retrieval system called Cobra. The system supports automatic extraction and retrieval of high-level

  14. Prenatal Care: A Content-Based ESL Curriculum.

    Science.gov (United States)

    Hassel, Elissa Anne

    A content-based curriculum in English as a Second Language (ESL) focusing on prenatal self-care is presented. The course was designed as a solution to the problem of inadequate prenatal care for limited-English-proficient Mexican immigrant women. The first three sections offer background information on and discussion of (1) content-based ESL…

  15. ADAPTIVE CONTENT BASED TEXTUAL INFORMATION SOURCE PRIORITIZATION

    Directory of Open Access Journals (Sweden)

    Nikhil Mitra

    2014-10-01

    Full Text Available The world-wide-web offers a posse of textual information sources which are ready to be utilized for several applications. In fact, given the rapidly evolving nature of online data, there is a real risk of information overload unless we continue to develop and refine techniques to meaningfully segregate these information sources. Specifically, there is a dearth of content-oriented and intelligent techniques which can learn from past search experiences and also adapt to a user’s specific requirements during her current search. In this paper, we tackle the core issue of prioritizing textual information sources on the basis of the relevance of their content to the central theme that a user is currently exploring. We propose a new Source Prioritization Algorithm that adopts an iterative learning approach to assess the proclivity of given information sources towards a set of user-defined seed words in order to prioritise them. The final priorities obtained serve as initial priorities for the next search request. This serves a dual purpose. Firstly, the system learns incrementally from several users’ cumulative search experiences and re-adjusts the source priorities to reflect the acquired knowledge. Secondly, the refreshed source priorities are utilized to direct a user’s current search towards more relevant sources while adapting also to the new set of keywords acquired from that user. Experimental results show that the proposed algorithm progressively improves the system’s ability to discern between different sources, even in the presence of several random sources. Further, it is able to scale well to identify the augmented information source when a new enriched information source is generated by clubbing existing ones.

  16. Bread Water Content Measurement Based on Hyperspectral Imaging

    DEFF Research Database (Denmark)

    Liu, Zhi; Møller, Flemming

    2011-01-01

    for bread quality based on near-infrared hyperspectral imaging against the conventional manual loss-in-weight method. For this purpose, the hyperspectral components unmixing technology is used for measuring the water content quantitatively. And the definition on bread water content index is presented......Water content is one of the most important properties of the bread for tasting assesment or store monitoring. Traditional bread water content measurement methods mostly are processed manually, which is destructive and time consuming. This paper proposes an automated water content measurement...... for this measurement. The proposed measurement scheme is relatively inexpensive to implement, easy to set up. The experimental results demonstrate the effectiveness....

  17. Mashup Based Content Search Engine for Mobile Devices

    Directory of Open Access Journals (Sweden)

    Kohei Arai

    2013-05-01

    Full Text Available Mashup based content search engine for mobile devices is proposed. Example of the proposed search engine is implemented with Yahoo!JAPAN Web SearchAPI, Yahoo!JAPAN Image searchAPI, YouTube Data API, and Amazon Product Advertising API. The retrieved results are also merged and linked each other. Therefore, the different types of contents can be referred once an e-learning content is retrieved. The implemented search engine is evaluated with 20 students. The results show usefulness and effectiveness on e-learning content searches with a variety of content types, image, document, pdf files, moving picture.

  18. 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.

  19. Quality-based content delivery over the Internet

    CERN Document Server

    Li, Xiang

    2011-01-01

    ""Quality-Based Content Delivery over the Internet"" mainly discusses the methodology of doing quality-based content delivery in an Internet environment. Because the network is becoming intelligent and active, more and more researchers are talking about achieving personalization and customization in Internet content delivery. As researchers are aware, by introducing intelligence into a web intermediary server, they can make the content delivery more efficient and of higher quality. Still, the detailed methodology of doing so is never illustrated fully. The most critical part will be the active

  20. CONTENT BASED VIDEO RETRIEVAL BASED ON HDWT AND SPARSE REPRESENTATION

    Directory of Open Access Journals (Sweden)

    Sajad Mohamadzadeh

    2016-04-01

    Full Text Available Video retrieval has recently attracted a lot of research attention due to the exponential growth of video datasets and the internet. Content based video retrieval (CBVR systems are very useful for a wide range of applications with several type of data such as visual, audio and metadata. In this paper, we are only using the visual information from the video. Shot boundary detection, key frame extraction, and video retrieval are three important parts of CBVR systems. In this paper, we have modified and proposed new methods for the three important parts of our CBVR system. Meanwhile, the local and global color, texture, and motion features of the video are extracted as features of key frames. To evaluate the applicability of the proposed technique against various methods, the P(1 metric and the CC_WEB_VIDEO dataset are used. The experimental results show that the proposed method provides better performance and less processing time compared to the other methods.

  1. Flow Cytometric Analysis of DNA Content in Parotid Tumor and Its Contiguous Acini

    Institute of Scientific and Technical Information of China (English)

    ZHU Shengrong; SHAO Lenan; CHEN Weimin; WU Huihua; WANG Xiuli; CHEN Xinming

    2000-01-01

    To investigate the relationship between proliferative capacity of salivary gland cells in contiguous acini of parotid tumors and recurrent neoplasma, DNA contents of 30 fresh specimens of parotid were studied by using cytometry in tumors, normal and shallow or deep lobe acini of the masses. The results showed that the DI was 1.369, S % 16.95, PI 26.18 in malignant tumors;DI was 1.171, S % 12.41, PI 15.54 in recurrent pleomorphic adenoma; DI was 1.141, S % 12.74, PI 13.07 in pleomorphic adenoma, DI was 0.999, S % 5.10, PI 8.00 in normal acini. Analysis of variance showed there was a significant difference (P<0.01). The average DNA contents of shallow on deep lobe of contiguous tumors was 1.08 in DI, 10. 65 in S %, 13.49 in PI in malignant tumor, 1.06 in DI, 8.96 in S % and 9.85 in PI in pleomorphic adenoma, which were all higher than in normal acini (P>0.05). It was concluded that the levels of DI and S % of parotid tumor and its contiguous acini are related to degree of malignancy or recurrent condition of the tumors, suggesting contiguous acini of parotid tumors had the strong capacity of proliferation,which might play an important role in recurrent or malignant change of the parotid tumors.

  2. Condylomata acuminata of the urinary bladder. Natural history, viral typing, and DNA content.

    Science.gov (United States)

    Del Mistro, A; Koss, L G; Braunstein, J; Bennett, B; Saccomano, G; Simons, K M

    1988-03-01

    Three patients with condylomata acuminata of the urinary bladder are reported. Two of the patients were immunosuppressed, and one had longstanding extensive condylomata acuminata of the external genitalia and adjacent areas. All lesions recurred at least once and were difficult to treat. The diagnosis was confirmed by in situ hybridization on archival material with human papillomavirus (HPV) DNA probes under stringent conditions. In two of the patients, probes for HPV types 6 and 11 were positive; HPV 11 only was identified in one patient. Probes for HPV types 16 and 18 and pBR322 vector controls were negative. In one patient with a strong hybridization signal, the lesion was also positive for common papillomavirus antigen. DNA content measured by cytophotometry of Feulgen-stained whole nuclei isolated from lesions in two patients revealed a markedly aneuploid DNA pattern. Whether this is a factor in the behavior of the lesions is not known at this time. Although rare, HPV infection of the urinary bladder may result in widespread condylomatosis and may mimic giant condylomas of Buschke-Löwenstein or even verrucous carcinomas, sometimes necessitating radical treatment. Nevertheless, until there is proof to the contrary, the lesions must be considered benign and should not be confused with squamous cancer of the bladder.

  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. Speech Transduction Based on Linguistic Content

    DEFF Research Database (Denmark)

    Juel Henrichsen, Peter; Christiansen, Thomas Ulrich

    Digital hearing aids use a variety of advanced digital signal processing methods in order to improve speech intelligibility. These methods are based on knowledge about the acoustics outside the ear as well as psychoacoustics. This paper investigates the recent observation that speech elements...

  7. AN INVESTIGATION OF TEACHERS’ PEDAGOGICAL SKILLS AND CONTENT KNOWLEDGE IN A CONTENT-BASED INSTRUCTION CONTEXT

    Directory of Open Access Journals (Sweden)

    Tengku Nor Rizan Tengku Mohamad Maasum

    2012-01-01

    Full Text Available Advocates of the content-based approach believed that a language can be learnt effectively when it is the medium of instruction rather than just a subject. Integrating English and content as part of instruction has become one of the cornerstones of second language pedagogy. Researchers claimed that there are many benefits of integrating English and content instruction. Among the benefits are the increase in students’ interest with content themes, meaningful input and understanding. In 2003, the Malaysian Ministry of Education introduced the teaching and learning of science and mathematics in English for Year One, Form One and Lower Six Form in all government public schools. This paper describes the challenges faced by teachers when they are required to teach content subjects such as science and mathematics in English. The focus of the paper is on the teachers’ pedagogical skills and content knowldge which comprises subject matter content, pedagogical approach, classroom management, use of resources, assessment, preparation of teaching materials, managing students, teachers’ compensatory communication strategies, use of first language and teachers’ perspectives of teaching content subjects in English. Data were obtained from a self-report questionnaire administered to 495 secondary school teachers in West Malaysia. Results from the study provide implications for school administrators in making decisions in assignment of capable teachers to teach the various levels of classes. Suggestions for teacher self-development and life-long learning efforts are also provided.

  8. Multi Feature Content Based Image Retrieval

    Directory of Open Access Journals (Sweden)

    Rajshree S. Dubey,

    2010-09-01

    Full Text Available There are numbers of methods prevailing for Image Mining Techniques. This Paper includes the features of four techniques I,e Color Histogram, Color moment, Texture, and Edge Histogram Descriptor. The nature of the Image is basically based on the Human Perception of the Image. The Machine interpretation of the Image is based on the Contours and surfaces of the Images. The study of the Image Mining is a very challenging task because it involves the Pattern Recognition which is a very important tool for the Machine Vision system. A combination of four feature extraction methods namely color istogram, Color Moment, texture, and Edge Histogram Descriptor. There is a provision to add new features in future for better retrievalefficiency. In this paper the combination of the four techniques are used and the Euclidian distances are calculated of the every features are added and the averages are made .The user interface is provided by the Mat lab. The image properties analyzed in this work are by using computer vision and image processing algorithms. For colorthe histogram of images are computed, for texture co occurrence matrix based entropy, energy, etc, are calculated and for edge density it is Edge Histogram Descriptor (EHD that is found. For retrieval of images, the averages of the four techniques are made and the resultant Image is retrieved.

  9. Calculation of the debris flow concentration based on clay content

    Institute of Scientific and Technical Information of China (English)

    CHEN Ningsheng; CUI Peng; LIU Zhonggang; WEI Fangqiang

    2003-01-01

    The debris flow clay content has very tremendous influence on its concentration (γC). It is reported that the concentration can be calculated by applying the relative polynomial based on the clay content. Here one polynomial model and one logarithm model to calculate the concentration based on the clay content for both the ordinary debris flow and viscous debris flow are obtained. The result derives from the statistics and analysis of the relationship between the debris flow concentrations and clay content in 45 debris flow sites located in the southwest of China. The models can be applied for the concentration calculation to those debris flows that are impossible to observe. The models are available to calculate the debris flow concentration, the principles of which are in the clay content affecting on the debris flow formation, movement and suspending particle diameter. The mechanism of the relationship of the clay content and concentration is clear and reliable. The debris flow is usually of micro-viscous when the clay content is low (<3%), by analyzing the developing tendency on the basics of the relationship between the clay content and debris flow concentration. Indeed, the less the clay content, the less the concentration for most debris flows. The debris flow tends to become the water rock flow or the hyperconcentrated flow with the clay content decrease. Through statistics it is apt to transform the soil into the viscous debris flow when the clay content of ranges is in 3%-18%. Its concentration increases with the increasing of the clay content when the clay content is between 5% and 10%. But the value decreases with the increasing of the clay content when the clay content is between 10% and 18%. It is apt to transform the soil into the mudflow, when the clay content exceeds 18%. The concentration of the mudflow usually decreases with the increase of the clay content, and this developing tendency reverses to that of the micro-viscous debris flow. There is

  10. Scientific Opinion on the substantiation of a health claim related to coffee C21, a coffee standardised by its content of caffeoylquinic acids, trigonelline and N-methylpyridinium, and reduction of DNA damage by decreasing spontaneous DNA strand breaks

    DEFF Research Database (Denmark)

    Tetens, Inge

    on the scientific substantiation of a health claim related to coffee C21 and reduction of DNA damage by decreasing spontaneous DNA strand breaks. The scope of the application was proposed to fall under a health claim based on newly developed scientific evidence. Coffee C21, a coffee standardised by its content...... intervention study showed that daily consumption of coffee C21 (750 ml/day) for four weeks decreased spontaneous DNA strand breaks in habitual coffee drinkers after coffee withdrawal over the previous four weeks, but that no other human studies in which these results have been replicated were provided......, and that no evidence was provided for a mechanism by which coffee (including coffee C21) could exert the claimed effect. The Panel concludes that a cause and effect relationship has not been established between the consumption of coffee C21, a coffee standardised by its content of caffeoylquinic acids, trigonelline...

  11. Web-Based Media Contents Editor for UCC Websites

    Science.gov (United States)

    Kim, Seoksoo

    The purpose of this research is to "design web-based media contents editor for establishing UCC(User Created Contents)-based websites." The web-based editor features user-oriented interfaces and increased convenience, significantly different from previous off-line editors. It allows users to edit media contents online and can be effectively used for online promotion activities of enterprises and organizations. In addition to development of the editor, the research aims to support the entry of enterprises and public agencies to the online market by combining the technology with various UCC items.

  12. Rotational invariant similarity measurement for content-based image indexing

    Science.gov (United States)

    Ro, Yong M.; Yoo, Kiwon

    2000-04-01

    We propose a similarity matching technique for contents based image retrieval. The proposed technique is invariant from rotated images. Since image contents for image indexing and retrieval would be arbitrarily extracted from still image or key frame of video, the rotation invariant property of feature description of image is important for general application of contents based image indexing and retrieval. In this paper, we propose a rotation invariant similarity measurement in cooperating with texture featuring base on HVS. To simplify computational complexity, we employed hierarchical similarity distance searching. To verify the method, experiments with MPEG-7 data set are performed.

  13. AN INVESTIGATION OF TEACHERS’ PEDAGOGICAL SKILLS AND CONTENT KNOWLEDGE IN A CONTENT-BASED INSTRUCTION CONTEXT

    Directory of Open Access Journals (Sweden)

    Tengku Nor Rizan Tengku Mohamad Maasum

    2012-01-01

    Full Text Available Abstract: Advocates of the content-based approach believed that a language can be learnt effectively when it is the medium of instruction rather than just a subject.  Integrating English and content as part of instruction has become one of the cornerstones of second language pedagogy. Researchers claimed that there are many benefits of integrating English and content instruction.  Among the benefits are the increase in students’ interest with content themes, meaningful input and understanding. In 2003, the Malaysian Ministry of Education introduced the teaching and learning of science and mathematics in English for Year One, Form One and Lower Six Form in all government public schools. This paper describes the challenges faced by teachers when they are required to teach content subjects such as science and mathematics in English.  The focus of the paper is on the teachers’ pedagogical skills  and content knowldge which comprises subject matter content, pedagogical approach, classroom management, use of resources, assessment, preparation of teaching materials, managing students, teachers’ compensatory communication strategies, use of first language and teachers’ perspectives of teaching content subjects in English. Data were obtained from a self-report questionnaire administered to 495 secondary school teachers in West Malaysia. Results from the study provide implications for school administrators in making decisions in assignment of  capable teachers to teach the various levels of classes. Suggestions for teacher self-development and life-long learning efforts are also provided.   Key words: Content-based instruction, ESL instruction, second language, first language and second language pedagogy

  14. Rock and Roll English Teaching: Content-Based Cultural Workshops

    Science.gov (United States)

    Robinson, Tim

    2011-01-01

    In this article, the author shares a content-based English as a Second/Foreign Language (ESL/EFL) workshop that strengthens language acquisition, increases intrinsic motivation, and bridges cultural divides. He uses a rock and roll workshop to introduce an organizational approach with a primary emphasis on cultural awareness content and a…

  15. Content-based analysis improves audiovisual archive retrieval

    NARCIS (Netherlands)

    Huurnink, B.; Snoek, C.G.M.; de Rijke, M.; Smeulders, A.W.M.

    2012-01-01

    Content-based video retrieval is maturing to the point where it can be used in real-world retrieval practices. One such practice is the audiovisual archive, whose users increasingly require fine-grained access to broadcast television content. In this paper, we take into account the information needs

  16. Privacy-preserving content-based recommender system

    NARCIS (Netherlands)

    Erkin, Z.; Beye, M.; Veugen, T.; Lagendijk, R.L.

    2012-01-01

    By offering personalized content to users, recommender systems have become a vital tool in e-commerce and online media applications. Content-based algorithms recommend items or products to users, that are most similar to those previously purchased or consumed. Unfortunately, collecting and storing r

  17. Content-based analysis improves audiovisual archive retrieval

    NARCIS (Netherlands)

    Huurnink, B.; Snoek, C.G.M.; de Rijke, M.; Smeulders, A.W.M.

    2012-01-01

    Content-based video retrieval is maturing to the point where it can be used in real-world retrieval practices. One such practice is the audiovisual archive, whose users increasingly require fine-grained access to broadcast television content. In this paper, we take into account the information needs

  18. Privacy-Preserving Content-Based Recommender System

    NARCIS (Netherlands)

    Erkin, Z.; Beye, M.; Veugen, P.J.M.; Lagendijk, R.L.

    2012-01-01

    By offering personalized content to users, recommender systems have become a vital tool in e-commerce and online media applications. Content-based algorithms recommend items or products to users, that are most similar to those previously purchased or consumed. Unfortunately, collecting and storing r

  19. Privacy-preserving content-based recommendations through homomorphic encryption

    NARCIS (Netherlands)

    Erkin, Z.; Beye, M.; Veugen, T.; Lagendijk, R.L.

    2012-01-01

    By offering personalized content to users, recommender systems have become a vital tool in ecommerce and online media applications. Content-based algorithms recommend items or products to users, that are most similar to those previously purchased or consumed. Unfortunately, collecting and storing ra

  20. Privacy-Preserving Content-Based Recommendations through Homomorphic Encryption

    NARCIS (Netherlands)

    Erkin, Z.; Beye, M.; Veugen, P.J.M.; Lagendijk, R.L.

    2012-01-01

    By offering personalized content to users, recommender systems have become a vital tool in ecommerce and online media applications. Content-based algorithms recommend items or products to users, that are most similar to those previously purchased or consumed. Unfortunately, collecting and storing ra

  1. An Efficient Content Based Image Retrieval Scheme

    Directory of Open Access Journals (Sweden)

    Zukuan WEI

    2013-11-01

    Full Text Available Due to the recent improvements in digital photography and storage capacity, storing large amounts of images has been made possible. Consequently efficient means to retrieve images matching a user’s query are needed. In this paper, we propose a framework based on a bipartite graph model (BGM for semantic image retrieval. BGM is a scalable data structure that aids semantic indexing in an efficient manner, and it can also be incrementally updated. Firstly, all the images are segmented into several regions with image segmentation algorithm, pre-trained SVMs are used to annotate each region, and final label is obtained by merging all the region labels. Then we use the set of images and the set of region labels to build a bipartite graph. When a query is given, a query node, initially containing a fixed number of labels, is created to attach to the bipartite graph. The node then distributes the labels based on the edge weight between the node and its neighbors. Image nodes receiving the most labels represent the most relevant images. Experimental results demonstrate that our proposed technique is promising.

  2. Mitochondrial DNA and STR analyses for human DNA from maggots crop contents: a forensic entomology case from central-southern China.

    Science.gov (United States)

    Li, X; Cai, J F; Guo, Y D; Xiong, F; Zhang, L; Feng, H; Meng, F M; Fu, Y; Li, J B; Chen, Y Q

    2011-08-01

    Insect larvae and adult insects found on human corpses can provide important forensic evidence however it is useful to be able to prove evidence of association. Without this, it could be claimed that the insect evidence was a contaminant or had been planted on the body. This paper describes how mitochondrial DNA (mtDNA) and STR analysis of the crop contents of larvae of the blowfly Aldrichina grahami collected from separated body parts was used to provide evidence of association.

  3. A “GC-rich” method for mammalian gene expression:A dominant role of non-coding DNA GC content in the regulation of mammalian gene expression

    Institute of Scientific and Technical Information of China (English)

    Gilbert; Rishton; Matthew; (Mizhou); HUI

    2010-01-01

    High mammalian gene expression was obtained for more than twenty different proteins in different cell types by just a few laboratory scale stable gene transfections for each protein.The stable expression vectors were constructed by inserting a naturally-occurring 1.006 kb or a synthetic 0.733 kb DNA fragment(including intron) of extremely GC-rich at the 5’ or/and 3’ flanking regions of these protein genes or their gene promoters.This experiment is the first experimental evidence showing that a non-coding extremely GC-rich DNA fragment is a super "chromatin opening element" and plays an important role in mammalian gene expression.This experiment has further indicated that chromatin-based regulation of mammalian gene expression is at least partially embedded in DNA primary structure,namely DNA GC-content.

  4. Sugar content of popular sweetened beverages based on objective laboratory analysis: focus on fructose content.

    Science.gov (United States)

    Ventura, Emily E; Davis, Jaimie N; Goran, Michael I

    2011-04-01

    The consumption of fructose, largely in the form of high fructose corn syrup (HFCS), has risen over the past several decades and is thought to contribute negatively to metabolic health. However, the fructose content of foods and beverages produced with HFCS is not disclosed and estimates of fructose content are based on the common assumption that the HFCS used contains 55% fructose. The objective of this study was to conduct an objective laboratory analysis of the sugar content and composition in popular sugar-sweetened beverages with a particular focus on fructose content. Twenty-three sugar-sweetened beverages along with four standard solutions were analyzed for sugar profiles using high-performance liquid chromatography (HPLC) in an independent, certified laboratory. Total sugar content was calculated as well as percent fructose in the beverages that use HFCS as the sole source of fructose. Results showed that the total sugar content of the beverages ranged from 85 to 128% of what was listed on the food label. The mean fructose content in the HFCS used was 59% (range 47-65%) and several major brands appear to be produced with HFCS that is 65% fructose. Finally, the sugar profile analyses detected forms of sugar that were inconsistent with what was listed on the food labels. This analysis revealed significant deviations in sugar amount and composition relative to disclosures from producers. In addition, the tendency for use of HFCS that is higher in fructose could be contributing to higher fructose consumption than would otherwise be assumed.

  5. 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.

  6. Content-based multimedia retrieval: indexing and diversification

    NARCIS (Netherlands)

    van Leuken, R.H.

    2009-01-01

    The demand for efficient systems that facilitate searching in multimedia databases and collections is vastly increasing. Application domains include criminology, musicology, trademark registration, medicine and image or video retrieval on the web. This thesis discusses content-based retrieval

  7. Providing content based billing architecture over Next Generation Network

    CERN Document Server

    Lakhtaria, Kamaljit I

    2010-01-01

    Mobile Communication marketplace has stressed that "content is king" ever since the initial footsteps for Next Generation Networks like 3G, 3GPP, IP Multimedia subsystem (IMS) services. However, many carriers and content providers have struggled to drive revenue for content services, primarily due to current limitations of certain types of desirable content offerings, simplistic billing models, and the inability to support flexible pricing, charging and settlement. Unlike wire line carriers, wireless carriers have a limit to the volume of traffic they can carry, bounded by the finite wireless spectrum. Event based services like calling, conferencing etc., only perceive charge per event, while the Content based charging system attracts Mobile Network Operators (MNOs) to maximize service delivery to customer and achieve best ARPU. With the Next Generation Networks, the number of data related services that can be offered, is increased significantly. The wireless carrier will be able to move from offering wireles...

  8. Text Content Pushing Technology Research Based on Location and Topic

    Science.gov (United States)

    Wei, Dongqi; Wei, Jianxin; Wumuti, Naheman; Jiang, Baode

    2016-11-01

    In the field, geological workers usually want to obtain related geological background information in the working area quickly and accurately. This information exists in the massive geological data, text data is described in natural language accounted for a large proportion. This paper studied location information extracting method in the mass text data; proposed a geographic location—geological content—geological content related algorithm based on Spark and Mapreduce2, finally classified content by using KNN, and built the content pushing system based on location and topic. It is running in the geological survey cloud, and we have gained a good effect in testing by using real geological data.

  9. A study of real-time content marketing : formulating real-time content marketing based on content, search and social media

    OpenAIRE

    Nguyen, Thi Kim Duyen

    2015-01-01

    The primary objective of this research is to understand profoundly the new concept of content marketing – real-time content marketing on the aspect of the digital marketing experts. Particularly, the research will focus on the real-time content marketing theories and how to build real-time content marketing strategy based on content, search and social media. It also finds out how marketers measure and keep track of conversion rates of their real-time content marketing plan. Practically, th...

  10. [Prognostic value of cell heterogeneity in cervical cancer determined by digital image analyzer of DNA content].

    Science.gov (United States)

    Pete, I; Gaudi, I; Szerdahelyi, A; Tóth, E; Pulay, T; Szentirmay, Z

    2000-10-01

    Frequency and prognostic value of cell heterogeneity in FIGO 1a-2a cervical cancer was examined, in 66 of patients underwent Wertheim type hysterectomy between 1989 and 1995 in National Institute of Cancer, Budapest, Hungary. A newly developed DNA image analyses (DNACE) was used in paraffin embedded tissues after enzymatic hydrolyses for evaluation of the DNA content in cervical cancer. In 30.3% of examined tissues (20/66) two subgroups was found. There was significant differences in the DNA indexes (DI) between the subgroups (p = 0.0001). In the remaining 69.7% of the cases only one subgroup was present. The frequency of two subgroups was higher between aneuploid (78.4%), or hyperploid (81.5%) type cervical cancer, however there was no significant difference between the two groups. On the other hand there was significant difference in the presence of two subgroups between the well and less differentiated cervical cancer. The frequency was higher between the less differentiated groups (p = 0.02). Looking at the prognostic value of subgroups, there was no significant correlation between the heterogeneity of cervical cancer and FIGO stage, or lymph node metastasis (p = 0.6855), or vascular/lymphatic space infiltration (p = 0.2558), or invasiveness of cancer (0.0823). There was neither significant value found between the outcome of disease and the number of subgroups present (p = 0.8738). It is though that the present of cellular heterogeneity in cervical cancer is connected with the differentiation of the cancer cells, and can be a good prognostic value in the anticipation of the aggressiveness of cervical cancer. Looking at the present result, there was no significant connection between the heterogeneity of cervical cancer and the outcome of the disease, so further examination should be done.

  11. Analysis of nuclear DNA content in Capsicum (Solanaceae) by flow cytometry and Feulgen densitometry.

    Science.gov (United States)

    Moscone, Eduardo A; Baranyi, Monika; Ebert, Irma; Greilhuber, Johann; Ehrendorfer, Friedrich; Hunziker, Armando T

    2003-07-01

    Flow cytometric measurements of nuclear DNA content were performed using ethidium bromide as the DNA stain (internal standard, Hordeum vulgare 'Ditta', 1C = 5.063 pg) in 25 samples belonging to nine diploid species and four varieties of Capsicum: C. chacoense, C. parvifolium, C. frutescens, C. chinense, C. annuum var. annuum, C. baccatum var. baccatum, C. baccatum var. pendulum, C. baccatum var. umbilicatum, C. eximium and C. pubescens, all with 2n = 24, and C. campylopodium with 2n = 26. In addition, one sample each of C. annuum var. annuum and C. pubescens were also analysed using Feulgen densitometry (standard, Allium cepa 'Stuttgarter Riesen', 1C = 16.75 pg). Both staining methods resulted in very similar relative values. Genome size displays significant variation between but not within species (except in C. campylopodium), and contributes to their taxonomic grouping. 1C-values range from 3.34-3.43 pg (3273-3361 Mbp) in C. chacoense and the C. annuum complex to 4.53-5.77 pg (4439-5655 Mbp) in C. campylopodium and C. parvifolium. The data obtained support conclusions on phylogenetic relationships in the genus derived from karyotype analyses using chromosome banding approaches. In Capsicum, constitutive heterochromatin amount is correlated with genome size, except in C. parvifolium, and is regarded as an additive genomic component.

  12. 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.

  13. Information Theoretic Similarity Measures for Content Based Image Retrieval.

    Science.gov (United States)

    Zachary, John; Iyengar, S. S.

    2001-01-01

    Content-based image retrieval is based on the idea of extracting visual features from images and using them to index images in a database. Proposes similarity measures and an indexing algorithm based on information theory that permits an image to be represented as a single number. When used in conjunction with vectors, this method displays…

  14. Senescence vs. changes in nuclear DNA, protein and dry mass contents in leaf mesophyll of two species differing in occurrence of endomitotic polyploidy.

    Science.gov (United States)

    Kuran, H

    1999-01-01

    DNA and Naphtol yellow S-staining (F-NYS) protein contents were measured cytophotometrically using the Feulgen method in the nuclei of the mesophyll from the basal and apical zone of young and old leaves in two perennial monocotyledonous species: Rhoeo discolor and Clivia miniata, differing in presence or absence of DNA endoreplication. Dry mass content was determined interferometrically using an uniform field with large image shearing method. It has been shown that nuclei with 2C DNA and below 2C DNA content dominate in old leaves. The decrease in dry mass content of nuclei correlated with the decrease in NYS protein content. Parallelly a significant increase in NYS protein and DNA contents observed in chromocenters Rhoeo discolor was proportional to the increase in their dry mass. The decrease in nuclear DNA content in mesophyll of old leaves in endoreplicating species was the same as in non-edoreplicating one, however the senescence was more intensive in endoreplicating species.

  15. 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....

  16. 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.

  17. Density-based similarity measures for content based search

    Energy Technology Data Exchange (ETDEWEB)

    Hush, Don R [Los Alamos National Laboratory; Porter, Reid B [Los Alamos National Laboratory; Ruggiero, Christy E [Los Alamos National Laboratory

    2009-01-01

    We consider the query by multiple example problem where the goal is to identify database samples whose content is similar to a coUection of query samples. To assess the similarity we use a relative content density which quantifies the relative concentration of the query distribution to the database distribution. If the database distribution is a mixture of the query distribution and a background distribution then it can be shown that database samples whose relative content density is greater than a particular threshold {rho} are more likely to have been generated by the query distribution than the background distribution. We describe an algorithm for predicting samples with relative content density greater than {rho} that is computationally efficient and possesses strong performance guarantees. We also show empirical results for applications in computer network monitoring and image segmentation.

  18. 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.

  19. Content Based Image Retrieval : Classification Using Neural Networks

    Directory of Open Access Journals (Sweden)

    Shereena V.B

    2014-10-01

    Full Text Available In a content-based image retrieval system (CBIR, the main issue is to extract the image features that effectively represent the image contents in a database. Such an extraction requires a detailed evaluation of retrieval performance of image features. This paper presents a review of fundamental aspects of content based image retrieval including feature extraction of color and texture features. Commonly used color features including color moments, color histogram and color correlogram and Gabor texture are compared. The paper reviews the increase in efficiency of image retrieval when the color and texture features are combined. The similarity measures based on which matches are made and images are retrieved are also discussed. For effective indexing and fast searching of images based on visual features, neural network based pattern learning can be used to achieve effective classification.

  20. Content Based Image Retrieval : Classification Using Neural Networks

    Directory of Open Access Journals (Sweden)

    Shereena V.B

    2014-11-01

    Full Text Available In a content-based image retrieval system (CBIR, the main issue is to extract the image features that effectively represent the image contents in a database. Such an extraction requires a detailed evaluation of retrieval performance of image features. This paper presents a review of fundamental aspects of content based image retrieval including feature extraction of color and texture features. Commonly used color features including color moments, color histogram and color correlogram and Gabor texture are compared. The paper reviews the increase in efficiency of image retrieval when the color and texture features are combined. The similarity measures based on which matches are made and images are retrieved are also discussed. For effective indexing and fast searching of images based on visual features, neural network based pattern learning can be used to achieve effective classification.

  1. 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.

  2. 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

  3. 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.

  4. Mashup Based Content Search Engine for Mobile Devices

    OpenAIRE

    Kohei Arai

    2013-01-01

    Mashup based content search engine for mobile devices is proposed. Example of the proposed search engine is implemented with Yahoo!JAPAN Web SearchAPI, Yahoo!JAPAN Image searchAPI, YouTube Data API, and Amazon Product Advertising API. The retrieved results are also merged and linked each other. Therefore, the different types of contents can be referred once an e-learning content is retrieved. The implemented search engine is evaluated with 20 students. The results show usefulness and effectiv...

  5. 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.

  6. 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....

  7. Content-Based Design and Implementation of Ambient Intelligence Applications

    NARCIS (Netherlands)

    Diggelen, J. van; Grootjen, M.; Ubink, E.M.; Zomeren, M. van; Smets, N.J.J.M.

    2013-01-01

    Optimal support of professionals in complex ambient task environments requires a system that delivers the Right Message at the Right Moment in the Right Modality: (RM)3. This paper describes a content-based design methodology and an agent-based architecture to enable real time decisions of informati

  8. 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.

  9. Content

    DEFF Research Database (Denmark)

    Keiding, Tina Bering

    Aim, content and methods are fundamental categories of both theoretical and practical general didactics. A quick glance in recent pedagogical literature on higher education, however, reveals a strong preoccupation with methods, i.e. how teaching should be organized socially (Biggs & Tang, 2007......; Race, 2001; Ramsden, 2003). This trend appears closely related to the ‘from-teaching-to-learning’ movement, which has had a strong influence on pedagogy since the early nineties (Keiding, 2007; Terhart, 2003). Another interpretation of the current interest in methodology can be derived from...... for selection of content (Klafki, 1985, 2000; Myhre, 1961; Nielsen, 2006). These attempts all share one feature, which is that criteria for selection of content appear very general and often, more or less explicitly, deal with teaching at the first Bologna-cycle; i.e. schooling at the primary and lower...

  10. 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.

  11. 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.

  12. Content-Based Book Recommending Using Learning for Text Categorization

    OpenAIRE

    Mooney, Raymond J.; Roy, Loriene

    1999-01-01

    Recommender systems improve access to relevant products and information by making personalized suggestions based on previous examples of a user's likes and dislikes. Most existing recommender systems use social filtering methods that base recommendations on other users' preferences. By contrast, content-based methods use information about an item itself to make suggestions. This approach has the advantage of being able to recommended previously unrated items to users with unique interests and...

  13. 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.

  14. Effect of X irradiation on a heterotransplanted human colonic carcinoma before and after a change in the cellular DNA content

    DEFF Research Database (Denmark)

    Spang-Thomsen, M; Vindeløv, L L; Nielsen, A

    1983-01-01

    A spontaneous change of cellular DNA content occurred in a hyperdiploid human colonic carcinoma grown in nude mice. After the change to hyperpentaploidy the tumor was exposed to single-dose X irradiation, and the effects on growth curves and on the cell cycle, determined by flow cytometric DNA...... analysis (FCM), were compared to results obtained with the tumor prior to the evolutionary event. The results showed that the radiation effects on growth rate and on cell kinetics had changed after the change in cellular DNA content. In the hyperpentaploid tumor the irradiation had no effect...... a partial synchronization of accumulated cells, whereas no synchronization effect was found in the hyperdiploid tumor. The redistribution time was 8-10 days for both tumors. The results indicate that clonal evolution may affect radiosensitivity, and that FCM analysis may prove to be a valuable method...

  15. Content Linking for UGC based on Word Embedding Model

    Directory of Open Access Journals (Sweden)

    Zhiqiao Gao

    2015-09-01

    Full Text Available There are huge amounts of User Generated Contents (UGCs consisting of authors’ articles of different themes and readers’ on-line comments on social networks every day. Generally, an article often gives rise to thousands of readers’ comments, which are related to specific points of the originally published article or previous comments. Hence it has suggested the urgent need for automated methods to implement the content linking task, which can also help other related applications, such as information retrieval, summarization and content management. So far content linking is still a relatively new issue. Because of the unsatisfactory of traditional ways based on feature extraction, we look forward to using deeper textual semantic analysis. The Word Embedding model based on deep learning has performed well in Natural Language Processing (NLP, especially in mining deep semantic information recently. Therefore, we study further on the Word Embedding model trained by different neural network models from which we can learn the structure, principles and training ways of the neural network language model in more depth to complete deep semantic feature extraction. With the aid of the semantic features, we expect to do further research on content linking between comments and their original articles from social networks, and finally verify the validity of the proposed method by comparison with traditional ways based on feature extraction.

  16. Content Based Video Retrieval using trajectory and Velocity features

    Directory of Open Access Journals (Sweden)

    Dr. S. D. Sawarkar

    2012-09-01

    Full Text Available The Internet forms today’s largest source of Information containing a high density of multimedia objects and its content is often semantically related. The identification of relevant media objects in such a vast collection poses a major problem that is studied in the area of multimedia information retrieval. Before the emergence of content-based retrieval, media was annotated with text, allowing the media to be accessed by text-based searching based on the classification of subject or semantics.In typical content-based retrieval systems, the contents of the media in the database are extracted and described by multi-dimensional feature vectors, also called descriptors. In our paper to retrieve desired data, users submit query examples to the retrieval system. The system then represents these examples with feature vectors. The distances (i.e.,similarities between the feature vectors of the query example and those of the media in the feature dataset are then computed and ranked. Retrieval is conducted by applying an indexing scheme to provide an efficient way to search the video database. Finally, the system ranks the search results and then returns the top search results that are most similar to the query examples.Therefore, a content-based retrieval system has four aspects: feature extraction and representation, dimension reduction of feature, indexing, and query specifications. With the search engine being developed, the user should have the ability to initiate a retrieval procedure by using video retrieval in a way that there is a better chance for a user to find the desired content.

  17. Content-based analysis and indexing of sports video

    Science.gov (United States)

    Luo, Ming; Bai, Xuesheng; Xu, Guang-you

    2001-12-01

    An explosion of on-line image and video data in digital form is already well underway. With the exponential rise in interactive information exploration and dissemination through the World-Wide Web, the major inhibitors of rapid access to on-line video data are the management of capture and storage, and content-based intelligent search and indexing techniques. This paper proposes an approach for content-based analysis and event-based indexing of sports video. It includes a novel method to organize shots - classifying shots as close shots and far shots, an original idea of blur extent-based event detection, and an innovative local mutation-based algorithm for caption detection and retrieval. Results on extensive real TV programs demonstrate the applicability of our approach.

  18. 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.

  19. Ploidy distribution and DNA content variations of Lonicera caerulea (Caprifoliaceae) in Japan

    OpenAIRE

    Miyashita, Tomomi; ARAKI, Hajime; Hoshino, Yoichiro

    2011-01-01

    Ploidy level and geographical distribution were investigated in Japanese Lonicera caerulea L. Flow cytometric analysis revealed the presence of DNA diploid and DNA tetraploid plants in Japan. Chromosome observation confirmed that diploid and tetraploid plants showed 2n = 2x = 18 and 2n = 4x = 36, respectively. The DNA diploid populations were found only in lowland mires, Betsukai, Bekanbeushi, Kushiro and Kiritappu located in eastern Hokkaido. On the other hand, DNA tetraploid populations wer...

  20. 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...

  1. Student Engagement with a Content-Based Learning Design

    Science.gov (United States)

    Padilla Rodriguez, Brenda Cecilia; Armellini, Alejandro

    2013-01-01

    While learning is commonly conceptualised as a social, collaborative process in organisations, online courses often provide limited opportunities for communication between people. How do students engage with content-based courses? How do they find answers to their questions? How do they achieve the learning outcomes? This paper aims to answer…

  2. Student engagement with a content-based learning design

    Directory of Open Access Journals (Sweden)

    Brenda Cecilia Padilla Rodriguez

    2013-09-01

    Full Text Available While learning is commonly conceptualised as a social, collaborative process in organisations, online courses often provide limited opportunities for communication between people. How do students engage with content-based courses? How do they find answers to their questions? How do they achieve the learning outcomes? This paper aims to answer these questions by focusing on students’ experiences in an online content-based course delivered in a large Mexican organisation. Sales supervisors (n=47 participated as students. Four main data sources were used to evaluate engagement with and learning from the course: surveys (n=40, think-aloud sessions (n=8, activity logs (n=47 and exams (n=43. Findings suggest that: (1 Students engage with a content-based course by following the guidance available and attempting to make the materials relevant to their own context. (2 Students are resourceful when trying to find support. If the materials do not provide the answers to their questions, they search for alternatives such as colleagues to talk to. (3 Content-based online learning designs may be engaging and effective. However, broadening the range of support options available to students may derive in more meaningful, contextualised and rewarding learning experiences.

  3. Text mining of web-based medical content

    CERN Document Server

    Neustein, Amy

    2014-01-01

    Text Mining of Web-Based Medical Content examines web mining for extracting useful information that can be used for treating and monitoring the healthcare of patients. This work provides methodological approaches to designing mapping tools that exploit data found in social media postings. Specific linguistic features of medical postings are analyzed vis-a-vis available data extraction tools for culling useful information.

  4. Human-Centered Content-Based Image Retrieval

    NARCIS (Netherlands)

    van den Broek, Egon

    2005-01-01

    Retrieval of images that lack a (suitable) annotations cannot be achieved through (traditional) Information Retrieval (IR) techniques. Access through such collections can be achieved through the application of computer vision techniques on the IR problem, which is baptized Content-Based Image

  5. An Integrated Approach for Image Retrieval based on Content

    Directory of Open Access Journals (Sweden)

    Kavita Choudhary

    2010-05-01

    Full Text Available The difficulties faced in an image retrieval system used for browsing, searching and retrieving of image in an image databases cannot be underestimated also the efficient management of the rapidly expanding visual information has become an urgent problem in science and technology. This requirement formed the driving force behind the emergence of image retrieval techniques. Image retrieval based on content also called content based image retrieval, is a technique which uses the visual contents to search an image in the scale database. This Image retrieval technique integrate both low-level visual features, addressing the more detailed perceptual aspects, and high-level semantic features underlying the more general conceptual aspects of visual data. In connection with this Content Based Image Retrieval is a technology that is being developed to address different application areas, remote sensing, geographic information systems, and weather forecasting, architectural and engineering design, multimedia documents for digital libraries. In this paper we present an approach that significantly automates the retrieving process by relying on image analysis techniques that are based on image visual features like color with spatial information, texture and shape.

  6. Concept-Based Content of Professional Linguistic Education

    Science.gov (United States)

    Makshantseva, Nataliia Veniaminovna; Bankova, Liudmila Lvovna

    2016-01-01

    The article deals with professional education of future linguists built on the basis of conceptual approach. The topic is exemplified by the Russian language and a successful attempt to implement the concept-based approach to forming the content of professional language education. Within the framework of the proposed research, the concept is…

  7. Content-Based Information Retrieval from Forensic Databases

    NARCIS (Netherlands)

    Geradts, Z.J.M.H.

    2002-01-01

    In forensic science, the number of image databases is growing rapidly. For this reason, it is necessary to have a proper procedure for searching in these images databases based on content. The use of image databases results in more solved crimes; furthermore, statistical information can be obtained

  8. Human-Centered Content-Based Image Retrieval

    NARCIS (Netherlands)

    Broek, van den Egon L.

    2005-01-01

    Retrieval of images that lack a (suitable) annotations cannot be achieved through (traditional) Information Retrieval (IR) techniques. Access through such collections can be achieved through the application of computer vision techniques on the IR problem, which is baptized Content-Based Image Retrie

  9. Application of Bayesian Classification to Content-Based Data Management

    Science.gov (United States)

    Lynnes, Christopher; Berrick, S.; Gopalan, A.; Hua, X.; Shen, S.; Smith, P.; Yang, K-Y.; Wheeler, K.; Curry, C.

    2004-01-01

    The high volume of Earth Observing System data has proven to be challenging to manage for data centers and users alike. At the Goddard Earth Sciences Distributed Active Archive Center (GES DAAC), about 1 TB of new data are archived each day. Distribution to users is also about 1 TB/day. A substantial portion of this distribution is MODIS calibrated radiance data, which has a wide variety of uses. However, much of the data is not useful for a particular user's needs: for example, ocean color users typically need oceanic pixels that are free of cloud and sun-glint. The GES DAAC is using a simple Bayesian classification scheme to rapidly classify each pixel in the scene in order to support several experimental content-based data services for near-real-time MODIS calibrated radiance products (from Direct Readout stations). Content-based subsetting would allow distribution of, say, only clear pixels to the user if desired. Content-based subscriptions would distribute data to users only when they fit the user's usability criteria in their area of interest within the scene. Content-based cache management would retain more useful data on disk for easy online access. The classification may even be exploited in an automated quality assessment of the geolocation product. Though initially to be demonstrated at the GES DAAC, these techniques have applicability in other resource-limited environments, such as spaceborne data systems.

  10. Content Analysis of a Computer-Based Faculty Activity Repository

    Science.gov (United States)

    Baker-Eveleth, Lori; Stone, Robert W.

    2013-01-01

    The research presents an analysis of faculty opinions regarding the introduction of a new computer-based faculty activity repository (FAR) in a university setting. The qualitative study employs content analysis to better understand the phenomenon underlying these faculty opinions and to augment the findings from a quantitative study. A web-based…

  11. Screening for Methylated Poly(⌊-histidine with Various Dimethylimidazolium/Methylimidazole/Imidazole Contents as DNA Carrier

    Directory of Open Access Journals (Sweden)

    Shoichiro Asayama

    2015-08-01

    Full Text Available Methylated poly(l-histidine (PLH-Me, our original polypeptide, has controlled the contents of dimethylimidazolium, τ/π-methylimidazole and imidazole groups for efficient gene delivery. The screening for the PLH-Me as DNA carrier has been carried out by use of the PLH with 25 mol% (τ-methyl, 16 mol%; π-methyl, 17 mol%; deprotonated imidazole, 41 mol%, 68 mol% (τ-methyl, 16 mol%; π-methyl, 8 mol%; deprotonated imidazole, 8 mol% and 87 mol% (τ-methyl, 7 mol%; π-methyl, 4 mol%; deprotonated imidazole, 2 mol% dimethylimidazolium groups, that is, PLH-Me(25, PLH-Me(68 and PLH-Me(87, respectively. The screening of the chemical structure of PLH-Me has been carried out for DNA carrier properties, which are the stability of its DNA polyion complexes and gene expression. The DNA complexes with the 25 mol% and 68 mol% dimethylated PLH-Me possessed almost same ability to retain DNA, as compared with the 87 mol% dimethylated PLH-Me, which was examined by competitive exchange with dextran sulfate. From the gene transfection experiment against HepG2 cells, human hepatoma cell line, the PLH-Me(25/DNA complex was revealed to mediate highest gene expression. These results suggest that the dimethyl-imidazolium/methylimidazole/imidazole balance of the PLH-Me is important for DNA carrier design.

  12. Screening for Methylated Poly(l-histidine) with Various Dimethylimidazolium/Methylimidazole/Imidazole Contents as DNA Carrier.

    Science.gov (United States)

    Asayama, Shoichiro; Kumagai, Takao; Kawakami, Hiroyoshi

    2015-08-25

    : Methylated poly(l-histidine) (PLH-Me), our original polypeptide, has controlled the contents of dimethylimidazolium, τ/π-methylimidazole and imidazole groups for efficient gene delivery. The screening for the PLH-Me as DNA carrier has been carried out by use of the PLH with 25 mol% (τ-methyl, 16 mol%; π-methyl, 17 mol%; deprotonated imidazole, 41 mol%), 68 mol% (τ-methyl, 16 mol%; π-methyl, 8 mol%; deprotonated imidazole, 8 mol%) and 87 mol% (τ-methyl, 7 mol%; π-methyl, 4 mol%; deprotonated imidazole, 2 mol%) dimethylimidazolium groups, that is, PLH-Me(25), PLH-Me(68) and PLH-Me(87), respectively. The screening of the chemical structure of PLH-Me has been carried out for DNA carrier properties, which are the stability of its DNA polyion complexes and gene expression. The DNA complexes with the 25 mol% and 68 mol% dimethylated PLH-Me possessed almost same ability to retain DNA, as compared with the 87 mol% dimethylated PLH-Me, which was examined by competitive exchange with dextran sulfate. From the gene transfection experiment against HepG2 cells, human hepatoma cell line, the PLH-Me(25)/DNA complex was revealed to mediate highest gene expression. These results suggest that the dimethyl-imidazolium/methylimidazole/imidazole balance of the PLH-Me is important for DNA carrier design.

  13. Reengineering the ESL Practitioner for Content-Based Instruction.

    Science.gov (United States)

    Haynes, Lilith M.

    The idea of content-based instruction (CBI) is at odds with the curricula of most English-as-a-Second-Language (ESL) teacher preparation programs. Nor does it fit easily with the skill-based texts and learning packages that are used widely in the field. There is also little agreement about the methods to be used to effect it at various levels of…

  14. K-mer Content, Correlation, and Position Analysis of Genome DNA Sequences for the Identification of Function and Evolutionary Features.

    Science.gov (United States)

    Sievers, Aaron; Bosiek, Katharina; Bisch, Marc; Dreessen, Chris; Riedel, Jascha; Froß, Patrick; Hausmann, Michael; Hildenbrand, Georg

    2017-04-19

    In genome analysis, k-mer-based comparison methods have become standard tools. However, even though they are able to deliver reliable results, other algorithms seem to work better in some cases. To improve k-mer-based DNA sequence analysis and comparison, we successfully checked whether adding positional resolution is beneficial for finding and/or comparing interesting organizational structures. A simple but efficient algorithm for extracting and saving local k-mer spectra (frequency distribution of k-mers) was developed and used. The results were analyzed by including positional information based on visualizations as genomic maps and by applying basic vector correlation methods. This analysis was concentrated on small word lengths (1 ≤ k ≤ 4) on relatively small viral genomes of Papillomaviridae and Herpesviridae, while also checking its usability for larger sequences, namely human chromosome 2 and the homologous chromosomes (2A, 2B) of a chimpanzee. Using this alignment-free analysis, several regions with specific characteristics in Papillomaviridae and Herpesviridae formerly identified by independent, mostly alignment-based methods, were confirmed. Correlations between the k-mer content and several genes in these genomes have been found, showing similarities between classified and unclassified viruses, which may be potentially useful for further taxonomic research. Furthermore, unknown k-mer correlations in the genomes of Human Herpesviruses (HHVs), which are probably of major biological function, are found and described. Using the chromosomes of a chimpanzee and human that are currently known, identities between the species on every analyzed chromosome were reproduced. This demonstrates the feasibility of our approach for large data sets of complex genomes. Based on these results, we suggest k-mer analysis with positional resolution as a method for closing a gap between the effectiveness of alignment-based methods (like NCBI BLAST) and the high pace of

  15. SeeDNA: A Visualization Tool for K-string Content of Long DNA Sequences and Their Randomized Counterparts

    Institute of Scientific and Technical Information of China (English)

    Junjie Shen; Shuyu Zhang; Hoong-Chien Lee; Bailin Hao

    2004-01-01

    An interactive tool to visualize the K-string composition of long DNA sequences including bacterial complete genomes is described. It is especially useful for exploring short palindromic structures in the sequences. The SeeDNA program runs on Red Hat Linux with GTK+ support. It displays two-dimensional (2D) or one-dimensional (1D) histograms of the K-string distribution of a given sequence and/or its randomized counterpart. It is also capable of showing the difference of K-string distributions between two sequences. The C source code using the GTK+package is freely available.

  16. A CONTENT ANALYSIS ON PROBLEM-BASED LEARNING APPROACH

    OpenAIRE

    BİBER, Mahir; Esen ERSOY; KÖSE BİBER, Sezer

    2014-01-01

    Problem Based Learning is one of the learning models that contain the general principles of active learning and students can use scientific process skills. Within this research it was aimed to investigate in detail the postgraduate thesis held in Turkey about PBL approach. The content analysis method was used in the research. The study sample was consisted of a total of 64 masters and PhD thesis made between the years 2012-2013 and reached over the web. A “Content Analysis Template” prepared ...

  17. A CONTENT ANALYSIS ON PROBLEM-BASED LEARNING APPROACH

    OpenAIRE

    BİBER, Mahir; Esen ERSOY; KÖSE BİBER, Sezer

    2015-01-01

    Problem Based Learning is one of the learning models that contain the general principles of active learning and students can use scientific process skills. Within this research it was aimed to investigate in detail the postgraduate thesis held in Turkey about PBL approach. The content analysis method was used in the research. The study sample was consisted of a total of 64 masters and PhD thesis made between the years 2012-2013 and reached over the web. A “Content Analysis Template” prepared ...

  18. 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...

  19. Cytogenetic characterization of olive flounder Paralichthys olivaceus: DNA content, karyotype, AgNORs and location of major ribosomal genes

    Institute of Scientific and Technical Information of China (English)

    WANG Xubo; ZHANG Quanqi; CHEN Yanjie; QI Jie; WANG Zhigang; WANG Xinglian

    2009-01-01

    A cytogenetic analysis of Paralichthys olivaceus was carried out using the flow cytometry method for DNA content, silver staining for the nucleolus organizer region (AgNORs) identification and one-color fluorescence in situ hybridization (FISH) for chromosomal mapping of major ribosomal genes. Nuclear DNA content was estimated by flow cytometry method using Gallus domesticus erythrocytes as the internal reference standard. The C-value of this species was (0.737±0.024) pg, and the DNA contents of each chromosome were estimated to be 16.51 Mb to 39.50 Mb after paired according to the average relative length. The FISH probe was made by PCR amplification of a DNA fragment containing internal transcribed spacers ITS1 between 18S and 5.8S ribosomal RNA gene, and labeled by PCR incorporation of bio-16-dUTP. FISH signals and AgNORs were both located on the secondary constrictions of chromosome 1. These results will provide a better understanding of the cytogenetic information of this species and would help for further research of the karyotype evolution in the order Pleuronectiformes.

  20. 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...

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. Resistive content addressable memory based in-memory computation architecture

    KAUST Repository

    Salama, Khaled N.

    2016-12-08

    Various examples are provided examples related to resistive content addressable memory (RCAM) based in-memory computation architectures. In one example, a system includes a content addressable memory (CAM) including an array of cells having a memristor based crossbar and an interconnection switch matrix having a gateless memristor array, which is coupled to an output of the CAM. In another example, a method, includes comparing activated bit values stored a key register with corresponding bit values in a row of a CAM, setting a tag bit value to indicate that the activated bit values match the corresponding bit values, and writing masked key bit values to corresponding bit locations in the row of the CAM based on the tag bit value.

  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. Cytological study of DNA content and nuclear morphometric analysis for aid in the diagnosis of high-grade dysplasia within oral leukoplakia.

    Science.gov (United States)

    Yang, Xi; Xiao, Xuan; Wu, Wenyan; Shen, Xuemin; Zhou, Zengtong; Liu, Wei; Shi, Linjun

    2017-09-01

    To quantitatively examine the DNA content and nuclear morphometric status of oral leukoplakia (OL) and investigate its association with the degree of dysplasia in a cytologic study. Oral cytobrush biopsy was carried out to obtain exfoliative epithelial cells from lesions before scalpel biopsy at the same location in a blinded series of 70 patients with OL. Analysis of nuclear morphometry and DNA content status using image cytometry was performed with oral smears stained with the Feulgen-thionin method. Nuclear morphometric analysis revealed significant differences in DNA content amount, DNA index, nuclear area, nuclear radius, nuclear intensity, sphericity, entropy, and fractal dimension (all P content analysis identified 34 patients with OL (48.6%) with DNA content abnormality. Nonhomogeneous lesion (P = .018) and high-grade dysplasia (P = .008) were significantly associated with abnormal DNA content. Importantly, the positive correlation between the degree of oral dysplasia and DNA content status was significant (P = .004, correlation coefficient = 0.342). Cytology analysis of DNA content and nuclear morphometric status using image cytometry may support their use as a screening and monitoring tool for OL progression. Copyright © 2017 Elsevier Inc. All rights reserved.

  8. Nuclear DNA Content and Chromatin Pattern of Rat Rhabdomyosarcoma Cell Sublines with Different Metastatic Potentials

    Directory of Open Access Journals (Sweden)

    Jean Dufer

    2000-01-01

    Full Text Available There is a constant need of features able to characterize potentially metastatic cells among the heterogeneous cell subpopulations which constitute a tumor. Image cytometry of metastatic tumor cells give rise to variable results, partly because of a heterogeneous origin of cells, or potential drug effects. The aim of this work was to characterize nuclear changes observed in metastatic cell clones issued in vitro from the same parental cell population The nuclear phenotypes of 6 cell sublines isolated from a rat rhabdomyosarcoma cell line and differing in their metastatic ability were evaluated by image cytometry on Feulgen‐stained preparations. Densitometric [5], geometric [3] and textural [9] features were computed from each nuclear image. For each cell subline, a metastatic score, ranging from 0 to 10, was calculated on the basis of in vitro invasivity data, by measuring the number of pulmonary metastases observed after s.c. graft of tumor cells in rats. Data obtained were compared to karyotype, growth characteristics, and oncogene expressions of cell lines. The nuclear DNA content, the chromosome numbers, the cell sublines doubling times, and the distribution of cells within the cell cycle appear unrelated with this score. On the contrary, increase in metastatic ability is accompanied by changes in chromatin pattern as assessed by textural features. Progressive increase in chromatin condensation can be observed in cell sublines with increasing metastatic score. These results were confirmed by an unsupervised multivariate partitioning of rhabdomyosarcoma cells which identified two separate subsets whose distributions within the analyzed cell lines correlate with their metastatic ability. These data suggest that, in rat rhabdomyosarcoma cell sublines, metastatic ability could be associated with nuclear morphological changes at the level of chromatin texture.

  9. CONTENTS

    Institute of Scientific and Technical Information of China (English)

    2012-01-01

    The Development and Evolution of the Idea of the Mandate of Heaven in the Zhou Dynasty The changes in the idea of Mandate of Heaven during the Shang and Zhou dynasties are of great significance in the course of the development of traditional Chinese culture. The quickening and awakening of the humanistic spirit was not the entire content of the Zhou idea of Mandate of Heaven. In the process of annihilating the Shang dynasty and setting up their state, the Zhou propagated the idea of the Mandate of Heaven out of practical needs. Their idea of the Mandate of Heaven was not very different from that of the Shang. From the Western Zhou on, the Zhou idea of Mandate of Heaven by no means developed in a linear way along a rational track. The intermingling of rationality and irrationality and of awakening and non-awakening remained the overall state of the Zhou intellectual superstructure after their "spiritual awakening".

  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. Content-Based Spam Filtering on Video Sharing Social Networks

    CERN Document Server

    da Luz, Antonio; Araujo, Arnaldo

    2011-01-01

    In this work we are concerned with the detection of spam in video sharing social networks. Specifically, we investigate how much visual content-based analysis can aid in detecting spam in videos. This is a very challenging task, because of the high-level semantic concepts involved; of the assorted nature of social networks, preventing the use of constrained a priori information; and, what is paramount, of the context dependent nature of spam. Content filtering for social networks is an increasingly demanded task: due to their popularity, the number of abuses also tends to increase, annoying the user base and disrupting their services. We systematically evaluate several approaches for processing the visual information: using static and dynamic (motionaware) features, with and without considering the context, and with or without latent semantic analysis (LSA). Our experiments show that LSA is helpful, but taking the context into consideration is paramount. The whole scheme shows good results, showing the feasib...

  14. CONTENTS

    Institute of Scientific and Technical Information of China (English)

    2012-01-01

    Grassroots Officials Promotion in Differentiated Model Association, The Researching of Rural Clan :Paradigm Should be Shifted Analysis Based on the Practice of Rural Community Construction in Ganzhou of Jiangxi Province and Yueping of Hubei Province

  15. Application of fuzzy logic in content-based image retrieval

    Institute of Scientific and Technical Information of China (English)

    WANG Xiao-ling; XIE Kang-lin

    2008-01-01

    We propose a fuzzy logic-based image retrieval system, in which the image similarity can be inferred in a nonlinear manner as human thinking. In the fuzzy inference process, weight assignments of multi-image features were resolved impliedly. Each fuzzy rule was embedded into the subjectivity of human perception of image contents. A color histogram called the average area histogram is proposed to represent the color features. Experimental results show the efficiency and feasibility of the proposed algorithms.

  16. A New Approach to Coding in Content Based MANETs

    OpenAIRE

    Joy, Joshua; Yu, Yu-Ting; Perez, Victor; Lu, Dennis; Gerla, Mario

    2015-01-01

    In content-based mobile ad hoc networks (CB-MANETs), random linear network coding (NC) can be used to reliably disseminate large files under intermittent connectivity. Conventional NC involves random unrestricted coding at intermediate nodes. This however is vulnerable to pollution attacks. To avoid attacks, a brute force approach is to restrict the mixing at the source. However, source restricted NC generally reduces the robustness of the code in the face of errors, losses and mobility induc...

  17. Active index for content-based medical image retrieval.

    Science.gov (United States)

    Chang, S K

    1996-01-01

    This paper introduces the active index for content-based medical image retrieval. The dynamic nature of the active index is its most important characteristic. With an active index, we can effectively and efficiently handle smart images that respond to accessing, probing and other actions. The main applications of the active index are to prefetch image and multimedia data, and to facilitate similarity retrieval. The experimental active index system is described.

  18. 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.

  19. 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.

  20. 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...

  1. Content based Image Retrieval from Forensic Image Databases

    Directory of Open Access Journals (Sweden)

    Swati A. Gulhane

    2015-03-01

    Full Text Available Due to the proliferation of video and image data in digital form, Content based Image Retrieval has become a prominent research topic. In forensic sciences, digital data have been widely used such as criminal images, fingerprints, scene images and so on. Therefore, the arrangement of such large image data becomes a big issue such as how to get an interested image fast. There is a great need for developing an efficient technique for finding the images. In order to find an image, image has to be represented with certain features. Color, texture and shape are three important visual features of an image. Searching for images using color, texture and shape features has attracted much attention. There are many content based image retrieval techniques in the literature. This paper gives the overview of different existing methods used for content based image retrieval and also suggests an efficient image retrieval method for digital image database of criminal photos, using dynamic dominant color, texture and shape features of an image which will give an effective retrieval result.

  2. Content-based Image Retrieval by Information Theoretic Measure

    Directory of Open Access Journals (Sweden)

    Madasu Hanmandlu

    2011-09-01

    Full Text Available Content-based image retrieval focuses on intuitive and efficient methods for retrieving images from databases based on the content of the images. A new entropy function that serves as a measure of information content in an image termed as 'an information theoretic measure' is devised in this paper. Among the various query paradigms, 'query by example' (QBE is adopted to set a query image for retrieval from a large image database. In this paper, colour and texture features are extracted using the new entropy function and the dominant colour is considered as a visual feature for a particular set of images. Thus colour and texture features constitute the two-dimensional feature vector for indexing the images. The low dimensionality of the feature vector speeds up the atomic query. Indices in a large database system help retrieve the images relevant to the query image without looking at every image in the database. The entropy values of colour and texture and the dominant colour are considered for measuring the similarity. The utility of the proposed image retrieval system based on the information theoretic measures is demonstrated on a benchmark dataset.Defence Science Journal, 2011, 61(5, pp.415-430, DOI:http://dx.doi.org/10.14429/dsj.61.1177

  3. Contents

    Directory of Open Access Journals (Sweden)

    Editor IJRED

    2012-11-01

    Full Text Available International Journal of Renewable Energy Development www.ijred.com Volume 1             Number 3            October 2012                ISSN 2252- 4940   CONTENTS OF ARTICLES page Design and Economic Analysis of a Photovoltaic System: A Case Study 65-73 C.O.C. Oko , E.O. Diemuodeke, N.F. Omunakwe, and E. Nnamdi     Development of Formaldehyde Adsorption using Modified Activated Carbon – A Review 75-80 W.D.P Rengga , M. Sudibandriyo and M. Nasikin     Process Optimization for Ethyl Ester Production in Fixed Bed Reactor Using Calcium Oxide Impregnated Palm Shell Activated Carbon (CaO/PSAC 81-86 A. Buasri , B. Ksapabutr, M. Panapoy and N. Chaiyut     Wind Resource Assessment in Abadan Airport in Iran 87-97 Mojtaba Nedaei       The Energy Processing by Power Electronics and its Impact on Power Quality 99-105 J. E. Rocha and B. W. D. C. Sanchez       First Aspect of Conventional Power System Assessment for High Wind Power Plants Penetration 107-113 A. Merzic , M. Music, and M. Rascic   Experimental Study on the Production of Karanja Oil Methyl Ester and Its Effect on Diesel Engine 115-122 N. Shrivastava,  , S.N. Varma and M. Pandey  

  4. Estimation of rice leaf nitrogen contents based on hyperspectral LIDAR

    Science.gov (United States)

    Du, Lin; Gong, Wei; Shi, Shuo; Yang, Jian; Sun, Jia; Zhu, Bo; Song, Shalei

    2016-02-01

    Precision agriculture has become a global research hotspot in recent years. Thus, a technique for rapidly monitoring a farmland in a large scale and for accurately monitoring the growing status of crops needs to be established. In this paper, a novel technique, i.e., hyperspectral LIDAR (HL) which worked based on wide spectrum emission and a 32-channel detector was introduced, and its potential in vegetation detection was then evaluated. These spectra collected by HL were used to classify and derive the nitrogen contents of rice under four different nitrogen content levels with support vector machine (SVM) regression. Meanwhile the wavelength selection and channel correction method for achieving high spectral resolution were discussed briefly. The analysis results show that: (1) the reflectance intensity of the selected characteristic wavelengths of HL system has high correlation with different nitrogen contents levels of rice. (2) By increasing the number of wavelengths in calculation, the classification accuracy is greatly improved (from 54% with 4 wavelengths to 83% with 32 wavelengths) and so the regression coefficient r2 is (from 0.51 with 4 wavelengths to 0.75 with 32 wavelengths). (3) Support vector machine (SVM) is a useful regression method for rice leaf nitrogen contents retrieval. These analysis results can help farmers to make fertilization strategies more accurately. The receiving channels and characteristic wavelengths of HL system can be flexibly selected according to different requirements and thus this system will be applied in other fields, such as geologic exploration and environmental monitoring.

  5. Image content authentication technique based on Laplacian Pyramid

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    This paper proposes a technique of image content authentication based on the Laplacian Pyramid to verify the authenticity of image content.First,the image is decomposed into Laplacian Pyramid before the transformation.Next,the smooth and detail properties of the original image are analyzed according to the Laplacian Pyramid,and the properties are classified and encoded to get the corresponding characteristic values.Then,the signature derived from the encrypted characteristic values is embedded in the original image as a watermark.After the reception,the characteristic values of the received image are compared with the watermark drawn out from the image.The algorithm automatically identifies whether the content is tampered by means of morphologic filtration.The information of tampered location is Presented at the same time.Experimental results show that the pro posed authentication algorithm can effectively detect the event and location when the original image content is tampered.Moreover,it can tolerate some distortions produced by compression,filtration and noise degradation.

  6. CONTENTS

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    In this article, the author presents his opinions on the extent of China ancient territory, viz. the territory administrated by integrated nation and separate states in China ancient history, which is based on his formal studies. The author also makes a comment on the new academic views since 1990s, and presents four new opinions on the development phases of China ancient territory.

  7. 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.

  8. 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

  9. Conserved balance of hepatocyte nuclear DNA content in mononuclear and binuclear hepatocyte populations during the course of chronic viral hepatitis

    Institute of Scientific and Technical Information of China (English)

    Hidenori Toyoda; Takashi Kumada; Olivier Bregerie; Christian Brechot; Chantal Desdouets

    2006-01-01

    AIM: To analyze the percentages of hepatocytes with increased nuclear DNA content, i.e., tetraploid (4n) and octoploid (8n) nuclei, and then compared mononuclear and binuclear hepatocyte populations:METHODS: The percentages of mononuclear diploid(2n), 4n, and 8n hepatocytes and those of binuclear 2× 2n, 2 × 4n, and 2 × 8n hepatocytes were determined with a method that can simultaneously measure hepatocyte nuclear DNA content and binuclearity in 62patients with chronic hepatitis B or C. The percentage of 4n and 8n hepatocytes in the mononuclear hepatocyte population was compared with the percentage of 2 ×4n and 2 × 8n hepatocytes in the binuclear hepatocyte population.RESULTS: The percentages of 4n and 8n hepatocytes in mononuclear hepatocytes and 2 × 4n and 2 × 8n hepatocytes in binuclear hepatocytes were similar,regardless of the activity or fibrosis grade of chronic hepatitis and regardless of the infecting virus.CONCLUSION: The distribution of nuclear DNA content within mononuclear and binuclear hepatocyte populations was conserved during the course of chronic viral hepatitis.

  10. Stability in chromosome number and DNA content in synthetic tetraploids of Lolium multiflorum after two generations of selection

    Directory of Open Access Journals (Sweden)

    Roselaine Cristina Pereira

    Full Text Available ABSTRACT: Chromosome doubling of Italian ryegrass genotypes ( Lolium multiflorum Lam. adapted to the brazilian edaphoclimatic conditions is an important strategy used by breeders and aims to obtain more vigorous genotypes with better forage quality and disease resistance. The effectiveness of chromosome doubling can be measured by genetic stability and fertility rates of plants over generations. However, a common problem in the polyploidization process is the regeneration of mixoploid plants that have impaired fertility and genetic stability. The objective of this study was to verify if progenies of recently tetraploidized plants remain stable regarding DNA content and chromosome number, over two generations. Progenies of L. multiflorum plants artificially tetraploidized with colchicine treatment were evaluated. Chromosome counting and estimates of the DNA content were used to evaluate the genetic stability. The percentage of tetraploid plants (4X increased over generations (18%, 34% and 91% in cycle 0, 1 and 2, respectively. All progenies identified as tetraploid by flow citometry showed variation in chromosome number (mixoploidy, but produced viable seeds. Results showed that stabilization in chromosome number and DNA content in tetraploidized plant progenies requires time and that the success of this procedure depends on a continuous and accurate screening and selection.

  11. Human circulating ribosomal DNA content significantly increases while circulating satellite III (1q12) content decreases under chronic occupational exposure to low-dose gamma- neutron and tritium beta-radiation.

    Science.gov (United States)

    Korzeneva, Inna B; Kostuyk, Svetlana V; Ershova, Elizaveta S; Skorodumova, Elena N; Zhuravleva, Veronika F; Pankratova, Galina V; Volkova, Irina V; Stepanova, Elena V; Porokhovnik, Lev N; Veiko, Natalia N

    A single exposure to ionizing radiation (IR) results in an elevated cell-free DNA (cfDNA) content in the blood plasma. In this case, the cfDNA concentration can be a marker of the cell death in the organism. However, a chronic exposure to a low-dose IR enhances both the endonuclease activity and titer of antibodies to DNA in blood plasma, resulting in a decrease of the total concentration of circulating cfDNA in exposed people. In this case, the total cfDNA concentration should not be considered as a marker of the cell death in an exposed body. We assumed that a pool of the cfDNA circulating in the exposed people contains DNA fragments, which are resistant to a double-strand break formation in the environment of the elevated plasma endonuclease activity, and can be accumulated in the blood plasma. In order to test this hypothesis, we studied the content of GC-rich sequences (69%GC) of the transcribed region of human ribosomal repeat (rDNA), as well as the content of AT-rich repeat (63%AT) of satellite III (1q12) in the cfDNA samples obtained from 285 individuals. We have found that a chronic exposure to gamma-neutron radiation (N=88) and tritium β-radiation (N=88) evokes an increase of the rDNA content (RrDNA index) and a decrease of the satellite III content (RsatIII index) in the circulating cfDNA as compared with the cfDNA of non-exposed people (N=109). Such index that simultaneously displays both the increase of rDNA content and decrease of satellite III content in the cfDNA (RrDNA/RsatIII) can be recommended as a marker of chronic processes in the body that involve the elevated cell death rate and/or increased blood plasma endonuclease activity. Copyright © 2016 Elsevier B.V. All rights reserved.

  12. 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

  13. 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.

  14. 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.``

  15. High-throughput monitoring of plant nuclear DNA contents via flow cytometry.

    Science.gov (United States)

    Galbraith, David W; Lambert, Georgina M

    2012-01-01

    Interest in measuring the nuclear holoploid genome sizes of higher plants reflects not just the status of the nucleus as a defining characteristic of eukaryotic organisms. Higher plants also attract interest in that they display an unusually large range of genome sizes, current measurements indicating an almost 2,500-fold difference between the smallest and the largest. Scientists would like to learn more about the significance of nuclear genome sizes, in terms of molecular and cytological mechanisms regulating the interaction of the nucleus with the cytoplasm and regulating the observed increases and decreases of genome sizes observed within and across families, genera, and species. We would like to understand their adaptive significance through charting their distribution within populations and ecosystems. Further, since genome size values are only available for a small minority of the ∼650,000 species of angiosperms (known and yet undiscovered), we would like to systematically survey plant genome sizes globally before their extinction as a consequence of anthropogenic change. Flow cytometry is accepted as the method of choice for genome size measurements, these measurements being based on fluorescent staining of the nuclear DNA. Flow cytometry offers exceptional ease of use, accompanied by high accuracy and reproducibility and low cost. This chapter provides a general discussion of flow cytometric methods for measuring plant genome sizes, and detailed methods for carrying out these analyses.

  16. Information Theoretical Analysis of Identification based on Active Content Fingerprinting

    OpenAIRE

    Farhadzadeh, F Farzad; Willems, FMJ Frans; Voloshynovskiy, S

    2014-01-01

    Content fingerprinting and digital watermarking are techniques that are used for content protection and distribution monitoring. Over the past few years, both techniques have been well studied and their shortcomings understood. Recently, a new content fingerprinting scheme called {\\em active content fingerprinting} was introduced to overcome these shortcomings. Active content fingerprinting aims to modify a content to extract robuster fingerprints than the conventional content fingerprinting....

  17. Information theoretical analysis of identification based on active content fingerprinting

    OpenAIRE

    Farhadzadeh, F Farzad; Willems, FMJ Frans; Voloshynovskiy, S

    2014-01-01

    Content fingerprinting and digital watermarking are techniques that are used for content protection and distribution monitoring. Over the past few years, both techniques have been well studied and their shortcomings understood. Recently, a new content fingerprinting scheme called {\\em active content fingerprinting} was introduced to overcome these shortcomings. Active content fingerprinting aims to modify a content to extract robuster fingerprints than the conventional content fingerprinting....

  18. 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.

  19. System refinement for content based satellite image retrieval

    Directory of Open Access Journals (Sweden)

    NourElDin Laban

    2012-06-01

    Full Text Available We are witnessing a large increase in satellite generated data especially in the form of images. Hence intelligent processing of the huge amount of data received by dozens of earth observing satellites, with specific satellite image oriented approaches, presents itself as a pressing need. Content based satellite image retrieval (CBSIR approaches have mainly been driven so far by approaches dealing with traditional images. In this paper we introduce a novel approach that refines image retrieval process using the unique properties to satellite images. Our approach uses a Query by polygon (QBP paradigm for the content of interest instead of using the more conventional rectangular query by image approach. First, we extract features from the satellite images using multiple tiling sizes. Accordingly the system uses these multilevel features within a multilevel retrieval system that refines the retrieval process. Our multilevel refinement approach has been experimentally validated against the conventional one yielding enhanced precision and recall rates.

  20. NEW APPROACH FOR IMAGE REPRESENTATION BASED ON GEOMETRIC STRUCTURAL CONTENTS

    Institute of Scientific and Technical Information of China (English)

    Jia Xiaomeng; Wang Guoyu

    2003-01-01

    This paper presents a novel approach for representation of image contents based on edge structural features. Edge detection is carried out for an image in the pre-processing stage.For feature representation, edge pixels are grouped into a set of segments through geometrical partitioning of the whole edge image. Then the invariant feature vector is computed for each edge-pixel segment. Thereby the image is represented with a set of spatially distributed feature vectors, each of which describes the local pattern of edge structures. Matching of two images can be achieved by the correspondence of two sets of feature vectors. Without the difficulty of image segmentation and object extraction due to the complexity of the real world images, the proposed approach provides a simple and flexible description for the image with complex scene, in terms of structural features of the image content. Experiments with real images illustrate the effectiveness of this new method.

  1. Identification and annotation of erotic film based on content analysis

    Science.gov (United States)

    Wang, Donghui; Zhu, Miaoliang; Yuan, Xin; Qian, Hui

    2005-02-01

    The paper brings forward a new method for identifying and annotating erotic films based on content analysis. First, the film is decomposed to video and audio stream. Then, the video stream is segmented into shots and key frames are extracted from each shot. We filter the shots that include potential erotic content by finding the nude human body in key frames. A Gaussian model in YCbCr color space for detecting skin region is presented. An external polygon that covered the skin regions is used for the approximation of the human body. Last, we give the degree of the nudity by calculating the ratio of skin area to whole body area with weighted parameters. The result of the experiment shows the effectiveness of our method.

  2. Content Authentication Based on JPEG-to-JPEG Watermarking

    Institute of Scientific and Technical Information of China (English)

    Hong-Xia Wang; Jie Hou; Ke Ding

    2009-01-01

    A content authentication technique based on JPEG-to-JPEG watermarking is proposed in this paper. In this technique, each 8×8 block in a JPEG compressed image is first processed by entropy decoding, and then the quantized discrete cosine transform (DCT) is applied to generate DCT coefficients: one DC coefficient and 63 AC coefficients in frequency coeffi- cients. The DCT AC coefficients are used to form zero planes in which the watermark is embedded by a chaotic map. In this way, the watermark information is embedded into JPEG compressed domain, and the output watermarked image is still a JPEG format. The proposed method is especially applicable to content authentication of JPEG image since the quantized coefficients are modified for embedding the watermark and the chaotic system possesses an important property with the high sensitivity on initial values. Experimental results show that the tamper regions are localized accurately when the watermarked JPEG image is maliciously tampered.

  3. Application of Near-Infrared Spectroscopy to Quantitatively Determine Relative Content of Puccnia striiformis f. sp. tritici DNA in Wheat Leaves in Incubation Period

    Directory of Open Access Journals (Sweden)

    Yaqiong Zhao

    2017-01-01

    Full Text Available Stripe rust caused by Puccinia striiformis f. sp. tritici (Pst is a devastating wheat disease worldwide. Potential application of near-infrared spectroscopy (NIRS in detection of pathogen amounts in latently Pst-infected wheat leaves was investigated for disease prediction and control. A total of 300 near-infrared spectra were acquired from the Pst-infected leaf samples in an incubation period, and relative contents of Pst DNA in the samples were obtained using duplex TaqMan real-time PCR arrays. Determination models of the relative contents of Pst DNA in the samples were built using quantitative partial least squares (QPLS, support vector regression (SVR, and a method integrated with QPLS and SVR. The results showed that the kQPLS-SVR model built with a ratio of training set to testing set equal to 3 : 1 based on the original spectra, when the number of the randomly selected wavelength points was 700, the number of principal components was 8, and the number of the built QPLS models was 5, was the best. The results indicated that quantitative detection of Pst DNA in leaves in the incubation period could be implemented using NIRS. A novel method for determination of latent infection levels of Pst and early detection of stripe rust was provided.

  4. 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.

  5. 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.

  6. Semantic-Based Requirements Content Management for Cloud Software

    Directory of Open Access Journals (Sweden)

    Jianqiang Hu

    2015-01-01

    Full Text Available Cloud Software is a software complex system whose topology and behavior can evolve dynamically in Cloud-computing environments. Given the unpredictable, dynamic, elasticity, and on-demand nature of the Cloud, it would be unrealistic to assume that traditional software engineering can “cleanly” satisfy the behavioral requirements of Cloud Software. In particular, the majority of traditional requirements managements take document-centric approaches, which have low degree of automation, coarse-grained management, and limited support for requirements modeling activities. Facing the challenges, based on metamodeling frame called RGPS (Role-Goal-Process-Service international standard, this paper firstly presents a hierarchical framework of semantic-based requirements content management for Cloud Software. And then, it focuses on some of the important management techniques in this framework, such as the native storage scheme, an ordered index with keywords, requirements instances classification based linear conditional random fields (CRFs, and breadth-first search algorithm for associated instances. Finally, a prototype tool called RGPS-RM for semantic-based requirements content management is implemented to provide supporting services for open requirements process of Cloud Software. The proposed framework applied to the Cloud Software development is demonstrated to show the validity and applicability. RGPS-RM also displays effect of fine-grained retrieval and breadth-first search algorithm for associated instance in visualization.

  7. 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.

  8. TOL Plasmid Carriage Enhances Biofilm Formation and Increases Extracellular DNA Content in Pseudomonas Putida KT2440

    DEFF Research Database (Denmark)

    Smets, Barth F.; D'Alvise, Paul; Yankelovich, T.;

    of extracellular polymeric substances: TOL carriage leads to more extracellular DNA (eDNA) in pellicles and biofilms. Pellicles were dissolved by DNAse I treatment. eDNA was observed as ominous fibrous structures. Quantitative analysis of live and dead cells in static cultures was performed by flow cytometry......Adherent growth of Pseudomonas putida KT2440 with and without the TOL plasmid (pWWO) at the solid-liquid and air-liquid interface was examined. We compared biofilm formation on glass in flow cells, and assayed pellicle (air-liquid interface biofilm) formation in stagnant liquid cultures by confocal...... combined with specific cytostains; release of cytoplasmic material was assayed by a β-glucosidase assay. Enhanced cell lysis due to plasmid carriage was ruled out as the mechanism for eDNA release. We report, for the first time, that carriage of a conjugative plasmid leads to increased biofilm formation...

  9. An association analysis between mitochondrial DNA content, G10398A polymorphism, HPV infection, and the prognosis of cervical cancer in the Chinese Han population.

    Science.gov (United States)

    Feng, Dali; Xu, Hui; Li, Xin; Wei, Yuehua; Jiang, Huangang; Xu, Hong; Luo, Aihua; Zhou, Fuxiang

    2016-04-01

    The aim was to analyze quantitative (mitochondrial DNA (mtDNA) content) and qualitative (G10398A polymorphism) mtDNA alterations as well as human papillomavirus (HPV) infection in cervical cancer prognosis. One hundred and twenty-two cases of formalin-fixed paraffin-embedded cervical carcinoma specimens were collected from the Yichang Tumor Hospital and Zhongnan Hospital of Wuhan University in the recent 10 years together with medical records. A quantitative real-time PCR (RT-PCR) was used to determine the copy number of the mitochondrial DNA and HPV expression levels. G10398A polymorphism was determined by PCR-RFLP assay. The overall survival of patients with higher mtDNA content was significantly reduced compared with lower mtDNA content patients (P = 0.029). But there was no difference of prognosis between the mtDNA 10398 A allele and G allele. However, the Kaplan-Meier survival curve illustrated a significantly reduced overall survival in the patients with 10398A plus high mtDNA copy number compared with the other groups (P content compared with 10398G (P content were positively related in the younger subgroup (≤45 years) (correlation coefficient = 0.456, P = 0.022). This study indicated that mtDNA content and HPV infection status are associated with cervical cancer prognosis. High mitochondrial DNA content plus 10398 A may be a marker of poor prognosis in cervical cancer. And mtDNA variation may potentially influence the predisposition to HPV infection and cervical carcinogenesis.

  10. 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.

  11. 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.

  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. PMID:23093912

  13. 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.

  14. 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).

  15. 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.

  16. 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.

  17. Comparative growth performance in different Japanese quail lines: the effect of muscle DNA content and fiber morphology.

    Science.gov (United States)

    Choi, Y M; Sarah, D; Shin, S; Wick, M P; Kim, B C; Lee, K

    2013-07-01

    The aim of this study was to investigate the DNA content and morphological characteristics of muscle fibers, and their relation to the growth performance in random bred control (RBC) and heavy weight (HW) Japanese quail lines. The 2 lines were of similar embryo size at 6 and 8 d of incubation; however, HW quail were significantly larger than their counterparts after 10 d of incubation (P quail line was approximately 1.3-fold higher than the RBC quail line (P quail lines. The RBC line showed a faster rate of increase in PMW (2.7- vs. 2.1-fold) and total DNA mass (2.2- vs. 1.6-fold) between 0 and 4 d posthatch. The HW line exhibited a greater rate of the PMW (33.0- vs. 12.9-fold) and total DNA mass (10.3- vs. 4.0-fold) between 4 and 15 d posthatch than the RBC line. Moreover, the greatest increase in total DNA mass occurred between 0 and 8 d posthatch for the RBC line and 4 to 15 d posthatch for the HW line. These differences in the DNA content indicate a difference in the hypertrophic potential of muscle fibers between the 2 quail lines. The cross-sectional area of muscle fibers was 1.3-fold greater in the HW line compared with the RBC line at 8 d posthatch (158.5 vs. 97.11 μm(2), P quail lines are between 0 to 8 d and 4 to 15 d posthatch, respectively. Rapid muscle growth rate and a greater muscle mass in the HW quail line may be partially due to the hypertrophic potential of muscle fibers, which is characterized by larger fiber size.

  18. Content-based retrieval in videos from laparoscopic surgery

    Science.gov (United States)

    Schoeffmann, Klaus; Beecks, Christian; Lux, Mathias; Uysal, Merih Seran; Seidl, Thomas

    2016-03-01

    In the field of medical endoscopy more and more surgeons are changing over to record and store videos of their endoscopic procedures for long-term archival. These endoscopic videos are a good source of information for explanations to patients and follow-up operations. As the endoscope is the "eye of the surgeon", the video shows the same information the surgeon has seen during the operation, and can describe the situation inside the patient much more precisely than an operation report would do. Recorded endoscopic videos can also be used for training young surgeons and in some countries the long-term archival of video recordings from endoscopic procedures is even enforced by law. A major challenge, however, is to efficiently access these very large video archives for later purposes. One problem, for example, is to locate specific images in the videos that show important situations, which are additionally captured as static images during the procedure. This work addresses this problem and focuses on contentbased video retrieval in data from laparoscopic surgery. We propose to use feature signatures, which can appropriately and concisely describe the content of laparoscopic images, and show that by using this content descriptor with an appropriate metric, we are able to efficiently perform content-based retrieval in laparoscopic videos. In a dataset with 600 captured static images from 33 hours recordings, we are able to find the correct video segment for more than 88% of these images.

  19. The Use of QBIC Content-Based Image Retrieval System

    Directory of Open Access Journals (Sweden)

    Ching-Yi Wu

    2004-03-01

    Full Text Available The fast increase in digital images has caught increasing attention on the development of image retrieval technologies. Content-based image retrieval (CBIR has become an important approach in retrieving image data from a large collection. This article reports our results on the use and users study of a CBIR system. Thirty-eight students majored in art and design were invited to use the IBM’s OBIC (Query by Image Content system through the Internet. Data from their information needs, behaviors, and retrieval strategies were collected through an in-depth interview, observation, and self-described think-aloud process. Important conclusions are:(1)There are four types of information needs for image data: implicit, inspirational, ever-changing, and purposive. The types of needs may change during the retrieval process. (2)CBIR is suitable for the example-type query, text retrieval is suitable for the scenario-type query, and image browsing is suitable for the symbolic query. (3)Different from text retrieval, detailed description of the query condition may lead to retrieval failure more easily. (4)CBIR is suitable for the domain-specific image collection, not for the images on the Word-Wide Web.[Article content in Chinese

  20. Content-based Image Retrieval by Spatial Similarity

    Directory of Open Access Journals (Sweden)

    Archana M. Kulkarn

    2002-07-01

    Full Text Available Similarity-based retrieval of images is an important task in image databases. Most of the user's queries are on retrieving those database images that are spatially similar to a query image. In defence strategies, one wants to know a number of armoured vehicles, such as battle tanks, portable missile launching vehicles, etc. moving towards it, so that one can decide counter strategy. Content-based spatial similarity retrieval of images can be used to locate spatial relationship of various objects in a specific area from the aerial photographs and to retrieve images similar to the query image from image database. A content-based image retrieval system that efficiently and effectively retrieves information from a defence image database along with the architecture for retrieving images by spatial similarity is presented. A robust algorithm SIMdef for retrieval by spatial similarity is proposed that utilises both directional and topological relations for computing similarity between images, retrieves similar images and recognises images even after they undergo modelling transformations (translation, scale and rotation. A case study for some of the common objects, used in defence applications using SIMdef algorithm, has been done.

  1. Knowledge-based approach to video content classification

    Science.gov (United States)

    Chen, Yu; Wong, Edward K.

    2001-01-01

    A framework for video content classification using a knowledge-based approach is herein proposed. This approach is motivated by the fact that videos are rich in semantic contents, which can best be interpreted and analyzed by human experts. We demonstrate the concept by implementing a prototype video classification system using the rule-based programming language CLIPS 6.05. Knowledge for video classification is encoded as a set of rules in the rule base. The left-hand-sides of rules contain high level and low level features, while the right-hand-sides of rules contain intermediate results or conclusions. Our current implementation includes features computed from motion, color, and text extracted from video frames. Our current rule set allows us to classify input video into one of five classes: news, weather, reporting, commercial, basketball and football. We use MYCIN's inexact reasoning method for combining evidences, and to handle the uncertainties in the features and in the classification results. We obtained good results in a preliminary experiment, and it demonstrated the validity of the proposed approach.

  2. 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.

  3. Relevance Feedback in Content Based Image Retrieval: A Review

    Directory of Open Access Journals (Sweden)

    Manesh B. Kokare

    2011-01-01

    Full Text Available This paper provides an overview of the technical achievements in the research area of relevance feedback (RF in content-based image retrieval (CBIR. Relevance feedback is a powerful technique in CBIR systems, in order to improve the performance of CBIR effectively. It is an open research area to the researcher to reduce the semantic gap between low-level features and high level concepts. The paper covers the current state of art of the research in relevance feedback in CBIR, various relevance feedback techniques and issues in relevance feedback are discussed in detail.

  4. Natural ingredients based cosmetics. Content of selected fragrance sensitizers

    DEFF Research Database (Denmark)

    Rastogi, Suresh Chandra; Johansen, J D; Menné, T

    1996-01-01

    In the present study, we have investigated 42 cosmetic products based on natural ingredients for content of 11 fragrance substances: geraniol, hydroxycitronellal, eugenol, isoeugenol, cinnamic aldehyde, cinnamic alcohol, alpha-amylcinnamic aldehyde, citral, coumarin, dihydrocoumarin and alpha...... cosmetic products (shampoos, creams, tonics, etc) were found to contain 0.0003-0.0820% of 1 to 3 of the target fragrances. Relatively high concentrations of hydroxycitronellal, coumarin, cinnamic alcohol and alpha-amyl cinnamic aldehyde were found in some of the investigated products. The detection...

  5. Nuclear DNA content in Sinningia (Gesneriaceae); intraspecific genome size variation and genome characterization in S. speciosa.

    Science.gov (United States)

    Zaitlin, David; Pierce, Andrew J

    2010-12-01

    The Gesneriaceae (Lamiales) is a family of flowering plants comprising >3000 species of mainly tropical origin, the most familiar of which is the cultivated African violet (Saintpaulia spp.). Species of Gesneriaceae are poorly represented in the lists of taxa sampled for genome size estimation; measurements are available for three species of Ramonda and one each of Haberlea, Saintpaulia, and Streptocarpus, all species of Old World origin. We report here nuclear genome size estimates for 10 species of Sinningia, a neotropical genus largely restricted to Brazil. Flow cytometry of leaf cell nuclei showed that holoploid genome size in Sinningia is very small (approximately two times the size of the Arabidopsis genome), and is small compared to the other six species of Gesneriaceae with genome size estimates. We also documented intraspecific genome size variation of 21%-26% within a group of wild Sinningia speciosa (Lodd.) Hiern collections. In addition, we analyzed 1210 genome survey sequences from S. speciosa to characterize basic features of the nuclear genome such as guanine-cytosine content, types of repetitive elements, numbers of protein-coding sequences, and sequences unique to S. speciosa. We included several other angiosperm species as genome size standards, one of which was the snapdragon (Antirrhinum majus L.; Veronicaceae, Lamiales). Multiple measurements on three accessions indicated that the genome size of A. majus is ~633 × 10⁶ base pairs, which is approximately 40% of the previously published estimate.

  6. 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.

  7. 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.

  8. Variation of karyotype and nuclear DNA content among four species of Plectranthus L’ Héritier, 1788 (Lamiaceae) from Brazil

    Science.gov (United States)

    Nani, Thaís Furtado; Mesquita, Amanda Teixeira; Bustamante, Fernanda de Oliveira; Barbosa, Sandro; Barbosa, João Vítor Calvelli; Davide, Lisete Chamma

    2015-01-01

    Abstract Plectranthus is a genus which includes species of ornamental and medicinal potential. It faces taxonomic problems due to aggregating species previously belonging to the genus Coleus, a fact that has contributed to the existence of various synonymies. The species Plectranthus amboinicus, Plectranthus barbatus, Plectranthus grandis and Plectranthus neochilus are included in this context. Some authors consider Plectranthus barbatus and Plectranthus grandis as synonyms. The present work was carried out with the aim of comparing plants of the above-mentioned species, originating from different localities in Brazil, with regards to chromosome number and karyotypic morphology, correlated to the nuclear DNA content. There was no variation in chromosome number among plants of the same species. Plectranthus amboinicus was the only species to exhibit 2n=34, whereas the others had 2n=30. No karyotypic differences were found among the plants of each species, except for Plectranthus barbatus. The plants of the Plectranthus species revealed little coincidence between chromosome pairs. The nuclear DNA content allowed grouping Plectranthus amboinicus and Plectranthus neochilus, with the highest mean values, and Plectranthus grandis and Plectranthus barbatus with the lowest ones. Differences in DNA amount among the plants were identified only for Plectranthus barbatus. These results allow the inference that the populations of Plectranthus amboinicus and Plectranthus neochilus present coincident karyotypes among their plants, and Plectranthus grandis is probably a synonym of Plectranthus barbatus. PMID:26753074

  9. Variation of karyotype and nuclear DNA content among four species of Plectranthus L' Héritier, 1788 (Lamiaceae) from Brazil.

    Science.gov (United States)

    Nani, Thaís Furtado; Mesquita, Amanda Teixeira; Bustamante, Fernanda de Oliveira; Barbosa, Sandro; Barbosa, João Vítor Calvelli; Davide, Lisete Chamma

    2015-01-01

    Plectranthus is a genus which includes species of ornamental and medicinal potential. It faces taxonomic problems due to aggregating species previously belonging to the genus Coleus, a fact that has contributed to the existence of various synonymies. The species Plectranthus amboinicus, Plectranthus barbatus, Plectranthus grandis and Plectranthus neochilus are included in this context. Some authors consider Plectranthus barbatus and Plectranthus grandis as synonyms. The present work was carried out with the aim of comparing plants of the above-mentioned species, originating from different localities in Brazil, with regards to chromosome number and karyotypic morphology, correlated to the nuclear DNA content. There was no variation in chromosome number among plants of the same species. Plectranthus amboinicus was the only species to exhibit 2n=34, whereas the others had 2n=30. No karyotypic differences were found among the plants of each species, except for Plectranthus barbatus. The plants of the Plectranthus species revealed little coincidence between chromosome pairs. The nuclear DNA content allowed grouping Plectranthus amboinicus and Plectranthus neochilus, with the highest mean values, and Plectranthus grandis and Plectranthus barbatus with the lowest ones. Differences in DNA amount among the plants were identified only for Plectranthus barbatus. These results allow the inference that the populations of Plectranthus amboinicus and Plectranthus neochilus present coincident karyotypes among their plants, and Plectranthus grandis is probably a synonym of Plectranthus barbatus.

  10. Demographic-Based Content Analysis of Web-Based Health-Related Social Media

    OpenAIRE

    2016-01-01

    Background An increasing number of patients from diverse demographic groups share and search for health-related information on Web-based social media. However, little is known about the content of the posted information with respect to the users’ demographics. Objective The aims of this study were to analyze the content of Web-based health-related social media based on users’ demographics to identify which health topics are discussed in which social media by which demographic groups and to he...

  11. Measuring the DNA Content of Cells in Apoptosis and at Different Cell-Cycle Stages by Propidium Iodide Staining and Flow Cytometry.

    Science.gov (United States)

    Crowley, Lisa C; Chojnowski, Grace; Waterhouse, Nigel J

    2016-10-03

    All cells are created from preexisting cells. This involves complete duplication of the parent cell to create two daughter cells by a process known as the cell cycle. For this process to be successful, the DNA of the parent cell must be faithfully replicated so that each daughter cell receives a full copy of the genetic information. During the cell cycle, the DNA content of the parent cell increases as new DNA is synthesized (S phase). When there are two full copies of the DNA (G2/M phase), the cell splits to form two new cells (G0/G1 phase). As such, cells in different stages of the cell cycle have different DNA contents. The cell cycle is tightly regulated to safeguard the integrity of the cell and any cell that is defective or unable to complete the cell cycle is programmed to die by apoptosis. When this occurs, the DNA is fragmented into oligonucleosomal-sized fragments that are disposed of when the dead cell is removed by phagocytosis. Consequently apoptotic cells have reduced DNA content compared with living cells. This can be measured by staining cells with propidium iodide (PI), a fluorescent molecule that intercalates with DNA at a specific ratio. The level of PI fluorescence in a cell is, therefore, directly proportional to the DNA content of that cell. This protocol describes the use of PI staining to determine the percentage of cells in each phase of the cell cycle and the percentage of apoptotic cells in a sample.

  12. TOL plasmid carriage enhances biofilm formation and increases extracellular DNA content in Pseudomonas putida KT2440

    DEFF Research Database (Denmark)

    D'Alvise, Paul; Sjoholm, O.R.; Yankelevich, T.;

    2010-01-01

    : TOL carriage leads to more extracellular DNA (eDNA) in pellicles and biofilms. Pellicles were dissolved by DNase I treatment. Enhanced cell lysis due to plasmid carriage was ruled out as the mechanism for eDNA release. We report, for the first time, that carriage of a conjugative plasmid leads......Adherent growth of Pseudomonas putida KT2440 with and without the TOL plasmid (pWWO) at the solid-liquid and air-liquid interface was examined. We compared biofilm formation on glass in flow cells, and assayed pellicle (air-liquid interface biofilm) formation in stagnant liquid cultures by confocal...... laser scanning microscopy. The TOL-carrying strains formed pellicles and thick biofilms, whereas the same strains without the plasmid displayed little adherent growth. Microscopy using fluorescent nucleic acid-specific stains revealed differences in the production of extracellular polymeric substances...

  13. Mobile Web Browsing Based On Content Preserving With Reduced Cost

    Directory of Open Access Journals (Sweden)

    Dr.N.Saravanaselvam

    2015-01-01

    Full Text Available Internet has played a drastic change in today’s life. Especially, web browsing has become more exclusive in compact devices. This tempts the people to migrate their innovations & skills into an unimaginable world. With these things in mind, it is necessary for us to concentrate more on the techniques that how the web data’s are accessed and accounted. Developed countries use a widely popular technique called Flat- rate pricing, which is solely independent on data usage. But whereas, developing countries are still behind the concept of “pay as you use”, which leads to high usage bills.With an effort to resolve the problem of high usage bills, we propose a cost effective technique, which reduces the data consumption in web mobile browsing. It reduces the usage bills in the mechanism of usage-based pricing. The key idea of our approach is to leverage the data plan of the user to compute a cost quota for each web request and a network middle-box to automatically adapt any web page to the cost quota. Here we use a simple but effective content adaption technique that highly decides which image or data best fits the mobile display with low cost and high quality resolution. It also emphasis on the trendy technique,” The Data Mining “which mines the requested & required data. The mined data’s are filtered based on the content adaption technique and fit into the display effectively. Interesting and noticeable feature in this concept is that only important web contents requested by the user are exhibited. A feedback process involves in this concept to retrieve the required data alone and also to improve the best fit resolution. With this proposed system web mobile browsing becomes cheaper & contributes an enormous logic for the future project in the field of Mobile browsing.

  14. Highly Selective Electrochemical Determination of Taxol Based on ds-DNA-Modified Pencil Electrode.

    Science.gov (United States)

    Taei, M; Hassanpour, F; Salavati, H; Sadeghi, Z; Alvandi, H

    2015-05-01

    In this research, TiO2/ZrO2 nanocomposite has been prepared using sol-gel method. The TiO2/ZrO2 composite was characterized by X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FT-IR), and transmission electron microscopy (TEM). A sensitive electrochemical biosensor is also presented for the determination of Taxol based on ds-DNA decorated multiwall carbon nanotubes-TiO2/ZrO2-chitosan-modified pencil electrode (ds-DNA-MWNTs-TiO2/ZrO2-CHIT-PGE). The UV spectroscopic data and differential pulse voltammetry revealed that there is a strong interaction between ds-DNA and Taxol. The groove binding of Taxol to ds-DNA helix has been characterized by a red shift (less than 8 nm) in wavelength and the decrease in the differential pulse voltammetry oxidation signal intensity of the Taxol at pencil graphite electrode (PGE) after its interaction with ds-DNA. Finally, a pretreated PGE modified with ds-DNA-MWNTs-TiO2/ZrO2-CHIT was tested in order to determine Taxol content in the solution. The dynamic range was from 0.7 to 1874.0 nmol L(-1) with a detection limit of 0.01 nmol L(-1). This sensing platform was successfully applied for the determination of Taxol in pharmaceutical and biological samples.

  15. 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

  16. SOME PRELIMINARY DATA ON THE TOTAL DNA CONTENT IN HYPOPHTHALMICHTHS MOLITRIX AND ARISTICHTHYS NOBILIS

    Directory of Open Access Journals (Sweden)

    Gabriela Vasile

    2006-08-01

    Full Text Available The work presents a comparative study between the total amount of DNA from five different types of tissues (gills, muscle, liver, spleen, kidneys in two cultured cyprinids species from the Ezreni accumulation, namely - silver carp (Hypophthalmichthys molitrix and bighead carp (Aristichthys nobilis. The results obtained show that for both Asian cyprinids species the highest average value of the total amount of DNA is to be found in the spleeny tissue comparatively with the muscular tissue, which has the lowest average value, confirming that the spleeny tissue has a more

  17. Content-based image database system for epilepsy.

    Science.gov (United States)

    Siadat, Mohammad-Reza; Soltanian-Zadeh, Hamid; Fotouhi, Farshad; Elisevich, Kost

    2005-09-01

    We have designed and implemented a human brain multi-modality database system with content-based image management, navigation and retrieval support for epilepsy. The system consists of several modules including a database backbone, brain structure identification and localization, segmentation, registration, visual feature extraction, clustering/classification and query modules. Our newly developed anatomical landmark localization and brain structure identification method facilitates navigation through an image data and extracts useful information for segmentation, registration and query modules. The database stores T1-, T2-weighted and FLAIR MRI and ictal/interictal SPECT modalities with associated clinical data. We confine the visual feature extractors within anatomical structures to support semantically rich content-based procedures. The proposed system serves as a research tool to evaluate a vast number of hypotheses regarding the condition such as resection of the hippocampus with a relatively small volume and high average signal intensity on FLAIR. Once the database is populated, using data mining tools, partially invisible correlations between different modalities of data, modeled in database schema, can be discovered. The design and implementation aspects of the proposed system are the main focus of this paper.

  18. Content-based image hashing using wave atoms

    Institute of Scientific and Technical Information of China (English)

    Liu Fang; Leung Hon-Yin; Cheng Lee-Ming; Ji Xiao-Yong

    2012-01-01

    It is well known that robustness,fragility,and security are three important criteria of image hashing; however how to build a system that can strongly meet these three criteria is still a challenge.In this paper,a content-based image hashing scheme using wave atoms is proposed,which satisfies the above criteria.Compared with traditional transforms like wavelet transform and discrete cosine transform (DCT),wave atom transform is adopted for the sparser expansion and better characteristics of texture feature extraction which shows better performance in both robustness and fragility.In addition,multi-frequency detection is presented to provide an application-defined trade-off.To ensure the security of the proposed approach and its resistance to a chosen-plaintext attack,a randomized pixel modulation based on the Rényi chaotic map is employed,combining with the nonliner wave atom transform.The experimental results reveal that the proposed scheme is robust against content-preserving manipulations and has a good discriminative capability to malicious tampering.

  19. Content-based microarray search using differential expression profiles

    Directory of Open Access Journals (Sweden)

    Thathoo Rahul

    2010-12-01

    Full Text Available Abstract Background With the expansion of public repositories such as the Gene Expression Omnibus (GEO, we are rapidly cataloging cellular transcriptional responses to diverse experimental conditions. Methods that query these repositories based on gene expression content, rather than textual annotations, may enable more effective experiment retrieval as well as the discovery of novel associations between drugs, diseases, and other perturbations. Results We develop methods to retrieve gene expression experiments that differentially express the same transcriptional programs as a query experiment. Avoiding thresholds, we generate differential expression profiles that include a score for each gene measured in an experiment. We use existing and novel dimension reduction and correlation measures to rank relevant experiments in an entirely data-driven manner, allowing emergent features of the data to drive the results. A combination of matrix decomposition and p-weighted Pearson correlation proves the most suitable for comparing differential expression profiles. We apply this method to index all GEO DataSets, and demonstrate the utility of our approach by identifying pathways and conditions relevant to transcription factors Nanog and FoxO3. Conclusions Content-based gene expression search generates relevant hypotheses for biological inquiry. Experiments across platforms, tissue types, and protocols inform the analysis of new datasets.

  20. Content patterns in topic-based overlapping communities.

    Science.gov (United States)

    Ríos, Sebastián A; Muñoz, Ricardo

    2014-01-01

    Understanding the underlying community structure is an important challenge in social network analysis. Most state-of-the-art algorithms only consider structural properties to detect disjoint subcommunities and do not include the fact that people can belong to more than one community and also ignore the information contained in posts that users have made. To tackle this problem, we developed a novel methodology to detect overlapping subcommunities in online social networks and a method to analyze the content patterns for each subcommunities using topic models. This paper presents our main contribution, a hybrid algorithm which combines two different overlapping sub-community detection approaches: the first one considers the graph structure of the network (topology-based subcommunities detection approach) and the second one takes the textual information of the network nodes into consideration (topic-based subcommunities detection approach). Additionally we provide a method to analyze and compare the content generated. Tests on real-world virtual communities show that our algorithm outperforms other methods.

  1. Motion feature extraction scheme for content-based video retrieval

    Science.gov (United States)

    Wu, Chuan; He, Yuwen; Zhao, Li; Zhong, Yuzhuo

    2001-12-01

    This paper proposes the extraction scheme of global motion and object trajectory in a video shot for content-based video retrieval. Motion is the key feature representing temporal information of videos. And it is more objective and consistent compared to other features such as color, texture, etc. Efficient motion feature extraction is an important step for content-based video retrieval. Some approaches have been taken to extract camera motion and motion activity in video sequences. When dealing with the problem of object tracking, algorithms are always proposed on the basis of known object region in the frames. In this paper, a whole picture of the motion information in the video shot has been achieved through analyzing motion of background and foreground respectively and automatically. 6-parameter affine model is utilized as the motion model of background motion, and a fast and robust global motion estimation algorithm is developed to estimate the parameters of the motion model. The object region is obtained by means of global motion compensation between two consecutive frames. Then the center of object region is calculated and tracked to get the object motion trajectory in the video sequence. Global motion and object trajectory are described with MPEG-7 parametric motion and motion trajectory descriptors and valid similar measures are defined for the two descriptors. Experimental results indicate that our proposed scheme is reliable and efficient.

  2. 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.

  3. 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.

  4. Effect of serotonin on the expression of antigens and DNA levels in Yersinia pestis cells with different plasmid content

    Science.gov (United States)

    Klueva, Svetlana N.; Korsukov, Vladimir N.; Schukovskaya, Tatyana N.; Kravtsov, Alexander L.

    2004-08-01

    Using flow cytometry (FCM) the influence of exogenous serotonin on culture growth, DNA content and fluorescence intensity of cells binding FITC-labelled plague polyclonal immunoglobulins was studied in Yersinia pestis EV (pFra+, pCad+, pPst+), Yersinia pestis KM218 (pFra-, pCad-, pPst-), Yersinia pestis KM 216 (pFra-, pCad-, pPst+). The results have been obtained by FCM showed serotonin accelerated Yersinia pestis EV (pFra+, pCad+, pPst+), Yersinia pestis KM218 (pFra-, pCad-, pPst-) culture growth during cultivation in Hottinger broth pH 7.2 at 28°C at concentration of 10-5 M. The presence of 10-5 M serotonin in nutrient broth could modulate DNA content in 37°C growing population of plague microbe independently of their plasmid content. Serotonin have been an impact on the distribution pattern of the cells according to their phenotypical characteristics, which was reflected in the levels of population heterogeneity in the intensity of specific immunofluorescence determined by FMC.

  5. Global Descriptor Attributes Based Content Based Image Retrieval of Query Images

    Directory of Open Access Journals (Sweden)

    Jaykrishna Joshi

    2015-02-01

    Full Text Available The need for efficient content-based image retrieval system has increased hugely. Efficient and effective retrieval techniques of images are desired because of the explosive growth of digital images. Content based image retrieval (CBIR is a promising approach because of its automatic indexing retrieval based on their semantic features and visual appearance. In this proposed system we investigate method for describing the contents of images which characterizes images by global descriptor attributes, where global features are extracted to make system more efficient by using color features which are color expectancy, color variance, skewness and texture feature correlation.

  6. Content Based Image Recognition by Information Fusion with Multiview Features

    Directory of Open Access Journals (Sweden)

    Rik Das

    2015-09-01

    Full Text Available Substantial research interest has been observed in the field of object recognition as a vital component for modern intelligent systems. Content based image classification and retrieval have been considered as two popular techniques for identifying the object of interest. Feature extraction has played the pivotal role towards successful implementation of the aforesaid techniques. The paper has presented two novel techniques of feature extraction from diverse image categories both in spatial domain and in frequency domain. The multi view features from the image categories were evaluated for classification and retrieval performances by means of a fusion based recognition architecture. The experimentation was carried out with four different popular public datasets. The proposed fusion framework has exhibited an average increase of 24.71% and 20.78% in precision rates for classification and retrieval respectively, when compared to state-of-the art techniques. The experimental findings were validated with a paired t test for statistical significance.

  7. Towards Better Retrievals in Content -Based Image Retrieval System

    Directory of Open Access Journals (Sweden)

    Kumar Vaibhava

    2014-04-01

    Full Text Available -This paper presents a Content-Based Image Retrieval (CBIR System called DEICBIR-2. The system retrieves images similar to a given query image by searching in the provided image database.Standard MPEG-7 image descriptors are used to find the relevant images which are similar to thegiven query image. Direct use of the MPEG-7 descriptors for creating the image database and retrieval on the basis of nearest neighbor does not yield accurate retrievals. To further improve the retrieval results, B-splines are used for ensuring smooth and continuous edges of the images in the edge-based descriptors. Relevance feedback is also implemented with user intervention. These additional features improve the retrieval performance of DEICBIR-2 significantly. Computational performance on a set of query images is presented and the performance of the proposed system is much superior to the performance of DEICBIR[9] on the same database and on the same set of query images.

  8. Novel Approach to Content Based Image Retrieval Using Evolutionary Computing

    Directory of Open Access Journals (Sweden)

    Muhammad Imran

    2014-08-01

    Full Text Available Content Based Image Retrieval (CBIR is an active research area in multimedia domain in this era of information technology. One of the challenges of CBIR is to bridge the gap between low level features and high level semantic. In this study we investigate the Particle Swarm Optimization (PSO, a stochastic algorithm and Genetic Algorithm (GA for CBIR to overcome this drawback. We proposed a new CBIR system based on the PSO and GA coupled with Support Vector Machine (SVM. GA and PSO both are evolutionary algorithms and in this study are used to increase the number of relevant images. SVM is used to perform final classification. To check the performance of the proposed technique, rich experiments are performed using coral dataset. The proposed technique achieves higher accuracy compared to the previously introduced techniques (FEI, FIRM, simplicity, simple HIST and WH.

  9. Permutation-based Homogeneous Block Content Authentication for Watermarking

    Directory of Open Access Journals (Sweden)

    S.Maruthuperumal

    2013-02-01

    Full Text Available In modern days, digital watermarking has become an admired technique for hitting data in digital images to help guard against copyright infringement. The proposed Permutation-based Homogeneous Block Content authentication (PHBC methods develop a secure and excellence strong watermarking algorithm that combines the reward of permutation-based Homogeneous block (PHB with that of significant and insignificant bit values with X0R encryption function using Max coefficient of least coordinate value for embedding the watermark. In the projected system uses the relationship between the permutation blocks to embed many data into Homogeneous blocks without causing solemn distortion to the watermarked image. The experimental results show that the projected system is very efficient in achieving perceptual invisibility with an increase in the Peak Signal to Noise Ratio (PSNR. Moreover, the projected system is robust to a variety of signal processing operations, such as image Cropping, Rotation, Resizing, Adding noise, Filtering , Blurring and Motion blurring.

  10. 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.

  11. 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.

  12. The DNA methylation level against the background of the genome size and t-heterochromatin content in some species of the genus Secale L

    Science.gov (United States)

    Kalinka, Anna; Poter, Paulina

    2017-01-01

    Methylation of cytosine in DNA is one of the most important epigenetic modifications in eukaryotes and plays a crucial role in the regulation of gene activity and the maintenance of genomic integrity. DNA methylation and other epigenetic mechanisms affect the development, differentiation or the response of plants to biotic and abiotic stress. This study compared the level of methylation of cytosines on a global (ELISA) and genomic scale (MSAP) between the species of the genus Secale. We analyzed whether the interspecific variation of cytosine methylation was associated with the size of the genome (C-value) and the content of telomeric heterochromatin. MSAP analysis showed that S. sylvestre was the most distinct species among the studied rye taxa; however, the results clearly indicated that these differences were not statistically significant. The total methylation level of the studied loci was very similar in all taxa and ranged from 60% in S. strictum ssp. africanum to 66% in S. cereale ssp. segetale, which confirmed the lack of significant differences in the sequence methylation pattern between the pairs of rye taxa. The level of global cytosine methylation in the DNA was not significantly associated with the content of t-heterochromatin and did not overlap with the existing taxonomic rye relationships. The highest content of 5-methylcytosine was found in S. cereale ssp. segetale (83%), while very low in S. strictum ssp. strictum (53%), which was significantly different from the methylation state of all taxa, except for S. sylvestre. The other studied taxa of rye had a similar level of methylated cytosine ranging from 66.42% (S. vavilovii) to 74.41% in (S. cereale ssp. afghanicum). The results obtained in this study are evidence that the percentage of methylated cytosine cannot be inferred solely based on the genome size or t-heterochromatin. This is a significantly more complex issue. PMID:28149679

  13. 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.

  14. Plasmodium species: Flow cytometry and microfluorometry assessments of DNA content and synthesis

    NARCIS (Netherlands)

    Janse, C.J.; Vianen, P.H. van; Tanke, H.J.; Mons, B.; Ponnudurai, T.; Overdulve, J.P.

    1987-01-01

    Fluorescence intensities were established by flow cytometry of different erythrocytic stages of Plasmodium berghei after staining of their DNA with Hoechst-33258 or Hoechst-33342. Parasites were obtained from highly synchronized infections or in vitro cultures. Most fluorescence measurements were pe

  15. TOL plasmid carriage enhances biofilm formation and increases extracellular DNA content in Pseudomonas putida KT2440.

    Science.gov (United States)

    D'Alvise, Paul W; Sjøholm, Ole R; Yankelevich, Tatiana; Jin, Yujie; Wuertz, Stefan; Smets, Barth F

    2010-11-01

    Adherent growth of Pseudomonas putida KT2440 with and without the TOL plasmid (pWWO) at the solid-liquid and air-liquid interface was examined. We compared biofilm formation on glass in flow cells, and assayed pellicle (air-liquid interface biofilm) formation in stagnant liquid cultures by confocal laser scanning microscopy. The TOL-carrying strains formed pellicles and thick biofilms, whereas the same strains without the plasmid displayed little adherent growth. Microscopy using fluorescent nucleic acid-specific stains revealed differences in the production of extracellular polymeric substances: TOL carriage leads to more extracellular DNA (eDNA) in pellicles and biofilms. Pellicles were dissolved by DNase I treatment. Enhanced cell lysis due to plasmid carriage was ruled out as the mechanism for eDNA release. We report, for the first time, that carriage of a conjugative plasmid leads to increased biofilm formation by production of eDNA. © 2010 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

  16. Content-based image retrieval with ontological ranking

    Science.gov (United States)

    Tsai, Shen-Fu; Tsai, Min-Hsuan; Huang, Thomas S.

    2010-02-01

    Images are a much more powerful medium of expression than text, as the adage says: "One picture is worth a thousand words." It is because compared with text consisting of an array of words, an image has more degrees of freedom and therefore a more complicated structure. However, the less limited structure of images presents researchers in the computer vision community a tough task of teaching machines to understand and organize images, especially when a limit number of learning examples and background knowledge are given. The advance of internet and web technology in the past decade has changed the way human gain knowledge. People, hence, can exchange knowledge with others by discussing and contributing information on the web. As a result, the web pages in the internet have become a living and growing source of information. One is therefore tempted to wonder whether machines can learn from the web knowledge base as well. Indeed, it is possible to make computer learn from the internet and provide human with more meaningful knowledge. In this work, we explore this novel possibility on image understanding applied to semantic image search. We exploit web resources to obtain links from images to keywords and a semantic ontology constituting human's general knowledge. The former maps visual content to related text in contrast to the traditional way of associating images with surrounding text; the latter provides relations between concepts for machines to understand to what extent and in what sense an image is close to the image search query. With the aid of these two tools, the resulting image search system is thus content-based and moreover, organized. The returned images are ranked and organized such that semantically similar images are grouped together and given a rank based on the semantic closeness to the input query. The novelty of the system is twofold: first, images are retrieved not only based on text cues but their actual contents as well; second, the grouping

  17. Free energy and information contents of conformons in proteins and DNA.

    Science.gov (United States)

    Ji, S

    2000-01-01

    Sequence-specific conformational strains (SSCS) of biopolymers that carry free energy and genetic information have been called conformons, a term coined independently by two groups over two and a half decades ago [Green, D.E., Ji, S., 1972. The electromechanochemical model of mitochondrial structure and function. In: Schultz, J., Cameron, B.F. (Eds.), Molecular Basis of Electron Transport. Academic Press, New York, pp. 1-44; Volkenstein, M.V., 1972. The Conformon. J. Theor. Biol. 34, 193-195]. Conformons provide the molecular mechanisms necessary and sufficient to account for all biological processes in the living cell on the molecular level in principle--including the origin of life, enzymic catalysis, control of gene expression, oxidative phosphorylation, active transport, and muscle contraction. A clear example of SSCS is provided by SIDD (strain-induced duplex destabilization) in DNA recently reported by Benham [Benham, C.J., 1996a. Duplex destabilization in superhelical DNA is predicted to occur at specific transcriptional regulatory regions. J. Mol. Biol. 255, 425-434; Benham, C.J., 1996b. Computation of DNA structural variability--a new predictor of DNA regulatory regions. CABIOS 12(5), 375-381]. Experimental as well as theoretical evidence indicates that conformons in proteins carry 8-16 kcal/mol of free energy and 40-200 bits of information, while those in DNA contain 500-2500 kcal/mol of free energy and 200-600 bits of information. The similarities and differences between conformons and solitons have been analyzed on the basis of the generalized Franck-Condon principle [Ji, S., 1974a. A general theory of ATP synthesis and utilization. Ann. N.Y. Acad. Sci. 227, 211-226; Ji, S., 1974b. Energy and negentropy in enzymic catalysis. Ann. N.Y. Acad. Sci. 227, 419-437]. To illustrate a practical application, the conformon theory was applied to the molecular-clamp model of DNA gyrase proposed by Berger and Wang [Berger, J.M., Wang, J.C., 1996. Recent developments

  18. 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.

  19. Content-based, Task-based, and Participatory Approaches (I)

    Institute of Scientific and Technical Information of China (English)

    Diane Larsen-Freeman

    2012-01-01

    1. Introduction In this chapter we will be investigating three more approaches that make communication central: content-based instruction, task-based instruction, and the participatory approach. The approaches we examine in this chapter do not begin with functions, or approaches we examine in this chapter don't begin with functions, or indeed, any other language items. Instead, they give priority to process over predetermined linguistic content. In these approaches rather than "learning to use English",

  20. 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...

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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 .

  6. Multimedia Content Based Image Retrieval Iii: Local Tetra Pattern

    Directory of Open Access Journals (Sweden)

    Nagaraja G S

    2014-06-01

    Full Text Available Content Based Image Retrieval methods face several challenges while presentation of results and precision levels due to various specific applications. To improve the performance and address these problems a novel algorithm Local Tetra Pattern (LTrP is proposed which is coded in four direction instead of two direction used in Local Binary Pattern (LBP, Local Derivative Pattern (LDP andLocal Ternary Pattern(LTP.To retrieve the images the surrounding neighbor pixel value is calculated by gray level difference, which gives the relation between various multisorting algorithms using LBP, LDP, LTP and LTrP for sorting the images. This method mainly uses low level features such as color, texture and shape layout for image retrieval.

  7. Content-Based Publish/Subscribe System for Web Syndication

    Institute of Scientific and Technical Information of China (English)

    Zeinab Hmedeh; Harry Kourdounakis; Vassilis Christophides; Cedric du Mouza; Michel Scholl; Nicolas Travers

    2016-01-01

    Content syndication has become a popular way for timely delivery of frequently updated information on the Web. Today, web syndication technologies such as RSS or Atom are used in a wide variety of applications spreading from large-scale news broadcasting to medium-scale information sharing in scientific and professional communities. However, they exhibit serious limitations for dealing with information overload in Web 2.0. There is a vital need for efficient real-time filtering methods across feeds, to allow users to effectively follow personally interesting information. We investigate in this paper three indexing techniques for users’ subscriptions based on inverted lists or on an ordered trie for exact and partial matching. We present analytical models for memory requirements and matching time and we conduct a thorough experimental evaluation to exhibit the impact of critical parameters of realistic web syndication workloads.

  8. Retrieval Architecture with Classified Query for Content Based Image Recognition

    Directory of Open Access Journals (Sweden)

    Rik Das

    2016-01-01

    Full Text Available The consumer behavior has been observed to be largely influenced by image data with increasing familiarity of smart phones and World Wide Web. Traditional technique of browsing through product varieties in the Internet with text keywords has been gradually replaced by the easy accessible image data. The importance of image data has portrayed a steady growth in application orientation for business domain with the advent of different image capturing devices and social media. The paper has described a methodology of feature extraction by image binarization technique for enhancing identification and retrieval of information using content based image recognition. The proposed algorithm was tested on two public datasets, namely, Wang dataset and Oliva and Torralba (OT-Scene dataset with 3688 images on the whole. It has outclassed the state-of-the-art techniques in performance measure and has shown statistical significance.

  9. Weighted feature fusion for content-based image retrieval

    Science.gov (United States)

    Soysal, Omurhan A.; Sumer, Emre

    2016-07-01

    The feature descriptors such as SIFT (Scale Invariant Feature Transform), SURF (Speeded-up Robust Features) and ORB (Oriented FAST and Rotated BRIEF) are known as the most commonly used solutions for the content-based image retrieval problems. In this paper, a novel approach called "Weighted Feature Fusion" is proposed as a generic solution instead of applying problem-specific descriptors alone. Experiments were performed on two basic data sets of the Inria in order to improve the precision of retrieval results. It was found that in cases where the descriptors were used alone the proposed approach yielded 10-30% more accurate results than the ORB alone. Besides, it yielded 9-22% and 12-29% less False Positives compared to the SIFT alone and SURF alone, respectively.

  10. Web Pages Content Analysis Using Browser-Based Volunteer Computing

    Directory of Open Access Journals (Sweden)

    Wojciech Turek

    2013-01-01

    Full Text Available Existing solutions to the problem of finding valuable information on the Websuffers from several limitations like simplified query languages, out-of-date in-formation or arbitrary results sorting. In this paper a different approach to thisproblem is described. It is based on the idea of distributed processing of Webpages content. To provide sufficient performance, the idea of browser-basedvolunteer computing is utilized, which requires the implementation of text pro-cessing algorithms in JavaScript. In this paper the architecture of Web pagescontent analysis system is presented, details concerning the implementation ofthe system and the text processing algorithms are described and test resultsare provided.

  11. Approach to extracting hot topics based on network traffic content

    Institute of Scientific and Technical Information of China (English)

    Yadong ZHOU; Xiaohong GUAN; Qindong SUN; Wei LI; Jing TAO

    2009-01-01

    This article presents the formal definition and description of popular topics on the Internet,analyzes the relationship between popular words and topics,and finally introduces a method that uses statistics and correlation of the popular words in traffic content and network flow characteristics as input for extracting popular topics on the Internet.Based on this,this article adapts a clustering algorithm to extract popular topics and gives formalized results.The test results show that this method has an accuracy of 16.7% in extracting popular topics on the Internet.Compared with web mining and topic detection and tracking (TDT),it can provide a more suitable data source for effective recovery of Internet public opinions.

  12. PERFORMANCE EVALUATION OF CONTENT BASED IMAGE RETRIEVAL FOR MEDICAL IMAGES

    Directory of Open Access Journals (Sweden)

    SASI KUMAR. M

    2013-04-01

    Full Text Available Content-based image retrieval (CBIR technology benefits not only large image collections management, but also helps clinical care, biomedical research, and education. Digital images are found in X-Rays, MRI, CT which are used for diagnosing and planning treatment schedules. Thus, visual information management is challenging as the data quantity available is huge. Currently, available medical databases utilization is limited image retrieval issues. Archived digital medical images retrieval is always challenging and this is being researched more as images are of great importance in patient diagnosis, therapy, medical reference, and medical training. In this paper, an image matching scheme using Discrete Sine Transform for relevant feature extraction is presented. The efficiency of different algorithm for classifying the features to retrieve medical images is investigated.

  13. Incorporating Semantics into Data Driven Workflows for Content Based Analysis

    Science.gov (United States)

    Argüello, M.; Fernandez-Prieto, M. J.

    Finding meaningful associations between text elements and knowledge structures within clinical narratives in a highly verbal domain, such as psychiatry, is a challenging goal. The research presented here uses a small corpus of case histories and brings into play pre-existing knowledge, and therefore, complements other approaches that use large corpus (millions of words) and no pre-existing knowledge. The paper describes a variety of experiments for content-based analysis: Linguistic Analysis using NLP-oriented approaches, Sentiment Analysis, and Semantically Meaningful Analysis. Although it is not standard practice, the paper advocates providing automatic support to annotate the functionality as well as the data for each experiment by performing semantic annotation that uses OWL and OWL-S. Lessons learnt can be transmitted to legacy clinical databases facing the conversion of clinical narratives according to prominent Electronic Health Records standards.

  14. 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.

  15. Nuclear DNA content and ultrastructure of secretory cells of Vicia faba L. stigma

    Directory of Open Access Journals (Sweden)

    Bogdan Wróbel

    2014-01-01

    Full Text Available The object of study was the level of nuclear DNA and the ultrastructural transformations in the secretory cells of the stigma in Vicia faba L. It has been found that the stigmal cells which are active in biogenesis and exudate secretion are diploid cells whose differentiation starts from 2C DNA level. The presence of a population of nuclei with an amount DNA of about 2.5 C suggests that the metabolic activity of those cells may be regulated through supplementary incomplete replication. The ultrastructural transformations of secretory cells point to three stages of biogenesis and secretion of exudate. Stage I, before the start of the cell's secretory functions, is characterized by the development of the protein synthesizing apparatus and the activity of dictyosomes. In development stage II vesicular electron-transparent exudate is secreted. Stage III of exudate biogenesis is production of lipids. They form mainly in the plastids and are secreted with the involvement of the cell's vacuolar system.

  16. Multilocus sequence analysis supports the taxonomic position of Astragalus glycyphyllos symbionts based on DNA-DNA hybridization.

    Science.gov (United States)

    Gnat, Sebastian; Małek, Wanda; Oleńska, Ewa; Wdowiak-Wróbel, Sylwia; Kalita, Michał; Rogalski, Jerzy; Wójcik, Magdalena

    2016-04-01

    In this study, the phylogenetic relationship and taxonomic status of six strains, representing different phenons and genomic groups of Astragalus glycyphyllos symbionts, originating from Poland, were established by comparative analysis of five concatenated housekeeping gene sequences (atpD, dnaK, glnA, recA and rpoB), DNA-DNA hybridization and total DNA G+C content. Maximum-likelihood phylogenetic analysis of combined atpD, dnaK, glnA, recA and rpoB sequence data placed the studied bacteria into the clade comprising the genus Mesorhizobium. In the core gene phylograms, four A. glycyphyllos nodule isolates (AG1, AG7, AG15 and AG27) formed a cluster common with Mesorhizobium ciceri, whereas the two other A. glycyphyllos symbionts (AG17 and AG22) were grouped together with Mesorhizobium amorphae and M. septentrionale. The species position of the studied bacteria was clarified by DNA-DNA hybridization. The DNA-DNA relatedness between isolates AG1, AG7, AG15 and AG27 and reference strain M. ciceri USDA 3383T was 76.4-84.2%, and all these A. glycyphyllos nodulators were defined as members of the genomospecies M. ciceri. DNA-DNA relatedness for isolates AG17 and AG22 and the reference strain M. amorphae ICMP 15022T was 77.5 and 80.1%, respectively. We propose that the nodule isolates AG17 and AG22 belong to the genomic species M. amorphae. Additionally, it was found that the total DNA G+C content of the six test A. glycyphyllos symbionts was 59.4-62.1 mol%, within the range for species of the genus Mesorhizobium.

  17. Monoclonal antibody-based, selective isolation of DNA fragments containing an alkylated base to be quantified in defined gene sequences.

    Science.gov (United States)

    Hochleitner, K; Thomale, J; Nikitin AYu; Rajewsky, M F

    1991-08-25

    We have established a sensitive, monoclonal antibody (Mab)-based procedure permitting the selective enrichment of sequences containing the miscoding alkylation product O6-ethylguanine (O6-EtGua) from mammalian DNA. H5 rat hepatoma cells were reacted with the N-nitroso carcinogen N-ethyl-N-nitrosourea in vitro, to give overall levels of greater than or equal to 25 O6-EtGua residues per diploid genome (corresponding to O6-EtGua/guanine molar ratios of greater than or equal to 10(-8). For analysis, enzymatically restricted DNA from these cells is incubated with an antibody specific for O6-ethyl-2'-deoxyguanosine, the resulting Mab-DNA complexes are separated from (O6-EtGua)-free fragments by filtration through a nitrocellulose (NC) membrane, and the DNA is recovered from the filter-bound complexes quantitatively. The efficiency of Mab binding to DNA fragments containing O6-EtGua is constant over a range of O6-EtGua/guanine molar ratios between 10(-5) and 10(-8). (O6-EtGua)-containing restriction fragments encompassing known gene sequences (e.g., the immunoglobulin E heavy chain gene of H5 rat hepatoma cells used as a model in this study) are subsequently amplified by PCR and quantified by slot-blot hybridisation. The content and distribution of a specific carcinogen-DNA adduct in defined sequences of genomic DNA can thus be analyzed as well as the kinetics of intragenomic (toposelective) repair of any DNA lesion for which a suitable Mab is available.

  18. Efficient content-based P2P image retrieval using peer content descriptions

    Science.gov (United States)

    Muller, Wolfgang T.; Eisenhardt, Martin; Henrich, Andreas

    2003-12-01

    Peer-to-peer (P2P) networks are overlay networks that connect independent computers (also called nodes or peers). In contrast to client/server solutions, all nodes offer and request services from other peers in a P2P network. P2P networks are very attractive in that they harness the computing power of many common desktop machines and necessitate little administrative overhead. While the resulting computing power is impressive, efficiently looking up data still is the major challenge in P2P networks. Current work comprises fast lookup of one-dimensional values (Distributed Hash Tables, DHT) and retrieval of texts using few keywords. However, the lookup of multimedia data in P2P networks is still attacked by very few groups. In this paper, we present experiments with efficient Content Based Image Retrieval in a P2P environment, thus a P2P-CBIR system. The challenge in such systems is to limit the number of messages sent, and to maximize the usefulness of each peer contacted in the query process. We achieve this by distributing peer data summaries over the network. Obviously, the data summaries have to be compact in order to limit the communication overhead. We propose an CBIR scheme based on a compact peer data summary. This peer data summary relies on cluster frequencies. To obtain the compact representation of a peer's collection, a global clustering of the data is efficiently calculated in a distributed manner. After that, each peer publishes how many of its images fall into each cluster. These cluster frequencies are then used by the querying peer to contact only those peers that have the largest number of images present in one cluster given by the query. In our paper we further detail the various challenges that have to be met by the designers of such a P2P-CBIR, and we present experiments with varying degree of data replication (duplicates of images), as well as quality of clustering within the network.

  19. 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.

  20. 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.

  1. AN EFFICIENT CONTENT AND SEGMENTATION BASED VIDEO COPY DETECTION

    Directory of Open Access Journals (Sweden)

    N. Kalaiselvi

    2015-10-01

    Full Text Available The field of multimedia technology has become easier to store, creation and access large amount of video data. This technology has editing and duplication of video data that will cause to violation of digital rights. So in this project we implemented an efficient content and segmentation based video copy detection concept to detect the illegal manipulation of video. In this Work or proposed system, Instead of SIFT matching algorithms, used combination of SIFT and SURF matching algorithms to detect the matching features in images. Because, SIFT is slow and not good at illumination changes, while it is invariant to rotation, scale changes and affine transformations and then SURF is fast and has good performance, but it is also have some issues that it is not stable to rotation and affine transformations. So combined the above two algorithms SIFT and SURF to extract the image features. Auto dual Threshold method is used to segment the video into segments and extract key frames from each segment and it also eliminate the redundant frame. SIFT and SURF features based on SVD is used to compare the two frames features sets points, where the SIFT and SURF features are extracted from the key frames of the segments. Graph-based video sequence matching method is used to match the sequence of query video and train video. It skillfully converts the video sequence matching result to a matching result graph.

  2. Natural ingredients based cosmetics. Content of selected fragrance sensitizers.

    Science.gov (United States)

    Rastogi, S C; Johansen, J D; Menné, T

    1996-06-01

    In the present study, we have investigated 42 cosmetic products based on natural ingredients for content of 11 fragrance substances: geraniol, hydroxycitronellal, eugenol, isoeugenol, cinnamic aldehyde, cinnamic alcohol, alpha-amylcinnamic aldehyde, citral, coumarin, dihydrocoumarin and alpha-hexylcinnamic aldehyde. The study revealed that the 91% (20/22) of the natural ingredients based perfumes contained 0.027%-7.706% of 1 to 7 of the target fragrances. Between 1 and 5 of the chemically defined synthetic constituents of fragrance mix were found in 82% (18/22) of the perfumes. 35% (7/20) of the other cosmetic products (shampoos, creams, tonics, etc) were found to contain 0.0003-0.0820% of 1 to 3 of the target fragrances. Relatively high concentrations of hydroxycitronellal, coumarin, cinnamic alcohol and alpha-amyl cinnamic aldehyde were found in some of the investigated products. The detection of hydroxycitronellal and alpha-hexylcinnamic aldehyde in some of the products demonstrates that artificial fragrances, i.e., compounds not yet regarded as natural substances, may be present in products claimed to be based on natural ingredients.

  3. 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.

  4. 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

  5. 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

  6. Removing external DNA contamination from arthropod predators destined for molecular gut-content analysis

    Science.gov (United States)

    Molecular gut-content analysis enables detection of arthropod predation with minimal disruption of ecosystem processes. Field and laboratory experiments have demonstrated that mass-collection methods, such as sweep-netting, vacuum sampling, and foliage beating, can lead to contamination of fed pred...

  7. Removing external DNA decontamination from arthropod predators destined for molecular gut-content analysis

    Science.gov (United States)

    Molecular gut-content analysis enables detection of arthropod predation with minimal disruption of ecosystem processes. Field and laboratory experiments have demonstrated that mass-collection methods, such as sweep-netting, vacuum sampling, and foliage beating, can lead to contamination of fed pred...

  8. Content Based Image Retrieval Using Singular Value Decomposition

    Directory of Open Access Journals (Sweden)

    K. Harshini

    2012-10-01

    Full Text Available A computer application which automatically identifies or verifies a person from a digital image or a video frame from a video source, one of the ways to do this is by com-paring selected facial features from the image and a facial database. Content based image retrieval (CBIR, a technique for retrieving images on the basis of automatically derived features. This paper focuses on a low-dimensional feature based indexing technique for achieving efficient and effective retrieval performance. An appearance based face recognition method called singular value decomposition (SVD is proposed in this paper and is different from principal component analysis (PCA, which effectively considers only Euclidean structure of face space for analysis which lead to poor classification performance in case of great facial variations such as expression, lighting, occlusion and so on, due to the fact the image gray value matrices on which they manipulate are very sensitive to these facial variations. We consider the fact that every image matrix can always have the well known singular value decomposition (SVD and can be regarded as a composition of a set of base images generated by SVD and we further point out that base images are sensitive to the composition of face image. Finally our experimental results show that SVD has the advantage of providing a better representation and achieves lower error rates in face recognition but it has the disadvantage that it drags the performance evaluation. So, in order to overcome that, we conducted experiments by introducing a controlling parameter ‘α’, which ranges from 0 to 1, and we achieved better results for α=0.4 when compared with the other values of ‘α’. Key words: Singular value decomposition (SVD, Euclidean distance, original gray value matrix (OGVM.

  9. 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

  10. 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

  11. EFFECTS OF PERIOPERATIVE CIMETIDINE ADMINISTRATION ON TUMOR CELL NUCLEAR MORPHOMETRY AND DNA CONTENT IN PATIENTS WITH GASTROINTESTINAL CANCER

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Objective: To explore the effects of perioperative cimetidine administration on tumor cell nuclear morphometric parameters and DNA content in patients with gastrointestinal adenocarcinoma. Methods: 49 patients with pathologically confirmed gastrointestinal adenocarcinoma were randomized into test group (n=25) and control group (n=24). The test group started oral cimetidine intake 400 mg, tid, 7-10d before operation, followed by standard curative operation. The control group did not receive cimetidine. Tumor specimens were paraffin embedded for microsection and stained with hematoxylin and eosin (HE) and Feulgen stain. Morphometric studies and DNA content of tumor nuclei were performed on IBAS Image Analyzer. Results: The tumor cell nuclear area (m m2), nuclear perimeter (m m), maximal nuclear diameter (m m) for test group/control group were 23.54 ± 5.08/34.69± 10.08 (Pquintuple ploidy tumor cells for test group/control group were 16.64± 2.58/5.33± 2.14 (P0.50), 12.42± 5.00/14.48± 0.74 (P>0.20), 31.11± 6.86/ 45.97± 3.82 (P<0.005), respectively. Conclusion: Perioperative administration of cimetidine in gasgtrointestinal cancer patients could decrease the nuclear size and raise the percentage of diploid tumor cells, and convert high aneuploid tumor cells into low-aneuploid tumor cells, which might help reduce the invasiveness of tumor cells.

  12. 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.

  13. 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.

  14. 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.

  15. Correlation of inter-locus polyglutamine toxicity with CAG•CTG triplet repeat expandability and flanking genomic DNA GC content.

    Directory of Open Access Journals (Sweden)

    Colm E Nestor

    Full Text Available Dynamic expansions of toxic polyglutamine (polyQ-encoding CAG repeats in ubiquitously expressed, but otherwise unrelated, genes cause a number of late-onset progressive neurodegenerative disorders, including Huntington disease and the spinocerebellar ataxias. As polyQ toxicity in these disorders increases with repeat length, the intergenerational expansion of unstable CAG repeats leads to anticipation, an earlier age-at-onset in successive generations. Crucially, disease associated alleles are also somatically unstable and continue to expand throughout the lifetime of the individual. Interestingly, the inherited polyQ length mediating a specific age-at-onset of symptoms varies markedly between disorders. It is widely assumed that these inter-locus differences in polyQ toxicity are mediated by protein context effects. Previously, we demonstrated that the tendency of expanded CAG•CTG repeats to undergo further intergenerational expansion (their 'expandability' also differs between disorders and these effects are strongly correlated with the GC content of the genomic flanking DNA. Here we show that the inter-locus toxicity of the expanded polyQ tracts of these disorders also correlates with both the expandability of the underlying CAG repeat and the GC content of the genomic DNA flanking sequences. Inter-locus polyQ toxicity does not correlate with properties of the mRNA or protein sequences, with polyQ location within the gene or protein, or steady state transcript levels in the brain. These data suggest that the observed inter-locus differences in polyQ toxicity are not mediated solely by protein context effects, but that genomic context is also important, an effect that may be mediated by modifying the rate at which somatic expansion of the DNA delivers proteins to their cytotoxic state.

  16. The relationships among IGF-1, DNA content, and protein accumulation during skeletal muscle hypertrophy

    Science.gov (United States)

    Adams, G. R.; Haddad, F.

    1996-01-01

    Insulin-like growth factor-1 (IGF-1) is known to have anabolic effects on skeletal muscle cells. This study examined the time course of muscle hypertrophy and associated IGF-1 peptide and mRNA expression. Data were collected at 3, 7, 14, and 28 days after surgical removal of synergistic muscles of both normal and hypophysectomized (HX) animals. Overloading increased the plantaris (Plant) mass, myofiber size, and protein-to-body weight ratio in both groups (normal and HX; P hypertrophy response, possibly via the mobilization of satellite cells to provide increases in muscle DNA.

  17. Comparison of two silica-based extraction methods for DNA isolation from bones.

    Science.gov (United States)

    Rothe, Jessica; Nagy, Marion

    2016-09-01

    One of the most demanding DNA extractions is from bones and teeth due to the robustness of the material and the relatively low DNA content. The greatest challenge is due to the manifold nature of the material, which is defined by various factors, including age, storage, environmental conditions, and contamination with inhibitors. However, most published protocols do not distinguish between different types or qualities of bone material, but are described as being generally applicable. Our laboratory works with two different extraction methods based on silica membranes or the use of silica beads. We compared the amplification success of the two methods from bone samples with different qualities and in the presence of inhibitors. We found that the DNA extraction using the silica membrane method results an in higher DNA yield but also in a higher risk of co-extracting impurities, which can act as inhibitors. In contrast the silica beads method shows decreased co-extraction of inhibitors but also less DNA yield. Related to our own experiences it has to be considered that each bone material should be reviewed independently regarding the analysis and extraction method. Therefore, the most ambitious task is determining the quality of the bone material, which requires substantial experience. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  18. Tetrahedral DNA nanostructure-based microRNA biosensor coupled with catalytic recycling of the analyte.

    Science.gov (United States)

    Miao, Peng; Wang, Bidou; Chen, Xifeng; Li, Xiaoxi; Tang, Yuguo

    2015-03-25

    MicroRNAs are not only important regulators of a wide range of cellular processes but are also identified as promising disease biomarkers. Due to the low contents in serum, microRNAs are always difficult to detect accurately . In this study, an electrochemical biosensor for ultrasensitive detection of microRNA based on tetrahedral DNA nanostructure is developed. Four DNA single strands are engineered to form a tetrahedral nanostructure with a pendant stem-loop and modified on a gold electrode surface, which largely enhances the molecular recognition efficiency. Moreover, taking advantage of strand displacement polymerization, catalytic recycling of microRNA, and silver nanoparticle-based solid-state Ag/AgCl reaction, the proposed biosensor exhibits high sensitivity with the limit of detection down to 0.4 fM. This biosensor shows great clinical value and may have practical utility in early diagnosis and prognosis of certain diseases.

  19. Content-Based Image Retrieval for Semiconductor Process Characterization

    Directory of Open Access Journals (Sweden)

    Kenneth W. Tobin

    2002-07-01

    Full Text Available Image data management in the semiconductor manufacturing environment is becoming more problematic as the size of silicon wafers continues to increase, while the dimension of critical features continues to shrink. Fabricators rely on a growing host of image-generating inspection tools to monitor complex device manufacturing processes. These inspection tools include optical and laser scattering microscopy, confocal microscopy, scanning electron microscopy, and atomic force microscopy. The number of images that are being generated are on the order of 20,000 to 30,000 each week in some fabrication facilities today. Manufacturers currently maintain on the order of 500,000 images in their data management systems for extended periods of time. Gleaning the historical value from these large image repositories for yield improvement is difficult to accomplish using the standard database methods currently associated with these data sets (e.g., performing queries based on time and date, lot numbers, wafer identification numbers, etc.. Researchers at the Oak Ridge National Laboratory have developed and tested a content-based image retrieval technology that is specific to manufacturing environments. In this paper, we describe the feature representation of semiconductor defect images along with methods of indexing and retrieval, and results from initial field-testing in the semiconductor manufacturing environment.

  20. Content-Based Object Movie Retrieval and Relevance Feedbacks

    Directory of Open Access Journals (Sweden)

    Lee Greg C

    2007-01-01

    Full Text Available Object movie refers to a set of images captured from different perspectives around a 3D object. Object movie provides a good representation of a physical object because it can provide 3D interactive viewing effect, but does not require 3D model reconstruction. In this paper, we propose an efficient approach for content-based object movie retrieval. In order to retrieve the desired object movie from the database, we first map an object movie into the sampling of a manifold in the feature space. Two different layers of feature descriptors, dense and condensed, are designed to sample the manifold for representing object movies. Based on these descriptors, we define the dissimilarity measure between the query and the target in the object movie database. The query we considered can be either an entire object movie or simply a subset of views. We further design a relevance feedback approach to improving retrieved results. Finally, some experimental results are presented to show the efficacy of our approach.

  1. A transport protocol for best-effort content-based networks

    OpenAIRE

    Malekpour, Amirhossein; Carzaniga, Antonio ; Pedone, Fernando

    2013-01-01

    Content-based publish/subscribe (or simply content-based) networking is a relatively new communication paradigm compared to IP networking, with a different approach to addressing network hosts. In content- based networking addressing as well as information dissemination center around information and interests. A host's address is represented by its interest and information is routed by a network of brokers to hosts with relevant interests. We advocate the idea that content-based network...

  2. 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.

  3. INVESTIGATION OF METHODS OF DNA EXTRACTION FROM PLANT ORIGIN OBJECTS AND FOODS BASED ON THEM

    Directory of Open Access Journals (Sweden)

    L. S. Dyshlyuk

    2014-01-01

    Full Text Available For the last decades modern and highly efficient methods of determining the quality and safety of food products, based on the application of the latest scientific achievements were developed in the world. A special place is given to the methods based on achievements of molecular biology and genetics. At the present stage of development in the field of assessing the quality of raw materials and processed food products much attention is given to highly accurate, sensitive and specific research methods, the method of polymerase chain reaction (PCR occupying a leading place among them. PCR is a sophisticated method that simulates the natural DNA replication and allows to detect a single specific DNA molecule in the presence of millions of other molecules. The key point in the preparation of material for PCR is the extraction of nucleic acids. The low content of DNA in plant material and the high concentration of secondary metabolites complicate the process of extraction. The key solution to this problem is highly effective method of extraction, which allows to obtain the DNA of adequate quality and purity. Comparative analysis of methods for the extraction of nucleic acids from fruit raw materials and products based on them was carried out in the study. General analysis of the experimental data allowed us to determine the most efficient method for DNA extracting. In the comparative analysis it was found out that to extract DNA from plant raw materials and food products prepared on their basis it is the most suitable to use "Sorb-GMO-A" reactants kit (set. The approach described gives us a brilliant opportunity to obtain deoxyribonucleic acid proper quality and purity.

  4. 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

  5. DNA methylation analysis of chromosome 21 gene promoters at single base pair and single allele resolution.

    Directory of Open Access Journals (Sweden)

    Yingying Zhang

    2009-03-01

    Full Text Available Differential DNA methylation is an essential epigenetic signal for gene regulation, development, and disease processes. We mapped DNA methylation patterns of 190 gene promoter regions on chromosome 21 using bisulfite conversion and subclone sequencing in five human cell types. A total of 28,626 subclones were sequenced at high accuracy using (long-read Sanger sequencing resulting in the measurement of the DNA methylation state of 580427 CpG sites. Our results show that average DNA methylation levels are distributed bimodally with enrichment of highly methylated and unmethylated sequences, both for amplicons and individual subclones, which represent single alleles from individual cells. Within CpG-rich sequences, DNA methylation was found to be anti-correlated with CpG dinucleotide density and GC content, and methylated CpGs are more likely to be flanked by AT-rich sequences. We observed over-representation of CpG sites in distances of 9, 18, and 27 bps in highly methylated amplicons. However, DNA sequence alone is not sufficient to predict an amplicon's DNA methylation status, since 43% of all amplicons are differentially methylated between the cell types studied here. DNA methylation in promoter regions is strongly correlated with the absence of gene expression and low levels of activating epigenetic marks like H3K4 methylation and H3K9 and K14 acetylation. Utilizing the single base pair and single allele resolution of our data, we found that i amplicons from different parts of a CpG island frequently differ in their DNA methylation level, ii methylation levels of individual cells in one tissue are very similar, and iii methylation patterns follow a relaxed site-specific distribution. Furthermore, iv we identified three cases of allele-specific DNA methylation on chromosome 21. Our data shed new light on the nature of methylation patterns in human cells, the sequence dependence of DNA methylation, and its function as epigenetic signal in gene

  6. 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

  7. Implementing a Web-based content management system.

    Science.gov (United States)

    Pomeroy, Brian; Crawford, Evan; Sinisi, Albert

    2003-01-01

    The Children's Hospital of Philadelphia transformed its web site to enhance patient satisfaction and attract new patients, as well as meet the needs of clinicians and the hospital's business plans. They accomplished this by implementing a content management system that would allow content creation and updating to be delegated to appropriate department staffers, thereby eliminating bottlenecks and unnecessary steps and ensuring that the web site receives fresh content much more quickly.

  8. Socioscientific Issues-Based Instruction: An Investigation of Agriscience Students' Content Knowledge Based on Student Variables

    Science.gov (United States)

    Shoulders, Catherine W.; Myers, Brian E.

    2013-01-01

    Numerous researchers in science education have reported student improvement in areas of scientific literacy resulting from socioscientific issues (SSI)-based instruction. The purpose of this study was to describe student agriscience content knowledge following a six-week SSI-based instructional unit focusing on the introduction of cultured meat…

  9. Content-based versus semantic-based retrieval: an LIDC case study

    Science.gov (United States)

    Jabon, Sarah A.; Raicu, Daniela S.; Furst, Jacob D.

    2009-02-01

    Content based image retrieval is an active area of medical imaging research. One use of content based image retrieval (CBIR) is presentation of known, reference images similar to an unknown case. These comparison images may reduce the radiologist's uncertainty in interpreting that case. It is, therefore, important to present radiologists with systems whose computed-similarity results correspond to human perceived-similarity. In our previous work, we developed an open-source CBIR system that inputs a computed tomography (CT) image of a lung nodule as a query and retrieves similar lung nodule images based on content-based image features. In this paper, we extend our previous work by studying the relationships between the two types of retrieval, content-based and semantic-based, with the final goal of integrating them into a system that will take advantage of both retrieval approaches. Our preliminary results on the Lung Image Database Consortium (LIDC) dataset using four types of image features, seven radiologists' rated semantic characteristics and two simple similarity measures show that a substantial number of nodules identified as similar based on image features are also identified as similar based on semantic characteristics. Furthermore, by integrating the two types of features, the similarity retrieval improves with respect to certain nodule characteristics.

  10. Content-based, Task-based, and Participatory Approaches (II)

    Institute of Scientific and Technical Information of China (English)

    Diane Larsen-Freeman

    2012-01-01

    4. Participatory Approach Although it originated in the early sixties with the work of Paulo Freire, and therefore antedates modern versions of content-based and task-based approaches, it was not until the 1980s that the participatory approach started being widely discussed in the language teaching literature.

  11. Folding thermodynamics of c-Myb DNA-binding domain in correlation with its α-helical contents.

    Science.gov (United States)

    Inaba, Satomi; Fukada, Harumi; Oda, Masayuki

    2016-01-01

    The conformational and thermal stabilities of the minimum functional unit for c-Myb DNA-binding domain, tandem repeat 2 and 3 (R2R3), were analyzed under different pH conditions, ranging from 4.0 to 7.5, using circular dichroism and differential scanning calorimetry. Secondary structure analysis showed that the solution pH largely affects the conformational stability of the protein domain. Of all conditions analyzed, the α-helical content was maximal at pH 6.5, and the thermal stability was highest at pH 5.0. Thermodynamic parameters for thermal unfolding of R2R3 were determined using differential scanning calorimetry, and the origin of folding thermodynamics at the different pHs and its correlation with the α-helical content were further analyzed. It should be noted that the α-helical content correlates well with the enthalpy change in the pH range from 4.5 to 7.5, suggesting that the strength of hydrogen bonds and salt bridges needed for maintenance of helical structure is related to enthalpy in the native state. Under physiological pH conditions, c-Myb R2R3 exists in the enthalpically unstable but entropically stable state. Due to loss of rigid structure and high stability, the protein can now obtain structural flexibility, befitting its function.

  12. 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.

  13. 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.

  14. Content Based Image Retrieval by Multi Features using Image Blocks

    Directory of Open Access Journals (Sweden)

    Arpita Mathur

    2013-12-01

    Full Text Available Content based image retrieval (CBIR is an effective method of retrieving images from large image resources. CBIR is a technique in which images are indexed by extracting their low level features like, color, texture, shape, and spatial location, etc. Effective and efficient feature extraction mechanisms are required to improve existing CBIR performance. This paper presents a novel approach of CBIR system in which higher retrieval efficiency is achieved by combining the information of image features color, shape and texture. The color feature is extracted using color histogram for image blocks, for shape feature Canny edge detection algorithm is used and the HSB extraction in blocks is used for texture feature extraction. The feature set of the query image are compared with the feature set of each image in the database. The experiments show that the fusion of multiple features retrieval gives better retrieval results than another approach used by Rao et al. This paper presents comparative study of performance of the two different approaches of CBIR system in which the image features color, shape and texture are used.

  15. Content-Based Human Motion Retrieval with Scene Description Language

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    As commercial motion capture systems are widely used, more and more 3D motion libraries become available, reinforcing the demand for efficient indexing and retrieving methods. Usually, the user will only have a sketchy idea of which kind of motion to look for in the motion database. As a result, how to clearly describe the user's demands is a bottleneck for motion retrieval system. This paper presented a framework that can handle this problem effectively for motion retrieval. This content-based retrieval system supports two kinds of query modes:textual query mode and query-by-example mode. In both query modes, user's input is translated into scene description language first, which can be processed by the system efficiently. By using various kinds of qualitative features and adaptive segments of motion capture data stream, indexing and retrieval methods are carried out at the segment level rather than at the frame level, making them quite efficient. Some experimental examples are given to demonstrate the effectiveness and efficiency of the proposed algorithms.

  16. Content-Based Analysis of Bumper Stickers in Jordan

    Directory of Open Access Journals (Sweden)

    Abdullah A. Jaradat

    2016-12-01

    Full Text Available This study has set out to investigate bumper stickers in Jordan focusing mainly on the themes of the stickers. The study hypothesized that bumper stickers in Jordan reflect a wide range of topics including social, economic, and political. Due to being the first study of this phenomenon, the study has adopted content-based analysis to determine the basic topics. The study has found that the purpose of most bumper sticker is fun and humor; most of them are not serious and do not carry any biting messages. They do not present any criticism to the most dominant problems at the level of society including racism, nepotism, anti-feminism, inflation, high taxes, and refugees. Another finding is that politics is still a taboo; no political bumper stickers were found in Jordan. Finally, the themes the stickers targeted are: lessons of life 28.85 %; challenging or warning other drivers 16%; funny notes about social issues 12%; religious sayings 8%; treating the car as a female 7%; the low economic status of the driver 6%; love and treachery 5.5%; the prestigious status of the car 5%; envy 4%; nicknames for the car or the driver 4%; irony 3 %; and English sayings 1.5 %. Keywords: bumper stickers, themes, politics

  17. Soil Moisture Content Monitoring Based on ERS Wind Scatterometer Data

    Institute of Scientific and Technical Information of China (English)

    WANG Jian-ming; SHI Jian-cheng; SHAO Yun; LIU Wei

    2005-01-01

    The ERS-1/2 wind scatterometer (WSC) has a low resolution cell of about 50 km but provides a high repetition rate (<4 d) and can make measurements at multiple incidence angles. In order to estimate effective surface reflectivity (related to soil moisture content) over bare soil using WSC data, an original methodology based on the advance integral equation model (AIEM) is presented, which takes advantage of its multiple view angular characteristics. This method includes two steps. First, a simplified two-parameter surface scattering model is calibrated by AIEM simulated-database over a wide parameter space. Second, regression analyses are carried out using the simulated database to build the relation between those parameters of our model at different incident angles from two observations of Mid and Fore beams. From the model simulated database, our technique works quite well in estimating Γ0. The possibility of applying the model to retrieve soil moisture is investigated using a set of data collected from the Intensive Observation Period field campaign in 1998 of the Asian Monsoon Experiment Tibet (GAME-Tibet). The retrieved values obtained for the bare land surface are consistent with ground measurements collected in these areas and the correlation coefficient between retrieved soil moisture and the measured one reaches 0.65.

  18. Automatic indexing of news video for content-based retrieval

    Science.gov (United States)

    Yang, Myung-Sup; Yoo, Cheol-Jung; Chang, Ok-Bae

    1998-06-01

    Since it is impossible to automatically parse a general video, we investigated an integrated solution for the content-based news video indexing and the retrieval. Thus, a specific structural video such as news video is parsed, because it is included both temporal and spatial characteristics that the news event with an anchor-person is iteratively appeared, a news icon and a caption are involved in some frame, respectively. To extract automatically the key frames by using the structured knowledge of news, the model used in this paper is consisted of the news event segmentation, caption recognition and search browser module. The following are three main modules represented in this paper: (1) The news event segmentation module (NESM) for both the recognition and the division of an anchor-person shot. (2) The caption recognition module (CRM) for the detection of the caption-frames in a news event, the extraction of their caption region in the frame by using split-merge method, and the recognition of the region as a text with OCR software. 3) The search browser module (SBM) for the display of the list of news events and news captions, which are included in selected news event. However, the SBM can be caused various searching mechanisms.

  19. 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.

  20. 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.

  1. The abundant extrachromosomal DNA content of the Spiroplasma citri GII3-3X genome

    Directory of Open Access Journals (Sweden)

    Carrère Sébastien

    2008-04-01

    Full Text Available Abstract Background Spiroplama citri, the causal agent of citrus stubborn disease, is a bacterium of the class Mollicutes and is transmitted by phloem-feeding leafhopper vectors. In order to characterize candidate genes potentially involved in spiroplasma transmission and pathogenicity, the genome of S. citri strain GII3-3X is currently being deciphered. Results Assembling 20,000 sequencing reads generated seven circular contigs, none of which fit the 1.8 Mb chromosome map or carried chromosomal markers. These contigs correspond to seven plasmids: pSci1 to pSci6, with sizes ranging from 12.9 to 35.3 kbp and pSciA of 7.8 kbp. Plasmids pSci were detected as multiple copies in strain GII3-3X. Plasmid copy numbers of pSci1-6, as deduced from sequencing coverage, were estimated at 10 to 14 copies per spiroplasma cell, representing 1.6 Mb of extrachromosomal DNA. Genes encoding proteins of the TrsE-TraE, Mob, TraD-TraG, and Soj-ParA protein families were predicted in most of the pSci sequences, in addition to members of 14 protein families of unknown function. Plasmid pSci6 encodes protein P32, a marker of insect transmissibility. Plasmids pSci1-5 code for eight different S. citri adhesion-related proteins (ScARPs that are homologous to the previously described protein P89 and the S. kunkelii SkARP1. Conserved signal peptides and C-terminal transmembrane alpha helices were predicted in all ScARPs. The predicted surface-exposed N-terminal region possesses the following elements: (i 6 to 8 repeats of 39 to 42 amino acids each (sarpin repeats, (ii a central conserved region of 330 amino acids followed by (iii a more variable domain of about 110 amino acids. The C-terminus, predicted to be cytoplasmic, consists of a 27 amino acid stretch enriched in arginine and lysine (KR and an optional 23 amino acid stretch enriched in lysine, aspartate and glutamate (KDE. Plasmids pSci mainly present a linear increase of cumulative GC skew except in regions presenting

  2. Copyright Protection for Modifiable Digital Content Based on Distributed Environment

    Science.gov (United States)

    Park, Heejae; Kim, Jong

    Today, users themselves are becoming subjects of content creation. The fact that blog, wiki, and UCC have become very popular shows that users want to participate to create and modify digital content. Users who participate in composing content also want to have their copyrights on their modification parts. Thus, a copyright protection system for the content which can be modified by multiple users is required. However, the conventional DRM (Digital Rights Management) systems like OMA DRM are not suitable for the modifiable content because they do not support the content created and modified by different users. Therefore in this paper, we propose a new copyright protection system which allows each modifier of the content created and modified by multiple users to have one's own copyright. We propose data formats and protocols, and analyze the proposed system in terms of the correctness and security. Performance evaluation in the view of response time shows that the proposed system is 2 to 18 times shorter than other comparative schemes.

  3. 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.

  4. 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.

  5. 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.

  6. Analysis of DNA Content of Various Types of Spermatogenic Cells in Rat after Testicular Heating with Flow Cytometry

    Institute of Scientific and Technical Information of China (English)

    Duo XU; Wei-jie ZHU; Zi-neng WANG; Da-nian QIN

    2005-01-01

    Objective To measure DNA contents of spermatogenic cells and analyze the efficiency of spermatogenesis aftef testicular heating in ratMethods Eighty adult male Sprague-Dawley rats were randomly divided into experimental group (43 ℃, 30 min) and control group (22 ℃, 30 min). According to day 0.5, 1, 3, 6, 10, 25, 35 and 50 after local testicular heating, every group was divided into 8 subgroups:experimental subgroups (n=6) and control subgroups (n=4). DNA contents of various types of germ cells were observed with flow cytometry (FCM) in all groups.Results Compared with control groups, percentages of 4C cell (primary spermatocyte)in 0. 5 -35 d groups and percentages of 1 C cell (spermatid and sperm) in 6-50 d groups significantly decreased in experimental groups (P<0. 05), and percentages of 2C cell (spermatogonium and second spermatocyte) in 3 -35 d experimental groups increased significantly after heating (P<0. 05). 4C:2C in all of 8 experimental groups and 1C:2C in 3-35 d experimental groups were down (P<0. 05), and in 1 d experimental group 1C:4C was up after heating (P<0. 05).Conclusions After being heated, the number of spermatocyte firstly decreased, and then that of spermatid and sperm decreased too. Heat influences several stages in spermatogenesis and results in suppression of spermatogenesis. Flow cytometry is an effective method for researching on the change of spermatogenesis and has significance on mechanism about changing of spermatogenic cells induced by heat.

  7. Teaching Concepts of Natural Sciences to Foreigners through Content-Based Instruction: The Adjunct Model

    Science.gov (United States)

    Satilmis, Yilmaz; Yakup, Doganay; Selim, Guvercin; Aybarsha, Islam

    2015-01-01

    This study investigates three models of content-based instruction in teaching concepts and terms of natural sciences in order to increase the efficiency of teaching these kinds of concepts in realization and to prove that the content-based instruction is a teaching strategy that helps students understand concepts of natural sciences. Content-based…

  8. 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.

  9. Development of Content Management System-based Web Applications

    NARCIS (Netherlands)

    Souer, J.

    2012-01-01

    Web engineering is the application of systematic and quantifiable approaches (concepts, methods, techniques, tools) to cost-effective requirements analysis, design, implementation, testing, operation, and maintenance of high quality web applications. Over the past years, Content Management Systems (

  10. Effects of Spent Pot Liner on mitotic activity and nuclear DNA content in meristematic cells of Allium cepa.

    Science.gov (United States)

    Andrade-Vieira, Larissa Fonseca; de Campos, José Marcello Salabert; Davide, Lisete Chamma

    2012-09-30

    Industrial waste usually contains complex mixtures of mutagenic chemicals. Spent Pot Liner (SPL) is a complex solid waste from the aluminum industry, which is composed of organics, fluoride salts, inorganic cyanides, metals, and sodium. Due to the toxicity of these compounds, this study sought to use cytogenetics and flow cytometry to assess the effects of SPL on cell cycle parameters and DNA content in meristematic cells of Allium cepa. Three concentrations of leachates from SPL-soil mixtures were used for the study: 0, 10, and 25%. Roots were collected and analyzed after 4, 8, 12, 24, and 36 h of exposure to the above SPL leachates. The results showed an overall mitodepressive effect accompanied by an increased percentage of condensed nuclei and genomic instability as evidenced by the presence of cellular/chromosomal abnormalities. Terminal deoxynucleotidyl transferase dUTP nick end labeling revealed nuclei with fragmented DNA, a marker of programmed cell death. This study also addressed the question of reversibility of the effects of SPL and found that 36 h of exposure to 25% SPL seemed to be the point at which the effects on the induction of apoptosis became irreversible.

  11. Bivariate flow cytometric analysis of DNA content versus immunopositivity for ribonucleotide reductase M1 subunit in the cell cycle.

    Science.gov (United States)

    Mangiarotti, R; Bottone, M G; Danova, M; Pellicciari, C

    1998-06-01

    Ribonucleotide reductase (RR) is a cytoplasmatic enzyme catalyzing the reduction of all four ribonucleotides to their corresponding deoxyribonucleotides. Its activity strongly correlates to the rate of DNA synthesis. By using a specific monoclonal antibody against the large M1 subunit of RR, we assessed the expression of M1-RR versus DNA content by dual-parameter flow cytometry. The aim of this paper was to compare the variations in the immunopositivity for M1-RR during the cell cycle to the positivity for other cell cycle markers identifying either proliferating cells (Ki-67 and PCNA) or quiescent cells (statin). To do this, normal human embryonic fibroblasts in different growth conditions as well as several other mammalian cell lines (rat C6 glioma cells; mouse 3T3 fibroblasts and B16 melanoma cells; human epithelial EUE cells and mammary carcinoma MCF-7 cells) were used. The expression of M1-RR antigen was found to correlate positively with the expression of Ki-67 and PCNA, and negatively with the expression of statin. During early G1 phase, M1-RR becomes detectable by specific antibodies relatively later compared to PCNA and Ki-67; therefore, the lack of immunopositivity for M1-RR cannot be taken as an absolute indication of cell quiescence in G0.

  12. 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.

  13. A personalized web page content filtering model based on segmentation

    CERN Document Server

    Kuppusamy, K S; 10.5121/ijist.2012.2104

    2012-01-01

    In the view of massive content explosion in World Wide Web through diverse sources, it has become mandatory to have content filtering tools. The filtering of contents of the web pages holds greater significance in cases of access by minor-age people. The traditional web page blocking systems goes by the Boolean methodology of either displaying the full page or blocking it completely. With the increased dynamism in the web pages, it has become a common phenomenon that different portions of the web page holds different types of content at different time instances. This paper proposes a model to block the contents at a fine-grained level i.e. instead of completely blocking the page it would be efficient to block only those segments which holds the contents to be blocked. The advantages of this method over the traditional methods are fine-graining level of blocking and automatic identification of portions of the page to be blocked. The experiments conducted on the proposed model indicate 88% of accuracy in filter...

  14. 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.

  15. Characterization of mitochondrial DNA in various Candida species: isolation, restriction endonuclease analysis, size, and base composition.

    Science.gov (United States)

    Su, C S; Meyer, S A

    1991-01-01

    A practical and effective method for the extraction of mitochondrial DNA from Candida species was developed. Zymolyase was used to induce yeast protoplasts, and mitochondrial DNA was extracted from DNase I-treated mitochondrial preparations. Restriction endonuclease analyses of mitochondrial DNAs from 19 isolates representing seven species of Candida (C. albicans, C. kefyr, C. lusitaniae, C. maltosa, C. parapsilosis, C. shehatae, and C. tropicalis) and Lodderomyces elongisporus revealed different cleavage patterns that appeared to be specific for the species. Few common restriction fragments were evident. The genome sizes of the mitochondrial DNAs ranged from 26.4 to 51.4 kilobase pairs, and the guanine-plus-cytosine contents ranged from 20.7 to 36.8 mol%. There was no correlation between the base compositions of nuclear and mitochondrial DNAs. Eight isolates of C. parapsilosis, including the type culture, and an ascosporogenous strain of L. elongisporus, which was once proposed as the teleomorph of C. parapsilosis, had similar mitochondrial DNA molecular sizes (30.2 and 28.8 kilobase pairs); however, restriction endonuclease patterns of these organisms were distinct. These data provide additional support for discrimination of these two species. The results of our experiments demonstrate that mitochondrial DNA analyses may provide useful criteria for the differentiation of yeast species.

  16. 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.

  17. 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

  18. Quantitative bioluminometric method for DNA-based species/varietal identification in food authenticity assessment.

    Science.gov (United States)

    Trantakis, Ioannis A; Christopoulos, Theodore K; Spaniolas, Stelios; Kalaitzis, Panagiotis; Ioannou, Penelope C; Tucker, Gregory A

    2012-02-01

    A method is reported for species quantification by exploiting single-nucleotide polymorphisms (SNPs). These single-base changes in DNA are particularly useful because they enable discrimination of closely related species and/or varieties. As a model, quantitative authentication studies were performed on coffee. These involved the determination of the percentage of Arabica and Robusta species based on a SNP in the chloroplastic trnL(UAA)-trnF(GAA) intraspacer region. Following polymerase chain reaction (PCR), the Robusta-specific and Arabica-specific fragments were subjected to 15 min extension reactions by DNA polymerase using species-specific primers carrying oligo(dA) tags. Biotin was incorporated into the extended strands. The products were captured in streptavidin-coated microtiter wells and quantified by using oligo(dT)-conjugated photoprotein aequorin. Aequorin was measured within 3 s via its characteristic flash-type bioluminescent reaction that was triggered by the addition of Ca(2+). Because of the close resemblance between the two DNA fragments, during PCR one species serves as an internal standard for the other. The percentage of the total luminescence signal obtained from a certain species was linearly related to the percent content of the sample with respect to this species. The method is accurate and reproducible. The microtiter well-based assay configuration allows high sample throughput and facilitates greatly the automation.

  19. Dihydropyridines decrease X-ray-induced DNA base damage in mammalian cells

    Energy Technology Data Exchange (ETDEWEB)

    Wojewodzka, M., E-mail: marylaw@ichtj.waw.pl [Center of Radiobiology and Biological Dosimetry, Institute of Nuclear Chemistry and Technology, Warszawa (Poland); Gradzka, I.; Buraczewska, I.; Brzoska, K.; Sochanowicz, B. [Center of Radiobiology and Biological Dosimetry, Institute of Nuclear Chemistry and Technology, Warszawa (Poland); Goncharova, R.; Kuzhir, T. [Institute of Genetics and Cytology, Belarussian National Academy of Sciences, Minsk (Belarus); Szumiel, I. [Center of Radiobiology and Biological Dosimetry, Institute of Nuclear Chemistry and Technology, Warszawa (Poland)

    2009-12-01

    Compounds with the structural motif of 1,4-dihydropyridine display a broad spectrum of biological activities, often defined as bioprotective. Among them are L-type calcium channel blockers, however, also derivatives which do not block calcium channels exert various effects at the cellular and organismal levels. We examined the effect of sodium 3,5-bis-ethoxycarbonyl-2,6-dimethyl-1,4-dihydropyridine-4-carboxylate (denoted here as DHP and previously also as AV-153) on X-ray-induced DNA damage and mutation frequency at the HGPRT (hypoxanthine-guanine phosphoribosyl transferase) locus in Chinese hamster ovary CHO-K1 cells. Using formamido-pyrimidine glycosylase (FPG) comet assay, we found that 1-h DHP (10 nM) treatment before X-irradiation considerably reduced the initial level of FPG-recognized DNA base damage, which was consistent with decreased 8-oxo-7,8-dihydro-2'-deoxyguanosine content and mutation frequency lowered by about 40%. No effect on single strand break rejoining or on cell survival was observed. Similar base damage-protective effect was observed for two calcium channel blockers: nifedipine (structurally similar to DHP) or verapamil (structurally unrelated). So far, the specificity of the DHP-caused reduction in DNA damage - practically limited to base damage - has no satisfactory explanation.

  20. 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...

  1. 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.

  2. Content-Based Filtering for Video Sharing Social Networks

    CERN Document Server

    Valle, Eduardo; Luz, Antonio da; de Souza, Fillipe; Coelho, Marcelo; Araújo, Arnaldo

    2011-01-01

    In this paper we compare the use of several features in the task of content filtering for video social networks, a very challenging task, not only because the unwanted content is related to very high-level semantic concepts (e.g., pornography, violence, etc.) but also because videos from social networks are extremely assorted, preventing the use of constrained a priori information. We propose a simple method, able to combine diverse evidence, coming from different features and various video elements (entire video, shots, frames, keyframes, etc.). We evaluate our method in three social network applications, related to the detection of unwanted content - pornographic videos, violent videos, and videos posted to artificially manipulate popularity scores. Using challenging test databases, we show that this simple scheme is able to obtain good results, provided that adequate features are chosen. Moreover, we establish a representation using codebooks of spatiotemporal local descriptors as critical to the success o...

  3. Development of flow cytometric protocol for nuclear DNA content estimation and determination of chromosome number in Pongamia pinnata L., a valuable biodiesel plant.

    Science.gov (United States)

    Ramesh, Aadi Moolam; Basak, Supriyo; Choudhury, Rimjhim Roy; Rangan, Latha

    2014-01-01

    The potentiality of Pongamia pinnata L. as a sustainable source of feedstock for the biodiesel industry is dependent on an extensive knowledge of the genome structure of the plant. Flow cytometry, with propidium iodide (PI) as the DNA stain, was used to estimate the nuclear DNA content of P. pinnata, with respect to Zea mays 'CE-777' as standard. The internal and pseudo-internal standardization was followed on account of the inhibitory effect of secondary compounds on PI intercalation. The antioxidants (PVP-40 and β-mercaptoethanol) were added to the nuclear isolation buffer for the reduction of inhibitory effect of P. pinnata cytosol. Nuclear DNA content estimation was done for P. pinnata leaves from different altitudes (37-117 m height from sea level) of Assam. Flow cytometry analysis indicated that the nuclear DNA content of P. pinnata is 2.66 pg with predicted 1C value of 1,300 Mb using Z. mays as standard. Coefficient of variation in flow cytometric analysis was within the limit of 5 % indicating that the results were reliable. Somatic chromosome numbers were counted from root-tip cells and was found to be 2n = 22 corresponding to the diploid level (x = 11). A decreasing trend in the nuclear DNA content was observed for the species of different altitudes.

  4. An E-Commerce Recommender System Based on Content-Based Filtering

    Institute of Scientific and Technical Information of China (English)

    HE Weihong; CAO Yi

    2006-01-01

    Content-based filtering E-commerce recommender system was discussed fully in this paper. Users' unique features can be explored by means of vector space model firstly. Then based on the qualitative value of products information, the recommender lists were obtained. Since the system can adapt to the users' feedback automatically, its performance were enhanced comprehensively. Finally the evaluation of the system and the experimental results were presented.

  5. 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.

  6. 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).

  7. 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.

  8. 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.

  9. Characterizing the DNA Damage Response by Cell Tracking Algorithms and Cell Features Classification Using High-Content Time-Lapse Analysis.

    Directory of Open Access Journals (Sweden)

    Walter Georgescu

    Full Text Available Traditionally, the kinetics of DNA repair have been estimated using immunocytochemistry by labeling proteins involved in the DNA damage response (DDR with fluorescent markers in a fixed cell assay. However, detailed knowledge of DDR dynamics across multiple cell generations cannot be obtained using a limited number of fixed cell time-points. Here we report on the dynamics of 53BP1 radiation induced foci (RIF across multiple cell generations using live cell imaging of non-malignant human mammary epithelial cells (MCF10A expressing histone H2B-GFP and the DNA repair protein 53BP1-mCherry. Using automatic extraction of RIF imaging features and linear programming techniques, we were able to characterize detailed RIF kinetics for 24 hours before and 24 hours after exposure to low and high doses of ionizing radiation. High-content-analysis at the single cell level over hundreds of cells allows us to quantify precisely the dose dependence of 53BP1 protein production, RIF nuclear localization and RIF movement after exposure to X-ray. Using elastic registration techniques based on the nuclear pattern of individual cells, we could describe the motion of individual RIF precisely within the nucleus. We show that DNA repair occurs in a limited number of large domains, within which multiple small RIFs form, merge and/or resolve with random motion following normal diffusion law. Large foci formation is shown to be mainly happening through the merging of smaller RIF rather than through growth of an individual focus. We estimate repair domain sizes of 7.5 to 11 µm2 with a maximum number of ~15 domains per MCF10A cell. This work also highlights DDR which are specific to doses larger than 1 Gy such as rapid 53BP1 protein increase in the nucleus and foci diffusion rates that are significantly faster than for spontaneous foci movement. We hypothesize that RIF merging reflects a "stressed" DNA repair process that has been taken outside physiological conditions when

  10. Hybrid Content-Based Collaborative-Filtering Music Recommendations

    NARCIS (Netherlands)

    Siles Del Castillo, H.

    2007-01-01

    Recommendation of music is emerging with force nowadays due to the huge amount of music content and because users normally do not have the time to search through these collections looking for new items. The main purpose of a recommendation system is to estimate the user’s preferences and present him

  11. Content Design Patterns for Game-Based Learning

    Science.gov (United States)

    Maciuszek, Dennis; Ladhoff, Sebastian; Martens, Alke

    2011-01-01

    To address the lack of documented best practices in the development of digital educational games, the authors have previously proposed a reference software architecture. One of its components is the rule system specifying learning and gameplay content. It contains quest, player character, non-player character, environment, and item rules.…

  12. Text Indexing of Images Based on Graphical Image Content.

    Science.gov (United States)

    Patrick, Timothy B.; Sievert, MaryEllen C.; Popescu, Mihail

    1999-01-01

    Describes an alternative method for indexing images in an image database. The method consists of manually indexing a selected reference image, and then using retrieval by graphical content to automatically transfer the manually assigned index terms from the reference image to the images to be indexed. (AEF)

  13. Empirically Based Recommendations for Content of Graduate Nursing Administration Programs.

    Science.gov (United States)

    Scalzi, Cynthia C.; Wilson, David L.

    1990-01-01

    To determine content for graduate programs in nursing administration, 184 nurse executives from acute care, home care, long-term care, and occupational health rated their job functions. All respondents spend time on activities requiring knowledge of law, health care policy, and organizational behavior. Ethics ranked lowest in terms of time spent.…

  14. Surface Electromyographic Onset Detection Based On Statistics and Information Content

    Science.gov (United States)

    López, Natalia M.; Orosco, Eugenio; di Sciascio, Fernando

    2011-12-01

    The correct detection of the onset of muscular contraction is a diagnostic tool to neuromuscular diseases and an action trigger to control myoelectric devices. In this work, entropy and information content concepts were applied in algorithmic methods to automatic detection in surface electromyographic signals.

  15. 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.

  16. Content-Based Image Retrieval Based on Electromagnetism-Like Mechanism

    Directory of Open Access Journals (Sweden)

    Hamid A. Jalab

    2013-01-01

    Full Text Available Recently, many researchers in the field of automatic content-based image retrieval have devoted a remarkable amount of research looking for methods to retrieve the best relevant images to the query image. This paper presents a novel algorithm for increasing the precision in content-based image retrieval based on electromagnetism optimization technique. The electromagnetism optimization is a nature-inspired technique that follows the collective attraction-repulsion mechanism by considering each image as an electrical charge. The algorithm is composed of two phases: fitness function measurement and electromagnetism optimization technique. It is implemented on a database with 8,000 images spread across 80 classes with 100 images in each class. Eight thousand queries are fired on the database, and the overall average precision is computed. Experimental results of the proposed approach have shown significant improvement in the retrieval performance in regard to precision.

  17. 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.

  18. 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.

  19. 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.

  20. On the way to identify microorganisms in drinking water distribution networks via DNA analysis of the gut content of freshwater isopods.

    Science.gov (United States)

    Mayer, Michael; Keller, Adrian; Szewzyk, Ulrich; Warnecke, Hans-Joachim

    2015-05-10

    Pure drinking water is the basis for a healthy society. In Germany the drinking water regulations demand for analysis of water via detection of certain microbiological parameters by cultivation only. However, not all prokaryotes can be detected by these standard methods. How to gain more and better information about the bacteria present in drinking water and its distribution systems? The biofilms in drinking water distribution systems are built by bacteria and therefore represent a valuable source of information about the species present. Unfortunately, these biofilms are badly accessible. We thus exploited the circumstance that a lot of metazoans graze the biofilms, so that the content of their guts partly reflects the respective biofilm biocenosis. Therefore, we collected omnivorous isopods, prepared their guts and examined and characterized their contents based on 16S und 18S rDNA analysis. These molecularbiological investigations provide a profound basis for the characterization of the biocenosis and thereby biologically assess the drinking water ecosystems. Combined with a thorough identification of the species and the knowledge of their habitats, this approach can provide useful indications for the assessment of drinking-water quality and the early detection of problems in the distribution system. Copyright © 2015 Elsevier B.V. All rights reserved.

  1. 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...

  2. A tree-based paradigm for content-based video retrieval and management

    Science.gov (United States)

    Fang, H.; Yin, Y.; Jiang, J.

    2006-01-01

    As video databases become increasingly important for full exploitation of multimedia resources, this paper aims at describing our recent efforts in feasibility studies towards building up a content-based and high-level video retrieval/management system. The study is focused on constructing a semantic tree structure via combination of low-level image processing techniques and high-level interpretation of visual content. Specifically, two separate algorithms were developed to organise input videos in terms of two layers: the shot layer and the key-frame layer. While the shot layer is derived by developing a multi-featured shot cut detection, the key frame layer is extracted automatically by a genetic algorithm. This paves the way for applying pattern recognition techniques to analyse those key frames and thus extract high level information to interpret the visual content or objects. Correspondingly, content-based video retrieval can be conducted in three stages. The first stage is to browse the digital video via the semantic tree at structural level, the second stage is match the key frame in terms of low-level features, such as colour, shape of objects, and texture etc. Finally, the third stage is to match the high-level information, such as conversation with indoor background, moving vehicles along a seaside road etc. Extensive experiments are reported in this paper for shot cut detection and key frame extraction, enabling the tree structure to be constructed.

  3. Reputation-based content dissemination for user generated wireless podcasting

    DEFF Research Database (Denmark)

    Hu, Liang; Dittmann, Lars; Le Boudec, J.-Y.

    2009-01-01

    User-generated podcasting service over human-centric opportunistic network can facilitate user-generated content sharing while humans are on the move beyond the coverage of infrastructure networks. We focus on the aspects of designing efficient forwarding and cache replacement schemes of such ser......User-generated podcasting service over human-centric opportunistic network can facilitate user-generated content sharing while humans are on the move beyond the coverage of infrastructure networks. We focus on the aspects of designing efficient forwarding and cache replacement schemes...... of such service under the constraints of limited capability of handheld device and limited network capacity. In particular, the design of those schemes is challenged by the lack of podcast channel popularity information at each node which is crucial for forwarding and caching decisions. We design a distributed...

  4. Location based content delivery solution using iBeacon

    OpenAIRE

    2015-01-01

    There is a growing trend of using mobile devices in retail stores. Access to instant product related information is desirable by consumers in making a purchase decision. This information may include offers or sales discount associated with a product, comparing prices, ingredients or materials composition and many more. Retail business owners have seen this as a big opportunity to increase their in-store sales and they are adapting various technologies to deliver helpful contents and informati...

  5. Content-Based Video Description for Automatic Video Genre Categorization

    OpenAIRE

    Ionescu, Bogdan; Seyerlehner, Klaus; Rasche, Christoph; Vertan, Constantin; Lambert, Patrick

    2012-01-01

    International audience; In this paper, we propose an audio-visual approach to video genre categorization. Audio information is extracted at block-level, which has the advantage of capturing local temporal information. At temporal structural level, we asses action contents with respect to human perception. Further, color perception is quantified with statistics of color distribution, elementary hues, color properties and relationship of color. The last category of descriptors determines statis...

  6. Nuclear DNA content in Galaxias maculatus (Teleostei: Osmeriformes: Galaxiidae Contenido de ADN nuclear en Galaxias maculatus (Teleostei: Osmeriformes: Galaxiidae

    Directory of Open Access Journals (Sweden)

    Pedro Jara-Seguel

    2008-01-01

    Full Text Available The nuclear DNA content (2C value was determined in the commercial fish Galaxias maculatus (Galaxiidae was determined by microdensitometry of erythrocyte nuclei after Feulgen staining; rainbow trout erythrocytes with a known 2C value were used as a standard. The 2C value of G. maculatus was 2.21 ± 0.12 pg and its C value was equivalent to 1.105 pg (1,082.9 Mbp. This C value is within the range recorded for other osmeriform species (0.62-3.2 pg. The average sperm head diameter of G. maculatus is lower than the average sperm head diameter of rainbow trout (used as a standard, which coincides with the differences observed in the nuclear DNA content of both species. This information increases the genome data available for G. maculatus and might be useful in future programs dealing with its genetic manipulation.El contenido de ADN nuclear (valor 2C fue determinado en el pez comercial Galaxias maculatus (Galaxiidae usando microdensitometría de núcleos de eritrocitos sometidos a tinción de Feulgen, utilizando como estándar eritrocitos de trucha arco iris con un valor 2C conocido. El valor 2C de G. maculatus fue 2,21 ± 0,12 pg y su valor C es equivalente a 1,105 pg (1.082,9 pMb. Este valor C está dentro del rango registrado para otras especies de osmeriformes (0,62-3,2 pg. El diámetro promedio de la cabeza del espermatozoide de G. maculatus es menor al promedio descrito para la trucha arco iris utilizado como estándar, lo que coincide con las diferencias observadas en el contenido de ADN nuclear entre ambas especies. Estos datos contribuyen a ampliar los antecedentes genómicos disponibles para G. maculatus y podrían ser útiles en futuros programas tendientes a su manipulación genética.

  7. Semantic Based Cluster Content Discovery in Description First Clustering Algorithm

    Directory of Open Access Journals (Sweden)

    MUHAMMAD WASEEM KHAN

    2017-01-01

    Full Text Available In the field of data analytics grouping of like documents in textual data is a serious problem. A lot of work has been done in this field and many algorithms have purposed. One of them is a category of algorithms which firstly group the documents on the basis of similarity and then assign the meaningful labels to those groups. Description first clustering algorithm belong to the category in which the meaningful description is deduced first and then relevant documents are assigned to that description. LINGO (Label Induction Grouping Algorithm is the algorithm of description first clustering category which is used for the automatic grouping of documents obtained from search results. It uses LSI (Latent Semantic Indexing; an IR (Information Retrieval technique for induction of meaningful labels for clusters and VSM (Vector Space Model for cluster content discovery. In this paper we present the LINGO while it is using LSI during cluster label induction and cluster content discovery phase. Finally, we compare results obtained from the said algorithm while it uses VSM and Latent semantic analysis during cluster content discovery phase.

  8. Content Sharing over Smartphone-Based Delay-Tolerant Networks

    Directory of Open Access Journals (Sweden)

    L. Ramya Rekha

    2014-10-01

    Full Text Available With the growing number of smartphone end users, peer-to-peer ad hoc content giving is likely to occur often. Thus, new articles sharing mechanisms must be developed since traditional information delivery schemes will not be efficient with regard to content sharing due to the sporadic connectivity between smartphones on the market. To obtain data delivery such challenging environments, researchers include proposed the employment of store-carry-forward methodologies, in which a node stores a communication and holds it until a forwarding prospect arises through an encounter together with other nodes. Most past works in this field have dedicated to the conjecture of whether two nodes could encounter the other, without thinking about the place and also time from the encounter. In this particular paper, we propose to her discover-predict-deliver as a possible efficient articles sharing scheme for delay-tolerant touch screen phone networks. In this proposed scheme, contents are usually shared while using the mobility information of people. Specifically, our strategy employs the mobility understanding algorithm to spot places inside your own home and outdoor.

  9. 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

  10. 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.

  11. 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

  12. 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...

  13. 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.

  14. 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.

  15. 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.

  16. 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/.

  17. 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...

  18. New type of outer membrane vesicle produced by the Gram-negative bacterium Shewanella vesiculosa M7T: implications for DNA content.

    Science.gov (United States)

    Pérez-Cruz, Carla; Carrión, Ornella; Delgado, Lidia; Martinez, Gemma; López-Iglesias, Carmen; Mercade, Elena

    2013-03-01

    Outer membrane vesicles (OMVs) from Gram-negative bacteria are known to be involved in lateral DNA transfer, but the presence of DNA in these vesicles has remained difficult to explain. An ultrastructural study of the Antarctic psychrotolerant bacterium Shewanella vesiculosa M7(T) has revealed that this Gram-negative bacterium naturally releases conventional one-bilayer OMVs through a process in which the outer membrane is exfoliated and only the periplasm is entrapped, together with a more complex type of OMV, previously undescribed, which on formation drag along inner membrane and cytoplasmic content and can therefore also entrap DNA. These vesicles, with a double-bilayer structure and containing electron-dense material, were visualized by transmission electron microscopy (TEM) after high-pressure freezing and freeze-substitution (HPF-FS), and their DNA content was fluorometrically quantified as 1.8 ± 0.24 ng DNA/μg OMV protein. The new double-bilayer OMVs were estimated by cryo-TEM to represent 0.1% of total vesicles. The presence of DNA inside the vesicles was confirmed by gold DNA immunolabeling with a specific monoclonal IgM against double-stranded DNA. In addition, a proteomic study of purified membrane vesicles confirmed the presence of plasma membrane and cytoplasmic proteins in OMVs from this strain. Our data demonstrate the existence of a previously unobserved type of double-bilayer OMV in the Gram-negative bacterium Shewanella vesiculosa M7(T) that can incorporate DNA, for which we propose the name outer-inner membrane vesicle (O-IMV).

  19. 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

  20. Study on the change of HPV DNA virus content, circulating blood and tissue miR indexes of patients with cervical cancer

    Institute of Scientific and Technical Information of China (English)

    Ru-Qiong Luo; LiangTang; Ping Xie; Yan-Mei Hu

    2016-01-01

    Objective:To study and observe the change status of HPV DNA virus content, circulating blood and tissue miR indexes of patients with cervical cancer.Methods:A total of 72 patients with cervical cancer in our hospital from February 2014 to September 2015 were selected as the observation group, 72 healthy women at the same period were selected as the control group, then the HPV DNA virus content and constitution, circulating blood and tissue miR indexes of two groups were analyzed and compared, and the detection results of observation group with stageⅠ,Ⅱ,Ⅲ andⅣ of cervical cancer were compared.Results:The rates of HPV DNA virus content and>500 in the observation group were all higher than those of control group, the circulating blood and tissue miR-21 were all higher than those of control group, while the circulating blood and tissue miR-126, miR-143 and miR-145 were all lower than those of control group, and the detection results of observation group with stageⅠ,Ⅱ,Ⅲ andⅣ of cervical cancer all had obvious differences, the differences were all significant.Conclusion:The changes of the status of HPV DNA virus content, circulating blood and tissue miR indexes of patients with cervical cancer are great, and the influence of cervical cancer stage for the detection results are great, so it has active guiding significance for the diagnosis and treatment of disease.

  1. The content of PPAR, LXR, and RXR and the PPAR DNA-binding activity in macrophages over the course of inflammation in mice.

    Science.gov (United States)

    Dushkin, M I; Khoshchenko, O M; Chasovsky, M A; Pivovarova, E N

    2009-03-01

    The content of peroxisome proliferation activating proteins PPAR-alpha and PPAR-gamma, liver X receptors (LXR), and retinoid X receptors (RXR) and activity of PPAR-alpha, PPAR-gamma, and PPAR-delta binding to DNA response elements in C57Bl/6 mouse macrophages were studied during different phases of aseptic inflammation, induced by intraperitoneal injection of 50 mg/kg zymosan A. The DNA-binding activities of PPAR-alpha and PPAR-gamma and the levels of PPAR-alpha, PPAR-gamma, LXR, and RXR in peritoneal macrophages dropped on days 1 and 3 after zymosan injection. On days 7 and 14 the DNA-binding activity of PPAR-gamma and content of PPAR-gamma and LXR-beta protein increased in comparison with the control, while the DNA-binding activity and content of PPAR-alpha in the cells remained low. Recovery of RXR protein content in macrophages was observed only on day 14 after zymosan injection.

  2. Pharmacodynamics of cisplatin in human head and neck cancer : correlation between platinum content, DNA adduct levels and drug sensitivity in vitro and in vivo

    NARCIS (Netherlands)

    Welters, M.J.P.; Fichtinger-Schepman, A.M.J.; Baan, R.A.; Jacobs-Bergmans, A.J.; Kegel, A.; Vijgh, W.J.F. van der; Braakhuis, B.J.M.

    1999-01-01

    Total platinum contents and cisplatin-DNA adduct levels were determined in vivo in xenografted tumour tissues in mice and in vitro in cultured tumour cells of head and neck squamous cell carcinoma (HNSCC), and correlated with sensitivity to cisplatin. In vivo, a panel of five HNSCC tumour lines grow

  3. Pharmacodynamics of cisplatin in human head and neck cancer : correlation between platinum content, DNA adduct levels and drug sensitivity in vitro and in vivo

    NARCIS (Netherlands)

    Welters, M.J.P.; Fichtinger-Schepman, A.M.J.; Baan, R.A.; Jacobs-Bergmans, A.J.; Kegel, A.; Vijgh, W.J.F. van der; Braakhuis, B.J.M.

    1999-01-01

    Total platinum contents and cisplatin-DNA adduct levels were determined in vivo in xenografted tumour tissues in mice and in vitro in cultured tumour cells of head and neck squamous cell carcinoma (HNSCC), and correlated with sensitivity to cisplatin. In vivo, a panel of five HNSCC tumour lines grow

  4. Content-based retrieval based on binary vectors for 2-D medical images

    Institute of Scientific and Technical Information of China (English)

    龚鹏; 邹亚东; 洪海

    2003-01-01

    In medical research and clinical diagnosis, automated or computer-assisted classification and retrieval methods are highly desirable to offset the high cost of manual classification and manipulation by medical experts. To facilitate the decision-making in the health-care and the related areas, in this paper, a two-step content-based medical image retrieval algorithm is proposed. Firstly, in the preprocessing step, the image segmentation is performed to distinguish image objects, and on the basis of the ...

  5. Analysis of the polycyclic aromatic hydrocarbon content of petrol and diesel engine lubricating oils and determination of DNA adducts in topically treated mice by 32P-postlabelling.

    Science.gov (United States)

    Carmichael, P L; Jacob, J; Grimmer, G; Phillips, D H

    1990-11-01

    Engine lubricating oils are known to accumulate carcinogenic polycyclic aromatic hydrocarbons (PAHs) during engine running. Oils from nine petrol-powered and 11 diesel-powered vehicles, in addition to samples of unused oil, were analysed for PAH content and ability to form DNA adducts when applied topically to mouse skin. The levels of 19 PAHs, determined by GC, were in total, approximately 22 times higher in used oils from petrol engines than in oils from diesel engines. Male Parkes mice were treated with 50 microliters of oil daily for 4 days before they were killed and DNA isolated from skin and lung tissue. DNA samples were analysed by nuclease P1-enhanced 32P-postlabelling. Used oils from both diesel and petrol engines showed several adduct spots on PEI-cellulose plates at total adduct levels of up to 0.57 fmol/microgram DNA [approximately 60 times greater than in experiments with samples of unused oil in which adduct levels (0.01-0.02 fmol adducts/microgram DNA) were close to the limit of detection]. Higher adduct levels were generally formed by petrol engine oils than by diesel engine oils. Lung DNA contained similar total adduct levels to those in skin although the adduct maps were less complex. Total adduct levels correlated with extent of oil use in the engine, the total PAH concentration in oils and with the concentrations of certain individual PAHs present in the oils. An adduct spot that co-eluted with that of the major benzo[a]pyrene-DNA adduct accounted for 9-26% of the total adducts in skin DNA, and approximately 8% of the adducts in lung DNA, of mice treated with petrol engine oils. A major, and as yet unidentified, adduct spot comprised up to 30% of the total adducts in skin DNA, and up to 89% of the total adducts in lung DNA, of these animals.

  6. A Content-Based Search Algorithm for Motion Estimation

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    The basic search algorithm toimplement Motion Estimation (ME) in the H. 263 encoder is a full search.It is simple but time-consuming. Traditional search algorithms are fast, but may cause a fall in image quality or an increase in bit-rate in low bit-rate applications. A fast search algorithm for ME with consideration on image content is proposed in this paper. Experiments show that the proposed algorithm can offer up to 70 percent savings in execution time with almost no sacrifice in PSNR and bit-rate, compared with the full search.

  7. 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...

  8. 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.

  9. 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.

  10. Web content adaptation for mobile device: A fuzzy-based approach

    Directory of Open Access Journals (Sweden)

    Frank C.C. Wu

    2012-03-01

    Full Text Available While HTML will continue to be used to develop Web content, how to effectively and efficiently transform HTML-based content automatically into formats suitable for mobile devices remains a challenge. In this paper, we introduce a concept of coherence set and propose an algorithm to automatically identify and detect coherence sets based on quantified similarity between adjacent presentation groups. Experimental results demonstrate that our method enhances Web content analysis and adaptation on the mobile Internet.

  11. Content-Based Hierarchical Analysis of News Video Using Audio and Visual Information

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    A schema for content-based analysis of broadcast news video is presented. First, we separate commercials from news using audiovisual features. Then, we automatically organize news programs into a content hierarchy at various levels of abstraction via effective integration of video, audio, and text data available from the news programs. Based on these news video structure and content analysis technologies, a TV news video Library is generated, from which users can retrieve definite news story according to their demands.

  12. Quality evaluation of methyl binding domain based kits for enrichment DNA-methylation sequencing.

    Directory of Open Access Journals (Sweden)

    Tim De Meyer

    Full Text Available DNA-methylation is an important epigenetic feature in health and disease. Methylated sequence capturing by Methyl Binding Domain (MBD based enrichment followed by second-generation sequencing provides the best combination of sensitivity and cost-efficiency for genome-wide DNA-methylation profiling. However, existing implementations are numerous, and quality control and optimization require expensive external validation. Therefore, this study has two aims: 1 to identify a best performing kit for MBD-based enrichment using independent validation data, and 2 to evaluate whether quality evaluation can also be performed solely based on the characteristics of the generated sequences. Five commercially available kits for MBD enrichment were combined with Illumina GAIIx sequencing for three cell lines (HCT15, DU145, PC3. Reduced representation bisulfite sequencing data (all three cell lines and publicly available Illumina Infinium BeadChip data (DU145 and PC3 were used for benchmarking. Consistent large-scale differences in yield, sensitivity and specificity between the different kits could be identified, with Diagenode's MethylCap kit as overall best performing kit under the tested conditions. This kit could also be identified with the Fragment CpG-plot, which summarizes the CpG content of the captured fragments, implying that the latter can be used as a tool to monitor data quality. In conclusion, there are major quality differences between kits for MBD-based capturing of methylated DNA, with the MethylCap kit performing best under the used settings. The Fragment CpG-plot is able to monitor data quality based on inherent sequence data characteristics, and is therefore a cost-efficient tool for experimental optimization, but also to monitor quality throughout routine applications.

  13. 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.

  14. 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.

  15. Genomic and Haplotype Comparison of Butanol Producing Bacteria Based on 16S rDNA

    Directory of Open Access Journals (Sweden)

    Ekwan Nofa Wiratno

    2016-04-01

    Full Text Available High butanol demand for transportation fuel triggers butanol production development. Exploration of butanolproducing bacteria using genomic comparison and biogeography will help to develop butanol industry. The objectives of this research were butanol production, genome comparison and haplotype analysis of butanolproducing bacteria from Ranu Pani Lake sediment using 16S rDNA sequences. The highest butanol concentrations were showed by Paenibacillus polymyxa RP 2.2 isolate (10.34 g.L-1, followed by Bacillus methylotrophicus RP 3.2 and B. methylotrophicus RP 7.2 isolate (10.11 g.L-1 and 9.63 g.L-1 respectively. Paenibacillus polymyxa RP 2.2 showed similarity in nucleotide composition (ATGC with B. methylotrophicus RP 3.2, B. methylotrophicus RP 7.2, P. polymyxa CR1, Bacillus amyloliquefaciens NELB-12, and Paenibacillus polymyxa WR-2. Clostridium acetobutylicum ATCC 824 showed similarity in nucleotide composition (ATGC with Clostridium saccharoperbutylacetonicum N1-4, and Clostridium saccharobutylicum Ox29. The lowest G+C content was C. saccharobutylicum Ox29 (51.35%, and the highest was B. methylotrophicus RP 7.2 (55.33%. Conserved region of 16S rDNA (1044 bp were consisted of 17 conserved sequences. The number of Parsimony Informative Site (PIS was 319 spot and single tone was 48 spot. We found in this study that all of butanolproducing bacterial DNA sequences have clustered to 8 haplotypes. Based on the origin of sample, there were three haplotype groups. Bacteria from group A were could produce butanol 8.9-10.34 g.L-1, group B 9.2-14.2 g.L-1 and group C was could produce butanol 0.47 g.L-1. The haplotype analysis of bacteria based on 16S rDNA sequences in this study could predict capability of butanol production.

  16. Efficient stereoscopic contents file format on the basis of ISO base media file format

    Science.gov (United States)

    Kim, Kyuheon; Lee, Jangwon; Suh, Doug Young; Park, Gwang Hoon

    2009-02-01

    A lot of 3D contents haven been widely used for multimedia services, however, real 3D video contents have been adopted for a limited applications such as a specially designed 3D cinema. This is because of the difficulty of capturing real 3D video contents and the limitation of display devices available in a market. However, diverse types of display devices for stereoscopic video contents for real 3D video contents have been recently released in a market. Especially, a mobile phone with a stereoscopic camera has been released in a market, which provides a user as a consumer to have more realistic experiences without glasses, and also, as a content creator to take stereoscopic images or record the stereoscopic video contents. However, a user can only store and display these acquired stereoscopic contents with his/her own devices due to the non-existence of a common file format for these contents. This limitation causes a user not share his/her contents with any other users, which makes it difficult the relevant market to stereoscopic contents is getting expanded. Therefore, this paper proposes the common file format on the basis of ISO base media file format for stereoscopic contents, which enables users to store and exchange pure stereoscopic contents. This technology is also currently under development for an international standard of MPEG as being called as a stereoscopic video application format.

  17. 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.

  18. 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.

  19. Histogram score contributes for reliability of DNA content estimatives in Brachiaria spp Notas do histograma contribuem para a confiabilidade das estimativas do conteúdo de DNA de Brachiaria spp

    Directory of Open Access Journals (Sweden)

    Ana Luiza de Oliveira Timbó

    2012-12-01

    Full Text Available Flow cytometry allows to estimate the DNA content of a large number of plants quickly. However, inadequate protocols can compromise the reliability of these estimates leading to variations in the values of DNA content the same species. The objective of this study was to propose an efficient protocol to estimate the DNA content of Brachiaria spp. genotypes with different ploidy levels using flow cytometry. We evaluated four genotypes (B. ruziziensis diploid and artificially tetraploidized; a tetraploid B. brizantha and a natural triploid hybrid, three buffer solutions (MgSO4, Galbraith and Tris-HCl and three species as internal reference standards (Raphanus sativus, Solanum lycopersicum e Pisum sativum. The variables measured were: histogram score (1-5, coefficient of variation and estimation of DNA content. The best combination for the analysis of Brachiaria spp. DNA content was the use of MgSO4 buffer with R. sativus as a internal reference standard. Genome sizes expressed in picograms of DNA are presented for all genotypes and the importance of the histogram score on the results reliability of DNA content analyses were discussed.A citometria de fluxo permite estimar o conteúdo de DNA de um grande número de plantas rapidamente. No entanto, protocolos inadequados podem comprometer a confiabilidade dessas estimativas, levando a variações nos valores de conteúdo de DNA para uma mesma espécie. Neste trabalho, objetivou-se propor um protocolo eficiente para a estimativa do conteúdo de DNA de genótipos de Brachiaria spp. com diferentes níveis de ploidia, utilizando a citometria de fluxo. Foram avaliados quatro genótipos (B. ruziziensis, diploide e tetraploidizada artificialmente; B. brizantha tetraploide e um híbrido natural triploide, 3 soluções tampões (MgSO4, Galbraith e Tris-HCl e três espécies como padrões de referência interno (Raphanus sativus, Solanum lycopersicum e Pisum sativum. As variáveis mensuradas foram: nota do

  20. Design and realisation of an efficient content based music playlist generation system

    NARCIS (Netherlands)

    Balkema, Jan Wietse

    2009-01-01

    This thesis is on the subject of content based music playlist generation systems. The primary aim is to develop algorithms for content based music playlist generation that are faster than the current state of technology while keeping the quality of the playlists at a level that is at least comparabl

  1. Exploring Programmable Self-Assembly in Non-DNA based Molecular Computing

    CERN Document Server

    Terrazas, German; Krasnogor, Natalio

    2013-01-01

    Self-assembly is a phenomenon observed in nature at all scales where autonomous entities build complex structures, without external influences nor centralised master plan. Modelling such entities and programming correct interactions among them is crucial for controlling the manufacture of desired complex structures at the molecular and supramolecular scale. This work focuses on a programmability model for non DNA-based molecules and complex behaviour analysis of their self-assembled conformations. In particular, we look into modelling, programming and simulation of porphyrin molecules self-assembly and apply Kolgomorov complexity-based techniques to classify and assess simulation results in terms of information content. The analysis focuses on phase transition, clustering, variability and parameter discovery which as a whole pave the way to the notion of complex systems programmability.

  2. 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)

  3. The Integration of Language and Content: Form-Focused Instruction in a Content-Based Language Program

    Directory of Open Access Journals (Sweden)

    Antonella Valeo

    2013-06-01

    Full Text Available Abstract This comparative, classroom-based study investigated the effect and effectiveness of introducing a focus on form approach to a content-based, occupation-specific language program for adults. Thirty-six adults in two classes participated in a 10-week study. One group of 16 adults received content-based instruction that included a focus on form component while the other group of 20 adults received the same content-based instruction with a focus on meaning only. Pre-tests/post-tests/delayed post-tests measured learning of two grammatical forms, the present conditional and the simple past tense, as well as occupational content knowledge. Results indicated significant gains on most of the language measures for both learner groups but significant advantages for the form-focused group on the content knowledge tests. The results are discussed in relation to the impact of specific strategies designed to focus on form and the relationship between attention to form and comprehension of content in the context of content-based language programs. Résumé Cette étude comparative menée en salle de classe a examiné l'effet et l'efficacité d’un enseignement mettant l’accent sur ​​la forme dans un programme de langues professionnelles pour adultes. Trente-six apprenants de deux classes intactes ont participé à cette recherche pendant 10 semaines. Un groupe de 16 personnes a reçu les instructions qui se concentraient sur la forme, tandis que l'autre groupe de 20 personnes a reçu les mêmes instructions qui portaient sur ​​le sens seulement. Des pré-tests, des post-tests ainsi que des post-tests retardés ont mesuré l'apprentissage de la langue et du contenu de deux traits grammaticaux; premièrement, la connaissance du conditionnel et du passé et, deuxièmement, la connaissance du contenu professionnel. Les résultats ont indiqué une amélioration sensible de la plupart des compétences linguistiques pour les deux groupes d

  4. 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...

  5. RETRIEVAL TIME RESEARCH IN TEMPORAL KNOWLEDGE BASES WITH DYNAMIC CONTENT

    Directory of Open Access Journals (Sweden)

    J. A. Koroleva

    2015-07-01

    Full Text Available Results of retrieval time research of actual data effectiveness search in temporal knowledge bases built in the basis of state of events have been proposed. This type of knowledge base gives the possibility for quick access to relevant states as well as for history based on events chronology. It is shown that data storage for deep retrospective increases significantly the search time due to the growth of the decision tree. The search time for temporal knowledge bases depending on the average number of events prior to the current state has been investigated. Experimental results confirm the advantage of knowledge bases in the basis of state of events over traditional methods for design of intelligent systems.

  6. Outcomes-based Teaching for Brain-based Learning Vis-à-vis Pedagogical Content Knowledge

    Directory of Open Access Journals (Sweden)

    Reynaldo B. Inocian

    2016-05-01

    Full Text Available The study determined the essential elements of an Outcomes-based Teaching and Learning (OBTL component of an Outcomes-based Education (OBE cycle. It sought to answer these objectives: (1 extrapolate notable teaching attributes based on the actual teaching demonstration of the 7 subjects; (2 describe each of the OBTL’s quadrant elements (3 design a prototype for an integrated arts-based OBTL.This study utilized a case analysis of the actual observation of recurring subtleties exhibited by the seven subject demonstrators during the In-service Training (INSET held last October 27, 2015 in one of the city divisions in Cebu, Philippines. Each of them was rated based on the specific skills used according to Hermann’s Learning Quadrants, after a short lecture on pedagogical content knowledge (PCK.A documentation of a sample Lesson Plan (LP for Quadrant Modelling for Teaching (QMT was juxtaposed as a noble exemplar.The quest for outcomes-based teaching for brain-based learning vis-à-vis pedagogical content knowledge or PCK cascaded with more brain-based inspired learning activities among teacher-demonstrators, with less emphasis on creativity, thus a teaching exemplar was created as part of its modelling. Though, an INSET in the public schools enhanced opportunities to exhibit teaching attributes such as: vivacity, sense of humor, creativity, inquisitiveness, concentration, cautiousness, and dynamism in the achievement of the 21st century skills, however these attributes remained uniquely apparent in every individual teacher. Dreaming to acquire many of these attributes among individual teachers propelled their authentic experience and sincerity to integrate appropriate OBTL activities, which emphasized its four spiral elements, by which the learners would:own knowledge in discovering experiences (sarili, master skills in critical evaluation (husay, engage understating and reflection in dialogical abstraction (saysay, and achieve wonderment in

  7. Evaluation of Genetic Variations in Maize Seedlings Exposed to Electric Field Based on Protein and DNA Markers

    Directory of Open Access Journals (Sweden)

    Asma A. AL-Huqail

    2015-01-01

    Full Text Available The current study analyzed proteins and nuclear DNA of electric fields (ELF exposed and nonexposed maize seedlings for different exposure periods using sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE, isozymes, random amplified polymorphic DNA (RAPD, and comet assay, respectively. SDS-PAGE analysis revealed total of 46 polypeptides bands with different molecular weights ranging from 186.20 to 36.00 KDa. It generated distinctive polymorphism value of 84.62%. Leucine-aminopeptidase, peroxidase, and catalase isozymes showed the highest values of polymorphism (100% based on zymograms number, relative front (Rf, and optical intensity while esterase isozyme generated polymorphism value of 83.33%. Amino acids were analyzed using high-performance liquid chromatography, which revealed the presence of 17 amino acids of variable contents ranging from 22.65% to 28.09%. RAPD revealed that 78 amplified DNA products had highly polymorphism value (95.08% based on band numbers, with variable sizes ranging from 120 to 992 base pairs and band intensity. Comet assay recorded the highest extent of nuclear DNA damage as percentage of tailed DNA (2.38% and tail moment unit (5.36 at ELF exposure of maize nuclei for 5 days. The current study concluded that the longer ELF exposing periods had genotoxic stress on macromolecules of maize cells and biomarkers used should be augmented for reliable estimates of genotoxicity after exposure of economic plants to ELF stressors.

  8. 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.

  9. mage Mining using Content Based Image Retrieval System

    OpenAIRE

    Rajshree S. Dubey; Niket Bhargava; Rajnish Choubey

    2010-01-01

    The image depends on the Human perception and is also based on the Machine Vision System. The Image Retrieval is based on the color Histogram, texture. The perception of the Human System of Image is based on the Human Neurons which hold the 1012 of Information; the Human brain continuously learns with the sensory organs like eye which transmits the Image to the brain which interprets the Image. The research challenge is that how the brain processes the informationin the semantic manner is hot...

  10. 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.

  11. 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.

  12. WormBase: new content and better access

    OpenAIRE

    Bieri, Tamberlyn; Blasiar, Darin; Ozersky, Philip; Antoshechkin, Igor; Bastiani, Carol; Canaran, Payan; Chan, Juancarlos; Chen, Nansheng; Chen, Wen J.; Davis, Paul; Fiedler, Tristan J.; Girard, Lisa; Han, Michael; Harris, Todd W.; Kishore, Ranjana

    2006-01-01

    WormBase (http://wormbase.org), a model organism database for Caenorhabditis elegans and other related nematodes, continues to evolve and expand. Over the past year WormBase has added new data on C.elegans, including data on classical genetics, cell biology and functional genomics; expanded the annotation of closely related nematodes with a new genome browser for Caenorhabditis remanei; and deployed new hardware for stronger performance. Several existing datasets including phenotype descripti...

  13. Dynamic heterogeneity of DNA methylation and hydroxymethylation in embryonic stem cell populations captured by single-cell 3D high-content analysis

    Energy Technology Data Exchange (ETDEWEB)

    Tajbakhsh, Jian, E-mail: tajbakhshj@cshs.org [Chromatin Biology Laboratory, Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA 90048 (United States); Translational Cytomics Group, Cedars-Sinai Medical Center, Los Angeles, CA 90048 (United States); Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048 (United States); Stefanovski, Darko [Translational Cytomics Group, Cedars-Sinai Medical Center, Los Angeles, CA 90048 (United States); Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048 (United States); Department of Clinical Studies, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19348 (United States); Tang, George [Chromatin Biology Laboratory, Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA 90048 (United States); Translational Cytomics Group, Cedars-Sinai Medical Center, Los Angeles, CA 90048 (United States); Wawrowsky, Kolja [Translational Cytomics Group, Cedars-Sinai Medical Center, Los Angeles, CA 90048 (United States); Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048 (United States); Liu, Naiyou; Fair, Jeffrey H. [Department of Surgery and UF Health Comprehensive Transplant Center, University of Florida College of Medicine, Gainesville, FL 32608 (United States)

    2015-03-15

    Cell-surface markers and transcription factors are being used in the assessment of stem cell fate and therapeutic safety, but display significant variability in stem cell cultures. We assessed nuclear patterns of 5-hydroxymethylcytosine (5hmC, associated with pluripotency), a second important epigenetic mark, and its combination with 5-methylcytosine (5mC, associated with differentiation), also in comparison to more established markers of pluripotency (Oct-4) and endodermal differentiation (FoxA2, Sox17) in mouse embryonic stem cells (mESC) over a 10-day differentiation course in vitro: by means of confocal and super-resolution imaging together with 3D high-content analysis, an essential tool in single-cell screening. In summary: 1) We did not measure any significant correlation of putative markers with global 5mC or 5hmC. 2) While average Oct-4 levels stagnated on a cell-population base (0.015 lnIU/day), Sox17 and FoxA2 increased 22-fold and 3-fold faster, respectively (Sox17: 0.343 lnIU/day; FoxA2: 0.046 lnIU/day). In comparison, global DNA methylation levels increased 4-fold faster (0.068 lnIU/day), and global hydroxymethylation declined at 0.046 lnIU/day, both with a better explanation of the temporal profile. 3) This progression was concomitant with the occurrence of distinct nuclear codistribution patterns that represented a heterogeneous spectrum of states in differentiation; converging to three major coexisting 5mC/5hmC phenotypes by day 10: 5hmC{sup +}/5mC{sup −}, 5hmC{sup +}/5mC{sup +}, and 5hmC{sup −}/5mC{sup +} cells. 4) Using optical nanoscopy we could delineate the respective topologies of 5mC/5hmC colocalization in subregions of nuclear DNA: in the majority of 5hmC{sup +}/5mC{sup +} cells 5hmC and 5mC predominantly occupied mutually exclusive territories resembling euchromatic and heterochromatic regions, respectively. Simultaneously, in a smaller subset of cells we observed a tighter colocalization of the two cytosine variants, presumably

  14. 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.

  15. Demographic-Based Content Analysis of Web-Based Health-Related Social Media

    Science.gov (United States)

    Shahbazi, Moloud; Wiley, Matthew T; Hristidis, Vagelis

    2016-01-01

    Background An increasing number of patients from diverse demographic groups share and search for health-related information on Web-based social media. However, little is known about the content of the posted information with respect to the users’ demographics. Objective The aims of this study were to analyze the content of Web-based health-related social media based on users’ demographics to identify which health topics are discussed in which social media by which demographic groups and to help guide educational and research activities. Methods We analyze 3 different types of health-related social media: (1) general Web-based social networks Twitter and Google+; (2) drug review websites; and (3) health Web forums, with a total of about 6 million users and 20 million posts. We analyzed the content of these posts based on the demographic group of their authors, in terms of sentiment and emotion, top distinctive terms, and top medical concepts. Results The results of this study are: (1) Pregnancy is the dominant topic for female users in drug review websites and health Web forums, whereas for male users, it is cardiac problems, HIV, and back pain, but this is not the case for Twitter; (2) younger users (0-17 years) mainly talk about attention-deficit hyperactivity disorder (ADHD) and depression-related drugs, users aged 35-44 years discuss about multiple sclerosis (MS) drugs, and middle-aged users (45-64 years) talk about alcohol and smoking; (3) users from the Northeast United States talk about physical disorders, whereas users from the West United States talk about mental disorders and addictive behaviors; (4) Users with higher writing level express less anger in their posts. Conclusion We studied the popular topics and the sentiment based on users' demographics in Web-based health-related social media. Our results provide valuable information, which can help create targeted and effective educational campaigns and guide experts to reach the right users on Web-based

  16. Proto-object based rate control for JPEG2000: an approach to content-based scalability.

    Science.gov (United States)

    Xue, Jianru; Li, Ce; Zheng, Nanning

    2011-04-01

    The JPEG2000 system provides scalability with respect to quality, resolution and color component in the transfer of images. However, scalability with respect to semantic content is still lacking. We propose a biologically plausible salient region based bit allocation mechanism within the JPEG2000 codec for the purpose of augmenting scalability with respect to semantic content. First, an input image is segmented into several salient proto-objects (a region that possibly contains a semantically meaningful physical object) and background regions (a region that contains no object of interest) by modeling visual focus of attention on salient proto-objects. Then, a novel rate control scheme distributes a target bit rate to each individual region according to its saliency, and constructs quality layers of proto-objects for the purpose of more precise truncation comparable to original quality layers in the standard. Empirical results show that the suggested approach adds to the JPEG2000 system scalability with respect to content as well as the functionality of selectively encoding, decoding, and manipulation of each individual proto-object in the image, with only some slightly trivial modifications to the JPEG2000 standard. Furthermore, the proposed rate control approach efficiently reduces the computational complexity and memory usage, as well as maintains the high quality of the image to a level comparable to the conventional post-compression rate distortion (PCRD) optimum truncation algorithm for JPEG2000.

  17. Watermarking Digital Images Based on a Content Based Image Retrieval Technique

    CERN Document Server

    Tsolis, Dimitrios K; Papatheodorou, Theodore S

    2008-01-01

    The current work is focusing on the implementation of a robust watermarking algorithm for digital images, which is based on an innovative spread spectrum analysis algorithm for watermark embedding and on a content-based image retrieval technique for watermark detection. The highly robust watermark algorithms are applying "detectable watermarks" for which a detection mechanism checks if the watermark exists or no (a Boolean decision) based on a watermarking key. The problem is that the detection of a watermark in a digital image library containing thousands of images means that the watermark detection algorithm is necessary to apply all the keys to the digital images. This application is non-efficient for very large image databases. On the other hand "readable" watermarks may prove weaker but easier to detect as only the detection mechanism is required. The proposed watermarking algorithm combine's the advantages of both "detectable" and "readable" watermarks. The result is a fast and robust watermarking algor...

  18. User-Based Interaction for Content-Based Image Retrieval by Mining User Navigation Patterns.

    Directory of Open Access Journals (Sweden)

    A. Srinagesh

    2013-09-01

    Full Text Available In Internet, Multimedia and Image Databases image searching is a necessity. Content-Based Image Retrieval (CBIR is an approach for image retrieval. With User interaction included in CBIR with Relevance Feedback (RF techniques, the results are obtained by giving more number of iterative feedbacks for large databases is not an efficient method for real- time applications. So, we propose a new approach which converges rapidly and can aptly be called as Navigation Pattern-Based Relevance Feedback (NPRF with User-based interaction mode. We combined NPRF with RF techniques with three concepts viz., query Re-weighting (QR, Query Expansion (QEX and Query Point Movement (QPM. By using, these three techniques efficient results are obtained by giving a small number of feedbacks. The efficiency of the proposed method with results is proved by calculating Precision, Recall and Evaluation measures.

  19. 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...

  20. 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...

  1. 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

  2. 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.

  3. 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.

  4. Identifying content for simulation-based curricula in urology

    DEFF Research Database (Denmark)

    Nayahangan, Leizl Joy; Bølling Hansen, Rikke; Lindorff-Larsen, Karen

    2017-01-01

    to identify technical procedures in urology that should be included in a simulation-based curriculum for residency training. MATERIALS AND METHODS: A national needs assessment was performed using the Delphi method involving 56 experts with significant roles in the education of urologists. Round 1 identified......OBJECTIVE: Simulation-based training is well recognized in the transforming field of urological surgery; however, integration into the curriculum is often unstructured. Development of simulation-based curricula should follow a stepwise approach starting with a needs assessment. This study aimed...... technical procedures that newly qualified urologists should perform. Round 2 included a survey using an established needs assessment formula to explore: the frequency of procedures; the number of physicians who should be able to perform the procedure; the risk and/or discomfort to patients when a procedure...

  5. Natural ingredients based cosmetics. Content of selected fragrance sensitizers

    DEFF Research Database (Denmark)

    Rastogi, Suresh Chandra; Johansen, J D; Menné, T

    1996-01-01

    -hexylcinnamic aldehyde. The study revealed that the 91% (20/22) of the natural ingredients based perfumes contained 0.027%-7.706% of 1 to 7 of the target fragrances. Between 1 and 5 of the chemically defined synthetic constituents of fragrance mix were found in 82% (18/22) of the perfumes. 35% (7/20) of the other...

  6. Evaluation of a Problem Based Learning Curriculum Using Content Analysis

    Science.gov (United States)

    Prihatiningsih, Titi Savitri; Qomariyah, Nurul

    2016-01-01

    Faculty of Medicine UGM has implemented Problem Based Learning (PBL) since 1985. Seven jump tutorial discussions are applied. A scenario is used as a trigger to stimulate students to identify learning objectives (LOs) in step five which are used as the basis for self study in step six. For each scenario, the Block Team formulates the LOs which are…

  7. GreenDelivery: Proactive Content Caching and Push with Energy-Harvesting-based Small Cells

    OpenAIRE

    Zhou, Sheng; Gong, Jie; ZHOU, Zhenyu; Chen, Wei; Niu, Zhisheng

    2015-01-01

    The explosive growth of mobile multimedia traffic calls for scalable wireless access with high quality of service and low energy cost. Motivated by the emerging energy harvesting communications, and the trend of caching multimedia contents at the access edge and user terminals, we propose a paradigm-shift framework, namely GreenDelivery, enabling efficient content delivery with energy harvesting based small cells. To resolve the two-dimensional randomness of energy harvesting and content requ...

  8. A NEW CONTENT BASED IMAGE RETRIEVAL SYSTEM USING GMM AND RELEVANCE FEEDBACK

    Directory of Open Access Journals (Sweden)

    N. Shanmugapriya

    2014-01-01

    Full Text Available Content-Based Image Retrieval (CBIR is also known as Query By Image Content (QBIC is the application of computer vision techniques and it gives solution to the image retrieval problem such as searching digital images in large databases. The need to have a versatile and general purpose Content Based Image Retrieval (CBIR system for a very large image database has attracted focus of many researchers of information-technology-giants and leading academic institutions for development of CBIR techniques. Due to the development of network and multimedia technologies, users are not fulfilled by the traditional information retrieval techniques. So nowadays the Content Based Image Retrieval (CBIR are becoming a source of exact and fast retrieval. Texture and color are the important features of Content Based Image Retrieval Systems. In the proposed method, images can be retrieved using color-based, texture-based and color and texture-based. Algorithms such as auto color correlogram and correlation for extracting color based images, Gaussian mixture models for extracting texture based images. In this study, Query point movement is used as a relevance feedback technique for Content Based Image Retrieval systems. Thus the proposed method achieves better performance and accuracy in retrieving images.

  9. Evolution-based Virtual Content Insertion with Visually Virtual Interactions in Videos

    Science.gov (United States)

    Chang, Chia-Hu; Wu, Ja-Ling

    With the development of content-based multimedia analysis, virtual content insertion has been widely used and studied for video enrichment and multimedia advertising. However, how to automatically insert a user-selected virtual content into personal videos in a less-intrusive manner, with an attractive representation, is a challenging problem. In this chapter, we present an evolution-based virtual content insertion system which can insert virtual contents into videos with evolved animations according to predefined behaviors emulating the characteristics of evolutionary biology. The videos are considered not only as carriers of message conveyed by the virtual content but also as the environment in which the lifelike virtual contents live. Thus, the inserted virtual content will be affected by the videos to trigger a series of artificial evolutions and evolve its appearances and behaviors while interacting with video contents. By inserting virtual contents into videos through the system, users can easily create entertaining storylines and turn their personal videos into visually appealing ones. In addition, it would bring a new opportunity to increase the advertising revenue for video assets of the media industry and online video-sharing websites.

  10. 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

  11. Mineral content prediction for unconventional oil and gas reservoirs based on logging data

    Science.gov (United States)

    Maojin, Tan; Youlong, Zou; Guoyue

    2012-09-01

    Coal bed methane and shale oil &gas are both important unconventional oil and gas resources, whose reservoirs are typical non-linear with complex and various mineral components, and the logging data interpretation model are difficult to establish for calculate the mineral contents, and the empirical formula cannot be constructed due to various mineral. The radial basis function (RBF) network analysis is a new method developed in recent years; the technique can generate smooth continuous function of several variables to approximate the unknown forward model. Firstly, the basic principles of the RBF is discussed including net construct and base function, and the network training is given in detail the adjacent clustering algorithm specific process. Multi-mineral content for coal bed methane and shale oil &gas, using the RBF interpolation method to achieve a number of well logging data to predict the mineral component contents; then, for coal-bed methane reservoir parameters prediction, the RBF method is used to realized some mineral contents calculation such as ash, volatile matter, carbon content, which achieves a mapping from various logging data to multimineral. To shale gas reservoirs, the RBF method can be used to predict the clay content, quartz content, feldspar content, carbonate content and pyrite content. Various tests in coalbed and gas shale show the method is effective and applicable for mineral component contents prediction

  12. 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].

  13. Content Based Image Retrieval Using Local Color Histogram

    Directory of Open Access Journals (Sweden)

    Metty Mustikasari, Eri Prasetyo,, Suryadi Harmanto

    2014-01-01

    Full Text Available —This paper proposes a technique to retrieve images based on color feature using local histogram. The image is divided into nine sub blocks of equal size. The color of each sub-block is extracted by quantifying the HSV color space into 12x6x6 histogram. In this retrieval system Euclidean distance and City block distance are used to measure similarity of images. This algorithm is tested by using Corel image database. The performance of retrieval system is measured in terms of its recall and precision. The effectiveness of retrieval system is also measured based on AVRR (Average Rank of Relevant Images and IAVRR (Ideal Average Rank of Relevant Images which is proposed by Faloutsos. The experimental results show that the retrieval system has a good performance and the evaluation results of city block has achieved higher retrieval performance than the evaluation results of the Euclidean distance.

  14. 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.

  15. Situational Requirements Engineering for the Development of Content Management System-based Web Applications

    OpenAIRE

    2005-01-01

    Web applications are evolving towards strong content-centered Web applications. The development processes and implementation of these applications are unlike the development and implementation of traditional information systems. In this paper we propose WebEngineering Method; a method for developing content management system (CMS) based Web applications. Critical to a successful development of CMS-based Web applications, is the adaptation to the dynamic business. We first define CMS-based Web...

  16. The application of content based teaching method in English writing in Senior High School

    Institute of Scientific and Technical Information of China (English)

    李素霞

    2016-01-01

    Content-based instruction (CBI) refers to an approach of subject integration to language teaching in which the teaching is organized around the subject or information that students will acquire. Based on the deficiency of the previous studies, the thesis proposes a Content-Based Instruction, in order to improve the quality of English Writing Teaching in senior school and students' actual level of writing.

  17. Content-based Image Retrieval Using Color Histogram

    Institute of Scientific and Technical Information of China (English)

    HUANG Wen-bei; HE Liang; GU Jun-zhong

    2006-01-01

    This paper introduces the principles of using color histogram to match images in CBIR. And a prototype CBIR system is designed with color matching function. A new method using 2-dimensional color histogram based on hue and saturation to extract and represent color information of an image is presented. We also improve the Euclidean-distance algorithm by adding Center of Color to it. The experiment shows modifications made to Euclidean-distance significantly elevate the quality and efficiency of retrieval.

  18. 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.

  19. Augmentation of French grunt diet description using combined visual and DNA-based analyses

    Science.gov (United States)

    Hargrove, John S.; Parkyn, Daryl C.; Murie, Debra J.; Demopoulos, Amanda W.J.; Austin, James D.

    2012-01-01

    Trophic linkages within a coral-reef ecosystem may be difficult to discern in fish species that reside on, but do not forage on, coral reefs. Furthermore, dietary analysis of fish can be difficult in situations where prey is thoroughly macerated, resulting in many visually unrecognisable food items. The present study examined whether the inclusion of a DNA-based method could improve the identification of prey consumed by French grunt, Haemulon flavolineatum, a reef fish that possesses pharyngeal teeth and forages on soft-bodied prey items. Visual analysis indicated that crustaceans were most abundant numerically (38.9%), followed by sipunculans (31.0%) and polychaete worms (5.2%), with a substantial number of unidentified prey (12.7%). For the subset of prey with both visual and molecular data, there was a marked reduction in the number of unidentified sipunculans (visual – 31.1%, combined &ndash 4.4%), unidentified crustaceans (visual &ndash 15.6%, combined &ndash 6.7%), and unidentified taxa (visual &ndash 11.1%, combined &ndash 0.0%). Utilising results from both methodologies resulted in an increased number of prey placed at the family level (visual &ndash 6, combined &ndash 33) and species level (visual &ndash 0, combined &ndash 4). Although more costly than visual analysis alone, our study demonstrated the feasibility of DNA-based identification of visually unidentifiable prey in the stomach contents of fish.

  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.